Supplementary. Table S1 A total of DEGs detected in this study (Gm) No. genename significance in annotation 1 At1g01020 D2 ARV1__expressed protein, similar to hypothetical protein DDB0188786 [Dictyostelium discoideum] (GB:EAL62332.1); contains InterPro domain Arv1-like protein (InterPro:IPR007290) 2 At1g01100 D2 60S acidic ribosomal protein P1 (RPP1A), similar to 60S ACIDIC RIBOSOMAL PROTEIN P1 GB:O23095 from (Arabidopsis thaliana) 3 At1g01120 D2, Dm KCS1__fatty acid elongase 3-ketoacyl-CoA synthase 1 (KCS1), nearly identical to GB:AAC99312 GI:4091810 from (Arabidopsis thaliana) 4 At1g01160 D1, D2, Dm GIF2__SSXT protein-related / transcription co-activator-related, similar to SYT/SSX4 fusion protein (GI:11127695) (Homo sapiens); supporting cDNA gi:21539891:gb:AY102640.1:; contains Pfam profile PF05030: SSXT protein (N-terminal region) 5 At1g01170 D2 ozone-responsive stress-related protein, putative, similar to stress-related ozone-induced protein AtOZI1 (GI:790583) (Arabidopsis thaliana); contains 1 predicted transmembrane domain;

6 At1g01240 D1, D2, Dm expressed protein 7 At1g01300 D2, Dm aspartyl protease family protein, contains Pfam domain, PF00026: eukaryotic aspartyl protease

8 At1g01320 D2 tetratricopeptide repeat (TPR)-containing protein, low similarity to SP:P46825 Kinesin light chain (KLC) {Loligo pealeii}; contains Pfam profile PF00515: TPR Domain 9 At1g01430 D2, Dm expressed protein, similar to hypothetical protein GB:CAB80917 GI:7267605 from (Arabidopsis thaliana) 10 At1g01470 D1, D2, Dm LEA14_LSR3__late embryogenesis abundant protein, putative / LEA protein, putative, similar to SP:P46518 Late embryogenesis abundant protein Lea14-A {Gossypium hirsutum}; contains Pfam profile PF03168: Late embryogenesis abundant protein 11 At1g01540 D2 protein kinase family protein, contains protein kinase domain, Pfam:PF00069; contains serine/threonine protein kinase domain, INTERPRO:IPR002290 12 At1g01630 D1, D2, Dm SEC14 cytosolic factor, putative / phosphoglyceride transfer protein, putative, contains Pfam PF00650 : CRAL/TRIO domain and PF03765 : CRAL/TRIO, N-terminus; similar to polyphosphoinositide binding protein Ssh2p GB:AAB94599 GI:2739046 from (Glycine max) 13 At1g01720 D1, D2, Dm ANAC002_ATAF1__no apical meristem (NAM) family protein, contains Pfam PF02365: No apical meristem (NAM) domain; similar to NAC domain protein NAM GB:AAD17313 GI:4325282 from (Arabidopsis thaliana) 14 At1g01725 D1, D2, Dm expressed protein 15 At1g01730 D1, Dm expressed protein 16 At1g01800 Dm short-chain dehydrogenase/reductase (SDR) family protein, similar to carbonyl reductase GI:1049108 from (Mus musculus) 17 At1g01820 Dm peroxisomal biogenesis factor 11 family protein / PEX11 family protein, contains Pfam PF05648: Peroxisomal biogenesis factor 11 (PEX11) 18 At1g01970 D1, Dm pentatricopeptide (PPR) repeat-containing protein, low similarity to 67 kD chloroplastic RNA- binding protein RSP67.2 (Raphanus sativus) GI:9755888; contains Pfam profile PF01535: PPR repeat 19 At1g02205 D1, D2, Dm CER1__CER1 protein, identical to maize gl1 homolog (glossy1 locus) GI:1209703 and CER1 GI:1199467 from (Arabidopsis thaliana) 20 At1g02280 D1, D2, Dm TOC33_ATTOC33_PPI1_TOC75-III__GTP-binding protein (TOC33), identical to atToc33 protein (GI:11557973) (Arabidopsis thaliana); Carboxyl-terminal end highly similar to GTP-binding protein SP:U43377, location of EST gb:AA394770 and gb:R30089; identical to cDNA for chloroplast atToc33 protein GI:11557972 21 At1g02300 D1, D2, Dm cathepsin B-like cysteine protease, putative, similar to cathepsin B-like cysteine proteinase GI:609175 from (Nicotiana rustica) 22 At1g02305 D1, D2, Dm cathepsin B-like cysteine protease, putative, similar to cathepsin B-like cysteine proteinase (Nicotiana rustica) GI:609175; contains Pfam profile PF00112: Papain family cysteine protease

23 At1g02450 D1, Dm NIMIN1__NPR1/NIM1-interacting protein 1 (NIMIN-1), identical to NIMIN-1 protein (Arabidopsis thaliana) gi:12057154:emb:CAC19844; identical to cDNA NIMIN-1 protein (nimin-1 gene)GI:12057153 24 At1g02475 D1, Dm expressed protein 25 At1g02560 D2 CLPP5_NCLPP1_NCLPP5__ATP-dependent Clp protease proteolytic subunit (ClpP1), identical to nClpP1 GB:BAA82065 GI:5360579 from (Arabidopsis thaliana); contains Pfam profile PF00574: Clp protease; contains TIGRfam profile TIGR00493: ATP-dependent Clp protease, proteolytic subunit ClpP 26 At1g02640 Dm BXL2_ATBXL2__glycosyl hydrolase family 3 protein, similar to beta-xylosidase GB:Z84377 GI:2102655 from (Aspergillus niger) 27 At1g02650 D1, Dm DNAJ heat shock N-terminal domain-containing protein, contains Pfam profile PF00226: DnaJ domain 28 At1g02730 D1 ATCSLD5_CSLD5__cellulose synthase family protein, similar to cellulose synthase catalytic subunit (gi:13925881) from Nicotiana alata, cellulose synthase-4 (gi:9622880) from Zea mays 29 At1g02740 Dm MRG family protein, member of Pfam PF05712: MRG; similar to Transcription factor-like protein MRG15 (MORF-related gene 15 protein) (MSL3-1 protein) (Protein HSPC008/HSPC061) (SP:Q9UBU8) {Homo sapiens} 30 At1g02780 D1 EMB2386__60S ribosomal protein L19 (RPL19A), similar to ribosomal protein L19 GI:36127 from (Homo sapiens) 31 At1g02850 Dm glycosyl hydrolase family 1 protein, contains Pfam PF00232 : Glycosyl hydrolase family 1 domain; TIGRFAM TIGR01233: 6-phospho-beta-galactosidase; similar to hydroxyisourate hydrolase (GI:19569603) (Glycine max) 32 At1g02930 D2, Dm ATGSTF6_ATGSTF3_ERD11_GST1_GSTF6__glutathione S-transferase, putative, similar to glutathione S-transferase GI:860955 from (Hyoscyamus muticus) 33 At1g03030 D1, Dm phosphoribulokinase/uridine kinase family protein, contains Pfam PF00485: Phosphoribulokinase / Uridine kinase family; Belongs to Interpro IPR006083 Phosphoribulokinase/uridine kinase family; similar to Uridine kinase (Uridine monophosphokinase) (SP:P27515) {Saccharomyces cerevisiae}; ESTs gb:AA585719, gb:AA728503 and gb:T22272 come from this gene

34 At1g03080 D1, D2, Dm kinase interacting family protein, similar to kinase interacting protein 1 (GI:13936326) (Petunia integrifolia) 35 At1g03290 D1, D2, Dm expressed protein, ESTs gb:H36966, gb:R65511, gb:T42324 and gb:T20569 come from this gene 36 At1g03300 D1, Dm agenet domain-containing protein, contains Pfam PF05641: Agenet domain 37 At1g03400 D2 2-oxoglutarate-dependent dioxygenase, putative, similar to 2A6 (GI:599622) and tomato ethylene synthesis regulatory protein E8 (SP:P10967); similar to ESTs emb:Z34690, gb:T04168, gb:H37738, gb:T76913, gb:T43801, amd gb:T21964 38 At1g03475 D1, Dm LIN2__coproporphyrinogen III oxidase, putative / coproporphyrinogenase, putative / coprogen oxidase, putative, similar to coproporphyrinogen III oxidase, chloroplast (precursor) from Glycine max (SP:P35055), Nicotiana tabacum (SP:Q42946), Hordeum vulgare (SP:Q42840), ESTs gb:AA586260 and dbj:D48620; contains Pfam domain coproporphyrinogen III oxidase, aerobic (PF01218) 39 At1g03490 D2 ANAC006__no apical meristem (NAM) family protein, contains Pfam PF02365: No apical meristem (NAM) domain; 40 At1g03630 D1, Dm POR_TFC C__protochlorophyllide reductase C, chloroplast / PCR C / NADPH-protochlorophyllide oxidoreductase C (PORC), identical to SP:O48741 protochlorophyllide reductase C, chloroplast precursor (EC 1.3.1.33) (PCR C) (NADPH-protochlorophyllide oxidoreductase C) (POR C) (Arabidopsis thaliana) 41 At1g03790 D1, D2, Dm zinc finger (CCCH-type) family protein, contains Pfam domain, PF00642: Zinc finger C-x8-C-x5- C-x3-H type (and similar) 42 At1g03870 D1, D2, Dm FLA9__fasciclin-like arabinogalactan-protein (FLA9), identical to gi_13377784_gb_AAK20861 43 At1g03880 D2 CRU2_CRB__12S seed storage protein (CRB), identical to 12S seed storage protein, gi:808937 (SP:P15456) (Plant Mol Biol 11:805-820 (1988)); contains Pfam profile PF00190 Cupin and Prosite 11-S plant seed storage proteins signature PS00305 44 At1g03900 D1, Dm ATNAP4__expressed protein 45 At1g03910 D1, D2, Dm expressed protein, low similarity to cactin (Drosophila melanogaster) GI:7673675; expression supported by MPSS 46 At1g04040 D1, D2, Dm acid phosphatase class B family protein, similar to SP:P15490 STEM 28 kDa glycoprotein precursor (Vegetative storage protein A) {Glycine max}, acid phosphatase (Glycine max) GI:3341443; contains Pfam profile PF03767: HAD superfamily (subfamily IIIB) phosphatase; supporting cDNA gi:13926197:gb:AF370572.1:AF370572 47 At1g04120 D1, D2, Dm ATMRP5_MRP5__ABC transporter family protein, Strong similarity to MRP-like ABC transporter gb:U92650 from A. thaliana and canalicular multi-drug resistance protein gb:L49379 from Rattus norvegicus 48 At1g04170 D2, Dm EIF2 GAMMA__eukaryotic translation initiation factor 2 subunit 3, putative / eIF2S3, putative / eIF-2-gamma, putative, similar to gb:U37354 from S. pombe. ESTs gb:T41979, gb:N37284 and gb:N37529 come from this gene 49 At1g04190 D2 tetratricopeptide repeat (TPR)-containing protein, low similarity to protein antigen LmSTI1 (Leishmania major) GI:1698880; contains Pfam profile PF00515 TPR Domain; EST gb:Z47802 and gb:Z48402 come from this gene 50 At1g04220 D1, D2, Dm beta-ketoacyl-CoA synthase, putative, Strong similarity to beta-keto-Coa synthase gb:U37088 from Simmondsia chinensis, GI:4091810 51 At1g04240 D1 SHY2_IAA3__auxin-responsive protein / indoleacetic acid-induced protein 3 (IAA3), identical to SP:Q38822 Auxin-responsive protein IAA3 (Indoleacetic acid-induced protein 3) {Arabidopsis thaliana}; EST gb:T04296 comes from this gene 52 At1g04270 D1, D2, Dm RPS15__40S ribosomal protein S15 (RPS15A), Strong similarity to Oryza 40S ribosomal protein S15. ESTs gb:R29788,gb:ATTS0365 come from this gene 53 At1g04280 D1 expressed protein 54 At1g04350 D1, Dm 2-oxoglutarate-dependent dioxygenase, putative, Similar to Arabidopsis 2A6 (gb:X83096) and to tomato ethylene synthesis regulatory protein E8 (SP:P10967); EST gb:T76913 comes from this gene 55 At1g04400 D1, D2, Dm CRY2_AT-PHH1_FHA_PHH1__cryptochrome 2 apoprotein (CRY2) / blue light photoreceptor (PHH1), 97% identical to photolysase (PHH1) (SP:Q96524) and cryptochrome 2 apoprotein (CRY2) (SP:U43397). ESTs gb:W43661 and gb:Z25638 come from this gene; contains Pfam profiles PF03441: FAD binding domain of DNA photolyase and PF00875: deoxyribodipyrimidine photolyase; identical to cDNA Cvi cryptochrome 2 (CRY2) GI:18026275 56 At1g04470 D1, Dm expressed protein, EST gb:ATTS5672 comes from this gene 57 At1g04480 D2 60S ribosomal protein L23 (RPL23A), identical to GB:AAB80655 58 At1g04530 D1, Dm expressed protein 59 At1g04640 D2, Dm LIP2__biotin/lipoate A/B protein ligase family protein, similar to lipoyltransferase (LIP2p) (Arabidopsis thaliana) GI:15887052; contains Pfam profile PF03099: Biotin/lipoate A/B protein ligase family 60 At1g04690 D1, Dm KAB1_KV-BETA1__potassium channel protein, putative, nearly identical to K+ channel protein (Arabidopsis thaliana) GI:1063415; contains Pfam profile PF00248: oxidoreductase, aldo/keto reductase family 61 At1g04710 D2, Dm acetyl-CoA C-acyltransferase, putative / 3-ketoacyl-CoA thiolase, putative, similar to 3- ketoacyl-CoA thiolase (E.C. 2.3.1.16) from (Arabidopsis thaliana) GI:2981616, (Cucumis sativus) GI:393707, (Cucurbita cv. Kurokawa Amakuri) GI:1694621; contains InterPro accession IPR002155: Thiolase 62 At1g04800 D1, Dm glycine-rich protein 63 At1g04850 Dm ubiquitin-associated (UBA)/TS-N domain-containing protein, weak similarity to SP:P45974 Ubiquitin carboxyl-terminal hydrolase 5 (EC 3.1.2.15) {Homo sapiens}; contains Pfam profile PF00627: UBA/TS-N domain 64 At1g04970 D1, Dm lipid-binding serum glycoprotein family protein, low similarity to SP:P17213 Bactericidal permeability-increasing protein precursor (BPI) {Homo sapiens}; contains Pfam profile PF02886: LBP / BPI / CETP family, C-terminal domain 65 At1g05010 D1, D2, Dm EFE_EAT1__1-aminocyclopropane-1-carboxylate oxidase / ACC oxidase / ethylene-forming enzyme (ACO) (EAT1), Identical to 1-aminocyclopropane-1-carboxylate oxidase (ACC oxidase) gb:X66719 (EAT1). ESTs gb:T43073, gb:T5714, gb:R90435, gb:R44023, gb:AA597926, gb:AI099676, gb:AA650810 and gb:29725 come from this gene 66 At1g05055 Dm basic transcription factor 2, 44kD subunit-related, contains weak similarity to Swiss- Prot:Q13888 TFIIH basal transcription factor complex p44 subunit (Basic transcription factor 2 44 kDa subunit, BTF2-p44, General transcription factor IIH polypeptide 2) (Homo sapiens) 67 At1g05130 D2 68 At1g05170 D2 galactosyltransferase family protein 69 At1g05190 D1, Dm EMB2394__ribosomal protein L6 family protein, Similar to Mycobacterium RlpF (gb:Z84395). ESTs gb:T75785,gb:R30580,gb:T04698 come from this gene 70 At1g05200 Dm ATGLR3.4_GLR3.4_GLUR3__glutamate receptor family protein (GLR3.4), plant glutamate receptor family, PMID:11379626 71 At1g05340 D1, D2, Dm expressed protein 72 At1g05460 D1 SDE3__RNA helicase SDE3 (SDE3), identical to RNA helicase SDE3 (Arabidopsis thaliana) GI:13811296 73 At1g05520 Dm transport protein, putative, similar to Swiss-Prot:Q15436 protein transport protein Sec23A (Homo sapiens) 74 At1g05805 D1, Dm basic helix-loop-helix (bHLH) family protein 75 At1g05870 D2, Dm expressed protein 76 At1g05940 D1 CAT9__amino acid permease family protein, low similarity to SP:P30823 High-affinity cationic amino acid transporter-1 (CAT-1) {Rattus norvegicus}; contains Pfam profile PF00324: Amino acid permease 77 At1g06110 D1, D2, Dm F-box family protein, contains similarity to F-box protein FBX3 GI:6103643 from (Homo sapiens) ; similar to SKP1 interacting partner 2 (SKIP2) TIGR_Ath1:At5g67250 78 At1g06130 D1 GLX2-4__hydroxyacylglutathione hydrolase, putative / glyoxalase II, putative, similar to glyoxalase II isozyme GB:AAC49865 GI:2570338 from (Arabidopsis thaliana) 79 At1g06180 D1, D2, Dm ATMYB13__myb family transcription factor, identical to GB:CAA90748 GI:1263093 from (Arabidopsis thaliana);contains PFAM profile:PF00249 80 At1g06210 D2 VHS domain-containing protein / GAT domain-containing protein, weak similarity to SP:Q9UJY5 ADP-ribosylation factor binding protein GGA1 {Homo sapiens}; contains Pfam profiles PF00790: VHS domain, PF03127: GAT domain 81 At1g06250 D2 lipase class 3 family protein, similar to lipase GB:AAD01804 GI:4103627 from (Dianthus caryophyllus); contains Pfam profile PF01764: Lipase 82 At1g06360 D2 fatty acid desaturase family protein, similar to delta 9 acyl-lipid desaturase (ADS1) GI:2970034 from (Arabidopsis thaliana) 83 At1g06430 D2 FTSH8__encodes a FtsH protease that is localized to the chloroplast 84 At1g06460 D1, D2, Dm ACD32.1_ACD31.2__31.2 kDa small heat shock family protein / hsp20 family protein, contains Pfam profile: PF00011 Hsp20/alpha crystallin family 85 At1g06570 D1, D2, Dm PDS1_HPD__4-hydroxyphenylpyruvate dioxygenase (HPD), identical to 4-hydroxyphenylpyruvate dioxygenase (HPD) SP:P93836 (Arabidopsis thaliana (Mouse-ear cress)) 86 At1g06650 D2 2-oxoglutarate-dependent dioxygenase, putative, similar to 2A6 (GI:599622) and tomato ethylene synthesis regulatory protein E8 (SP:P10967); contains Pfam profile: PF00671 Iron/Ascorbate oxidoreductase family 87 At1g06670 D2 NIH__DEIH-box RNA/DNA helicase, identical to DEIH-box RNA/DNA helicase GB:BAA84364 GI:5881579 (Arabidopsis thaliana) 88 At1g06760 D2, Dm histone H1, putative, similar to histone H1-1 GB:CAA44312 GI:16314 from (Arabidopsis thaliana); identical to cDNA H1-1C mRNA for histone H1-1 (partial) GI:732560 89 At1g06830 D1, D2, Dm glutaredoxin family protein, contains INTERPRO Domain IPR002109, Glutaredoxin (thioltransferase) 90 At1g06950 D2, Dm ATTIC110_TIC110__Encodes a protein thought to be a part of the translocon at the chloroplast inner envelope. Involved in protein import into the chloroplast and chloroplast biogenesis. 91 At1g06980 D2 expressed protein, similar to hypothetical protein GI:2347189 from (Arabidopsis thaliana) 92 At1g07010 D2, Dm calcineurin-like phosphoesterase family protein, contains Pfam profile: PF00149 calcineurin- like phosphoesterase 93 At1g07040 D1, D2, Dm expressed protein 94 At1g07070 D1, D2, Dm 60S ribosomal protein L35a (RPL35aA), similar to ribosomal protein L35a GI:57118 from (Rattus norvegicus) 95 At1g07080 D1, D2, Dm gamma interferon responsive lysosomal thiol reductase family protein / GILT family protein, similar to SP:P13284 Gamma-interferon inducible lysosomal thiol reductase precursor {Homo sapiens}; contains Pfam profile PF03227: Gamma interferon inducible lysosomal thiol reductase (GILT) 96 At1g07090 D1, Dm expressed protein, contains Pfam profile PF04852: Protein of unknown function (DUF640) 97 At1g07110 D2 F2KP_ATF2KP_FKFBP__fructose-6-phosphate 2-kinase / fructose-2,6-bisphosphatase (F2KP), identical to fructose-6-phosphate 2-kinase/fructose-2,6-bisphosphatase (F2KP) (Arabidopsis thaliana) GI:13096098 98 At1g07135 D2 glycine-rich protein 99 At1g07180 D2 ATNDI1_NDA1__Internal NAD(P)H dehydrogenase in mitochondria. The predicted protein sequence has high homology with other designated NAD(P)H DHs from microorganisms; the capacity for matrix NAD(P)H oxidation via the rotenone-insensitive pathway is significantly reduced in the Atndi1 mutant plant line; the in vitro translation product of AtNDI1 is imported into isolated mitochondria and located on the inside of the inner membrane. 100 At1g07230 D1, D2, Dm phosphoesterase family protein, low similarity to SP:P95246 Phospholipase C 2 precursor (EC 3.1.4.3) {Mycobacterium tuberculosis}; contains Pfam profile PF04185: Phosphoesterase family 101 At1g07310 D2, Dm C2 domain-containing protein, contains similarity to shock protein SRC2 (Glycine max) gi:2055230:dbj:BAA19769 ; contains Pfam profile PF00168:C2 domain 102 At1g07320 D1, D2, Dm RPL4__50S ribosomal protein L4, chloroplast (CL4), identical to SP:O50061 from (Arabidopsis thaliana) 103 At1g07360 D1, Dm zinc finger (CCCH-type) family protein / RNA recognition motif (RRM)-containing protein, similar to SP:O59800 Cell cycle control protein cwf5 {Schizosaccharomyces pombe}, RNA Binding Protein 47 (Nicotiana plumbaginifolia) GI:9663769; contains Pfam profile: PF00076 RNA recognition motif (aka RRM, RBD, or RNP domain) 104 At1g07370 D1 PCNA1__proliferating cell nuclear antigen 1 (PCNA1), identical to SP:Q9M7Q7 Proliferating cellular nuclear antigen 1 (PCNA 1) {Arabidopsis thaliana}; nearly identical to SP:Q43124 Proliferating cell nuclear antigen (PCNA) {Brassica napus}; contains Pfam profiles PF00705: Proliferating cell nuclear antigen N-terminal domain, PF02747: Proliferating cell nuclear antigen C-terminal domain 105 At1g07400 Dm 17.8 kDa class I heat shock protein (HSP17.8-CI), similar to 17.5 kDa class I heat shock protein SP:P04793 from (Glycine max); contains Pfam PF00011: Hsp20/alpha crystallin family 106 At1g07430 D1, D2, Dm protein phosphatase 2C, putative / PP2C, putative, similar to GB:CAB90633 from (Fagus sylvatica) 107 At1g07440 D1 tropinone reductase, putative / tropine dehydrogenase, putative, similar to tropinone reductase SP:P50165 from (Datura stramonium) 108 At1g07500 Dm expressed protein, ; expression supported by MPSS 109 At1g07510 D1, Dm FTSH10__encodes an FtsH protease that is localized to the mitochondrion 110 At1g07570 D1 APK1A_APK1__protein kinase (APK1a), identical to Protein kinase APK1A from (Arabidopsis thaliana) SWISS-PROT:Q06548 111 At1g07590 D1, D2, Dm MT1A_ATMT-2_ATMT-Q_LSR4_MT1_MT-Q__pentatricopeptide (PPR) repeat-containing protein, low similarity to DNA-binding protein (Triticum aestivum) GI:6958202; contains Pfam profile PF01535: PPR repeat 112 At1g07610 D1, D2, Dm MT1C__metallothionein-like protein 1C (MT-1C), identical to Metallothionein-like protein 1C (MT-1C). (SP:Q38804) (Arabidopsis thaliana) 113 At1g07700 D1, D2, Dm thioredoxin family protein, low similarity to thioredoxin (Gallus gallus) GI:212766; contains Pfam profile: PF00085 Thioredoxin 114 At1g07720 D1, D2, Dm beta-ketoacyl-CoA synthase family protein, similar to GB:AAC99312 from (Arabidopsis thaliana) (Plant J. (1999) In press) 115 At1g07820 Dm histone H4, identical to histone H4 from Lycopersicon esculentum GI:297150, Lolium temulentum SP:P02308, Acropora formosa GI:455652, Citrus jambhiri GI:16797797 116 At1g07870 D2 protein kinase family protein, contains protein kinase domain, Pfam:PF00069 117 At1g07990 Dm SIT4 phosphatase-associated family protein, contains Pfam profile: PF04499 SIT4 phosphatase- associated protein 118 At1g08000 D1 zinc finger (GATA type) family protein, similar to PIR:T05288 from (Arabidopsis thaliana) 119 At1g08180 Dm expressed protein 120 At1g08200 D2 AXS2__expressed protein 121 At1g08210 Dm aspartyl protease family protein, contains Pfam profile PF00026: Eukaryotic aspartyl protease; similar to CND41, chloroplast nucleoid DNA binding protein (GI:2541876) {Nicotiana tabacum}

122 At1g08315 Dm armadillo/beta-catenin repeat family protein, contains Pfam profile: PF00514 armadillo/beta- catenin-like repeat 123 At1g08360 D1, Dm 60S ribosomal protein L10A (RPL10aA), similar to 60S ribosomal protein L10A GB:AAC73045 GI:3860277 from (Arabidopsis thaliana) 124 At1g08460 D1, Dm HDA08_HDA8__histone deacetylase family protein (HDA8), identical to HDA8 (Arabidopsis thaliana) GI:21360988low similarity to SP:Q9Z2V5 Histone deacetylase 6 (HD6) (Histone deacetylase mHDA2) {Mus musculus}; contains Pfam profile PF00850: Histone deacetylase family; supporting cDNA gi:21360987:gb:AF510167.1: 125 At1g08540 D1, D2, Dm SIGB_SIG2_SIGA__RNA polymerase sigma subunit SigB (sigB) / sigma factor 2 (SIG2), identical to sigma factor SigB (Arabidopsis thaliana) GI:5478446, plastid RNA polymerase sigma-subunit (Arabidopsis thaliana) GI:2879922, sigma factor (Arabidopsis thaliana) GI:2597831, sigma factor 2 (SIG2) (Arabidopsis thaliana) GI:2353173; contains Pfam profiles PF04545: Sigma-70, region 4, PF04539: Sigma-70 region 3, PF04542: Sigma-70 region 2 126 At1g08570 D1, D2, Dm thioredoxin family protein, contains Pfam profile: PF00085 Thioredoxin; similar to ESTs gb:T46281, gb:R83933, gb:N65879, emb:F14466, gb:N96726, gb:AA042340, and emb:Z18150 127 At1g08580 D2 expressed protein 128 At1g08650 D1 PPCK1__phosphoenolpyruvate carboxylase kinase, identical to phosphoenolpyruvate carboxylase kinase (Arabidopsis thaliana) gi:6318613:gb:AAF06968; contains protein kinase domain, Pfam:PF00069 129 At1g08830 D1 CSD1__superoxide dismutase (Cu-Zn) (SODCC) / copper/zinc superoxide dismutase (CSD1), identical to SWISS-PROT: P24704 130 At1g08930 D1, D2, Dm ERD6__early-responsive to dehydration stress protein (ERD6) / sugar transporter family protein, identical to ERD6 protein {Arabidopsis thaliana} GI:3123712; contains Pfam profile PF00083: major facilitator superfamily protein; contains TIGRfam TIGR00879: Sugar transporter

131 At1g09140 Dm ATSRP30.1_ATSRP30_ATSRP30.2__SF2/ASF-like splicing modulator (SRP30), nearly identical to SF2/ASF-like splicing modulator Srp30 (Arabidopsis thaliana) GI:4775270 132 At1g09160 D2, Dm protein phosphatase 2C-related / PP2C-related, similar to GB:AAC16260 133 At1g09200 D1, Dm histone H3, identical to histone H3 from Zea mays SP:P05203, Medicago sativa GI:166384, Encephalartos altensteinii SP:P08903, Pisum sativum SP:P02300; contains Pfam profile PF00125 Core histone H2A/H2B/H3/H4 134 At1g09250 Dm expressed protein 135 At1g09310 D1, D2, Dm expressed protein, contains Pfam profile PF04398: Protein of unknown function, DUF538 136 At1g09340 D1 expressed protein 137 At1g09490 D1, D2, Dm similar to Eucalyptus gunnii alcohol dehydrogenase of unknown physiological function (GI:1143445), Vigna unguiculata (gi:1854445), NOT a cinnamyl-alcohol dehydrogenase; Location of EST gb:H37170, gb:H77227 and gb:AA605565 138 At1g09500 D2 similar to Eucalyptus gunnii alcohol dehydrogenase of unknown physiological function (GI:1143445), Vigna unguiculata (gi:1854445), NOT a cinnamyl-alcohol dehydrogenase 139 At1g09530 D1, D2, Dm PIF3_PAP3_POC1__phytochrome interacting factor 3 (PIF3), identical to phytochrome interacting factor 3 (PIF3) GI:3929585 from (Arabidopsis thaliana) 140 At1g09550 D2, Dm pectinacetylesterase, putative, similar to pectinacetylesterase precursor GI:1431629 from (Vigna radiata) 141 At1g09590 D1, Dm 60S ribosomal protein L21 (RPL21A), Similar to L21 family of ribosomal protein; amino acid sequence is identical to F21M12.8 142 At1g09620 D2, Dm similar to leucyl-tRNA synthetase, putative / leucine--tRNA ligase, putative [Arabidopsis thaliana] (TAIR:At4g04350.1); similar to leucyl tRNA synthetase [Homo sapiens] (GB:BAA95667.1); similar to SYLC_HUMAN Leucyl-tRNA synthetase, cytoplasmic (Leucine--tRNA ligase) (LeuRS) (GB:Q9P2J5); similar to KIAA1352 protein [Homo sapiens] (GB:BAA92590.1); similar to MGC82093 protein [Xenopus laevis] (GB:AAH79713.1); similar to PREDICTED: similar to Leucyl-tRNA synthetase, cytoplasmic (Leucine--tRNA ligase) (LeuRS) [Canis familiaris] (GB:XP_535229.1); contains InterPro domain Aminoacyl-tRNA synthetase, class I (InterPro:IPR001412); contains InterPro domain Leucyl-tRNA synthetase archae/euk cytosolic, class Ia (InterPro:IPR004493); contains InterPro domain Aminoacyl-tRNA synthetase, class Ia (InterPro:IPR002300) 143 At1g09740 D2, Dm ethylene-responsive protein, putative, similar to ER6 protein (Lycopersicon esculentum) GI:5669654; contains Pfam profile PF00582: universal stress protein family 144 At1g09750 D1, D2, Dm chloroplast nucleoid DNA-binding protein-related, contains Pfam profile PF00026: Eukaryotic aspartyl protease;b similar to CND41, chloroplast nucleoid DNA binding protein (GI:2541876) (Nicotiana tabacum) 145 At1g09770 Dm ATCDC5_CDC5__myb family transcription factor, contains Pfam profile: PF00249 myb-like DNA- binding domain 146 At1g09780 D1, Dm 2,3-biphosphoglycerate-independent phosphoglycerate mutase, putative / phosphoglyceromutase, putative, strong similarity to SP:Q42908 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.1) (Phosphoglyceromutase) {Mesembryanthemum crystallinum}; contains Pfam profile PF01676: Metalloenzyme superfamily 147 At1g09795 D2 ATATP-PRT2__ATP phosphoribosyl transferase 2 (ATP-PRT2), identical to ATP phosphoribosyl transferase (AtATP-PRT2) (Arabidopsis thaliana) GI:6683619; supporting cDNA gi:6683618:dbj:AB025250.1: 148 At1g09830 D2 phosphoribosylamine--glycine ligase (PUR2), Identical to phosphoribosylamine--glycine ligase, chloroplast (precursor) SP:P52420 from (Arabidopsis thaliana) 149 At1g09840 Dm shaggy-related protein kinase kappa / ASK-kappa (ASK10), identical to shaggy-related protein kinase kappa SP:Q39019 GI:717180 from (Arabidopsis thaliana) 150 At1g09870 D2, Dm histidine acid phosphatase family protein, contains Pfam profile PF00328: Histidine acid phosphatase; similar to multiple inositol polyphosphate phosphatase (GI:4105496)(Mus musculus); EST gb:R64758 comes from this gene 151 At1g09970 D2 leucine-rich repeat transmembrane protein kinase, putative, Similar to A. thaliana receptor- like protein kinase (gb:RLK5_ARATH). ESTs gb:ATTS0475,gb:ATTS4362 come from this gene isoform contains a TG acceptor site at intron. 152 At1g10020 Dm expressed protein 153 At1g10030 Dm integral membrane family protein, contains Pfam PF03694: Erg28 like protein 154 At1g10090 D1, Dm expressed protein 155 At1g10140 D1, D2, Dm expressed protein, similar to EST gb:AA598098 156 At1g10200 D2 transcription factor LIM, putative, strong similarity to transcription factor Ntlim1 (Nicotiana tabacum) GI:5689136, LIM domain protein WLIM-1 (Helianthus annuus) GI:5070280; contains Pfam profile PF00412: LIM domain 157 At1g10230 D2, Dm ASK18__E3 ubiquitin ligase SCF complex subunit SKP1/ASK1 (At18), putative, E3 ubiquitin ligase; similar to Skp1 homolog Skp1a GI:3068807 (Arabidopsis thaliana) 158 At1g10240 Dm far-red impaired responsive protein, putative, similar to far-red impaired response protein FAR1 (Arabidopsis thaliana) gi:5764395:gb:AAD51282; contains Pfam:PF03101 domain: FAR1 family

159 At1g10270 D2 pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile: PF01535 PPR repeat; similar to ESTs gb:R30192 and gb:AA651017 160 At1g10290 Dm ADL6_DRP2A__dynamin-like protein 6 (ADL6), identical to dynamin-like protein 6 (ADL6) (Arabidopsis thaliana) GI:6651399; contains Pfam profiles PF01031: Dynamin central region, PF00350: Dynamin family, PF02212: Dynamin GTPase effector domain, PF00169: PH domain 161 At1g10300 Dm GTP-binding protein-related, contains similarity to nucleolar GTP-binding protein 1 SP: Q9BZE4 from (Homo sapiens); 162 At1g10360 D2 ATGSTU18_GST29__glutathione S-transferase, putative, similar to glutathione S-transferase (sp:Q03666:GTX4_TOBAC); similar to EST gb:H36275 gb:AB039930. 163 At1g10385 Dm expressed protein 164 At1g10420 Dm expressed protein 165 At1g10470 D1, D2, Dm ARR4_ATRR1_IBC7__two-component responsive regulator / response regulator 4 (ARR4), identical to responce regulator1 GI:3273195 from (Arabidopsis thaliana); identical to cDNA ARR4 mRNA for response regulator 4 GI:3953596 166 At1g10500 D1, D2, Dm ATCPISCA__Involved in chloroplast Fe-S cluster assembly. Located in the chloroplast stroma. Expressed preferentially in green tissues. 167 At1g10522 D2, Dm expressed protein 168 At1g10560 Dm armadillo/beta-catenin repeat family protein / U-box domain-containing protein, contains Pfam domain, PF00514: Armadillo/beta-catenin-like repeats and Pfam, PF04564: U-box domain 169 At1g10660 Dm expressed protein 170 At1g10840 Dm TIF3H1__eukaryotic translation initiation factor 3 subunit 3 / eIF-3 gamma / eIF3h (TIF3H1), identical to SP:Q9C5Z2 Eukaryotic translation initiation factor 3 subunit 3 (eIF-3 gamma) (eIF3 p38 subunit) (eIF3h) {Arabidopsis thaliana}; contains Pfam profile PF01398: Mov34/MPN/PAD-1 family 171 At1g10850 Dm Leucine-rich repeat protein kinase family protein; FUNCTIONS IN: protein serine/threonine kinase activity, protein kinase activity, ATP binding; INVOLVED IN: transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation; 172 At1g10940 D2, Dm ASK1__serine/threonine protein kinase, putative, similar to serine/threonine-protein kinase ASK1 (Arabidopsis thaliana) SWISS-PROT:P43291 173 At1g11120 D2, Dm expressed protein 174 At1g11190 D2 BFN1__bifunctional nuclease (BFN1), identical to bifunctional nuclease bfn1 (Arabidopsis thaliana) gi:4099831:gb:AAD00693 175 At1g11210 D2, Dm expressed protein, contains similarity to cotton fiber expressed protein 1 (Gossypium hirsutum) gi:3264828:gb:AAC33276 176 At1g11260 D1, D2, Dm glucose transporter (STP1), nearly identical to glucose transporter GB:P23586 SP:P23586 from (Arabidopsis thaliana) 177 At1g11410 Dm S-locus protein kinase, putative, similar to receptor-like protein kinase (Arabidopsis thaliana) gi:4008008:gb:AAC95352; contains S-locus glycoprotein family domain, Pfam:PF00954 178 At1g11430 D1, D2, Dm plastid developmental protein DAG, putative, similar to DAG protein, chloroplast precursor (Garden snapdragon) SWISS-PROT:Q38732 179 At1g11480 D1, Dm eukaryotic translation initiation factor-related, contains weak similarity to Swiss- Prot:P23588 eukaryotic translation initiation factor 4B (eIF-4B) (Homo sapiens) 180 At1g11530 D1 Encodes a single cysteine active site thioredoxin-related protein, similar to thioredoxin H- type from Arabidopsis thaliana SP:P29448, Nicotiana tabacum SP:Q07090; contains Pfam profile: PF00085 Thioredoxin; 181 At1g11545 Dm xyloglucan:xyloglucosyl transferase, putative / xyloglucan endotransglycosylase, putative / endo-xyloglucan transferase, putative, similar to endo-xyloglucan transferase GI:2244732 from (Gossypium hirsutum) 182 At1g11700 D2, Dm expressed protein, contains Pfam profile PF04520: Protein of unknown function, DUF584 183 At1g11720 D2 ATSS3__Encodes a starch synthase that in addition to its role in starch biosynthesis also has a negative regulatory function in the biosynthesis of transient starch. 184 At1g11760 D1, D2, Dm expressed protein, weak similarity to Pfam PF01648: 4`-phosphopantetheinyl transferase superfamily 185 At1g11840 D1, D2, Dm ATGLX1__lactoylglutathione lyase, putative / glyoxalase I, putative, highly similar to putative lactoylglutathione lyase SP:Q39366 from (Brassica oleracea) 186 At1g11860 D1 aminomethyltransferase, putative, similar to aminomethyltransferase, mitochondrial precursor SP:O49849 from (Flaveria anomala) 187 At1g11910 D1, D2, Dm aspartyl protease family protein, contains Pfam profiles: PF00026 eukaryotic aspartyl protease, PF03489 surfactant protein B, PF05184 saposin-like type B, region 1 188 At1g12000 D2, Dm pyrophosphate--fructose-6-phosphate 1-phosphotransferase beta subunit, putative / pyrophosphate-dependent 6-phosphofructose-1-kinase, putative, strong similarity to SP:Q41141 Pyrophosphate--fructose 6-phosphate 1-phosphotransferase beta subunit (EC 2.7.1.90) (PFP) ((PPI-PFK) {Ricinus communis}; contains Pfam profile PF00365: Phosphofructokinase 189 At1g12010 D2, Dm 1-aminocyclopropane-1-carboxylate oxidase, putative / ACC oxidase, putative, Strong similarity to amino-cyclopropane-carboxylic acid oxidase (ACC ox2) (GI:559407) from Brassica napus. ESTs gb:Z48548 and gb:Z48549 come from this gene 190 At1g12250 Dm thylakoid lumenal protein-related, weak similarity to SP:O22160 Thylakoid lumenal 15 kDa protein, chloroplast precursor (p15) {Arabidopsis thaliana}; contains Pfam profile PF00805: Pentapeptide repeats (8 copies) 191 At1g12380 D1 expressed protein 192 At1g12500 D2 phosphate translocator-related, low similarity to glucose-6-phosphate/phosphate-translocator precursor (Zea mays) GI:2997589, phosphoenolpyruvate/phosphate translocator precursor (Mesembryanthemum crystallinum) GI:9295275, SP:P21727:CPTR_PEA Triose phosphate/phosphate translocator, chloroplast precursor (CTPT) {Pisum sativum} 193 At1g12520 D1, Dm CCS1_ATCCS__superoxide dismutase copper chaperone, putative, similar to copper chaperone for superoxide dismutase (Homo sapiens) gi:2431868:gb:AAC51764 194 At1g12560 D1, D2, Dm ATEXPA7_ATEXP7_ATHEXP ALPHA 1.26_EXP7__expansin, putative (EXP7), similar to expansin GI:2828241 from (Brassica napus); alpha-expansin gene family, PMID:11641069 195 At1g12580 Dm protein kinase family protein, contains protein kinase domain, Pfam:PF00069; contains similarity to calcium-dependent protein kinase GI:5162877 from (Marchantia polymorpha) 196 At1g12780 D2, Dm Encodes a UDP-glucose epimerase that catalyzes the interconversion of the sugar nucleotides UDP-glucose UDP-galactose via a UDP-4-keto-hexose intermediate. 197 At1g12800 D1, Dm S1 RNA-binding domain-containing protein, contains Pfam domain, PF00575: S1 RNA binding domain

198 At1g12845 D2, Dm expressed protein 199 At1g12900 D1, D2, Dm glyceraldehyde 3-phosphate dehydrogenase, chloroplast, putative / NADP-dependent glyceraldehydephosphate dehydrogenase, putative, similar to SP:P25856 Glyceraldehyde 3- phosphate dehydrogenase A, chloroplast precursor (EC 1.2.1.13) (NADP-dependent glyceraldehydephosphate dehydrogenase subunit A) {Arabidopsis thaliana}; contains Pfam profiles PF02800: Glyceraldehyde 3-phosphate dehydrogenase C-terminal domain, PF00044: Glyceraldehyde 3-phosphate dehydrogenase NAD binding domain 200 At1g12990 Dm glycosyl transferase family 17 protein, low similarity to beta-1,4-mannosyl-glycoprotein beta- 1,4-N-acetylglucosaminyltransferase (EC 2.4.1.144) from Mus musculus (SP:Q10470), Rattus norvegicus (SP:Q02527), Homo sapiens (SP:Q09327); contains Pfam profile PF04724 :Glycosyltransferase family 17 201 At1g13020 Dm eukaryotic translation initiation factor, putative (EIF4B5), eukaryotic initiation factor 4B (GI:6739522) {Arabidopsis thaliana}; EST gb:T22808 comes from this gene 202 At1g13080 D2 CYP71B2__cytochrome P450 family protein, identical to gb:D78605 cytochrome P450 monooxygenase from Arabidopsis thaliana and is a member of the PF:00067 Cytochrome P450 family. ESTs gb:Z18072, gb:Z35218 and gb:T43466 come from this gene 203 At1g13090 D1 CYP71B28__cytochrome P450 71B28, putative (CYP71B28), Identical to Cytochrome P450 (SP:Q9SAE3) (Arabidopsis thaliana); strong similarity to gb:X97864 cytochrome P450 from Arabidopsis thaliana and is a member of the PF:00067 Cytochrome P450 family. ESTs gb:N65665, gb:T14112, gb:T76255, gb:T20906 and gb:AI100027 come from this gene 204 At1g13110 D1, D2, Dm CYP71B7__cytochrome P450 71B7 (CYP71B7), identical to (SP:Q96514) cytochrome P450 71B7 (Arabidopsis thaliana); PF:00067 Cytochrome P450 family. ESTs gb:T44875, gb:T04814, gb:R65111, gb:T44310 and gb:T04541 come from this gene; identical to cDNA cytochrome P450 GI:1523795, ATCYP71B7 205 At1g13220 D1, D2 nuclear matrix constituent protein-related, similar to nuclear matrix constituent protein 1 (NMCP1) (Daucus carota) GI:2190187 206 At1g13260 D2, Dm RAV1__DNA-binding protein RAV1 (RAV1), identical to SP:Q9ZWM9 DNA-binding protein RAV1 {Arabidopsis thaliana}, RAV1 GI:3868857 from (Arabidopsis thaliana) 207 At1g13360 D2 expressed protein 208 At1g13440 D2 glyceraldehyde 3-phosphate dehydrogenase, cytosolic, putative / NAD-dependent glyceraldehyde- 3-phosphate dehydrogenase, putative, very strong similarity to SP:P25858 Glyceraldehyde 3- phosphate dehydrogenase, cytosolic (EC 1.2.1.12) {Arabidopsis thaliana}; contains Pfam profiles PF02800: Glyceraldehyde 3-phosphate dehydrogenase C-terminal domain, PF00044: Glyceraldehyde 3-phosphate dehydrogenase NAD binding domain 209 At1g13760 D2, Dm expressed protein 210 At1g13820 D2 hydrolase, alpha/beta fold family protein, contains Pfam profile PF00561: hydrolase, alpha/beta fold family 211 At1g13930 D1, D2, Dm expressed protein, weakly similar to drought-induced protein SDi-6 (PIR:S71562) common sunflower (fragment) 212 At1g13990 D1, D2, Dm expressed protein 213 At1g14205 D1, Dm ribosomal protein L18 family protein, similar to SP:P09415 50S ribosomal protein L18 {Bacillus stearothermophilus} 214 At1g14250 D1, Dm nucleoside phosphatase family protein / GDA1/CD39 family protein, low similarity to SP:P97687 Ectonucleoside triphosphate diphosphohydrolase 1 (EC 3.6.1.5) (Ecto-apyrase) {Rattus norvegicus}; contains Pfam profile PF01150: GDA1/CD39 (nucleoside phosphatase) family 215 At1g14270 D1, D2, Dm CAAX amino terminal protease family protein, contains Pfam profile PF02517: CAAX amino terminal protease family 216 At1g14320 Dm 60S ribosomal protein L10 (RPL10A) / Wilm`s tumor suppressor protein-related, similar to tumor suppressor GI:575354 from (Oryza sativa) 217 At1g14345 D1, Dm expressed protein, contains one transmembrane domain 218 At1g14400 D2 UBC1_ATUBC1__ubiquitin-conjugating enzyme 1 (UBC1), E2; identical to gi:431259, SP:P25865 219 At1g14410 D1, Dm ATWHY1__DNA-binding protein-related, similar to DNA-binding protein p24 GI:9651810 from (Solanum tuberosum) 220 At1g14610 Dm TWN2_VALRS__valyl-tRNA synthetase / valine--tRNA ligase (VALRS), nearly identical to SP:P93736 Valyl-tRNA synthetase (EC 6.1.1.9) (Valine--tRNA ligase) (ValRS) {Arabidopsis thaliana}

221 At1g14840 D1 ATMAP70-4__Encodes a microtubule associated protein (MAP70-4). Expressed in all tissues. 222 At1g14870 D2, Dm expressed protein, similar to PGPS/D12 (Petunia x hybrida) GI:4105794; contains Pfam profile PF04749: Protein of unknown function, DUF614 223 At1g14930 D1, Dm major latex protein-related / MLP-related, low similarity to major latex protein {Papaver somniferum}(GI:20810) ; contains Pfam profile PF00407: Pathogenesis-related protein Bet v I family 224 At1g14980 D2, Dm CPN10__10 kDa chaperonin (CPN10), identical to SP:P34893 from (Arabidopsis thaliana) 225 At1g15040 D2, Dm glutamine amidotransferase-related 226 At1g15060 Dm expressed protein 227 At1g15080 Dm ATPAP2_ATLPP2_LPP2__phosphatidic acid phosphatase family protein / PAP2 family protein, similar to phosphatidic acid phosphatase 2a2 (Cavia porcellus) GI:3641336; contains Pfam profile PF01569 PAP2 superfamily 228 At1g15140 D2, Dm oxidoreductase NAD-binding domain-containing protein, Contains Pfam profile PF00175: Oxidoreductase NAD-binding domain; ESTs gb:H76345 and gb:AA651465 come from this gene 229 At1g15230 D1, D2, Dm expressed protein, ESTs gb:R30529, gb:Z48463, gb:Z48467, gb:AA597369 and gb:AA394772 come from this gene 230 At1g15270 D2 expressed protein, ESTs gb:AA650895, gb:AA720043 and gb:R29777 come from this gene 231 At1g15310 D1 ATHSRP54A_SRP54-1__signal recognition particle 54 kDa protein 1 / SRP54 (SRP-54) (SRP-54A), identical to Swiss-Prot:P37106 signal recognition particle 54 kDa protein 1 (SRP54) (Arabidopsis thaliana) 232 At1g15400 D2, Dm expressed protein, ESTs gb:H37295 and gb:R64895 come from this gene 233 At1g15670 D2, Dm kelch repeat-containing F-box family protein, similar to SP:Q9ER30 Kelch-related protein 1 (Sarcosin) {Rattus norvegicus}; contains Pfam profiles PF01344: Kelch motif, PF00646: F-box domain 234 At1g15690 D1, D2, Dm AVP1_ATAVP3_AVP-3__pyrophosphate-energized vacuolar membrane proton pump / pyrophosphate- energized inorganic pyrophosphatase (AVP-3), identical to pyrophosphate-energized vacuolar membrane proton pump (pyrophosphate-energized inorganic pyrophosphatase) SP:P31414 from (Arabidopsis thaliana) 235 At1g15730 Dm PRLI-interacting factor L, putative, strong similarity to PRLI-interacting factor L GI:11139268 from (Arabidopsis thaliana); contains Pfam profile PF02492: Cobalamin synthesis protein/P47K 236 At1g15740 Dm leucine-rich repeat family protein 237 At1g15880 Dm GOS11_ATGOS11__Golgi SNARE 11 protein, identical to Golgi SNARE 11 protein (GI:13898893) {Arabidopsis thaliana}; similar to putative cis-Golgi SNARE protein GI:2583133 from (Arabidopsis thaliana);similar toSP:O95249: 28 kDa Golgi SNARE protein (28 kDa cis-Golgi SNARE p28) (GOS-28). (Homo sapiens); similar to Golgi SNARE protein (Golgi SNAP receptor complex member 1) (28 kDa cis-Golgi SNARE p28) (GOS-28) (SP:Q62931) {Rattus norvegicus} 238 At1g15930 D1, Dm 40S ribosomal protein S12 (RPS12A), similar to 40S ribosomal protein S12 GI:4263712 from (Arabidopsis thaliana) 239 At1g15950 D2, Dm CCR1_ATCCR1_IRX4__cinnamoyl-CoA reductase, putative, nearly identical to CCR1 (GI:12034897), similar to cinnamoyl CoA reductase GI:2058310 from (Eucalyptus gunnii) 240 At1g15960 D2, Dm NRAMP6_ATNRAMP6__similar to NRAMP metal ion transporter 4 (NRAMP4) [Arabidopsis thaliana] (TAIR:At5g67330.1); similar to root-specific metal transporter [Malus baccata] (GB:AAU00158.1); similar to root-specific metal transporter [Lycopersicon esculentum] (GB:AAP21818.1); contains InterPro domain Natural resistance-associated macrophage protein (InterPro:IPR001046) 241 At1g16000 Dm expressed protein 242 At1g16080 D2 expressed protein 243 At1g16180 D1, Dm TMS membrane family protein / tumour differentially expressed (TDE) family protein, contains Pfam domain, PF03348: TMS membrane protein/tumour differentially expressed protein (TDE) 244 At1g16240 D1, D2, Dm SYP51_ATSYP51__syntaxin 51 (SYP51), identical to SP:Q9SA23 Syntaxin 51 (AtSYP51) {Arabidopsis thaliana}; supporting cDNA gi:13811643:gb:AF355755.1:AF355755 245 At1g16320 D1 expressed protein, ESTs gb:T76348, gb:N65615 and gb:Z18119 come from this gene 246 At1g16410 D1, Dm CYP79F1_BUS1_SPS1__cytochrome P450, putative, similar to gb:AF069494 cytochrome P450 from Sinapis alba and is a member of the PF:00067 Cytochrome P450 family 247 At1g16730 Dm expressed protein 248 At1g16810 D2, Dm expressed protein 249 At1g16840 D1, Dm expressed protein 250 At1g16850 D1, D2, Dm expressed protein 251 At1g16880 D1, Dm uridylyltransferase-related, similar to (Protein-PII) uridylyltransferase (PII uridylyl- transferase) (Uridylyl removing enzyme) (UTase)(SP:Q9AC53) (Caulobacter crescentus) 252 At1g16890 D1, Dm ubiquitin-conjugating enzyme, putative, nearly identical to ubiquitin-conjugating enzyme E2 (Catharanthus roseus) GI:5381319; contains Pfam profile PF00179: Ubiquitin-conjugating enzyme

253 At1g16920 Dm RAB11_ATRABA4B__Ras-related GTP-binding protein, putative, similar to GTP binding protein GI:218228 from (Vicia faba); identical to cDNA small GTP-binding protein (Rab11) GI:451859 254 At1g17000 Dm ATTPS3_TPS3__alpha, alpha-trehalose-phosphate synthase, UDP-forming, putative / trehalose-6- phosphate synthase, putative / UDP-glucose-glucosephosphate glucosyltransferase, putative, similar to trehalose-6-phosphate synthase SL-TPS/P (Selaginella lepidophylla) GI:4100325, GI:4468259 from (Pichia angusta); contains Pfam profiles PF00982: Glycosyltransferase family 20, PF02358: Trehalose-phosphatase 255 At1g17050 D1, Dm geranyl diphosphate synthase, putative / GPPS, putative / dimethylallyltransferase, putative / prenyl transferase, putative, similar to GI:11322965; Except for first 55 amino acids, 52% identical to Prenyl transferase (Cyanophora paradoxa) (gi 99282). Location of est 120E9T7 (gb:T43950) 256 At1g17100 D1, D2, Dm SOUL heme-binding family protein, similar to SOUL protein (Mus musculus) GI:4886906; contains Pfam profile PF04832: SOUL heme-binding protein 257 At1g17220 D2, Dm translation initiation factor IF-2, chloroplast, putative, similar to SP:P57997:IF2C_PHAVU Translation initiation factor IF-2, chloroplast precursor (PvIF2cp) {Phaseolus vulgaris} 258 At1g17370 D1 oligouridylate-binding protein, putative, similar to oligouridylate binding protein (Nicotiana plumbaginifolia) GI:6996560; contains InterPro entry IPR000504: RNA-binding region RNP-1 (RNA recognition motif) (RRM) 259 At1g17470 Dm ATDRG1_ATDRG__developmentally regulated GTP-binding protein (DRG1), identical to developmentally regulated GTP binding protein (DRG1) (Arabidopsis thaliana) GI:2345150 260 At1g17530 D1, D2, Dm ATTIM23-1__mitochondrial import inner membrane translocase subunit Tim17/Tim22/Tim23 family protein, contains Pfam PF02466: Mitochondrial import inner membrane translocase subunit Tim17

261 At1g17550 D2, Dm HAB2__protein phosphatase 2C-related / PP2C-related, similar to protein phosphatase 2C GI:3242077 from (Arabidopsis thaliana) 262 At1g17650 D1 similar to 6-phosphogluconate dehydrogenase NAD-binding domain-containing protein [Arabidopsis thaliana] (TAIR:At3g25530.1); similar to putative gamma hydroxybutyrate dehydrogenase [Oryza sativa (japonica cultivar-group)] (GB:NP_918497.1); contains InterPro domain 6- phosphogluconate dehydrogenase, NAD binding domain (InterPro:IPR006115) 263 At1g17700 D2, Dm prenylated rab acceptor (PRA1) family protein, weak similarity to prenylated Rab acceptor 1 (PRA1) (Homo sapiens) GI:4877285; contains Pfam profile PF03208: Prenylated rab acceptor (PRA1) 264 At1g17830 Dm expressed protein 265 At1g17870 D1, D2, Dm S2P-like putative metalloprotease, also contain transmembrane helices near their C-termini and many of them, five of seven, contain a conserved zinc-binding motif HEXXH. Homolog of EGY1. Each of the EGY1 and EGY-like proteins share two additional highly conserved motifs, the previously reported NPDG motif (aa 442聳454 in EGY1, Rudner et al., 1999) and a newly defined GNLR motif (aa 171聳179 in EGY1). The GNLR motif is a novel signature motif unique to EGY1 and EGY-like proteins as well as other EGY1 orthologs found in cyanobacteria. 266 At1g17880 D1, D2, Dm nascent polypeptide-associated complex (NAC) domain-containing protein / BTF3b-like transcription factor, putative, similar to SP:P20290 Transcription factor BTF3 (RNA polymerase B transcription factor 3) {Homo sapiens}; contains Pfam profile PF01849: NAC domain; identical to cDNA BTF3b-like factor GI:5912423 267 At1g17940 D2, Dm expressed protein 268 At1g17950 D2 MYB52_ATMYB52_BW52__myb family transcription factor (MYB52), similar to myb-like protein GI:6979341 from (Oryza sativa) 269 At1g17990 D1 12-oxophytodienoate reductase, putative, similar to OPR1 (GI:3882355) and OPR2 (GI:3882356) 270 At1g18060 D2 expressed protein 271 At1g18080 D1, D2, Dm ATARCA__WD-40 repeat family protein / auxin-dependent protein (ARCA) / guanine nucleotide- binding protein beta subunit, putative, identical to SP:O24456 Guanine nucleotide-binding protein beta subunit-like protein (WD-40 repeat auxin-dependent protein ARCA) {Arabidopsis thaliana}; contains 7 WD-40 repeats (PF00400) 272 At1g18120 D2, Dm pseudogene, putative myrosinase-associated protein 273 At1g18250 D1, D2, Dm ATLP-1__thaumatin, putative, identical to SP:P50699 Thaumatin-like protein precursor {Arabidopsis thaliana}; strong similarity to pathogenesis-related group 5 protein GI:2749943 from (Brassica rapa) 274 At1g18270 Dm ketose-bisphosphate aldolase class-II family protein, low similarity to KbaY (tagatose-1,6- bisphosphate aldolase) (Escherichia coli) GI:8895753; contains Pfam profile PF01116: Fructose- bisphosphate aldolase class-II 275 At1g18300 Dm ATNUDT4__MutT/nudix family protein, similar to SP:Q09790 Diadenosine 5`,5```-P1,P6- hexaphosphate hydrolase (EC 3.6.1.-) (Ap6A hydrolase) {Schizosaccharomyces pombe}; contains Pfam profile PF00293: NUDIX domain 276 At1g18540 D1, D2, Dm 60S ribosomal protein L6 (RPL6A), similar to 60S ribosomal protein L6 GI:7208784 from (Cicer arietinum) 277 At1g18620 D1, D2, Dm expressed protein 278 At1g18800 D2 nucleosome assembly protein (NAP) family protein, similar to SP:Q01105:SET protein (HLA-DR associated protein II) (PHAPII) (Phosphatase 2A inhibitor I2PP2A) {Homo sapiens}; contains Pfam profile PF00956: Nucleosome assembly protein (NAP) 279 At1g18870 Dm isochorismate synthase, putative / isochorismate mutase, putative, similar to GI:17223087 280 At1g19000 D2 myb family transcription factor, similar to MybSt1 GI:7705206 from (Solanum tuberosum) 281 At1g19090 Dm RKF2__serine/threonine protein kinase (RKF2), nearly identical to receptor-like serine/threonine kinase GI:2465925 from (Arabidopsis thaliana); intron 3 was added to circumvent a frameshift. Either a sequencing error exists or this may be a pseudogene. 282 At1g19120 Dm small nuclear ribonucleoprotein, putative / snRNP, putative / Sm protein, putative, similar to U6 snRNA-associated Sm-like protein LSm1 (Small nuclear ribonuclear CaSm, Cancer-associated Sm-like) (Homo sapiens) SWISS-PROT:O15116 283 At1g19150 D1, Dm LHCA2*1__chlorophyll A-B binding protein, putative / LHCI type II, putative, very strong similarity to PSI type II chlorophyll a/b-binding protein Lhca2*1 GI:541565 from (Arabidopsis thaliana); contains Pfam profile: PF00504 chlorophyll A-B binding protein 284 At1g19190 D2 expressed protein, contains similarity to anther-specific and pathogenesis response protein (PrMC3) GI:5487873 from (Pinus radiata) 285 At1g19370 D1, Dm expressed protein 286 At1g19380 D1, D2, Dm expressed protein 287 At1g19400 Dm expressed protein 288 At1g19440 D1 very-long-chain fatty acid condensing enzyme, putative, similar to GB:AAD37122 from (Arabidopsis thaliana) 289 At1g19450 D1, D2, Dm integral membrane protein, putative / sugar transporter family protein, similar to GB:U43629 GI:1209756 integral membrane protein from (Beta vulgaris); contains Pfam profile PF00083: major facilitator superfamily protein; contains TIGRfam TIGR00879: Sugar transporter 290 At1g19570 D1, D2, Dm DHAR__dehydroascorbate reductase, putative, similar to GB:BAA90672 from (Oryza sativa) 291 At1g19640 D2 JMT__S-adenosyl-L-methionine:jasmonic acid carboxyl methyltransferase (JMT), nearly identical to gi:13676829 292 At1g19650 Dm SEC14 cytosolic factor, putative / phosphoglyceride transfer protein, putative, similar to SP:P24859 from (Kluyveromyces lactissimilar to phosphatidylinositol transfer-like protein IV (GI:14486707) (Lotus japonicus); contains Pfam PF00650 : CRAL/TRIO domain; contains Pfam PF03765 : CRAL/TRIO, N-terminus 293 At1g19660 D1, D2, Dm wound-responsive family protein, similar to wound inducive gene (GI:8096273)(Nicotiana tabacum) 294 At1g19670 D1, Dm ATCLH1_ATHCOR1_CORI1__coronatine-responsive protein / coronatine-induced protein 1 (CORI1), identical to coronatine-induced protein 1 (CORI1) GI:30912637 from (Arabidopsis thaliana) 295 At1g19715 D2 jacalin lectin family protein, similar to agglutinin (Castanea crenata) GI:25528883; contains Pfam profile PF01419: Jacalin-like lectin domain 296 At1g19910 D1, D2, Dm AVA-P2_AVA-2PE__vacuolar ATP synthase 16 kDa proteolipid subunit 2 / V-ATPase 16 kDa proteolipid subunit 2 (AVAP2) (AVA-P2), identical to SP:Q39039 Vacuolar ATP synthase 16 kDa proteolipid subunit 2 (EC 3.6.3.14) (V-ATPase 16 kDa proteolipid subunit 2 {Arabidopsis thaliana}, nearly identical to vacuolar H+-ATPase proteolipid (16 kDa) subunit GI:755147 from (Gossypium hirsutum) 297 At1g19920 D1, D2, Dm APS2_ASA1_AMT1_TRP5_WEI2__sulfate adenylyltransferase 2 / ATP-sulfurylase 2 (ASA1) (MET3-1) (APS2), identical to ATP sulfurylase (APS2) (Arabidopsis thaliana) GI:1575324 298 At1g19960 D2 expressed protein 299 At1g20010 D1, D2, Dm TUB5__tubulin beta-5 chain (TUB5), nearly identical to SP:P29513 Tubulin beta-5 chain {Arabidopsis thaliana} 300 At1g20020 Dm ferredoxin--NADP(+) reductase, putative / adrenodoxin reductase, putative, strong similarity to Ferredoxin--NADP reductase, chloroplast precursor (EC 1.18.1.2) (FNR) from {Pisum sativum} SP:P10933, {Mesembryanthemum crystallinum} SP:P41343, {Spinacia oleracea} SP:P00455, (Capsicum annuum) GI:6899972 301 At1g20080 D2, Dm C2 domain-containing protein, contains INTERPRO:IPR000008 C2 domain 302 At1g20090 D2 ARAC4_ATRAC4_ATROP2_ROP2__Member of the Rho GTPase family. Functions to organize the microtubular cytoskeleton in combination with RIC1 and RIC4. These interactions affect pavement cell morphogenesis and pollen tube growth. ROP2 expression is stimulated by brassinosteroid treatment (PMID 16141452). 303 At1g20160 D1, D2, Dm subtilase family protein, similar to subtilisin-type protease precursor GI:14150446 from (Glycine max) 304 At1g20190 Dm ATEXPA11_ATEXP11_ATHEXP ALPHA 1.14_EXP11__expansin, putative (EXP11), similar to GB:U30460 from (Cucumis sativus); alpha-expansin gene family, PMID:11641069 305 At1g20330 D1, D2, Dm SMT2_CVP1_FRL1__S-adenosyl-methionine-sterol-C-methyltransferase, identical to sterol-C- methyltransferase GI:1061040 from (Arabidopsis thaliana) 306 At1g20440 D1, D2, Dm COR47__dehydrin (COR47), identical to dehydrin COR47 (Cold-induced COR47 protein) (Arabidopsis thaliana) SWISS-PROT:P31168 307 At1g20450 D1, D2, Dm LTI29_ERD10_LTI45__dehydrin (ERD10), identical to dehydrin ERD10 (Low-temperature-induced protein LTI45) (Arabidopsis thaliana) SWISS-PROT:P42759 308 At1g20650 D1, Dm protein kinase family protein, contains Pfam domain PF00069: Protein kinase domain 309 At1g20696 D1, D2, Dm HMGB3_NFD03_NFD3__high mobility group protein beta2 (HMGbeta2) / HMG protein beta2, nearly identical to HMG protein (HMGbeta2) (Arabidopsis thaliana) GI:2832361 310 At1g20780 D1, Dm armadillo/beta-catenin repeat protein-related / U-box domain-containing protein, low similarity to immediate-early fungal elicitor protein CMPG1 (Petroselinum crispum) GI:14582200; contains Pfam profile PF04564: U-box domain 311 At1g20840 D2, Dm transporter-related, low similarity to D-xylose proton-symporter (Lactobacillus brevis) GI:2895856; contains Pfam profile PF00083: major facilitator superfamily protein 312 At1g20850 D1, Dm XCP2__cysteine endopeptidase, papain-type (XCP2), identical to papain-type cysteine endopeptidase XCP2 GI:6708183 from (Arabidopsis thaliana) 313 At1g20890 Dm expressed protein, Location of ESTs OAO242 5` end, gb:Z30466 and OAO242 3` end, gb:Z30467 314 At1g21000 D1, D2, Dm zinc-binding family protein, similar to zinc-binding protein (Pisum sativum) GI:16117799; contains Pfam profile PF04640 : Protein of unknown function, DUF597 315 At1g21065 D1, D2, Dm expressed protein 316 At1g21080 D2 DNAJ heat shock N-terminal domain-containing protein, similar to SP:P39101 CAJ1 protein (Saccharomyces cerevisiae); contains Pfam profile PF00226 DnaJ domain; 317 At1g21190 D2, Dm small nuclear ribonucleoprotein, putative / snRNP, putative / Sm protein, putative, similar to SWISS-PROT:Q9Y4Z1 U6 snRNA-associated Sm-like protein LSm3 (MDS017) (Mouse) 318 At1g21270 D1, Dm WAK2__wall-associated kinase 2 (WAK2), identical to wall-associated kinase 2 (Arabidopsis thaliana) GI:4826399; induced by salicylic acid or INA (PMID:10380805) 319 At1g21400 D1, D2, Dm 2-oxoisovalerate dehydrogenase, putative / 3-methyl-2-oxobutanoate dehydrogenase, putative / branched-chain alpha-keto acid dehydrogenase E1 alpha subunit, putative, similar to branched- chain alpha-keto acid dehydrogenase E1-alpha subunit (Gallus gallus) GI:12964598; contains Pfam profile PF00676: Dehydrogenase E1 component 320 At1g21410 D1, D2, Dm F-box family protein, similar to SKP1 interacting partner 2 (SKIP2) TIGR_Ath1:At5g67250 321 At1g21450 D2 SCL1__scarecrow-like transcription factor 1 (SCL1), identical to scarecrow-like 1 GB:AAF21043 GI:6644390 from (Arabidopsis thaliana) 322 At1g21460 D2, Dm nodulin MtN3 family protein, contains similarity to MTN3 (nodule development protein) GB:Y08726 GI:1619601 from (Medicago truncatula) 323 At1g21500 D1, Dm expressed protein 324 At1g21550 Dm calcium-binding protein, putative, contains similarity to calcium-binding protein GB:CAB63264 GI:6580549 from (Lotus japonicus) 325 At1g21590 D1, D2, Dm protein kinase family protein, contains Pfam domain, PF00069: Protein kinase domain 326 At1g21600 D2 expressed protein, similar to hypothetical protein GB:AAD41412 GI:5263310 from (Arabidopsis thaliana) 327 At1g21680 D2, Dm expressed protein, similar to TolB protein precursor (SP:Q9ZDM5) {Rickettsia prowazekii}; ESTs gb:N96028, gb:F14286, gb:T20680, gb:F14443, gb:AA657300 and gb:N65244 come from this gene 328 At1g21690 Dm EMB1968__replication factor C 37 kDa, putative, Similar to SWISS-PROT:P35249 activator 1 37 kDa subunit (Replication factor C 37 kDa subunit, A1 37 kDa subunit, RF-C 37 kDa subunit, RFC37) (Homo sapiens); contains Pfam domain, PF00004: ATPase, AAA family 329 At1g21770 D2 expressed protein 330 At1g21780 D1, Dm BTB/POZ domain-containing protein. Contains similarity to gb:AJ000644 SPOP (speckle-type POZ protein) from Homo sapiens and contains a PF:00651 BTB/POZ domain. ESTs gb:T75841, gb:R89974, gb:R30221, gb:N96386, gb:T76457, gb:AI100013 and gb:T76456 come from this gene;supported by full-length. Interacts with CUL3A and CUL3B. 331 At1g21910 D2, Dm encodes a member of the DREB subfamily A-5 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 15 members in this subfamily including RAP2.1, RAP2.9 and RAP2.10. 332 At1g21920 D1, Dm MORN (Membrane Occupation and Recognition Nexus) repeat-containing protein /phosphatidylinositol-4-phosphate 5-kinase-related, similar to phosphatidylinositol-4- phosphate 5-kinase AtPIP5K1 (Arabidopsis thaliana) GI:3702691; contains Pfam profile PF02493: MORN repeat 333 At1g22015 Dm galactosyltransferase family protein, contains Pfam profile: PF01762 galactosyltransferase 334 At1g22070 Dm TGA3__bZIP family transcription factor (TGA3), identical to transcription factor GI:304113 from (Arabidopsis thaliana) 335 At1g22160 D1, D2, Dm senescence-associated protein-related, similar to senescence-associated protein SAG102 (GI:22331931) (Arabidopsis thaliana) 336 At1g22360 D2 UDP-glucoronosyl/UDP-glucosyl transferase family protein, contains Pfam profile: PF00201 UDP- glucoronosyl and UDP-glucosyl transferase 337 At1g22370 D2, Dm UDP-glucoronosyl/UDP-glucosyl transferase family protein, glycosyltransferase family 338 At1g22460 Dm expressed protein, similar to axi 1 (Nicotiana tabacum) GI:559921; contains Pfam profile PF03138: Plant protein family 339 At1g22480 Dm plastocyanin-like domain-containing protein 340 At1g22530 D1, D2, Dm SEC14 cytosolic factor family protein / phosphoglyceride transfer family protein, contains Pfam PF00650 : CRAL/TRIO domain; contains Pfam PF03765 : CRAL/TRIO, N-terminus; similar to SEC14-like protein 2 (Alpha-tocopherol associated protein) (TAP) (bTAP) (Fragment) (SP:P58875) {Bos taurus} 341 At1g22640 D1, D2, Dm ATMYB21_ATMYB3_MYB3_ATMYB3__myb family transcription factor (MYB4), similar to myb-related protein GI:1020155 from (Arabidopsis thaliana) 342 At1g22690 D1, D2, Dm gibberellin-responsive protein, putative, similar to SP:P46688 Gibberellin-regulated protein 2 precursor {Arabidopsis thaliana}; contains Pfam profile PF02704: Gibberellin regulated protein 343 At1g22710 D1, D2, Dm SUC2_ATSUC2_SUT1__sucrose transporter / sucrose-proton symporter (SUC2), nearly identical to sucrose-proton symporter SUC2 (Arabidopsis thaliana) GI:407092 344 At1g22750 D2 expressed protein 345 At1g22770 D2 GI_FB__gigantea protein (GI), identical to gigantea protein SP:Q9SQI2 from (Arabidopsis thaliana) 346 At1g22780 D2, Dm PFL_PFL1_RPS18A__40S ribosomal protein S18 (RPS18A), Match to ribosomal S18 gene mRNA gb:Z28701, DNA gb:Z23165 from A. thaliana. ESTs gb:T21121, gb:Z17755, gb:R64776 and gb:R30430 come from this gene 347 At1g22900 D1, D2, Dm similar to disease resistance-responsive family protein [Arabidopsis thaliana] (TAIR:At5g42500.1); similar to At5g42500 [Oryza sativa (japonica cultivar-group)] (GB:AAX96290.1); contains InterPro domain Plant disease resistance response protein (InterPro:IPR004265) 348 At1g22930 D1, D2, Dm T-complex protein 11, contains Pfam PF05794: T-complex protein 11 349 At1g22980 D2 expressed protein 350 At1g23030 D2, Dm armadillo/beta-catenin repeat family protein / U-box domain-containing protein, contains Pfam domain, PF00514: Armadillo/beta-catenin-like repeats and Pfam, PF04564: U-box domain 351 At1g23040 D1, D2, Dm hydroxyproline-rich glycoprotein family protein, contains proline-rich domains, INTERPRO:IPR000694 352 At1g23100 Dm 10 kDa chaperonin, putative, similar to 10 kDa chaperonin SP:P34893 from (Arabidopsis thaliana) 353 At1g23130 D2, Dm Bet v I allergen family protein, similar to Csf-2 (Cucumis sativus)(GI:5762258)(J Am Soc Hortic Sci 124, 136-139 (1999)); location of ESTs gb:T45139 and gb:T43456 ; contains Pfam profile PF00407: Pathogenesis-related protein Bet v I family 354 At1g23190 D1, D2, Dm phosphoglucomutase, cytoplasmic, putative / glucose phosphomutase, putative, strong similarity to SP:P93805 Phosphoglucomutase, cytoplasmic 2 (EC 5.4.2.2) (Glucose phosphomutase 2) (PGM 2) {Zea mays}; contains InterPro accession IPR006352: Phosphoglucosamine mutase

355 At1g23280 D2 MAK16 protein-related, contains similarity to MAK16 protein SP:P10962 from (Saccharomyces cerevisiae) 356 At1g23290 D1, D2, Dm RPL27AB_RPL27A__Regulated by TCP20. 357 At1g23310 D1, D2, Dm GGT1_AOAT1__glutamate:glyoxylate aminotransferase 1 (GGT1), identical to glutamate:glyoxylate aminotransferase 1 (Arabidopsis thaliana) GI:24461827; similar to alanine aminotransferase GI:4730884 from (Oryza sativa); contains Pfam profile PF00155: aminotransferase, classes I and II 358 At1g23480 D1, D2, Dm ATCSLA03_ATCSLA3_CSLA03__glycosyl transferase family 2 protein, similar to cellulose synthase from Agrobacterium tumeficiens (gi:710492) and Agrobacterium radiobacter (gi:710493); contains Pfam glycosyl transferase, group 2 family protein domain PF00535 isoform contains GG acceptor splice site at intron 1 359 At1g23490 Dm ATARF_ATARF1_ATARFA1A__Gene encoding ADP-ribosylation factor and similar to other ARFs and ARF-like proteins. Members of this family are known to be essential for vesicle coating and uncoating and functions in GTP-binding. The gene is shown to play a role in cell division, cell expansion and cellulose production using antisense construct. 360 At1g23740 D1, D2, Dm oxidoreductase, zinc-binding dehydrogenase family protein, contains Pfam profile PF00107: oxidoreductase, zinc-binding dehydrogenase family 361 At1g23950 D1 expressed protein 362 At1g23960 D1, D2, Dm expressed protein, contains Pfam profile PF04776: Protein of unknown function (DUF626) 363 At1g24145 D2, Dm expressed protein 364 At1g24340 D2 EMB2421__similar to phenol 2-monooxygenase like FAD dependent oxidoreductase of plant origin in apicomplexans [Cryptosporidium parvum] (GB:EAK89698.1); contains InterPro domain Flavoprotein monooxygenase (InterPro:IPR000733); contains InterPro domain Monooxygenase, FAD- binding (InterPro:IPR002938); contains InterPro domain NAD-binding site (InterPro:IPR000205); contains InterPro domain Aromatic-ring hydroxylase (InterPro:IPR003042)

365 At1g24360 D2, Dm 3-oxoacyl-(acyl-carrier protein) reductase, chloroplast / 3-ketoacyl-acyl carrier protein reductase, identical to 3-oxoacyl-(acyl-carrier protein) reductase SP:P33207 from (Arabidopsis thaliana) 366 At1g24510 D2 T-complex protein 1 epsilon subunit, putative / TCP-1-epsilon, putative / chaperonin, putative, identical to SWISS-PROT:O04450- T-complex protein 1, epsilon subunit (TCP-1-epsilon) (Arabidopsis thaliana); strong similarity to SP:P54411 T-complex protein 1, epsilon subunit (TCP-1-epsilon) (CCT-epsilon) (TCP-K36) {Avena sativa}; contains Pfam:PF00118 domain, TCP- 1/cpn60 chaperonin family 367 At1g25141 D1 UDP-3-0-acyl N-acetylglucosamine deacetylase family protein / F-box protein-related, contains weak hit to TIGRFAM TIGR01640 : F-box protein interaction domain and weak hit to Pfam PF00646: F-box domain; 368 At1g25230 D2 purple acid phosphatase family protein, contains Pfam profile: PF00149 calcineurin-like phosphoesterase; similar to purple acid phosphatase (GI:20257479) (Arabidopsis thaliana) 369 At1g25240 D2 epsin N-terminal homology (ENTH) domain-containing protein / clathrin assembly protein- related, contains Pfam PF01417: ENTH domain. ENTH (Epsin N-terminal homology) domain; similar to clathrin assembly protein AP180 (GI:6492344) (Xenopus laevis) 370 At1g25380 D1, D2, Dm mitochondrial substrate carrier family protein, contains Pfam profile: PF00153 mitochondrial carrier protein 371 At1g25400 Dm expressed protein, similar to unknown protein GI:6714347 from (Arabidopsis thaliana) 372 At1g25440 D2, Dm zinc finger (B-box type) family protein, similar to zinc finger protein GI:3618318 from (Oryza sativa) 373 At1g25490 D2 RCN1_ATB BETA BETA_EER1_PR65_REGA__serine/threonine protein phosphatase 2A (PP2A) regulatory subunit A (RCN1), identical to phosphoprotein phosphatase 2A, regulatory subunit A GI:1262171 from (Arabidopsis thaliana) 374 At1g25530 D1, D2, Dm lysine and histidine specific transporter, putative, similar to lysine and histidine specific transporter GI:2576361 from (Arabidopsis thaliana); contains Pfam profile PF01490: Transmembrane amino acid transporter protein 375 At1g26220 D1 GCN5-related N-acetyltransferase (GNAT) family protein, low similarity to SP:P09453 Ribosomal- protein-alanine acetyltransferase (EC 2.3.1.128) {Escherichia coli}; contains Pfam profile PF00583: acetyltransferase, GNAT family 376 At1g26240 D1, Dm proline-rich extensin-like family protein, similar to hydroxyproline-rich glycoprotein precursor gi:727264:gb:AAA87902; contains proline-rich extensin domains, INTERPRO:IPR002965 377 At1g26550 D2 peptidyl-prolyl cis-trans isomerase PPIC-type family protein, similar to SP:Q9Y237 Peptidyl- prolyl cis-trans isomerase NIMA-interacting 4 (EC 5.2.1.8) (Rotamase Pin4) (PPIase Pin4) (Parvulin 14) {Homo sapiens}; contains Pfam profile PF00639: PPIC-type PPIASE domain 378 At1g26580 Dm expressed protein, similar to putative MYB family transcription factor GB:AAD17429 GI:4335752 from (Arabidopsis thaliana) 379 At1g26630 D2 eukaryotic translation initiation factor 5A, putative / eIF-5A, putative, strong similariy to SP:Q9AXQ6 Eukaryotic translation initiation factor 5A-1 (eIF-5A 1) {Lycopersicon esculentum}

380 At1g26670 D2, Dm VTI12_ATVTI12_VTI1B__vesical transport v-SNARE 12 (VTI12) / vesicle soluble NSF attachment protein receptor VTI1b (VTI1B) receptor VTI1b, identical to SP:Q9SEL5 Vesicle transport v- SNARE 12 (AtVTI12) (Vesicle transport v-SNARE protein VTI1b) (Vesicle soluble NSF attachment protein receptor VTI1b) (AtVTI1b) {Arabidopsis thaliana} 381 At1g26800 D2 zinc finger (C3HC4-type RING finger) family protein, contains Pfam profile: PF00097 zinc finger, C3HC4 type (RING finger) 382 At1g26880 D2, Dm 60S ribosomal protein L34 (RPL34A), identical to GB:Q42351, location of EST 105E2T7, gb:T22624

383 At1g26910 D1, D2, Dm 60S ribosomal protein L10 (RPL10B), Nearly identical to ribosomal protein L10.e, Wilm`s tumor suppressor homologue, gi:17682 (Z15157), however differences in sequence indicate this is a different member of the L10 family 384 At1g26920 Dm expressed protein, Location of EST 228A16T7A, gb:N65686 385 At1g26970 Dm protein kinase, putative, similar to protein kinase (Arabidopsis thaliana) gi:2852449:dbj:BAA24695; contains protein kinase domain, Pfam:PF00069 386 At1g27020 D2 expressed protein 387 At1g27030 Dm expressed protein 388 At1g27100 D2 expressed protein, contains Pfam profile: PF04601 protein of unknown function (DUF569 389 At1g27150 D1, D2, Dm expressed protein 390 At1g27200 Dm expressed protein, contains Pfam PF01697: Domain of unknown function 391 At1g27300 D1, Dm expressed protein 392 At1g27390 D2 TOM20-2__mitochondrial import receptor subunit TOM20-2 (TOM20-2), identical to mitochondrial import receptor subunit TOM20-2 SP:P82873 from (Arabidopsis thaliana) 393 At1g27400 D1, D2, Dm 60S ribosomal protein L17 (RPL17A), similar to GB:P51413 from (Arabidopsis thaliana); similar to ESTs gb:L33542 and gb:AA660016 394 At1g27460 D1, Dm NPGR1__calmodulin-binding protein, similar to calmodulin-binding protein MPCBP (Zea mays) GI:10086260; contains Pfam profile PF00515: TPR Domain 395 At1g27520 Dm glycoside hydrolase family 47 protein, Similar to gb:U04299 mannosyl-oligosaccharide alpha- 1,2-mannosidase from Mus musculus. ESTs gb:R84145 and gb:AA394707 come from this gene 396 At1g27530 D2, Dm expressed protein, Similar to gb:AF151884 CGI-126 protein from Homo sapiens. EST gb:Z18048 comes from this gene 397 At1g27730 D1, D2, Dm ZAT10_STZ__Salt tolerance zinc finger protein responsive to chitin oligomers. 398 At1g27950 D2, Dm lipid transfer protein-related, low similarity to lipid transfer protein Picea abies GI:2627141; contains Pfam profile: PF00234: Protease inhibitor/seed storage/LTP family 399 At1g27970 D2 nuclear transport factor 2 (NTF2), putative, similar to Swiss-Prot:P33331 nuclear transport factor 2 (NTF-2) (Nuclear transport factor P10) (Saccharomyces cerevisiae) 400 At1g28060 D1, D2, Dm small nuclear ribonucleoprotein family protein / snRNP family protein, contains similarity to U4/U6 small nuclear ribonucleoprotein hPrp3 (Homo sapiens) gi:2708307:gb:AAC51926 401 At1g28120 D1, Dm expressed protein 402 At1g28140 D1, D2, Dm expressed protein, contains similarity to cytochrome oxidase I GI:1289267 from (Xantholinus sp.) 403 At1g28150 D2 expressed protein 404 At1g28240 D1, Dm expressed protein 405 At1g28260 D1, D2, Dm expressed protein 406 At1g28280 D1 VQ motif-containing protein, contains PF05678: VQ motif 407 At1g28330 D1, Dm DRM1__dormancy-associated protein, putative (DRM1), identical to dormancy-associated protein (Arabidopsis thaliana) GI:2995990; similar to dormancy-associated protein GI:2605887 from (Pisum sativum); contains Pfam profile PF05564: Dormancy/auxin associated protein 408 At1g28360 Dm ATERF12_ERF12__encodes a member of the ERF (ethylene response factor) subfamily B-1 of ERF/AP2 transcription factor family (ERF12). The protein contains one AP2 domain. There are 15 members in this subfamily including ATERF-3, ATERF-4, ATERF-7, and leafy petiole. 409 At1g28510 Dm expressed protein 410 At1g28540 Dm expressed protein 411 At1g28550 D1 Ras-related GTP-binding protein, putative, similar to GTP-binding protein GI:303742 from (Pisum sativum) 412 At1g28610 Dm GDSL-motif lipase, putative, similar to lipase (Arabidopsis thaliana) GI:1145627; contains Pfam profile: PF00657 Lipase/Acylhydrolase with GDSL-like motif 413 At1g28660 D2 lipase, putative, strong similarity to lipase (Arabidopsis thaliana) GI:1145627 414 At1g28960 D1, Dm atnudt15_AT1G28960__MutT/nudix family protein, similar to coenzyme A diphosphatase (Mus musculus) GI:12746410; contains Pfam profile PF00293: NUDIX domain 415 At1g29070 D1, D2, Dm ribosomal protein L34 family protein, similar to plastid ribosomal protein L34 precursor GB:AAF64157 GI:7578860 from (Spinacia oleracea) 416 At1g29250 D1, D2, Dm expressed protein, contains TIGRFAM TIGR00285: conserved hypothetical protein TIGR00285 417 At1g29280 D1, D2, Dm WRKY65_ATWRKY65__WRKY family transcription factor, similar to DNA binding protein WRKY3 GB:U56834 GI:1432055 from (Petroselinum crispum) 418 At1g29320 D2 transducin family protein / WD-40 repeat family protein, contains 3 WD-40 repeats (PF00400); similar to meiotic recombination protein REC14 (GI:11139242) (Homo sapiens); similar to unknown protein GI:13623493 (Homo sapiens) 419 At1g29390 D1, D2, Dm COR314-TM2__stress-responsive protein, putative, similar to cold acclimation WCOR413-like protein gamma form (Hordeum vulgare) gi:18449100:gb:AAL69988; similar to stress-regulated protein SAP1 (Xerophyta viscosa) gi:21360378:gb:AAM47505 420 At1g29430 D1, D2, Dm auxin-responsive family protein, similar to auxin-induced protein 10a 6B {SP:P33083) (Glycine max) 421 At1g29450 D1, Dm auxin-responsive protein, putative, similar to auxin-induced protein 6B (SP:P33083) (Glycine max) 422 At1g29470 D2, Dm dehydration-responsive protein-related, similar to early-responsive to dehydration stress ERD3 protein (Arabidopsis thaliana) GI:15320410; contains Pfam profile PF03141: Putative methyltransferase 423 At1g29490 D1, Dm auxin-responsive family protein, similar to auxin-induced protein X10A (SP:P33080) (Glycine max) 424 At1g29660 D1, D2, Dm GDSL-motif lipase/hydrolase family protein, low similarity to family II lipase EXL1 (Arabidopsis thaliana) GI:15054382; contains InterPro Entry IPR001087 Lipolytic enzyme, G-D-S- L family 425 At1g29670 D2, Dm GDSL-motif lipase/hydrolase family protein, similar to family II lipase EXL1 GI:15054382 from (Arabidopsis thaliana); contains Pfam profile: PF00657 Lipase/Acylhydrolase with GDSL-like motif 426 At1g29700 D2 expressed protein 427 At1g29880 D1, D2, Dm glycyl-tRNA synthetase / glycine--tRNA ligase, identical to SP:O23627 Glycyl-tRNA synthetase (EC 6.1.1.14) (Glycine--tRNA ligase) (GlyRS) {Arabidopsis thaliana} 428 At1g29900 D2 CARB__carbamoyl-phosphate synthase family protein, similar to carbamoylphosphate synthetase GI:6552726 from (Medicago sativa); contains Pfam profiles PF02786: Carbamoyl-phosphate synthase L chain ATP binding domain, PF00289: Carbamoyl-phosphate synthase L chain N-terminal domain, PF02787: Carbamoyl-phosphate synthetase large chain oligomerisation domain 429 At1g30080 Dm glycosyl hydrolase family 17 protein, similar to beta-1,3-glucanase precursor GI:4097948 from (Oryza sativa) 430 At1g30190 D1, D2, Dm expressed protein, ; expression supported by MPSS 431 At1g30220 Dm sugar transporter family protein, similar to SP:Q96QE2 Proton myo-inositol co-transporter (Hmit) (Homo sapiens); contains Pfam profile PF00083: major facilitator superfamily protein 432 At1g30260 D2, Dm AGL79__expressed protein 433 At1g30360 D1 early-responsive to dehydration stress protein (ERD4), nearly identical to ERD4 protein (early-responsive to dehydration stress) (Arabidopsis thaliana) GI:15375406; contains Pfam profile PF02714: Domain of unknown function DUF221 434 At1g30440 Dm phototropic-responsive NPH3 family protein, contains NPH3 family domain, Pfam:PF03000 435 At1g30500 D2, Dm CCAAT-binding transcription factor (CBF-B/NF-YA) family protein, contains Pfam profile: PF02045 CCAAT-binding transcription factor (CBF-B/NF-YA) 436 At1g30520 D1, D2, Dm acyl-activating enzyme 14 (AAE14), identical to acyl-activating enzyme 14 (Arabidopsis thaliana); similar to SP:Q42524 4-coumarate--CoA ligase 1 (EC 6.2.1.12) (4-coumaroyl-CoA synthase 1) {Arabidopsis thaliana}; contains Pfam profile PF00501: AMP-binding enzyme; identical to cDNA acyl-activating enzyme 14 (At1g30520) GI:29893263 437 At1g30610 Dm EMB2279__pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat 438 At1g30620 D2, Dm MUR4_UXE1__UDP-D-xylose 4-epimerase, putative (MUR4), similar to SP:P55180 UDP-glucose 4- epimerase (EC 5.1.3.2) from Bacillus subtilis, GI:3021357 UDP-galactose 4-epimerase from Cyamopsis tetragonoloba; contains Pfam profile PF01370 NAD dependent epimerase/dehydratase family; contains TIGRfam profile TIGR01179: UDP-glucose 4-epimerase 439 At1g30680 Dm toprim domain-containing protein, contains Pfam profile: PF01751 toprim domain 440 At1g30690 D2, Dm SEC14 cytosolic factor family protein / phosphoglyceride transfer family protein, contains Pfam PF00650 : CRAL/TRIO domain; contains Pfam PF03765 : CRAL/TRIO, N-terminus; similar to cytosolic factor (Phosphatidylinositol/phosphatidylcholine transfer protein) (PI/PCTP) (SP:P24280) (Saccharomyces cerevisiae); ESTs gb:T76582, gb:N06574 and gb:Z25700 come from this gene 441 At1g30720 D1, D2, Dm FAD-binding domain-containing protein, similar to SP:P30986 reticuline oxidase precursor (Berberine-bridge-forming enzyme) (BBE) (Tetrahydroprotoberberine synthase) (Eschscholzia californica); contains PF01565 FAD binding domain 442 At1g30820 D2, Dm CTP synthase, putative / UTP--ammonia ligase, putative, similar to SP:P17812 CTP synthase (EC 6.3.4.2) (UTP--ammonia ligase) {Homo sapiens}; contains Pfam profile PF00117: glutamine amidotransferase class-I; similar to ESTs gb:AA660762, gb:AA220982, dbj:AU008137, gb:AI054783, and gb:AA100804 443 At1g30880 D1, D2, Dm expressed protein, similar to ESTs gb:R30049 and gb:T46176 444 At1g31010 Dm expressed protein, contains Pfam PF05329: Protein of unknown function (DUF731) 445 At1g31100 Dm transposable_element_gene 446 At1g31170 D1, D2, Dm parB-like nuclease domain-containing protein, contains Pfam profile PF02195: ParB-like nuclease domain 447 At1g31350 D1, D2, Dm F-box family protein, similar to hypothetical protein GB:AAF24593 GI:6692128 from (Arabidopsis thaliana) ; similar to SKP1 interacting partner 2 (SKIP2) TIGR_Ath1:At5g67250 448 At1g31420 D2, Dm leucine-rich repeat transmembrane protein kinase, putative, contains Pfam profile: PF00069: Eukaryotic protein kinase domain 449 At1g31440 Dm SH3 domain-containing protein 1 (SH3P1), nearly identical to SH3 domain-containing protein 1 (Arabidopsis thaliana) GI:16974676; contains Pfam profile PF00018: SH3 domain 450 At1g31580 D1, Dm ECS1_CXC750__expressed protein, identical to ORF1 (Arabidopsis thaliana) gi:457716:emb:CAA50905 451 At1g31750 D1, D2, Dm proline-rich family protein, contains proline rich extensin domains, INTERPRO:IPR002965 452 At1g31812 D1, D2, Dm acyl-CoA binding protein / ACBP, identical to acyl-CoA-binding protein (ACBP) (Arabidopsis thaliana) SWISS-PROT:P57752 453 At1g31817 Dm chloroplast 30S ribosomal protein S11, putative, contains Pfam profile: PF00411: Ribosomal protein S11 454 At1g31820 D1, Dm amino acid permease family protein, weak similarity to asc-type amino acid transporter 2 (Mus musculus) GI:18148438; contains Pfam profile PF00324: Amino acid permease 455 At1g31860 D2 AT-IE__histidine biosynthesis bifunctional protein (HISIE), identical to histidine biosynthesis bifunctional protein hisIE, chloroplast (precursor) SP: O82768 from (Arabidopsis thaliana); identical to cDNA phosphoribosyl-ATP pyrophosphohydrolase GI:3461883 456 At1g31970 D2, Dm DEAD/DEAH box helicase, putative, similar to p68 RNA helicase (Schizosaccharomyces pombe) GI:173419 457 At1g32080 D1 membrane protein, putative, contains 12 transmembrane domains; similar to yohK (GI:405873) (Escherichia coli) 458 At1g32100 D1, D2, Dm pinoresinol-lariciresinol reductase, putative, similar to pinoresinol-lariciresinol reductase TH1 (Tsuga heterophylla)(GI:7578915); contains isoflavone reductase domain PF02716 459 At1g32200 D1, Dm ATS1_ACT1__glycerol-3-phosphate acyltransferase, chloroplast (ATS1), identical to SP:Q43307:PLSB_ARATH Glycerol-3-phosphate acyltransferase, chloroplast precursor (EC 2.3.1.15) (GPAT) (ATS1) {Arabidopsis thaliana}; contains Pfam profile PF01553: Acyltransferase

460 At1g32450 D1, D2, Dm proton-dependent oligopeptide transport (POT) family protein, contains Pfam profile: PF00854 POT family 461 At1g32460 D2 expressed protein 462 At1g32470 D1, Dm glycine cleavage system H protein, mitochondrial, putative, similar to SP:P25855 Glycine cleavage system H protein 1, mitochondrial precursor {Arabidopsis thaliana}; contains Pfam profile PF01597: Glycine cleavage H-protein 463 At1g32480 D2 isocitrate/isopropylmalate dehydrogenase family protein, similar to NAD+ dependent isocitrate dehydrogenase subunit 2 (Arabidopsis thaliana) GI:1766048; contains Pfam profile PF00180 dehydrogenase, isocitrate/isopropylmalate family 464 At1g32500 D2 ATNAP6__ATP-binding-cassette transporter, putative, similar to ATP-binding-cassette transporter (ABC1) described in PMID:11156608 465 At1g32540 D1, D2, Dm LOL1__zinc finger protein, putative, similar to zinc-finger protein Lsd1 (Arabidopsis thaliana) gi:1872521:gb:AAC49660 466 At1g32700 Dm zinc-binding family protein, similar to zinc-binding protein (Pisum sativum) GI:16117799; contains Pfam profile PF04640 : Protein of unknown function, DUF597 467 At1g32750 D1, D2, Dm HAF01_GTD1_HAC13_HAF1__HAC13 protein (HAC13), identical to HAC13 (Arabidopsis thaliana) gi:21105767:gb:AAM34782; contains Pfam domains, PF00439: Bromodomain and PF00240: Ubiquitin family 468 At1g32810 Dm expressed protein 469 At1g32900 D1, Dm PRPL11__starch synthase, putative, similar to starch synthase SP:Q42857 from (Ipomoea batatas)

470 At1g32920 D2, Dm expressed protein 471 At1g32990 D1, Dm PRPL11__ribosomal protein L11 family protein, similar to chloroplast ribosomal protein L11 GI:21312 from (Spinacia oleracea) 472 At1g33170 D1, Dm dehydration-responsive family protein, similar to early-responsive to dehydration stress ERD3 protein (Arabidopsis thaliana) GI:15320410; contains Pfam profile PF03141: Putative methyltransferase 473 At1g33230 Dm expressed protein 474 At1g33270 D1, Dm patatin-related, contains Patatin domain PF01734 475 At1g33480 D1, D2, Dm zinc finger (C3HC4-type RING finger) family protein, contains Pfam profile: PF00097 zinc finger, C3HC4 type (RING finger) 476 At1g33530 D2 F-box family protein, contains F-box domain Pfam:PF00646; contains TIGRFAM TIGR01640: F-box protein interaction domain 477 At1g33590 Dm disease resistance protein-related / LRR protein-related, contains leucine rich-repeat domains Pfam:PF00560, INTERPRO:IPR001611; similar to Hcr2-5D (Lycopersicon esculentum) gi:3894393:gb:AAC78596 478 At1g33730 D1, Dm CYP76C5__cytochrome P450, putative, Similar to cytochrome P450 76C2 (SP:O64637)(Arabidopsis thaliana); contains Pfam profile: PF00067 cytochrome P450 479 At1g33811 Dm GDSL-motif lipase/hydrolase family protein, similar to family II lipases EXL3 GI:15054386, EXL1 GI:15054382, EXL2 GI:15054384 from (Arabidopsis thaliana); contains Pfam profile PF00657: GDSL-like Lipase/Acylhydrolase 480 At1g33930 D2, Dm avirulence-responsive family protein / avirulence induced gene (AIG1) family protein, similar to SP:P54120 AIG1 protein {Arabidopsis thaliana}; contains Pfam profile PF04548: AIG1 family

481 At1g33970 D2 avirulence-responsive protein, putative / avirulence induced gene protein, putative / AIG protein, putative, similar to SP:P54120 AIG1 protein {Arabidopsis thaliana}; contains Pfam profile PF04548: AIG1 family 482 At1g34030 D2, Dm 40S ribosomal protein S18 (RPS18B), similar to ribosomal protein S18 GI:38422 from (Homo sapiens) 483 At1g34060 D1 alliinase family protein, contains Pfam profiles: PF04864 allinase C-terminal domain, PF04863 alliinase EGF-like domain 484 At1g34200 D2, Dm oxidoreductase family protein, similar to AX110P (Daucus carota) GI:285739; contains Pfam profiles PF01408: Oxidoreductase family NAD-binding Rossmann fold, PF02894: Oxidoreductase family C-terminal alpha/beta domain 485 At1g34355 Dm forkhead-associated domain-containing protein / FHA domain-containing protein 486 At1g34420 D2, Dm leucine-rich repeat family protein / protein kinase family protein, contains leucine rich repeat (LRR) domains, Pfam:PF00560; contains protein kinase domain, Pfam:PF00069 487 At1g34750 D2 protein phosphatase 2C, putative / PP2C, putative, similar to GB:AAD17805 from (Lotus japonicus) (Proc. Natl. Acad. Sci. U.S.A. 96 (4), 1738-1743 (1999)) 488 At1g35516 D2, Dm myb-like transcription factor family protein 489 At1g35660 Dm expressed protein 490 At1g35680 D1, Dm 50S ribosomal protein L21, chloroplast / CL21 (RPL21), identical to 50S ribosomal protein L21, chloroplast precursor (CL21) (Arabidopsis thaliana) SWISS-PROT:P51412 491 At1g35720 D1, D2, Dm ANNAT1_ATOXY5_OXY5__annexin 1 (ANN1), identical to annexin (AnnAt1) (Arabidopsis thaliana) GI:4959106 492 At1g36160 D2, Dm ACC1_AT-ACC1_EMB22_GK_PAS3__similar to acetyl-CoA carboxylase 2 (ACC2) [Arabidopsis thaliana] (TAIR:At1g36180.1); similar to putative acetyl-CoA carboxylase [Oryza sativa (japonica cultivar-group)] (GB:AAP53321.1); similar to acetyl-CoA carboxylase [Medicago sativa] (GB:AAB42144.1); similar to acetyl-CoA carboxylase [Brassica napus] (GB:CAC19875.1); similar to acetyl-CoA carboxylase [Brassica napus] (GB:CAC19876.1); similar to acetyl CoA carboxylase (GB:AAA75528.1); contains InterPro domain Carboxyl transferase (InterPro:IPR000022); contains InterPro domain Carbamoyl-phosphate synthetase large chain, N-terminal (InterPro:IPR005481); contains InterPro domain Biotin carboxylase, C-terminal (InterPro:IPR005482); contains InterPro domain Biotin/lipoyl attachment (InterPro:IPR000089); contains InterPro domain Carbamoyl-phosphate synthase L chain, ATP-binding (InterPro:IPR005479)

493 At1g36230 D1 hypothetical protein 494 At1g36240 D1, Dm 60S ribosomal protein L30 (RPL30A), similar to GI:6984132 from (Euphorbia esula) 495 At1g36280 D1, D2, Dm adenylosuccinate lyase, putative / adenylosuccinase, putative, similar to SP:P25739 Adenylosuccinate lyase (EC 4.3.2.2) (Adenylosuccinase) {Escherichia coli}; contains Pfam profile PF00206: Lyase 496 At1g36310 Dm expressed protein 497 At1g36380 D2, Dm expressed protein, similar to vanilloid receptor-like protein GB:AAD26363 from (Homo sapiens)

498 At1g36980 D2, Dm expressed protein 499 At1g37130 D2 NIA2_B29_CHL3_NIA2-1_NR_NR2__nitrate reductase 2 (NR2), identical to SP:P11035 Nitrate reductase 2 (formerly EC 1.6.6.1) (NR2) {Arabidopsis thaliana} 500 At1g41810 D1, Dm expressed protein 501 At1g41825 D1 transposable element gene 502 At1g41880 D1, D2, Dm 60S ribosomal protein L35a (RPL35aB), identical to GB:CAB81600 from (Arabidopsis thaliana) 503 At1g42430 Dm expressed protein 504 At1g42960 Dm expressed protein localized to the inner membrane of the chloroplast. 505 At1g42990 D1 ATBZIP60__AtbZIP60 consists of a bZIP DNA binding domain followed by a putative transmembrane domain. GFP fusions containing the first 260 amino acids (AtbZIP60deltaC) are nuclear- localized. AtbZIP60 is upregulated by the addition of tunicamycin (ER stress response inductor), DTT (inhibitor of disulfide bond formation) and azetin-2-carboxylate (proline analog perturbing protein structure). It is hypothesized that upon ER stress the protein is proteolyzed and the soluble part translocalized into the nucleus. AtbZIP60deltaC can activate the promoters of the ER chaperones BiP1, BiP2 and BiP3 and CNX1 and CNX2 via binding to the ER stress response element (ERSE) and the plant unfolded protein response element(P-UPRE). It can also activate its own transcription. 506 At1g43190 Dm polypyrimidine tract-binding protein, putative / heterogeneous nuclear ribonucleoprotein, putative, similar to Polypyrimidine tract-binding protein 1 (PTB) (Heterogeneous nuclear ribonucleoprotein I) (hnRNP I) from {Rattus norvegicus} SP:Q00438, {Homo sapiens} SP:P26599, (Homo sapiens) GI:35770; contains InterPro entry IPR000504: RNA-binding region RNP-1 (RNA recognition motif) (RRM) 507 At1g43560 D1, Dm thioredoxin family protein, contains Pfam profile: PF00085 Thioredoxin; similar to thioredoxin GI:142153 from (Synechococcus PCC6301) 508 At1g43670 D1, Dm fructose-1,6-bisphosphatase, putative / D-fructose-1,6-bisphosphate 1-phosphohydrolase, putative / FBPase, putative, very strong similarity to SP:P46267 Fructose-1,6-bisphosphatase, cytosolic (EC 3.1.3.11) (D-fructose-1,6- bisphosphate 1-phosphohydrolase) (FBPase) {Brassica napus}; contains Pfam profile PF00316: fructose-1,6-bisphosphatase 509 At1g43700 D2, Dm VIP1__VirE2-interacting protein (VIP1), identical to VirE2-interacting protein VIP1 GB:AAF37279 GI:7258340 from (Arabidopsis thaliana) 510 At1g43890 Dm ATRAB18__Ras-related GTP-binding protein, putative, similar to GTP-binding protein(RAB1Y) GI:1370173 from (Lotus japonicus) 511 At1g44446 D2 CH1_ATCAO_CAO__chlorophyll a oxygenase (CAO) / chlorophyll b synthase, identical to chlorophyll a oxygenase GI:5853117 from (Arabidopsis thaliana); contains Pfam PF00355 Rieske (2Fe-2S) domain 512 At1g44770 D2 expressed protein 513 At1g44790 D1 ChaC-like family protein, contains Pfam profile: PF04752 ChaC-like protein 514 At1g44800 D2, Dm nodulin MtN21 family protein, similar to MtN21 (Medicago truncatula) GI:2598575; contains Pfam profile PF00892: Integral membrane protein 515 At1g44810 D2 expressed protein, contains Pfam profile: PF04504 protein of unknown function, DUF573 516 At1g44940 D1, D2, Dm unknown protein 517 At1g45050 D1, Dm ATUBC2-1__ubiquitin-conjugating enzyme 15 (UBC15), E2; identical to ubiquitin-conjugating enzyme 15 GI:2801442 from (Arabidopsis thaliana) 518 At1g45249 Dm ABF2_AREB1__similar to ABA-responsive element-binding protein 2 (AREB2) [Arabidopsis thaliana] (TAIR:At3g19290.1); similar to putative ripening-related bZIP protein [Vitis vinifera] (GB:CAB85632.1); contains InterPro domain Basic-leucine zipper (bZIP) transcription factor (InterPro:IPR004827) 519 At1g45976 D2, Dm SBP1__expressed protein 520 At1g46768 D1 RAP2.1__encodes a member of the DREB subfamily A-5 of ERF/AP2 transcription factor family (RAP2.1). The protein contains one AP2 domain. There are 16 members in this subfamily including RAP2.9 and RAP2.10. 521 At1g47128 D1, D2, Dm cysteine proteinase (RD21A) / thiol protease, identical to SP:P43297 Cysteine proteinase RD21A precursor (EC 3.4.22.-) {Arabidopsis thaliana}, thiol protease RD21A SP:P43297 from (Arabidopsis thaliana) 522 At1g47270 D1, Dm F-box family protein / tubby family protein, contains Pfam profiles: PF00646 F-box domain, PF01167 Tub family; similar to Chain A, C-Terminal Domain Of Mouse Brain Tubby Protein Length(GI:6730158) (Mus musculus); similar to phosphodiesterase (GI:467578) (Mus musculus); similar to Tubby protein homolog (Swiss-Prot:O88808) (Rattus norvegicus) 523 At1g47490 D2 ATRBP47C__RNA-binding protein 47 (RBP47), putative, similar to DNA binding protein GI:1899187 from (Nicotiana tabacum) 524 At1g47740 Dm expressed protein 525 At1g47940 Dm expressed protein 526 At1g47960 D1, D2, Dm C/VIF1_ATC/VIF1__invertase/pectin methylesterase inhibitor family protein, low similarity to SP:P83326 Pectinesterase inhibitor (Pectin methylesterase inhibitor) (PMEI) {Actinidia chinensis}; contains Pfam profile PF04043: Plant invertase/pectin methylesterase inhibitor 527 At1g48000 D2, Dm MYB112__myb family transcription factor, similar to myb-related transcription factor (cpm10) GB:U33915 GI:1002795 from (Craterostigma plantagineum) 528 At1g48230 D2 phosphate translocator-related, low similarity to phosphoenolpyruvate/phosphate translocator precursor (Mesembryanthemum crystallinum) GI:9295275, SP:P52178 Triose phosphate/phosphate translocator, non-green plastid, chloroplast precursor (CTPT) {Brassica oleracea} 529 At1g48300 D1, D2, Dm expressed protein 530 At1g48320 D1, D2, Dm thioesterase family protein, similar to ComAB (Bacillus licheniformis) GI:1834379; contains Pfam profile PF03061: thioesterase family protein 531 At1g48420 D2 desulfhydrase family, similar to similar to D-cysteine desulfhydrase (EC 4.4.1.15). (Swiss- Prot:P59329) (Escherichia coli O6); contains TIGRFAM TIGR01275: pyridoxal phosphate-dependent enzymes, D-cysteine desulfhydrase family profile 532 At1g48440 D2 expressed protein 533 At1g48520 D1 GATB__glutamyl-tRNA(Gln) amidotransferase B family protein, contains Pfam profiles: PF02934 PET112 family, N terminal region, PF02637 GatB/Yqey domain, PF01162 PET112 family, C terminal region 534 At1g48570 D2 zinc finger (Ran-binding) family protein, contains Pfam domain, PF00641: Zn-finger in Ran binding protein and others 535 At1g48630 D1, D2, Dm guanine nucleotide-binding family protein / activated protein kinase C receptor, putative / RACK, putative, contains 7 WD-40 repeats (PF00400); very similar to guanine nucleotide-binding protein; activated protein kinase C receptor; RACK1 (GI:9294068) {Arabidopsis thaliana}; similar to WD-40 repeat auxin-dependent protein ARCA (SP:O24456) (Arabidopsis thaliana);

536 At1g48750 D1, D2, Dm protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, similar to TED4 (Zinnia elegans) GI:493721; contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 537 At1g48790 D1, Dm mov34 family protein, similar to AMSH (Homo sapiens) GI:4098124; contains Pfam profile PF01398: Mov34/MPN/PAD-1 family 538 At1g48830 D1, Dm 40S ribosomal protein S7 (RPS7A), similar to 40S ribosomal protein S7 homolog GI:5532505 from (Brassica oleracea) 539 At1g48840 D2 expressed protein, contains Pfam profile: PF04842 plant protein of unknown function (DUF639) 540 At1g48920 D2 nucleolin, putative, similar to nuM1 protein GI:1279562 from (Medicago sativa) 541 At1g49150 D2 expressed protein 542 At1g49230 D2 zinc finger (C3HC4-type RING finger) family protein, contains Pfam domain, PF00097: Zinc finger, C3HC4 type (RING finger) 543 At1g49240 D1, D2, Dm ACT8__actin 8 (ACT8), identical to SP:Q96293 Actin 8 {Arabidopsis thaliana}; nearly identical to SP:Q96292 Actin 2 (Arabidopsis thaliana) GI:1669387, and to At3g18780 544 At1g49300 Dm Ras-related GTP-binding protein, putative, contains Pfam profile: PF00071 Ras family 545 At1g49400 D1, Dm EMB1129__ribosomal protein S17 family protein, similar to 40S ribosomal protein S17 GI:1620985 from (Nicotiana plumbaginifolia) 546 At1g49410 D2 TOM6__expressed protein 547 At1g49490 Dm leucine-rich repeat family protein / extensin family protein, contains similarity to disease resistance protein GI:3894383 from (Lycopersicon esculentum); contains leucine-rich repeats, Pfam:PF00560; contains proline rich extensin domains, INTERPRO:IPR002965 548 At1g49500 D2, Dm expressed protein 549 At1g49510 D2, Dm EMB1273__expressed protein 550 At1g49590 Dm formin-binding protein-related, similar to formin binding protein 21 (GI:3550080) (Homo sapiens); similar to formin binding protein 21 (GI:3550077) (Mus musculus); similar to Dinap1- interacting protein 1 (GI:8745458) (Crypthecodinium cohnii) 551 At1g49600 D1, D2, Dm ATRBP47A__RNA-binding protein 47 (RBP47), putative, similar to DNA binding protein ACBF GB:U90212 GI:1899187 from (Nicotiana tabacum) 552 At1g49660 D1, Dm expressed protein 553 At1g49670 D2 ARP protein (REF), identical to ARP protein GB:CAA89858 GI:886434 from (Arabidopsis thaliana); contains Pfam profile PF00107: oxidoreductase, zinc-binding dehydrogenase family 554 At1g49720 Dm ABF1__ABA-responsive element-binding protein / abscisic acid responsive elements-binding factor (ABRE), identical to abscisic acid responsive elements-binding factor GB:AAF27179 GI:6739274 from (Arabidopsis thaliana); identical to cDNA abscisic acid responsive elements- binding factor (ABRE) mRNA, complete cds GI:6739273 555 At1g49750 D1, D2, Dm leucine-rich repeat family protein, contains leucine-rich repeats, Pfam:PF00560 556 At1g49760 D2 PAB8__polyadenylate-binding protein, putative / PABP, putative, similar to poly(A)-binding protein GB:AAF66825 GI:7673359 from (Nicotiana tabacum). Highly and ubiquitously expressed. Member of the class II PABP family. 557 At1g49970 D2, Dm CLPR1_NCLPP5__ATP-dependent Clp protease proteolytic subunit (ClpR1) (nClpP5), identical to nClpP5 GB:BAA82069 GI:5360595 from (Arabidopsis thaliana); identical to cDNA nClpP5 (nuclear encoded ClpP5) GI:5360594 558 At1g50010 D1, D2, Dm TUA2__tubulin alpha-2/alpha-4 chain (TUA2), identical to tubulin alpha-2/alpha-4 chain SP:P29510 GB:P29510 from (Arabidopsis thaliana) 559 At1g50020 D1, D2, Dm expressed protein 560 At1g50250 D1, D2, Dm FTSH1__encodes an FTSH protease that is localized to the chloroplast. Involved in the D1 repair cycle of Photosystem II. FtsH1 and FtsH5 are interchangeable in thylakoid membranes. 561 At1g50450 Dm expressed protein 562 At1g50480 D1, D2, Dm THFS__formate--tetrahydrofolate ligase / 10-formyltetrahydrofolate synthetase (THFS), identical to 10-formyltetrahydrofolate synthetase (Arabidopsis thaliana) GI:5921663 563 At1g50840 D2 POLGAMMA2__DNA Polymerase gamma2. Dual targeting to mitochondria and plastids due to alternative translation initiation. 564 At1g50900 D1, D2, Dm expressed protein 565 At1g50920 D2, Dm GTP-binding protein-related, similar to GTP-binding protein SP:Q99ME9 from (Mus musculus) 566 At1g51030 Dm expressed protein 567 At1g51060 D1, Dm histone H2A, putative, similar to histone H2A GI:7595337 from Arabidopsis thaliana, Triticum aestivum GI:536892, Picea abies SP:P35063; contains Pfam profile PF00125 Core histone H2A/H2B/H3/H4 568 At1g51070 D2 basic helix-loop-helix (bHLH) family protein, similar to bHLH transcription factor GI:3757520 from (Arabidopsis thaliana) 569 At1g51140 D1, D2, Dm basic helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain 570 At1g51200 D1, D2, Dm zinc finger (AN1-like) family protein, contains Pfam domains, PF01428: AN1-like Zinc finger and PF01754: A20-like zinc finger 571 At1g51400 D1 photosystem II 5 kD protein, 100% identical to GI:4836947 (F5D21.10) 572 At1g51500 D1, D2, Dm CER5_D3__ABC transporter family protein, similar to GB:AAF61569 from (Bombyx mori) 573 At1g51510 Dm RNA-binding protein, putative, similar to RNA-binding protein 8 (Ribonucleoprotein RBM8) SP:Q9Y5S9 from (Homo sapiens), RNA-binding protein Y14 (Xenopus laevis) GI:11034807; contains InterPro entry IPR000504: RNA-binding region RNP-1 (RNA recognition motif) (RRM) 574 At1g51570 D1, Dm C2 domain-containing protein, contains INTERPRO:IPR000008 C2 domain 575 At1g51700 D1, D2, Dm ADOF1__Dof-type zinc finger domain-containing protein (ADOF1), identical to cDNA adof1 mRNA for dof zinc finger protein, GI:3608260; contains Pfam profile PF02701: Dof domain, zinc finger 576 At1g51710 D2 UBP6__ubiquitin-specific protease 6, putative (UBP6), similar to GI:11993465 577 At1g51805 D1, Dm leucine-rich repeat protein kinase, putative, similar to light repressible receptor protein kinase (Arabidopsis thaliana) gi:1321686:emb:CAA66376; contains leucine rich repeat (LRR) domains, Pfam:PF00560; contains protein kinase domain, Pfam:PF00069 578 At1g51830 Dm leucine-rich repeat protein kinase, putative, similar to light repressible receptor protein kinase GI:1321686 from (Arabidopsis thaliana) 579 At1g51940 D2 protein kinase family protein / peptidoglycan-binding LysM domain-containing protein, contains protein kinases ATP-binding region signature, PROSITE:PS00107 580 At1g51980 D1, Dm mitochondrial processing peptidase alpha subunit, putative, similar to mitochondrial processing peptidase alpha subunit, mitochondrial precursor, Alpha-MPP (Ubiquinol-cytochrome C reductase subunit II) (Potato) SWISS-PROT:P29677 581 At1g52000 D2, Dm jacalin lectin family protein, similar to myrosinase binding protein (Brassica napus) GI:1711296, myrosinase-binding protein homolog (Arabidopsis thaliana) GI:2997767; contains Pfam profile: PF01419 jacalin-like lectin domain 582 At1g52030 D2 MBP2_F-ATMBP_MBP1.2__myrosinase-binding protein, putative (F-ATMBP), identical to SP:Q9SAV1 Myrosinase binding protein-like f-AtMBP (Arabidopsis thaliana); similar to myrosinase binding protein GI:1711295 from (Brassica napus); contains Pfam PF01419: Jacalin-like lectin domain; identical to cDNA myrosinase-binding protein-like protein (MBP1.2) GI:6760446 583 At1g52040 D2, Dm MBP1_ATMBP__jacalin lectin family protein, nearly identical to myrosinase-binding protein homolog GI:2997767 from (Arabidopsis thaliana); contains Pfam profile PF01419 jacalin-like lectin domain; identical to cDNA myrosinase-binding protein homolog GI:2997766 584 At1g52190 D1, D2, Dm proton-dependent oligopeptide transport (POT) family protein, contains Pfam profile: PF00854 POT family 585 At1g52200 Dm expressed protein, similar to PGPS/D12 (Petunia x hybrida) GI:4105794; contains Pfam profile PF04749: Protein of unknown function, DUF614 586 At1g52220 D1, D2 expressed protein 587 At1g52230 D1, Dm photosystem I reaction center subunit VI, chloroplast, putative / PSI-H, putative (PSAH2), identical to SP:Q9SUI6; similar to PSI-H precursor (Nicotiana sylvestris) GI:407355; contains Pfam profile PF03244: Photosystem I reaction centre subunit VI 588 At1g52300 D1, D2, Dm 60S ribosomal protein L37 (RPL37B), similar to SP:Q43292 from (Arabidopsis thaliana) 589 At1g52400 D2, Dm BG1_BGL1__glycosyl hydrolase family 1 protein / beta-glucosidase, putative (BG1), contains Pfam PF00232 : Glycosyl hydrolase family 1 domain; TIGRFAM TIGR01233: 6-phospho-beta- galactosidase; identical to GI:6651430 from (Arabidopsis thaliana) 590 At1g52440 D1, Dm expressed protein 591 At1g52590 D1, D2, Dm expressed protein 592 At1g52690 D1, D2, Dm late embryogenesis abundant protein, putative / LEA protein, putative, similar to SP:P13934 Late embryogenesis abundant protein 76 (LEA 76) {Brassica napus}; contains Pfam profile PF02987: Late embryogenesis abundant protein 593 At1g52720 Dm expressed protein 594 At1g52740 D2, Dm histone H2A, putative, similar to histone H2A.F/Z Arabidopsis thaliana GI:2407800; contains Pfam profile PF00125 Core histone H2A/H2B/H3/H4 595 At1g52760 D1, D2, Dm esterase/lipase/thioesterase family protein, low similarity to monoglyceride lipase from (Homo sapiens) GI:14594904, (Mus musculus) GI:2632162; contains Interpro entry IPR000379 596 At1g52870 D1, D2, Dm peroxisomal membrane protein-related, contains weak similarity to Swiss-Prot:Q07066 22 kDa peroxisomal membrane protein (Rattus norvegicus) 597 At1g52880 Dm ANAC018_NAM_ATNAM__no apical meristem (NAM) family protein, contains Pfam PF02365: No apical meristem (NAM) domain; similar to NAM (no apical meristem) GB:CAA63101 from (Petunia x hybrida); identical to cDNA NAC domain protein GI:4325285 598 At1g52890 D2, Dm ANAC019__no apical meristem (NAM) family protein, contains Pfam PF02365: No apical meristem (NAM) domain; similar to NAM (no apical meristem) GB:CAA63101 from (Petunia x hybrida) 599 At1g52930 D2 brix domain-containing protein, contains Pfam domain, PF04427: Brix domain 600 At1g53000 Dm cytidylyltransferase family, contains Pfam profile: PF02348 cytidylyltransferase 601 At1g53190 D2, Dm zinc finger (C3HC4-type RING finger) family protein, similar to RING-H2 finger protein RHG1a GI:3822225 from (Arabidopsis thaliana); contains Pfam profile PF00097: Zinc finger, C3HC4 type (RING finger) 602 At1g53200 Dm expressed protein 603 At1g53210 D1, D2, Dm sodium/calcium exchanger family protein / calcium-binding EF hand family protein, contains Pfam profiles: PF01699 sodium/calcium exchanger protein, PF00036 EF hand 604 At1g53230 D2 TCP3__TCP family transcription factor 3 (TCP3), identical to transcription factor 3 (TCP3) (Arabidopsis thaliana) (GI:3243274); similar to flower development protein cycloidea (cyc3) GI:6358611 from (Misopates orontium) 605 At1g53240 D1, D2, Dm malate dehydrogenase (NAD), mitochondrial, identical to mitochondrial NAD-dependent malate dehydrogenase GI:3929649 SP:Q9ZP06 from (Arabidopsis thaliana); contains InterPro entry IPR001236: Lactate/malate dehydrogenase 606 At1g53270 D1 ABC transporter family protein, contains similarity to ABC transporter GI:10280532 from (Homo sapiens) 607 At1g53280 D2 DJ-1 family protein, similar to DJ-1 protein (Homo sapiens) GI:1780755; similar to DJ-1 beta (GI:18642508) (Drosophila melanogaster); contains Pfam profile: PF01965 ThiJ/PfpI family; TIGRFAM TIGR01383: DJ-1 family protein 608 At1g53430 Dm leucine-rich repeat family protein / protein kinase family protein, contains Pfam domains PF00560: Leucine Rich Repeat and PF00069: Protein kinase domain 609 At1g53480 D2 expressed protein 610 At1g53500 D1, Dm MUM4_RHM2__NAD-dependent epimerase/dehydratase family protein, low similarity to dTDP-D- glucose-4,6-dehydratase from Aneurinibacillus thermoaerophilus GI:16357461, Sphingomonas sp. GI:1314581; contains Pfam profile PF01370: NAD dependent epimerase/dehydratase family; putative NDP-rhamnose synthase (rhm2 gene) GI:31559258 611 At1g53580 D1, D2, Dm GLX2-3__hydroxyacylglutathione hydrolase, putative / glyoxalase II, putative, similar to glyoxalase II GI:1644427 from (Arabidopsis thaliana) 612 At1g53620 D2 similar to hypothetical protein [Arabidopsis thaliana] (TAIR:At1g53610.1); similar to hypothetical protein [Neurospora crassa] (GB:XP_330065.1); similar to Hypothetical protein E02A10.2 [Caenorhabditis elegans] (GB:CAB02877.1); similar to ORF; able to induce HR-like lesions [Nicotiana tabacum] (GB:AAC49971.1); contains domain GLY_RICH (PS50315) 613 At1g53670 D2, Dm transcription factor-related, similar to pilin-like transcription factor (Homo sapiens) GI:5059062; contains Pfam profile PF01641: SelR domain 614 At1g53730 D2 leucine-rich repeat transmembrane protein kinase, putative, similar to GI:3360289 from (Zea mays) (Plant Mol. Biol. 37 (5), 749-761 (1998)) 615 At1g53800 D2, Dm expressed protein 616 At1g53840 Dm ATPME1__pectinesterase family protein, contains Pfam profile: PF01095 pectinesterase 617 At1g53890 D2 expressed protein, contains Pfam profile PF04525: Protein of unknown function (DUF567) 618 At1g53910 D1, Dm RAP2.12__encodes a member of the ERF (ethylene response factor) subfamily B-2 of ERF/AP2 transcription factor family (RAP2.12). The protein contains one AP2 domain. There are 5 members in this subfamily including RAP2.2 AND RAP2.12. 619 At1g54020 D2, Dm myrosinase-associated protein, putative, strong similarity to myrosinase-associated proteins GI:1769968, GI:1769970, GI:1216389,GI:1216391 from (Brassica napus); contains InterPro Entry IPR001087 Lipolytic enzyme, G-D-S-L family 620 At1g54100 D1, D2, Dm ALDH7B4__aldehyde dehydrogenase, putative / antiquitin, putative, strong similarity to SP:Q41247 Aldehyde dehydrogenase family 7 member A1 (EC 1.2.1.3) (Antiquitin 1) (Brassica turgor-responsive/drought-induced gene 26 protein) (Btg-26) {Brassica napus}; similar to turgor-responsive protein 26G (aldehyde dehydrogenase family 7 member A1) (Pisum sativum) SWISS-PROT:P25795 621 At1g54115 D1, D2, Dm cation exchanger, putative 622 At1g54120 D2 expressed protein 623 At1g54130 D2, Dm RSH3_AT-RSH3__RelA/SpoT protein, putative (RSH3), identical to RSH3 (RelA/SpoT homolog) GI:7141308 from (Arabidopsis thaliana); contains Pfam profiles PF01966: HD domain, PF04607: Region found in RelA / SpoT proteins 624 At1g54160 D1, Dm CCAAT-binding transcription factor (CBF-B/NF-YA) family protein, contains Pfam profile: PF02045 CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B 625 At1g54310 D1 expressed protein 626 At1g54410 D1, Dm dehydrin family protein, contains Pfam domain, PF00257: Dehydrin 627 At1g54520 Dm expressed protein 628 At1g54780 D1, D2, Dm thylakoid lumen 18.3 kDa protein, SP:Q9ZVL6 629 At1g54830 D1, D2, Dm CCAAT-box binding transcription factor Hap5a, putative, similar to heme activated protein GI:6289057 from (Arabidopsis thaliana) GI:14577940 CCAAT-binding protein subunit HAP5 {Hypocrea jecorina} similar to Transcription factor GB:CAA74053 GI:2398533 from (Arabidopsis thaliana) similarity to transcription factor Hap5a similar to transcription factor Hap5a (Arabidopsis thaliana)(GI:6523090) 630 At1g54970 Dm ATPRP1__proline-rich family protein, similar to proline-rich protein GI:170048 from (Glycine max) 631 At1g55000 D2 peptidoglycan-binding LysM domain-containing protein, contains Pfam profile PF01476: LysM domain 632 At1g55160 D1, Dm expressed protein 633 At1g55210 Dm disease resistance response protein-related/ dirigent protein-related, smimilar to dirigent protein (Thuja plicata) gi:6694699:gb:AAF25360; similar to pathogenesis-related protein (Pisum sativum) gi:4585273:gb:AAD25355 634 At1g55260 D2 protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 635 At1g55310 D1, D2, Dm SR33_ATSCL33_SCL33__SC35-like splicing factor, 33 kD (SCL33), nearly identical to SC35-like splicing factor SCL33, 33 kD (Arabidopsis thaliana) GI:9843659 636 At1g55330 D1, D2, Dm AGP21__arabinogalactan-protein (AGP21) 637 At1g55450 D1, D2, Dm embryo-abundant protein-related, similar to embryo-abundant protein GI:1350531 from (Picea glauca) 638 At1g55480 D1 expressed protein 639 At1g55680 D1, D2, Dm WD-40 repeat family protein, contains 2 (1 significant) WD-40 repeats (PF0400); similar to Trp-Asp repeat protein (PIR:T40094) (Schizosaccharomyces) 640 At1g55830 D1 expressed protein, similar to M-type 9 protein (GI:507127) (Streptococcus pyogenes) 641 At1g56020 D2 expressed protein 642 At1g56070 D1, D2, Dm AT1G56075.1_LOS1__elongation factor 2, putative / EF-2, putative, similar to ELONGATION FACTOR 2 GB:O14460 from (Schizosaccharomyces pombe) 643 At1g56110 D1, D2, Dm NOP56__nucleolar protein Nop56, putative, similar to XNop56 protein (Xenopus laevis) GI:14799394; contains Pfam profile PF01798: Putative snoRNA binding domain 644 At1g56170 D1, D2, Dm HAP5B_ATHAP5B__transcription factor, putative, similar to Transcription factor GB:CAA74053 GI:2398533 from (Arabidopsis thaliana) similarity to transcription factor Hap5a similar to transcription factor Hap5a (Arabidopsis thaliana)(GI:6523090) 645 At1g56220 D2 dormancy/auxin associated family protein, similar to Auxin-repressed 12.5 kDa protein (Swiss- Prot:Q05349) (Fragaria ananassa); similar to auxin-repressed protein (GI:927034) (Fragaria x ananassa); similar to dormancy-associated protein (GI:2605887) (Pisum sativum) 646 At1g56280 D1, D2, Dm ATDI19__drought-responsive family protein, contains an AT-AC intron 3, potentially contains a frameshift. An alternate model provides a translation more consistent with homologous proteins but lacks the AT-AC intron; similar to drought-induced mRNA, Di19 (Arabidopsis thaliana) gi:469110:emb:CAA55321 647 At1g56300 D2, Dm DNAJ heat shock N-terminal domain-containing protein, similar to SP:Q9QYI7 DnaJ homolog subfamily B member 8 Mus musculus; contains Pfam profile: PF00226: DnaJ domain 648 At1g56330 Dm ATSARA1B_SAR1_ATSAR1__GTP-binding protein (SAR1B), identical to GTP-binding protein (SAR1B) (Arabidopsis thaliana) SP:Q01474 649 At1g56340 D1, D2, Dm CRT1__calreticulin 1 (CRT1), identical to calreticulin (crt1) GI:2052379 (Arabidopsis thaliana) 650 At1g56400 D2, Dm F-box family protein, contains Pfam:PF00646 F-box domain 651 At1g56570 D2, Dm pentatricopeptide (PPR) repeat-containing protein, contains INTERPRO:IPR002885 PPR repeats 652 At1g56600 D1, D2, Dm galactinol synthase, putative, similar to galactinol synthase, isoform GolS-1 GI:5608497 from (Ajuga reptans) 653 At1g56650 D1, D2, Dm PAP1_MYB75_SIAA1__myb family transcription factor (MYB75), contains Pfam profile: PF00249 myb- like DNA-binding domain; identical to cDNA putative transcription factor (MYB75) GI:3941507 654 At1g56700 D1, D2, Dm pyrrolidone-carboxylate peptidase family protein, similar to Pyrrolidone-carboxylate peptidase (5-oxoprolyl- peptidase) (Pyroglutamyl-peptidase I) (PGP-I) (Pyrase). (Swiss-Prot:O73944) (Pyrococcus furiosus); similar to Pyrrolidone-carboxylate peptidase (5-oxoprolyl- peptidase) (Pyroglutamyl-peptidase I) (PGP-I). (Swiss-Prot:O07883) (Thermococcus litoralis); contains Pfam PF01470: pyrrolidone-carboxylate peptidase 655 At1g57590 D1, D2, Dm similar to pectinacetylesterase, putative [Arabidopsis thaliana] (TAIR:At5g26670.1); similar to putative pectinacetylesterase precursor [Oryza sativa (japonica cultivar-group)] (GB:NP_918013.1); contains InterPro domain Pectinacetylesterase (InterPro:IPR004963) 656 At1g57640 D2, Dm transposable element gene 657 At1g57680 D2, Dm expressed protein 658 At1g57860 D1, D2, Dm 60S ribosomal protein L21, similar to 60S ribosomal protein L21 GI:3885884 from (Oryza sativa)

659 At1g57870 D1, Dm shaggy-related protein kinase kappa, putative / ASK-kappa, putative, similar to shaggy-related protein kinase kappa SP:Q39019 GI:717180 from (Arabidopsis thaliana) 660 At1g57990 D1, D2, Dm ATPUP18__purine permease-related, low similarity to purine permease (Arabidopsis thaliana) GI:7620007; contains Pfam profile PF03151: Domain of unknown function, DUF250 661 At1g58030 D1, Dm CAT2__amino acid permease family protein, similar to SP:P18581 Low-affinity cationic amino acid transporter-2 (CAT-2) (T-cell early activation protein) {Mus musculus}; contains Pfam profile PF00324: Amino acid permease 662 At1g58180 D1, D2, Dm carbonic anhydrase family protein / carbonate dehydratase family protein, similar to SP:P46512 Carbonic anhydrase 1 (EC 4.2.1.1) (Carbonate dehydratase 1) {Flaveria linearis}; contains Pfam profile PF00484: Carbonic anhydrase 663 At1g58250 Dm SAB__SABRE, putative, similar to SABRE (GI:719291) (Arabidopsis thaliana) 664 At1g58270 D1, D2, Dm ZW9__meprin and TRAF homology domain-containing protein / MATH domain-containing protein, similar to ubiquitin-specific protease 12 (Arabidopsis thaliana) GI:11993471; contains Pfam profile PF00917: MATH domain 665 At1g58280 D2 expressed protein 666 At1g58360 D1, Dm AAP1_NAT2__amino acid permease I (AAP1), identical to amino acid permease I GI:22641 from (Arabidopsis thaliana) 667 At1g58380 D1, D2, Dm XW6__40S ribosomal protein S2 (RPS2A), similar to ribosomal protein S2 GI:939717 from (Urechis caupo) 668 At1g58520 D1, D2, Dm RXW8__early-responsive to dehydration protein-related / ERD protein-related, low similarity to ERD4 protein (early-responsive to dehydration stress) (Arabidopsis thaliana) GI:15375406; contains Pfam profile PF02714: Domain of unknown function DUF221 669 At1g59520 D2, Dm CW7__expressed protein (CW7) 670 At1g59675 D1 F-box family protein, similar to SKP1 interacting partner 2 (SKIP2) TIGR_Ath1:At5g67250 671 At1g59700 D1, D2, Dm ATGSTU16__glutathione S-transferase, putative, similar to glutathione S-transferase GB:AAF29773 GI:6856103 from (Gossypium hirsutum) 672 At1g59710 D2 expressed protein, contains Pfam profile: PF04601 protein of unknown function (DUF569 673 At1g59870 D1, D2, Dm ABC transporter family protein, similar to PDR5-like ABC transporter GI:1514643 from (Spirodela polyrhiza) 674 At1g59990 D2 DEAD/DEAH box helicase, putative (RH22), similar to RNA helicase GI:3776015 from (Arabidopsis thaliana); contains Pfam profiles PF00271: Helicase conserved C-terminal domain, PF00270: DEAD/DEAH box helicase; matches EST OAO811-2 675 At1g60040 D2 MADS-box family protein, contains similarity to hypothetical proteins of (Arabidopsis thaliana) 676 At1g60070 Dm gamma-adaptin, putative, similar to gamma-adaptin GI:2765190 from (Homo sapiens); contains Pfam profiles PF01602: Adaptin N terminal region, PF02883: Adaptin C-terminal domain 677 At1g60190 D1, Dm armadillo/beta-catenin repeat family protein / U-box domain-containing protein, contains Pfam domain, PF00514: Armadillo/beta-catenin-like repeats and Pfam, PF04564: U-box domain 678 At1g60230 D1, D2, Dm radical SAM domain-containing protein, contains Pfam profile PF04055: radical SAM domain protein 679 At1g60420 D2 DC1 domain-containing protein, contains Pfam domain PF03107: DC1 domain 680 At1g60550 D1, Dm naphthoate synthase, putative / dihydroxynaphthoic acid synthetase, putative / DHNA synthetase, putative, contains similarity to MENB from Escherichia coli (SP:P27290), Bacillus subtilis (SP:P23966); contains Pfam profile PF00378 enoyl-CoA hydratase/isomerase family protein 681 At1g60630 D2, Dm leucine-rich repeat family protein, similar to receptor kinase GI:498278 from (Petunia integrifolia); contains protein kinase domain, Pfam:PF00069; contains leucine-rich repeats, Pfam:PF00560 682 At1g60660 D1, Dm B5 #5__cytochrome b5 domain-containing protein, contains InterPro accession IPR001199: Cytochrome b5 683 At1g60710 D2 ATB2__aldo/keto reductase family protein, contains Pfam profile PF00248: oxidoreductase, aldo/keto reductase family 684 At1g60740 D1, D2, Dm peroxiredoxin type 2, putative, strong similarity to type 2 peroxiredoxin (Brassica rapa subsp. pekinensis) GI:4928472; contains Pfam profile: PF00578 AhpC/TSA (alkyl hydroperoxide reductase and thiol-specific antioxidant) family 685 At1g60800 D1, Dm leucine-rich repeat family protein / protein kinase family protein, contains Pfam domains PF00560: Leucine Rich Repeat and PF00069: Protein kinase domain 686 At1g60940 D2 serine/threonine protein kinase, putative, similar to serine/threonine-protein kinase ASK1 from (Arabidopsis thaliana), SWISS-PROT:P43291 687 At1g61100 D2, Dm disease resistance protein (TIR class), putative, domain signature TIR exists, suggestive of a disease resistance protein. 688 At1g61200 D1 homeobox-leucine zipper protein-related, similar to SP:Q02283 Homeobox-leucine zipper protein HAT5 (HD-ZIP protein 5) (HD-ZIP protein ATHB-1) {Arabidopsis thaliana} 689 At1g61250 D2, Dm SC3__secretory carrier membrane protein (SCAMP) family protein (SC3), contains Pfam domain, PF04144: SCAMP family 690 At1g61430 Dm S-locus protein kinase, putative, similar to receptor protein kinase (Ipomoea trifida) gi:836954:gb:AAC23542; contains S-locus glycoprotein family domain, Pfam:PF00954 691 At1g61520 D1, Dm LHCA3*1__chlorophyll A-B binding protein / LHCI type III (LHCA3.1), nearly identical to PSI type III chlorophyll a/b-binding protein GI:430947; contains Pfam profile: PF00504 chlorophyll A-B binding protein; similar to PSI type III chlorophyll a/b-binding protein GI:430947 from (Arabidopsis thaliana) 692 At1g61570 D2 TIM13__mitochondrial import inner membrane translocase (TIM13), identical to mitochondrial import inner membrane translocase subunit Tim13 (Arabidopsis thaliana) Swiss-Prot:Q9XH48; contains Pfam domain, PF02953: Tim10/DDP family zinc finger 693 At1g61580 D2, Dm ARP2_RPL3B__60S ribosomal protein L3 (RPL3B), identical to ribosomal protein GI:806279 from (Arabidopsis thaliana) 694 At1g61660 D1 basic helix-loop-helix (bHLH) family protein, contains Pfam domain, PF00010: Helix-loop-helix DNA-binding domain 695 At1g61670 Dm expressed protein, similar to membrane protein PTM1 precursor isolog GI:1931644 from (Arabidopsis thaliana) 696 At1g61890 D1, D2, Dm MATE efflux family protein, similar to ripening regulated protein DDTFR18 (Lycopersicon esculentum) GI:12231296; contains Pfam profile PF01554: Uncharacterized membrane protein family 697 At1g62020 Dm coatomer protein complex, subunit alpha, putative, contains Pfam PF00400: WD domain, G-beta repeat; similar to Coatomer alpha subunit (Alpha-coat protein) (Alpha-COP) (HEPCOP) (HEP-COP) (SP:P53621) (Homo sapiens) 698 At1g62040 D2 autophagy 8c (APG8c), identical to autophagy 8c (Arabidopsis thaliana) GI:19912155; contains Pfam profile PF02991: Microtubule associated protein 1A/1B, light chain 3 699 At1g62180 D2 APR2_APSR_ATAPR2_PRH_PRH43__5`-adenylylsulfate reductase 2, chloroplast (APR2) (APSR) / adenosine 5`-phosphosulfate 5`-adenylylsulfate (APS) sulfotransferase 2 / 3`-phosphoadenosine- 5`-phosphosulfate (PAPS) reductase homolog 43 (PRH-43), identical to SP:P92981 5`- adenylylsulfate reductase 2, chloroplast precursor (EC 1.8.4.9) (Adenosine 5`-phosphosulfate 5`-adenylylsulfate sulfotransferase 2) (APS sulfotransferase 2) (Thioredoxin independent APS reductase 2) (3`-phosphoadenosine-5`-phosphosulfate reductase homolog 43) (PAPS reductase homolog 43) (Prh-43) {Arabidopsis thaliana}; identical to cDNA PAPS reductase homolog (PRH43) GI:1710115 700 At1g62225 D2 expressed protein 701 At1g62250 Dm expressed protein 702 At1g62290 D1, D2, Dm aspartyl protease family protein, contains Pfam profiles: PF00026 eukaryotic aspartyl protease, PF03489 surfactant protein B, PF05184 saposin-like type B, region 1 703 At1g62390 D2 octicosapeptide/Phox/Bem1p (PB1) domain-containing protein / tetratricopeptide repeat (TPR)- containing protein, contains Pfam profiles PF00564: PB1 domain, PF00515: TPR Domain 704 At1g62480 D1, D2, Dm vacuolar calcium-binding protein-related, contains weak similarity to vacuolar calcium binding protein (Raphanus sativus) gi:9049359:dbj:BAA99394 705 At1g62510 D1, D2, Dm protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 706 At1g62520 D2 expressed protein 707 At1g62570 D1, Dm flavin-containing monooxygenase family protein / FMO family protein, low similarity to flavin- containing monooxygenase FMO3 (Rattus norvegicus) GI:12006730; contains Pfam profile PF00743: Flavin-binding monooxygenase-like 708 At1g62610 D1, D2, Dm short-chain dehydrogenase/reductase (SDR) family protein, contains similarity to 3-oxoacyl- (acyl-carrier protein) reductase SP:P51831 from (Bacillus subtilis) 709 At1g62710 D1, D2, Dm BETA-VPE_BETAVPE__vacuolar processing enzyme beta / beta-VPE, identical to SP:Q39044 Vacuolar processing enzyme, beta-isozyme precursor (EC 3.4.22.-) (Beta-VPE) {Arabidopsis thaliana}

710 At1g62750 D1, D2, Dm elongation factor Tu family protein, similar to elongation factor G SP:P34811 (Glycine max (Soybean)) 711 At1g62780 D1, D2, Dm expressed protein 712 At1g62910 Dm pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat 713 At1g63000 Dm NRS/ER__expressed protein 714 At1g63010 D1, Dm SPX (SYG1/Pho81/XPR1) domain-containing protein, contains Pfam profile PF03105: SPX domain 715 At1g63230 D2 pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat 716 At1g63280 Dm serpin-related / serine protease inhibitor-related, similar to protein zx (Hordeum vulgare subsp. vulgare) GI:19071, serpin (Triticum aestivum) GI:1885346 717 At1g63290 D2 ribulose-phosphate 3-epimerase, cytosolic, putative / pentose-5-phosphate 3-epimerase, putative, strong similarity to D-ribulose-5-phosphate 3-epimerase (Oryza sativa) GI:6007803; contains Pfam profile PF00834: Ribulose-phosphate 3 epimerase family 718 At1g63370 D1 flavin-containing monooxygenase family protein / FMO family protein, similar to FMO5 from Cavia porcellus (SP:P49109); contains Pfam profile: PF00743 Flavin-binding monooxygenase-like

719 At1g63660 D2 GMP synthase (glutamine-hydrolyzing), putative / glutamine amidotransferase, putative, similar to SP:P38625 GMP synthase (glutamine-hydrolyzing) (EC 6.3.5.2) (Glutamine amidotransferase) (GMP synthetase) {Saccharomyces cerevisiae}; contains Pfam profile PF00117: glutamine amidotransferase class-I 720 At1g63700 D1 YDA_MAPKKK4__protein kinase, putative, contains protein kinase domain, Pfam:PF00069; similar to MEK kinase (MAP3Ka) (Arabidopsis thaliana) gi:4204912:gb:AAD10848 721 At1g63800 D2, Dm ubiquitin-conjugating enzyme 5 (UBC5), E2; identical to gi:431269, SP:P42749 722 At1g63840 D1, Dm zinc finger (C3HC4-type RING finger) family protein, similar to RING-H2 finger protein RHA1a (GI:3790554) (Arabidopsis thaliana)` similar to BRH1 RING finger protein (Arabidopsis thaliana) GI:4689366; contains Pfam profile PF00097: Zinc finger, C3HC4 type (RING finger) 723 At1g63970 D2, Dm ISPF__2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, putative, similar to 2C-methyl-D- erythritol 2,4-cyclodiphosphate synthase GI:7621712 from (Catharanthus roseus) 724 At1g64090 D2, Dm reticulon family protein (RTNLB3), weak similarity to SP:O95197 Reticulon protein 3 (Neuroendocrine-specific protein-like) {Homo sapiens}; contains Pfam profile PF02453: Reticulon 725 At1g64110 D1, D2, Dm AAA-type ATPase family protein, contains Pfam domain, PF00004: ATPase, AAA family 726 At1g64140 D2, Dm expressed protein, similar to putative disease resistance protein GB:CAB40943 GI:4586107 from (Arabidopsis thaliana); weak similarity to Loricrin (Swiss-Prot:P23490) (Homo sapiens) 727 At1g64230 D1, D2, Dm ubiquitin-conjugating enzyme, putative, identical or nearly so to Ubiquitin-conjugating enzymes SP:P35132, SP:P35131, SP:P35133 from {Arabidopsis thaliana}; contains Pfam profile PF00179: Ubiquitin-conjugating enzyme 728 At1g64355 Dm expressed protein 729 At1g64360 D1, D2, Dm expressed protein 730 At1g64370 D1, D2, Dm expressed protein 731 At1g64500 D2 glutaredoxin family protein 732 At1g64640 D2 plastocyanin-like domain-containing protein, contains InterPro:IPR003245 plastocyanin-like domain 733 At1g64660 D1, D2, Dm Cys/Met metabolism pyridoxal-phosphate-dependent enzyme family protein, similar to SP:P13254 Methionine gamma-lyase (EC 4.4.1.11) (L-methioninase) {Pseudomonas putida}; contains Pfam profile PF01053: Cys/Met metabolism PLP-dependent enzyme 734 At1g64680 D2, Dm expressed protein 735 At1g64710 D1 alcohol dehydrogenase, putative, similar to alcohol dehydrogenase GI:551257 from (Nicotiana tabacum) 736 At1g64720 D1, D2, Dm CP5__expressed protein, weak similarity to SP:P53809 Phosphatidylcholine transfer protein (PC- TP) {Rattus norvegicus} 737 At1g64750 D2 DSS1/SEM1 family protein, contains Pfam profile PF05160: DSS1/SEM1 family 738 At1g64770 D1, D2, Dm expressed protein 739 At1g64790 D1, Dm translational activator family protein, similar to HsGCN1 (Homo sapiens) GI:2282576 740 At1g64850 D1, D2, Dm calcium-binding EF hand family protein, contains INTERPRO:IPR002048 calcium-binding EF-hand domain 741 At1g64880 D2 ribosomal protein S5 family protein, contains similarity to 30S ribosomal protein S5 GI:6969105 from (Campylobacter jejuni) 742 At1g64920 Dm glycosyltransferase family protein, contains Pfam profile: PF00201 UDP-glucoronosyl and UDP- glucosyl transferase 743 At1g64950 D1, D2, Dm CYP89A5__cytochrome P450, putative, similar to cytochrome P450 89A2 (CYPLXXXIX) (SP:Q42602) (Arabidopsis thaliana);similar to cytochrome P450 (GI:438242) (Solanum melongena) 744 At1g64970 D1, D2, Dm G-TMT_TMT1_VTE4__expressed protein 745 At1g65230 D2 expressed protein 746 At1g65260 D2 PspA/IM30 family protein, contains Pfam PF04012: PspA/IM30 family profile; similar to Membrane-associated 30 kDa protein, chloroplast precursor (M30) (Swiss-Prot:Q03943) (Pisum sativum); similar to phage shock protein A (GI:28806161) (Vibrio parahaemolyticus); similar to Phage shock protein A. (Swiss-Prot:P23853) (Shigella flexneri) 747 At1g65420 Dm expressed protein, contains Pfam profile PF04483: Protein of unknown function (DUF565) 748 At1g65480 D2 FT__flowering locus T protein (FT), identical to SP:Q9SXZ2 FLOWERING LOCUS T protein {Arabidopsis thaliana}; contains Pfam profile PF01161: Phosphatidylethanolamine-binding protein 749 At1g65590 Dm glycosyl hydrolase family 20 protein, contains Pfam PF00728: Glycosyl hydrolase family 20, catalytic domain; contains Pfam PF02838: Glycosyl hydrolase family 20, domain 2; similar to Beta-hexosaminidase beta chain precursor (EC 3.2.1.52) (N-acetyl-beta- glucosaminidase) (Beta- N-acetylhexosaminidase) (Hexosaminidase B) (Swiss-Prot:P07686) (Homo sapiens) 750 At1g65720 D1, D2, Dm expressed protein 751 At1g65820 D1, D2, Dm microsomal glutathione s-transferase, putative, similar to MGST3_HUMAN SP:O14880 752 At1g65840 Dm amine oxidase family protein, similar to polyamine oxidase SP:O64411 (Zea mays); contains Pfam profile PF01593 amine oxidase, flavin-containing 753 At1g65845 D2 expressed protein, (Arabidopsis thaliana) 754 At1g65930 D1, D2, Dm isocitrate dehydrogenase, putative / NADP+ isocitrate dehydrogenase, putative, strong similarity to isocitrate dehydrogenase SP:Q40345 from (Medicago sativa) 755 At1g65970 D1, D2, Dm TPX2__peroxiredoxin type 2, putative, strong similarity to type 2 peroxiredoxin (Brassica rapa subsp. pekinensis) GI:4928472; contains Pfam profile: PF00578 AhpC/TSA (alkyl hydroperoxide reductase and thiol-specific antioxidant) family 756 At1g65980 D1, D2, Dm TPX1__peroxiredoxin type 2, putative, strong similarity to type 2 peroxiredoxin (Brassica rapa subsp. pekinensis) GI:4928472; contains Pfam profile: PF00578 AhpC/TSA (alkyl hydroperoxide reductase and thiol-specific antioxidant) family 757 At1g66090 D1, D2 disease resistance protein (TIR-NBS class), putative, domain signature TIR-NBS exists, suggestive of a disease resistance protein. 758 At1g66100 D2, Dm thionin, putative, similar to thionin (Arabidopsis thaliana) GI:1181533 759 At1g66130 D1, D2, Dm oxidoreductase N-terminal domain-containing protein, similar to AX110P (Daucus carota) GI:285739; contains Pfam profile PF01408: Oxidoreductase family NAD-binding Rossmann fold 760 At1g66150 D1, D2, Dm TMK1__leucine-rich repeat protein kinase, putative (TMK1), identical to protein kinase TMK1 gi:166888:gb:AAA32876, SP:P43298 Putative receptor protein kinase TMK1 precursor (EC 2.7.1.-) {Arabidopsis thaliana} 761 At1g66180 D2, Dm aspartyl protease family protein, contains Pfam PF00026: Eukaryotic aspartyl protease profile; similar to CND41, chloroplast nucleoid DNA binding protein (GI:2541876) (Nicotiana tabacum)

762 At1g66200 D1, D2, Dm ATGSR2__glutamine synthetase, putative, similar to glutamine synthetase, cytosolic isozyme (Glutamate-- ammonia ligase, GS1) (Lotus japonicus) SWISS-PROT:Q42899 763 At1g66240 D1, D2, Dm copper homeostasis factor, putative / copper chaperone, putative (CCH), similar to gi:3168840 contains Pfam profile PF00403: Heavy-metal-associated domain 764 At1g66330 D2, Dm senescence-associated family protein, similar to senescence-associated protein (GI:12836895) (Ipomoea batatas) 765 At1g66410 D1 CAM4_ACAM-4__calmodulin-1/4 (CAM4), identical to calmodulin (Arabidopsis thaliana) GI:16223; nearly identical to SP:P25854 Calmodulin-1/4 {Arabidopsis thaliana} 766 At1g66890 D2, Dm expressed protein 767 At1g66900 D1, D2, Dm expressed protein 768 At1g66970 D1, Dm glycerophosphoryl diester phosphodiesterase family protein, contains Pfam PF03009 : Glycerophosphoryl diester phosphodiesterase family 769 At1g67020 D1 hypothetical protein 770 At1g67070 D1, Dm DIN9__phosphomannose isomerase, putative (DIN9), contains Pfam profile: PF01238 phosphomannose isomerase type I ;similar to phosphomannose isomerase GI:10834550 from (Arabidopsis thaliana); identical to cDNA phosphomannose isomerase (din9) partial cds GI:10834549 771 At1g67290 Dm glyoxal oxidase-related, contains similarity to glyoxal oxidase precursor (Phanerochaete chrysosporium) gi:1050302:gb:AAA87594 772 At1g67300 D1, D2, Dm hexose transporter, putative, similar to hexose transporters from Solanum tuberosum (GI:8347246), Nicotiana tabacum (GI:8347244), Arabidopsis thaliana (GI:8347250); contains Pfam profile PF00083: major facilitator superfamily protein 773 At1g67320 D1, Dm DNA primase, large subunit family, contains Pfam profile PF04104: Eukaryotic-type DNA primase, large subunit; similar to DNA primase large subunit (EC 2.7.7.-) (DNA primase 58 kDa subunit) (p58) (Swiss-Prot:P49643) (Homo sapiens) 774 At1g67360 D2, Dm rubber elongation factor (REF) family protein, contains Pfam profile: PF05755 rubber elongation factor protein (REF) 775 At1g67430 D1, D2, Dm 60S ribosomal protein L17 (RPL17B), similar to ribosomal protein GI:19101 from (Hordeum vulgare) 776 At1g67520 Dm lectin protein kinase family protein, contains Pfam domains PF00069: Protein kinase domain and PF01453: Lectin (probable mannose binding) 777 At1g67620 D2 expressed protein, contains Pfam domain PF02410: Domain of unknown function DUF143 778 At1g67700 D1, Dm expressed protein 779 At1g67810 D1, Dm Fe-S metabolism associated domain-containing protein, contains Pfam PF02657: Fe-S metabolism associated domain 780 At1g67860 D1, Dm expressed protein 781 At1g67870 D1, D2, Dm glycine-rich protein, contains non-consensus GG donor splice site at exon2; modeled to est match. 782 At1g67920 D1, D2, Dm expressed protein 783 At1g68010 D2, Dm HPR__glycerate dehydrogenase / NADH-dependent hydroxypyruvate reductase, identical to hydroxypyruvate reductase (HPR) GB:D85339 (Arabidopsis thaliana) (Plant Cell Physiol 1997 Apr;38(4):449-55) 784 At1g68110 Dm epsin N-terminal homology (ENTH) domain-containing protein / clathrin assembly protein- related, similar to clathrin assembly protein AP180 (GI:6492344) (Xenopus laevis); contains Pfam profile: PF01417 ENTH domain, suggesting involvement in endocytosis or cytoskeletal machinery 785 At1g68140 D1, Dm expressed protein 786 At1g68180 Dm zinc finger (C3HC4-type RING finger) family protein, contains Pfam profile: PF00097 zinc finger, C3HC4 type (RING finger) 787 At1g68190 Dm zinc finger (B-box type) family protein 788 At1g68300 D2 universal stress protein (USP) family protein, similar to ER6 protein (Lycopersicon esculentum) GI:5669654; contains Pfam profile PF00582: universal stress protein family 789 At1g68400 Dm leucine-rich repeat transmembrane protein kinase, putative, similar to receptor kinase GB:AAA33715 from (Petunia integrifolia) 790 At1g68440 D2 expressed protein 791 At1g68520 D2 zinc finger (B-box type) family protein, contains Pfam profile: PF00643 B-box zinc finger 792 At1g68560 D1, D2, Dm XYL1__alpha-xylosidase (XYL1), identical to alpha-xylosidase precursor GB:AAD05539 GI:4163997 from (Arabidopsis thaliana); contains Pfam profile PF01055: Glycosyl hydrolases family 31; identical to cDNA alpha-xylosidase precursor (XYL1) partial cds GI:4163996 793 At1g68570 D1, D2, Dm proton-dependent oligopeptide transport (POT) family protein, contains Pfam profile: PF00854 POT family 794 At1g68590 D1, D2, Dm plastid-specific 30S ribosomal protein 3, putative / PSRP-3, putative, similar to SP:P82412 Plastid-specific 30S ribosomal protein 3, chloroplast precursor (PSRP-3) {Spinacia oleracea}; contains Pfam profile PF04839: Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65)

795 At1g68600 D1, D2, Dm expressed protein, contains Pfam profile PF01027: Uncharacterized protein family UPF0005 796 At1g68660 D1, Dm expressed protein 797 At1g68830 D2, Dm STN7 protein kinase; required for state transitions, phosphorylation of the major antenna complex (LHCII) between PSII and PSI, and light adaptation 798 At1g68840 D1, D2, Dm RAP2.8_RAV2__DNA-binding protein RAV2 (RAV2) / AP2 domain-containing protein RAP2.8, identical to RAV2 GI:3868859 from (Arabidopsis thaliana), AP2 domain containing protein RAP2.8 (Arabidopsis thaliana) GI:2281641; contains Pfam profile: PF00847 AP2-domain 799 At1g68900 D1, Dm mandelate racemase/muconate lactonizing enzyme C-terminal domain-containing protein / hydrolase, alpha/beta fold family protein, contains Pfam profiles PF01188: Mandelate racemase / muconate lactonizing enzyme, C-terminal domain, PF00561: hydrolase, alpha/beta fold family

800 At1g69030 D1, Dm similar to BSD domain-containing protein [Arabidopsis thaliana] (TAIR:At1g26300.1); contains InterPro domain BSD domain (InterPro:IPR005607) 801 At1g69040 D1, D2, Dm ACR4_ACT REPEAT 4__ACT domain containing protein (ACR4), low similarity to uridylyltransferase (Gluconacetobacter diazotrophicus) GI:17226253; contains Pfam profile PF01842: ACT domain

802 At1g69110 D1, D2, Dm pseudogene, 40S ribosomal protein S20 803 At1g69140 D2, Dm pseudogene, hypothetical protei 804 At1g69200 D2, Dm pfkB-type carbohydrate kinase family protein, contains Pfam profile: PF00294 pfkB family carbohydrate kinase 805 At1g69250 D2 nuclear transport factor 2 (NTF2) family protein / RNA recognition motif (RRM)-containing protein, contains Pfam profiles PF02136: Nuclear transport factor 2 (NTF2) domain, PF00076: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain) 806 At1g69390 D2 ATMINE1__Encodes an Arabidopsis homologue of the bacterial MinE topological specificity factor ensuring correct division site placement. It is an essential integral component of the plastid division machinery. 807 At1g69410 D1, D2, Dm eukaryotic translation initiation factor 5A, putative / eIF-5A, putative, strong similarity to eukaryotic initiation factor 5A (2) (Nicotiana plumbaginifolia) GI:19702, SP:Q9AXQ6: Eukaryotic translation initiation factor 5A-1 (eIF-5A 1) {Lycopersicon esculentum} 808 At1g69490 D1, D2, Dm ANAC029_NAP__no apical meristem (NAM) family protein, similar to N-term half of NAC domain protein NAM (Arabidopsis thaliana) GI:4325282 809 At1g69510 D2, Dm expressed protein 810 At1g69530 D1, D2, Dm ATEXPA1_ATEXP1_AT-EXP1_ATHEXP ALPHA 1.2_EXP1__expansin, putative (EXP1), identical to expansin (At-EXP1) (Arabidopsis thaliana) GI:1041702; alpha-expansin gene family, PMID:11641069

811 At1g69620 D1, Dm RPL34__60S ribosomal protein L34 (RPL34B), similar to SP:Q42351 from (Arabidopsis thaliana) 812 At1g69740 D1, D2, Dm porphobilinogen synthase, putative / delta-aminolevulinic acid dehydratase, putative, similar to delta-aminolevulinic acid dehydratase (Alad) GI:493019 (SP:P43210) from Glycine max, SP:P24493 from Spinacia oleracea, SP:P30124 from Pisum sativum 813 At1g69770 Dm CMT3__chromomethylase 3 (CMT3), nearly identical to chromomethylase CMT3 (Arabidopsis thaliana) GI:14583092, GI:14647157 814 At1g69780 D2, Dm ATHB13__homeobox-leucine zipper protein 13 (HB-13) / HD-ZIP transcription factor 13, identical to homeobox gene 13 protein (GP:12325190) (Arabidopsis thaliana) 815 At1g69820 D1, Dm gamma-glutamyltranspeptidase family protein, similar to SP:P19440 Gamma-glutamyltranspeptidase 1 precursor (EC 2.3.2.2) (Gamma-glutamyltransferase 1) (CD224 antigen) {Homo sapiens}; contains Pfam profilePF01019: Gamma-glutamyltranspeptidase 816 At1g69890 D2 expressed protein, contains Pfam profile: PF04601 protein of unknown function (DUF569 817 At1g69930 D2 ATGSTU11__glutathione S-transferase, putative, similar to glutathione transferase GB:CAA09188 (Alopecurus myosuroides) 818 At1g70070 Dm PDE317__DEAD/DEAH box helicase, putative, similar to SP:P35207 Antiviral protein SKI2 {Saccharomyces cerevisiae}; contains Pfam profiles PF00270: DEAD/DEAH box helicase, PF00271: Helicase conserved C-terminal domain 819 At1g70280 Dm NHL repeat-containing protein, contains Pfam profile PF01436: NHL repeat 820 At1g70300 D2, Dm KUP6__potassium transporter, putative, similar to potassium transporter HAK2p (Mesembryanthemum crystallinum) gi:14091471:gb:AAK53759; KUP/HAK/KT Transporter family member, PMID:11500563; contains Pfam profile PF02705: K+ potassium transporter 821 At1g70410 D2, Dm carbonic anhydrase, putative / carbonate dehydratase, putative, similar to SP:P42737 Carbonic anhydrase 2 (EC 4.2.1.1) (Carbonate dehydratase 2) {Arabidopsis thaliana}; contains Pfam profile PF00484: Carbonic anhydrase 822 At1g70580 D2, Dm AOAT2_GGT2__glutamate:glyoxylate aminotransferase 2 (GGT2), identical to glutamate:glyoxylate aminotransferase 2 (Arabidopsis thaliana) GI:24461829; similar to alanine aminotransferase from Panicum miliaceum (SP:P34106), GI:4730884 from Oryza sativa; contains Pfam profile PF00155: aminotransferase, classes I and II 823 At1g70600 D2, Dm 60S ribosomal protein L27A (RPL27aC), identical to 60S ribosomal protein L27A GB:P49637 (Arabidopsis thaliana) 824 At1g70780 D2, Dm expressed protein 825 At1g70830 D1, D2, Dm similar to Bet v I allergen family protein [Arabidopsis thaliana] (TAIR:At1g70850.2); similar to Csf-2 [Cucumis sativus] (GB:BAA83470.1); contains InterPro domain Bet v I allergen (InterPro:IPR000916) 826 At1g70840 Dm Bet v I allergen family protein, similar to Csf-2 (Cucumis sativus)(GI:5762258)(J Am Soc Hortic Sci 124, 136-139 (1999)) ; contains Pfam profile PF00407: Pathogenesis-related protein Bet v I family 827 At1g70885 D2, Dm pseudogene, similar to major latex-like protein, blastp match of 64% identity and 7.2e-16 P- value to GP|13172242|gb|AAK14060.1|AF239177_1|AF239177 major latex-like protein {Prunus persica} 828 At1g70890 D1, D2, Dm major latex protein-related / MLP-related, low similarity to major latex protein {Papaver somniferum}(GI:294062) ; contains Pfam profile PF00407: Pathogenesis-related protein Bet v I family 829 At1g71030 D2, Dm ATMYBL2__Encodes a putative myb family transcription factor. In contrast to most other myb- like proteins its myb domain consists of a single repeat. A proline-rich region potentially involved in transactivation is found in the C-terminal part of the protein. Its transcript accumulates mainly in leaves. 830 At1g71050 D2 heavy-metal-associated domain-containing protein / copper chaperone (CCH)-related, low similarity to copper homeostasis factor (GI:3168840)(PMID:9701579); similar to farnesylated protein ATFP7 (GI:4097555); contains heavy-metal-associated domain PF00403 831 At1g71070 D1, Dm glycosyltransferase family 14 protein / core-2/I-branching enzyme family protein, similar to glucosaminyl (N-acetyl) transferase GB:4758422 from (Homo sapiens) 832 At1g71080 D2 expressed protein 833 At1g71130 D2 encodes a member of the ERF (ethylene response factor) subfamily B-5 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 7 members in this subfamily.

834 At1g71330 D2, Dm ATNAP5__ABC transporter family protein, contains Pfam profile: PF00005 ABC transporter 835 At1g71360 Dm expressed protein, low similarity to PIR:JC7185 chromosome 1 C1orf9 protein (Homo sapiens) 836 At1g71480 D1, D2, Dm nuclear transport factor 2 (NTF2) family protein, contains Pfam domain, PF02136: Nuclear transport factor 2 (NTF2) domain 837 At1g71500 D1, Dm Rieske (2Fe-2S) domain-containing protein, contains Pfam profile PF00355: iron-sulfur cluster- binding protein, rieske family 838 At1g71520 D2, Dm encodes a member of the DREB subfamily A-5 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 16 members in this subfamily including RAP2.1, RAP2.9 and RAP2.10. 839 At1g71695 D1, D2, Dm peroxidase 12 (PER12) (P12) (PRXR6), identical to SP:Q96520 Peroxidase 12 precursor (EC 1.11.1.7) (Atperox P12) (PRXR6) (ATP4a) {Arabidopsis thaliana} 840 At1g71720 D1, D2, Dm S1 RNA-binding domain-containing protein, contains Pfam domain, PF00575: S1 RNA binding domain

841 At1g71880 D2, Dm SUC1_ATSUC1__sucrose transporter / sucrose-proton symporter (SUC1), identical to sucrose- proton symporter SUC1 (Arabidopsis thaliana) GI:407094 842 At1g71890 D2, Dm ATSUC5_SUC5__Encodes a sucrose transporter that is expressed in the endosperm. Mutants have delayed accumulation of fatty acids and embryo maturation. 843 At1g71950 D2 expressed protein, similar to Pi starvation-induced protein GB:BAA06151 from (Nicotiana tabacum) 844 At1g72010 D1, D2, Dm TCP family transcription factor, putative, PCF2 (GP:2580440) (Oryza sativa) 845 At1g72160 D1, D2, Dm SEC14 cytosolic factor family protein / phosphoglyceride transfer family protein, similar to GI:807956 from (Saccharomyces cerevisiae)similar to polyphosphoinositide binding protein Ssh2p (GI:2739046) {Glycine max}; contains Pfam PF00650 : CRAL/TRIO domain; contains Pfam PF03765 : CRAL/TRIO, N-terminus 846 At1g72320 D1 pumilio/Puf RNA-binding domain-containing protein, contains Pfam profile: PF00806 Pumilio- family RNA binding domains (aka PUM-HD, Pumilio homology domain) (5 copies) 847 At1g72370 D1, D2, Dm P40_AP40_RP40_RPSAA__40S ribosomal protein SA (RPSaA), identical to laminin receptor-like protein GB:U01955 (Arabidopsis thaliana); identical to cDNA laminin receptor homologue GI:16379 848 At1g72430 D2, Dm auxin-responsive protein-related, similar to auxin-induced protein TGSAUR22 (GI:10185820) (Tulipa gesneriana) 849 At1g72440 D2, Dm CCAAT-box-binding transcription factor-related, similar to CCAAT-box-binding transcription factor (CCAAT-binding factor) (CBF) (Swiss-Prot:Q03701) (Homo sapiens), GB:P53569 (Mus musculus) 850 At1g72450 D1, D2, Dm expressed protein 851 At1g72490 Dm expressed protein, similar to hypothetical protein [Arabidopsis thaliana] (TAIR:At1g17400.1); similar to unknown protein [Oryza sativa (japonica cultivar-group)] (GB:BAD36146.1)

852 At1g72510 D1, D2, Dm expressed protein 853 At1g72610 D1, D2, Dm GLP1__germin-like protein (GER1), identical to germin-like protein subfamily 3 member 1 SP:P94040; contains Pfam profile: PF01072 Germin family 854 At1g72770 D1, D2, Dm HAB1__protein phosphatase 2C P2C-HA / PP2C P2C-HA (P2C-HA), identical to protein phosphatase 2C (AtP2C-HA) GB:AJ003119 (Arabidopsis thaliana) (Plant Mol. Biol. 38 (5), 879-883 (1998)) 855 At1g72970 D1, D2, Dm HTH__glucose-methanol-choline (GMC) oxidoreductase family protein, similar to mandelonitrile lyase from Prunus serotina (SP:P52706, SP:P52707); contains Pfam profile PF00732 GMC oxidoreductase 856 At1g73010 D2 expressed protein, similar to phosphatase, orphan 1 (GI:20196841) (Mus musculus), (GI:20196839) (Homo sapiens); contains TIGRFAM TIGR01489: 2,3-diketo-5-methylthio-1- phosphopentane phosphatase profile; contains TIGRFAM TIGR01488: HAD-superfamily hydrolase, subfamily IB (PSPase-like) 857 At1g73030 Dm SNF7 family protein, contains Pfam domain, PF03357: SNF7 family 858 At1g73060 Dm expressed protein 859 At1g73170 D1, D2, Dm expressed protein 860 At1g73230 D2 nascent polypeptide-associated complex (NAC) domain-containing protein, similar to SP:P20290 Transcription factor BTF3 (RNA polymerase B transcription factor 3) {Homo sapiens}; contains Pfam profile PF01849: NAC domain 861 At1g73260 D1 trypsin and protease inhibitor family protein / Kunitz family protein, similar to trypsin inhibitor propeptide (Brassica oleracea) GI:841208; contains Pfam profile PF00197: Trypsin and protease inhibitor 862 At1g73330 D2, Dm ATDR4__protease inhibitor, putative (DR4), identical to Dr4 GI:469114 from (Arabidopsis thaliana); contains Pfam profile PF00197: Trypsin and protease inhibitor 863 At1g73390 D2, Dm expressed protein 864 At1g73500 D2, Dm ATMKK9__mitogen-activated protein kinase kinase (MAPKK), putative (MKK9), mitogen-activated protein kinase kinase (MAPKK) family, PMID:12119167 865 At1g73600 D2 phosphoethanolamine N-methyltransferase 3, putative (NMT3), strong similarity to SP:Q9FR44 Phosphoethanolamine N-methyltransferase 1 (EC 2.1.1.103) (PEAMT 1) (AtNMT1) {Arabidopsis thaliana}; identical to SP:Q9C6B9 Putative phosphoethanolamine N-methyltransferase 3 {Arabidopsis thaliana} 866 At1g73655 D1 immunophilin / FKBP-type peptidyl-prolyl cis-trans isomerase family protein, similar to (Peptidyl-prolyl cis-trans isomerase) (PPiase) (Rotamase) (SP:Q26486) (Spodoptera frugiperda); contains Pfam PF00254: peptidyl-prolyl cis-trans isomerase, FKBP-type 867 At1g73670 D2 ATMPK15__mitogen-activated protein kinase, putative / MAPK, putative (MPK15), similar to mitogen-activated protein kinase GB:A56042 (Dictyostelium discoideum); mitogen-activated protein kinase (MAPK)(AtMPK15), PMID:12119167; contains Pfam profile: PF00069 Eukaryotic protein kinase domain 868 At1g73830 D2 basic helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain 869 At1g73840 D1, D2, Dm hydroxyproline-rich glycoprotein family protein, similar to proline-rich protein precursor GB:AAC34889 (Glycine max) 870 At1g73870 D2 zinc finger (B-box type) family protein 871 At1g73910 Dm ATARP4A_ATARP5__Encodes a gene similar to actin-related proteins in other organisms. Member of nuclear ARP family of genes. Component of chromatin remodeling complexes, involved in chromatin-mediated gene regulation. 872 At1g74000 D2 SS3__similar to strictosidine synthase family protein [Arabidopsis thaliana] (TAIR:At1g74020.1); similar to strictosidine synthase (GB:AAB40594.1); contains InterPro domain Strictosidine synthase (InterPro:IPR004141) 873 At1g74020 D2, Dm SS2__strictosidine synthase family protein, similar to strictosidine synthase (Rauvolfia serpentina)(SP:P15324); contains strictosidine synthase domain PF03088 874 At1g74070 Dm peptidyl-prolyl cis-trans isomerase cyclophilin-type family protein, contains Pfam domain, PF00160: peptidyl-prolyl cis-trans isomerase, cyclophilin-type 875 At1g74260 D1, Dm AIR synthase-related family protein, contains Pfam profiles: PF00586 AIR synthase related protein, N-terminal domain, PF02769 AIR synthase related protein, C-terminal domain 876 At1g74270 D2 60S ribosomal protein L35a (RPL35aC), similar to ribosomal protein L33B GB:NP_014877 from (Saccharomyces cerevisiae) 877 At1g74340 D1, D2, Dm dolichol phosphate-mannose biosynthesis regulatory protein-related, similar to dolichol phosphate-mannose biosynthesis regulatory protein SP:Q9Z324 from (Mus musculus) 878 At1g74370 D2 zinc finger (C3HC4-type RING finger) family protein, contains Pfam profile: PF00097 zinc finger, C3HC4 type (RING finger) 879 At1g74380 Dm galactosyl transferase GMA12/MNN10 family protein, very low similarity to alpha-1,2- galactosyltransferase, Schizosaccharomyces pombe (SP:Q09174) 880 At1g74560 D2 nucleosome assembly protein (NAP) family protein, similar to SP:Q01105 SET protein (HLA-DR associated protein II) (PHAPII) (Phosphatase 2A inhibitor I2PP2A) {Homo sapiens}; contains Pfam profile: PF00956 nucleosome assembly protein (NAP) 881 At1g74640 D1, D2, Dm expressed protein, contains Pfam profile: PF00561 alpha/beta hydrolase fold 882 At1g74660 D2 zinc finger homeobox family protein / ZF-HD homeobox family protein, contains Pfam PF04770: ZF-HD protein dimerisation region; contains TIGRFAM TIGR01566: ZF-HD homeobox protein Cys/His- rich dimerization domain; similar to ZF-HD homeobox protein (GI:13374061) (Flaveria bidentis)

883 At1g74670 D1, D2, Dm gibberellin-responsive protein, putative, similar to SP:P46690 Gibberellin-regulated protein 4 precursor {Arabidopsis thaliana} GASA4; contains Pfam profile PF02704: Gibberellin regulated protein 884 At1g74710 Dm ICS1_EDS16_SID2__isochorismate synthase 1 (ICS1) / isochorismate mutase, identical to GI:17223087 and GB:AF078080; contains Pfam profile PF00425: chorismate binding enzyme; contains TIGRfam profile TIGR00543: isochorismate synthases; identical to cDNA isochorismate synthase 1 precursor (ICS1) nuclear gene for plastid product GI:17223086 885 At1g74730 D1 expressed protein 886 At1g74810 D1, Dm anion exchange family protein, contains Pfam profile: PF00955 Anion exchanger family 887 At1g74850 Dm pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat 888 At1g74890 Dm ARR15__two-component responsive regulator / response regulator 15 (ARR15), identical to response regulator 15 GI:11870065 from (Arabidopsis thaliana); contains Pfam profile: PF00072 response regulator receiver domain 889 At1g74910 D1, D2, Dm ADP-glucose pyrophosphorylase family protein, contains Pfam profile PF00483: Nucleotidyl transferase; low similarity to mannose-1-phosphate guanylyltransferase (Hypocrea jecorina) GI:3323397 890 At1g74920 D1, D2, Dm ALDH10A8__betaine-aldehyde dehydrogenase, putative, identical to betaine-aldehyde dehydrogenase, chloroplast precursor (BADH) (Arabidopsis thaliana) SWISS-PROT:Q9S795; strong similarity to betaine aldehyde dehydrogenase (Amaranthus hypochondriacus) GI:2388710 891 At1g74940 D2, Dm senescence-associated protein-related, similar to senescence-associated protein SAG102 (GI:22331931) (Arabidopsis thaliana) 892 At1g74950 D2 expressed protein 893 At1g75040 D2, Dm PR5_PR-5__pathogenesis-related protein 5 (PR-5), identical to SP:P28493 Pathogenesis-related protein 5 precursor (PR-5) {Arabidopsis thaliana}; contains Pfam profile: PF00314 Thaumatin family 894 At1g75200 D2 flavodoxin family protein / radical SAM domain-containing protein, contains Pfam profiles PF00258: Flavodoxin, PF04055: radical SAM domain protein 895 At1g75210 Dm 5` nucleotidase family protein, contains Pfam profile: PF05761 5` nucleotidase family 896 At1g75220 D1, D2, Dm integral membrane protein, putative, strong similarity to integral membrane protein GI:1209756 from (Beta vulgaris); contains Pfam profile PF00083: major facilitator superfamily protein

897 At1g75240 Dm zinc finger homeobox family protein / ZF-HD homeobox family protein 898 At1g75280 D1, D2, Dm isoflavone reductase, putative, identical to SP:P52577 Isoflavone reductase homolog P3 (EC 1.3.1.-) {Arabidopsis thaliana}; contains Pfam profile PF02716: isoflavone reductase. Involved in response to oxidative stress. 899 At1g75300 D2, Dm isoflavone reductase, putative, identical to SP:P52577 Isoflavone reductase homolog P3 (EC 1.3.1.-) {Arabidopsis thaliana}; contains Pfam profile PF02716: Isoflavone reductase 900 At1g75310 D1 AUL1__DNAJ heat shock N-terminal domain-containing protein, low similarity to SP:Q27974 Auxilin {Bos taurus}; contains Pfam profile PF00226: DnaJ domain 901 At1g75350 D1 EMB2184__ribosomal protein L31 family protein, similar to SP:O46917 from (Guillardia theta) 902 At1g75380 D2 wound-responsive protein-related, similar to wound inducive gene GI:8096273 from (Nicotiana tabacum) 903 At1g75400 D2, Dm expressed protein 904 At1g75410 D1, D2, Dm BLH3__BEL1-like homeodomain 3 protein (BLH3), identical to BEL1-like homeodomain 3 (GI:13877515) (Arabidopsis thaliana) 905 At1g75500 D1, D2, Dm nodulin MtN21 family protein, similar to MtN21 GB:CAA75575 GI:2598575 from (Medicago truncatula) (Mol. Plant Microbe Interact. 9 (4), 233-242 (1996)); contains Pfam profile PF00892: Integral membrane protein 906 At1g75580 D2 auxin-responsive protein, putative, similar to auxin-induced protein TGSAUR22 (GI:10185820) (Tulipa gesneriana) 907 At1g75590 Dm auxin-responsive family protein, similar to auxin-induced protein TGSAUR22 (GI:10185820) (Tulipa gesneriana) 908 At1g75630 D1, D2, Dm AVA-P__vacuolar ATP synthase 16 kDa proteolipid subunit 4 / V-ATPase 16 kDa proteolipid subunit 4 (AVAP4) (AVA-P4), identical to SP:P59229 Vacuolar ATP synthase 16 kDa proteolipid subunit 4 (EC 3.6.3.14) (V-ATPase 16 kDa proteolipid subunit 4) {Arabidopsis thaliana}; contains Pfam profile PF00137: ATP synthase subunit C 909 At1g75680 D1, Dm glycosyl hydrolase family 9 protein, similar to endo-beta-1,4-glucanase GB:AAC12685 GI:3025470 from (Pinus radiata) 910 At1g75690 D1, Dm chaperone protein dnaJ-related, contains Pfam PF00684 : DnaJ central domain (4 repeats); similar to bundle sheath defective protein 2 (GI:4732091) (Zea mays) 911 At1g75710 Dm zinc finger (C2H2 type) family protein, contains zinc finger, C2H2 type, domain, PROSITE:PS00028 912 At1g75750 D1, D2, Dm GASA1_GASA5__gibberellin-regulated protein 1 (GASA1) / gibberellin-responsive protein 1, identical to SP:P46689 Gibberellin-regulated protein 1 precursor {Arabidopsis thaliana}; supporting cDNA gi:887938:gb:U11766.1:ATU11766 913 At1g75780 D1, D2, Dm TUB1__tubulin beta-1 chain (TUB1), nearly identical to SP:P12411 Tubulin beta-1 chain {Arabidopsis thaliana} 914 At1g75820 D1 CLV1_FAS3_FLO5__CLAVATA1 receptor kinase (CLV1), identical to receptor kinase (CLV1) GB:AAB58929 GI:2160756 (Arabidopsis thaliana) 915 At1g75830 D1, Dm LCR67_PDF1.1__plant defensin-fusion protein, putative (PDF1.1), identical to SP:P30224 Cysteine-rich antifungal protein 1 precursor (AFP1) (Anther-specific protein S18 homolog) {Arabidopsis thaliana} 916 At1g76020 D1, Dm expressed protein 917 At1g76090 D1, D2, Dm SMT3__S-adenosyl-methionine-sterol-C-methyltransferase, identical to S-adenosyl-methionine- sterol-C-methyltransferase GI:2246456 from (Arabidopsis thaliana) 918 At1g76100 Dm plastocyanin, identical to plastocyanin GI:1865683 from (Arabidopsis thaliana) 919 At1g76110 D2, Dm high mobility group (HMG1/2) family protein / ARID/BRIGHT DNA-binding domain-containing protein, low similarity to high mobility group protein (Plasmodium falciparum) GI:790198; contains Pfam profiles PF00505: HMG (high mobility group) box, PF01388: ARID/BRIGHT DNA binding domain 920 At1g76160 D1, D2, Dm SKS5__multi-copper oxidase type I family protein, similar to pollen-specific BP10 protein (SP:Q00624)(Brassica napus); contains Pfam profile: PF00394 Multicopper oxidase 921 At1g76180 D1, D2, Dm ERD14__dehydrin (ERD14), identical to SP:P42763 Dehydrin ERD14 {Arabidopsis thaliana} 922 At1g76380 Dm DNA-binding bromodomain-containing protein, contains bromodomain, INTERPRO:IPR001487 923 At1g76405 D2 expressed protein 924 At1g76490 D1, Dm HMG1_HMGR1__similar to 3-hydroxy-3-methylglutaryl-CoA reductase 2 / HMG-CoA reductase 2 (HMGR2) [Arabidopsis thaliana] (TAIR:At2g17370.1); similar to 3-hydroxy-3-methylglutaryl coenzyme A reductase [Hevea brasiliensis] (GB:AAU08214.1); similar to HMG-CoA reductase [Cucumis melo] (GB:BAA36291.1); similar to 3-hydroxy-3-methylglutaryl-coenzyme A reductase [Hevea brasiliensis] (GB:AAQ63055.1); similar to hydroxymethylglutaryl-CoA reductase (NADPH) [Raphanus sativus] (GB:CAA48610.1); similar to 3-hydroxy-3-methylglutaryl coenzyme A reductase; HMG-CoA reductase; EuHMGR [Eucommia ulmoides] (GB:AAV54051.1); contains InterPro domain 3-hydroxy-3-methylglutaryl Coenzyme A reductase (InterPro:IPR004554); contains InterPro domain Hydroxymethylglutaryl-coenzyme A reductase (InterPro:IPR002202) 925 At1g76570 D2, Dm chlorophyll A-B binding family protein, similar to chlorophyll A-B binding protein GB:P12470 (Nicotiana plumbaginifolia); contains Pfam profile: PF00504 Chlorophyll A-B binding proteins 926 At1g76580 D1, Dm similar to squamosa promoter-binding protein-like 1 (SPL1) [Arabidopsis thaliana] (TAIR:At2g47070.1); similar to putative SBP-domain protein [Oryza sativa (japonica cultivar- group)] (GB:XP_470314.1); contains domain SER_RICH (PS50324) 927 At1g76590 D1, D2, Dm zinc-binding family protein, similar to zinc-binding protein (Pisum sativum) GI:16117799; contains Pfam profile PF04640 : Protein of unknown function, DUF597 928 At1g76670 D2 transporter-related, low similarity to glucose-6-phosphate/phosphate-translocator precursor (Solanum tuberosum) GI:2997593, GDP-Mannose transporter (Arabidopsis thaliana) GI:15487237; contains Pfam profile PF00892: Integral membrane protein 929 At1g76680 D1, D2, Dm OPR1__12-oxophytodienoate reductase (OPR1), identical to 12-oxophytodienoate reductase OPR1 GB:AAC78440 (Arabidopsis thaliana) 930 At1g76690 D2, Dm OPR2__12-oxophytodienoate reductase (OPR2), identical to 12-oxophytodienoate reductase OPR2 GB:AAC78441 (Arabidopsis thaliana) 931 At1g76890 D2 GT2_AT-GT2__trihelix DNA-binding protein / GT-2 factor (GT2), identical to GT2 factor (Arabidopsis thaliana) GI:416490, GI:2664202 (DNA binding factor GT-2 from Arabidopsis) 932 At1g76960 Dm expressed protein 933 At1g76980 Dm expressed protein 934 At1g76990 D1, D2, Dm ACR3__ACT domain containing protein, low similarity to uridylyltransferase SP:P56884 from Rhizobium meliloti; contains Pfam ACT domain PF01842 935 At1g77000 D1, D2, Dm F-box family protein, similar to GP:21554029: F-box protein AtFBL5 from (Arabidopsis thaliana); similar to F-box protein FBL2 GI:6063090 from (Homo sapiens) 936 At1g77060 D1 mutase family protein, similar to carboxyvinyl-carboxyphosphonate phosphorylmutase GB:O49290 from (Arabidopsis thaliana); similar to carboxyphosphonoenolpyruvate mutase (GI:47149) (Streptomyces hygroscopicus); contains Prosite PS00161: Isocitrate lyase signature 937 At1g77090 D1, D2, Dm thylakoid lumenal 29.8 kDa protein, identical to SP:O49292:TL30_ARATH (Arabidopsis thaliana);contains a PsbP domain AF370571; SIMILAR TO GI:13926195--F22K20.16 938 At1g77180 D1, Dm chromatin protein family, contains Pfam domain, PF02731: SKIP/SNW domain found in chromatin proteins. 939 At1g77320 D1, Dm MEI1__BRCT domain-containing protein, contains Pfam profile PF00533: BRCA1 C Terminus (BRCT) domain 940 At1g77330 D2, Dm 1-aminocyclopropane-1-carboxylate oxidase, putative / ACC oxidase, putative, similar to 1- aminocyclopropane-1-carboxylate oxidase GI:3386565 from (Sorghum bicolor) 941 At1g77370 D1, D2, Dm glutaredoxin, putative, similar to glutaredoxin (Ricinus communis) gi:1732424:emb:CAA89699 942 At1g77440 Dm PBC2__20S proteasome beta subunit C (PBC2), identical to residues 14-204 of 20S proteasome beta subunit PBC2 GB:AAC32069 (Arabidopsis thaliana) 943 At1g77450 D1, D2, Dm ANAC032__no apical meristem (NAM) family protein, contains Pfam PF02365: No apical meristem (NAM) domain; similar to GRAB1 protein GB:CAA09371, a novel member of the NAC domain family 944 At1g77490 D1 L-ascorbate peroxidase, thylakoid-bound (tAPX), identical to thylakoid-bound ascorbate peroxidase GB:CAA67426 (Arabidopsis thaliana) 945 At1g77630 D2 peptidoglycan-binding LysM domain-containing protein, contains Pfam profile PF01476: LysM domain 946 At1g77710 D1, D2, Dm expressed protein, similar to hypothetical protein GB:P34661 (Caenorhabditis elegans) 947 At1g77740 D1, Dm 1-phosphatidylinositol-4-phosphate 5-kinase, putative / PIP kinase, putative / PtdIns(4)P-5- kinase, putative / diphosphoinositide kinase, putative, strong similarity to phosphatidylinositol-4-phosphate 5-kinase AtPIP5K1 (Arabidopsis thaliana) GI:3702691; contains Pfam profiles PF01504: Phosphatidylinositol-4-phosphate 5-Kinase, PF02493: MORN repeat

948 At1g77760 D1, Dm NIA1_GNR1_NR1__nitrate reductase 1 (NR1), identical to SP:P11832 Nitrate reductase 1 (formerly EC 1.6.6.1) (NR1){Arabidopsis thaliana} 949 At1g77930 D1, D2, Dm DNAJ heat shock N-terminal domain-containing protein, similar to J-Domain (Residues 1-77) Of The Escherichia Coli N-Terminal Fragment (Residues 1-104) Of The Molecular Chaperone Dnaj GI:5542126; contains Pfam profile PF00226 DnaJ domain 950 At1g78060 Dm glycosyl hydrolase family 3 protein, similar to xylosidase GI:2102655 from (Aspergillus niger)

951 At1g78090 D2, Dm ATTPPB__trehalose-6-phosphate phosphatase (TPPB), identical to trehalose-6-phosphate phosphatase (AtTPPB) GI:2944180 (Arabidopsis thaliana) 952 At1g78100 D2 F-box family protein, contains F-box domain Pfam:PF00646 953 At1g78110 D2 expressed protein 954 At1g78140 Dm methyltransferase-related, similar to Probable delta(24)-sterol C-methyltransferase (Swiss- Prot:O14321) (Schizosaccharomyces pombe); similar to C5-O-methyltransferase (GI:5921167) (Streptomyces avermitilis); similar to S-adenosyl-methionine-sterol-C- methyltransferase (GI:3560474) (Nicotiana tabacum) 955 At1g78200 D2 protein phosphatase 2C, putative / PP2C, putative, similar to protein phosphatase 2C GB:CAA72341 (Medicago sativa); contains Pfam profile: PF00481 Protein phosphatase 2C 956 At1g78370 D2 ATGSTU20__glutathione S-transferase, putative, similar to 2,4-D inducible glutathione S- transferase GI:2920666 from (Glycine max) 957 At1g78380 D2, Dm ATGSTU19_GST8__glutathione S-transferase, putative, similar to glutathione transferase GI:2853219 from (Carica papaya) 958 At1g78460 D2 SOUL heme-binding family protein, weak similarity to SOUL protein (Mus musculus) GI:4886906; contains Pfam profile PF04832: SOUL heme-binding protein 959 At1g78500 D2 pentacyclic triterpene synthase, putative, similar to pentacyclic triterpene synthase (04C11) (gi:6650208) (PMID:11247608); similar to beta-Amyrin Synthase GI:3688600 from (Panax ginseng)

960 At1g78570 D2 RHM1__NAD-dependent epimerase/dehydratase family protein, similar to dTDP-glucose 4,6- dehydratase from Aneurinibacillus thermoaerophilus GI:16357461, RmlB from Leptospira borgpetersenii GI:4234803; contains Pfam profile PF01370 NAD dependent epimerase/dehydratase family 961 At1g78600 D1, D2, Dm zinc finger (B-box type) family protein, similar to zinc finger protein GI:3618316 from (Oryza sativa) 962 At1g78630 D1, Dm EMB1473__ribosomal protein L13 family protein, similar to ribosomal protein L13 GI:170132 from (Spinacia oleracea) 963 At1g78670 D1, D2, Dm ATGGH3__gamma-glutamyl hydrolase, putative / gamma-Glu-X carboxypeptidase, putative / conjugase, putative, similar to gamma glutamyl hydrolase GI:1679658 SP:P93164 from (Glycine max) 964 At1g78680 D1, D2, Dm ATGGH2__The Arabidopsis protein AtGGH2 is a gamma-glutamyl hydrolase acting specifically on monoglutamates. The enzyme is involved in the tetrahydrofolate metabolism and located to the vacuole. 965 At1g78830 D2 curculin-like (mannose-binding) lectin family protein, similar to S glycoprotein (Brassica rapa) GI:2351186; contains Pfam profile PF01453: Lectin (probable mannose binding) 966 At1g78850 D1, D2, Dm curculin-like (mannose-binding) lectin family protein, low similarity to ser/thr protein kinase from Zea mays (GI:2598067); contains Pfam lectin (probable mannose binding) domain PF01453 but not the protein kinase domain of the Z. mays protein 967 At1g78860 D1, D2, Dm curculin-like (mannose-binding) lectin family protein, low similarity to Ser/Thr protein kinase (Zea mays) GI:2598067; contains Pfam profile PF01453: Lectin (probable mannose binding) but not the protein kinase domain of the Z. mays protein 968 At1g78870 D2 similar to ubiquitin-conjugating enzyme, putative [Arabidopsis thaliana] (TAIR:At1g16890.2); similar to ubiquitin-conjugating enzyme E2 [Catharanthus roseus] (GB:AAD42941.1); contains InterPro domain Ubiquitin-conjugating enzymes (InterPro:IPR000608) 969 At1g78960 D1, Dm ATLUP2__lupeol synthase, putative / 2,3-oxidosqualene-triterpenoid cyclase, putative, similar to lupeol synthase GI:1762150 from (Arabidopsis thaliana), 2,3-oxidosqualene-triterpenoid cyclase (Arabidopsis thaliana) GI:2738027 970 At1g79040 Dm photosystem II 10 kDa polypeptide, identical to photosystem II 10 kDa polypeptide, chloroplast (precursor) SP:P27202 from (Arabidopsis thaliana); contains Pfam profile: PF04725 photosystem II 10 kDa polypeptide PsbR 971 At1g79110 D2 expressed protein 972 At1g79140 D1, D2, Dm expressed protein 973 At1g79270 D1, D2, Dm ECT8__expressed protein, contains Pfam profile PF04146: YT521-B-like family 974 At1g79340 Dm latex-abundant protein, putative (AMC7) / caspase family protein, similar to latex-abundant protein (Hevea brasiliensis) gb:AAD13216; contains Pfam domain, PF00656: ICE-like protease (caspase) p20 domain 975 At1g79600 D2 ABC1 family protein, contains Pfam domain, PF03109: ABC1 family 976 At1g79720 Dm aspartyl protease family protein, contains Pfam domain, PF00026: eukaryotic aspartyl protease

977 At1g79750 D1, Dm ATNADP-ME4__The malic enzyme (EC 1.1.1.40) encoded by AtNADP-ME4 is localized to chloroplasts. The gene is expressed throughout the whole plant and during embryogenesis and germination. A possible involvement in the fatty acid biosynthesis has been proposed. 978 At1g79850 D1, Dm RPS17_CS17_ORE4_PRPS17__30S ribosomal protein S17, chloroplast / CS17 (RPS17), identical to 30S ribosomal protein S17, chloroplast precursor GB:P16180 (Arabidopsis thaliana) 979 At1g79870 D2 oxidoreductase family protein, contains Pfam profile: PF02826 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain; similar to glyoxylate reductase from Thermococcus litoralis (gi:13515409) 980 At1g79920 D2 heat shock protein 70, putative / HSP70, putative, contains Pfam profile: PF00012 Heat shock hsp70 proteins; similar to heat-shock proteins GB:CAA94389, GB:AAD55461 (Arabidopsis thaliana)

981 At1g79970 D1, D2, Dm expressed protein 982 At1g80070 D1 SUS2_EMB14_EMB158_EMB177_EMB33__splicing factor, putative, strong similarity to splicing factor Prp8 (Homo sapiens) GI:3661610; contains Pfam profile PF01398: Mov34/MPN/PAD-1 family 983 At1g80110 D1, D2, Dm ATPP2-B11__expressed protein, contains similarity to SKP1 interacting partner 3 (Arabidopsis thaliana) GI:10716951 984 At1g80120 D2, Dm expressed protein, contains Pfam profile PF04525: Protein of unknown function (DUF567) 985 At1g80130 D2, Dm expressed protein 986 At1g80160 D1, D2, Dm lactoylglutathione lyase family protein / glyoxalase I family protein, contains glyoxalase family protein domain, Pfam:PF00903 987 At1g80180 D2, Dm expressed protein 988 At1g80270 D2 DNA-binding protein, putative, similar to DNA-binding protein (Triticum aestivum) GI:6958202; contains Pfam profile: PF01535 PPR repeat 989 At1g80300 D2 chloroplast ADP, ATP carrier protein 1 / ADP, ATP translocase 1 / adenine nucleotide translocase 1 (AATP1), identical to SP:Q39002 Chloroplast ADP,ATP carrier protein 1, chloroplast precursor (ADP/ATP translocase 1) (Adenine nucleotide translocase 1) {Arabidopsis thaliana} 990 At1g80310 D1, D2, Dm expressed protein 991 At1g80380 D1, D2, Dm encodes a glycerate kinase which catalyzes the last step of photorespiration C2 cycle. 992 At1g80410 D2 EMB2753__acetyltransferase-related, low similarity to acetyltransferase Tubedown-1 (Mus musculus) GI:8497318, N-TERMINAL ACETYLTRANSFERASE GB:P12945 from (Saccharomyces cerevisiae); contains Pfam profile PF00515 TPR Domain 993 At1g80560 D2, Dm 3-isopropylmalate dehydrogenase, chloroplast, putative, strong similarity to 3-ISOPROPYLMALATE DEHYDROGENASE PRECURSOR GB:P29102 SP:P29102 from (Brassica napus) 994 At1g80640 D2 protein kinase family protein, contains protein kinase domain, Pfam:PF00069 995 At1g80780 D1, D2, Dm CCR4-NOT transcription complex protein, putative, similar to SWISS-PROT:Q60809 CCR4-NOT transcription complex, subunit 7 (CCR4-associated factor 1, (CAF1) (Mus musculus) 996 At1g80920 D1, D2, Dm J8__DNAJ heat shock N-terminal domain-containing protein, similar to SP:Q05646 Chaperone protein dnaJ Erysipelothrix rhusiopathiae, SP:P45555 Chaperone protein dnaJ (HSP40) Staphylococcus aureus; contains Pfam profile PF00226 DnaJ domain 997 At2g01110 D2 APG2_PGA2_TATC__thylakoid membrane formation protein / cpTatC (APG2), identical to thylakoid membrane formation protein (cpTatC) GI:15004994 from (Arabidopsis thaliana); contains Pfam profile PF00902: MttB family; identical to cDNA apg2 for cpTatC GI:15004993 998 At2g01250 D2, Dm 60S ribosomal protein L7 (RPL7B) 999 At2g01270 D2, Dm ATQSOX2__Encodes a protein disulfide isomerase-like (PDIL) protein, a member of a multigene family within the thioredoxin (TRX) superfamily. This protein also belongs to the quiescin- sulfhydryl oxidase (QSOX) family, which possess an Erv1-like domain at the COOH terminus in addition to a TRX domain. 1000 At2g01420 D1, D2, Dm PIN4__auxin transport protein, putative, similar to auxin transport protein PIN7(Arabidopsis thaliana) gi:5817305:gb:AAD52697 1001 At2g01470 D2, Dm STL2P_ATSEC12__St12p protein (ST12p) / SEC12p protein, putative, 99.8% identical to St12p protein (GI:166878) {Arabidopsis thaliana} 1002 At2g01490 D1, D2, Dm phytanoyl-CoA dioxygenase (PhyH) family protein, contains Pfam profile PF05721: Phytanoyl-CoA dioxygenase (PhyH); weak similarity to Phytanoyl-CoA dioxygenase, peroxisomal precursor (EC 1.14.11.18) (Phytanoyl-CoA alpha-hydroxylase) (PhyH) (Phytanic acid oxidase) (Swiss- Prot:O14832) (Homo sapiens) 1003 At2g01530 D1, D2, Dm major latex protein-related / MLP-related, low similarity to major latex protein {Papaver somniferum}(GI:20810) 1004 At2g01680 Dm ankyrin repeat family protein, contains ankyrin repeat domains, Pfam:PF00023 1005 At2g01830 Dm WOL_AHK4_CRE1_WOL1__histidine kinase (AHK4) (WOL), identical to histidine kinase AHK4 (Arabidopsis thaliana) gi:13537200:dbj:BAB40776; contains Pfam profiles PF03924: CHASE domain, PF02518: ATPase, histidine kinase-, DNA gyrase B-, and HSP90-like domain protein, PF00512: His Kinase A (phosphoacceptor) domain, PF00072: Response regulator receiver domain 1006 At2g01850 D2 EXGT-A3_ATXTH27_XTH27__xyloglucan:xyloglucosyl transferase / xyloglucan endotransglycosylase / endo-xyloglucan transferase (EXGT-A3), identical to endoxyloglucan transferase (Arabidopsis thaliana) GI:5533313 1007 At2g01890 D2 ATPAP8_PAP8__purple acid phosphatase, putative, contains Pfam profile: PF00149 calcineurin- like phosphoesterase; identical to purple acid phosphatase (GI:20257479) (Arabidopsis thaliana); 1008 At2g01910 D1 ATMAP65-6__Binds microtubules. Induces a crisscross mesh of microtubules, not bundles. Not involved in microtubule polymerization nor nucleation. Localizes to mitochondria. 1009 At2g02130 D2 LCR68_PDF2.3__plant defensin-fusion protein, putative (PDF2.3), plant defensin protein family member, personal communication, Bart Thomma ([email protected]) 1010 At2g02180 Dm TOM3__tobamovirus multiplication protein 3 (TOM3), identical to tobamovirus multiplication protein (TOM3) GI:15425641 from (Arabidopsis thaliana) 1011 At2g02320 D1, D2, Dm ATPP2-B7__F-box family protein / SKP1 interacting partner 3-related, contains similarity to SKP1 interacting partner 3 GI:10716951 from (Arabidopsis thaliana) 1012 At2g02390 D1, D2, Dm ATGSTZ1_GST18__glutathione S-transferase zeta 1 (GSTZ1) (GST18), identical to SP:Q9ZVQ3:GTZ1_ARATH Glutathione S-transferase zeta-class 1 (EC 2.5.1.18) (AtGSTZ1) (Maleylacetone isomerase) (EC 5.2.1.-) (MAI) {Arabidopsis thaliana}; contains Pfam profiles PF02798: Glutathione S-transferase, N-terminal domain and PF00043:Glutathione S-transferase, C-terminal domain 1013 At2g02930 Dm ATGSTF3_GST16__glutathione S-transferase, putative 1014 At2g02950 D2 PKS1__phytochrome kinase substrate 1 (PKS1), identical to Swiss-Prot:Q9SWI1 phytochrome kinase substrate 1 (Arabidopsis thaliana) 1015 At2g03020 Dm heat shock protein-related, Prosite PS00430: TonB-dependent receptor proteins signature 1; contains some similar to Small heat shock protein, chloroplast precursor (SP:P30222) {Petunia hybrida} 1016 At2g03120 Dm signal peptide peptidase family protein, contains Pfam domain PF04258: Membrane protein of unknown function (DUF435) 1017 At2g03170 D2 ASK14__E3 ubiquitin ligase SCF complex subunit SKP1/ASK1 (At14), putative, E3 ubiquitin ligase; similar to Skp1 homolog Skp1b GI:3068809, UIP2 GI:3719211 from (Arabidopsis thaliana)

1018 At2g03420 D1, D2, Dm expressed protein 1019 At2g03550 D1, D2, Dm expressed protein, similar to PrMC3 (Pinus radiata) GI:5487873; contains an esterase/lipase/thioesterase active site serine domain (prosite: PS50187) 1020 At2g04030 D2 EMB1956_CR88__heat shock protein, putative, strong similarity to heat shock protein (Arabidopsis thaliana) GI:1906830; contains Pfam profiles PF02518: ATPase, histidine kinase-, DNA gyrase B-, and HSP90-like domain protein, PF00183: Hsp90 protein 1021 At2g04160 D1, D2, Dm AIR3__subtilisin-like protease (AIR3), almost identical to subtilisin-like protease AIR3 GI:4218991 from (Arabidopsis thaliana), missing 200 aa at N-terminus 1022 At2g04240 D2, Dm zinc finger (C3HC4-type RING finger) family protein, contains Pfam profile: PF00097 zinc finger, C3HC4 type (RING finger) 1023 At2g04350 D1, D2, Dm long-chain-fatty-acid--CoA ligase family protein / long-chain acyl-CoA synthetase family protein (LACS8), similar to LACS 4 (SP:O35547) from Rattus norvegicus, LACS 4 (SP:O60488) from Homo sapiens; contains Pfam HMM hit: AMP-binding enzymes PF00501 1024 At2g04360 Dm expressed protein 1025 At2g04390 D1, D2, Dm 40S ribosomal protein S17 (RPS17A) 1026 At2g04410 Dm expressed protein 1027 At2g04520 D1 eukaryotic translation initiation factor 1A, putative / eIF-1A, putative / eIF-4C, putative, strong similarity to translation initiation factor (eIF-1A) (Beta vulgaris) GI:17977975; contains Pfam profile PF01176: Eukaryotic initiation factor 1A 1028 At2g04690 D1, D2, Dm cellular repressor of E1A-stimulated genes (CREG) family, contains 1 transmembrane domain; similar to CREG2 (GI:24371079) (Homo sapiens) and (GI:24371081) (Mus musculus); similar to cellular repressor of E1A-stimulated genes CREG (GI:3550343) (Homo sapiens) 1029 At2g04900 D1 expressed protein 1030 At2g05200 D2 transposable element gene 1031 At2g05210 D2, Dm expressed protein, similar to expressed protein [Arabidopsis thaliana] (TAIR:At5g06310.1) 1032 At2g05220 D1, D2, Dm 40S ribosomal protein S17 (RPS17B) 1033 At2g05310 D2 expressed protein 1034 At2g05380 D1, D2, Dm GRP3S__glycine-rich protein (GRP3S), identical to cDNA glycine-rich protein 3 short isoform (GRP3S) GI:4206766 1035 At2g05520 D2, Dm GRP-3__glycine-rich protein (GRP), identical to glycine-rich protein; atGRP (GI:259447) (Arabidopsis thaliana) 1036 At2g05530 D1, D2, Dm glycine-rich protein 1037 At2g05540 D2, Dm glycine-rich protein 1038 At2g05590 D2 expressed protein, similar to nucleolar protein C7C (GI:13540302) (Rattus norvegicus) 1039 At2g05620 D2 PGR5__expressed protein 1040 At2g05990 D1, D2, Dm ENR1_ENR-A_MOD1_ENR1__enoyl-(acyl-carrier protein) reductase (NADH), chloroplast, putative / NADH-dependent enoyl-ACP reductase, putative, strong similarity to enoyl-(acyl-carrier protein) reductase (NADH) SP:P80030 from (Brassica napus) 1041 At2g06230 D1, D2, Dm expressed protein 1042 At2g06850 D1, D2, Dm EXGT-A1_EXT_EXGT-A1__xyloglucan:xyloglucosyl transferase / xyloglucan endotransglycosylase / endo-xyloglucan transferase (EXT) (EXGT-A1), identical to endo-xyloglucan transferase (ext) GI:469484 and endoxyloglucan transferase (EXGT-A1) GI:5533309 from (Arabidopsis thaliana) 1043 At2g07090 D1, D2, Dm expressed protein 1044 At2g07290 D1 expressed protein 1045 At2g07640 D2, Dm D2,D4-dienoyl-CoA reductase-related, contains similarity to peroxisomal D2,D4-dienoyl-CoA reductase (Mus musculus) GI:5031508 1046 At2g09970 D2 expressed protein 1047 At2g10930 Dm expressed protein 1048 At2g10940 D1, D2, Dm protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, similar to proline-rich cell wall protein (Medicago sativa) GI:3818416; contains Pfam profile PF00234 Protease inhibitor/seed storage/LTP family 1049 At2g13360 D1, D2, Dm AGT_AGT1__serine-glyoxylate aminotransferase-related, similar to serine-glyoxylate aminotransferase (GI:21535798)(Methylobacterium dichloromethanicum; contains TIGRFAM TIGR01364: phosphoserine aminotransferase; contains Pfam PF00266: aminotransferase, class V) 1050 At2g14080 D1, Dm disease resistance protein (TIR-NBS-LRR class), putative, domain signature TIR-NBS-LRR exists, suggestive of a disease resistance protein. 1051 At2g14260 D1, D2, Dm PIP__proline iminopeptidase, identical to GP:1710151:U72711 1052 At2g14300 D2 transposable element gene 1053 At2g14610 D1, D2 PR1_PR-1-LIKE_PR1_PR-1__pathogenesis-related protein 1 (PR-1), identical to GB:M90508 SP:P33154 1054 At2g14720 D1, D2, Dm VSR-2__vacuolar sorting receptor, putative, identical to GB:U79960 GI:1737220; contains a calcium-binding EGF-like domain signature 1055 At2g14750 D2, Dm APK__adenylylsulfate kinase 1 (AKN1), identical to adenylylsulfate kinase 1, chloroplast precursor (APS kinase, Adenosine-5`phosphosulfate kinase, ATP adenosine-5`- phosphosulfate 3`- phosphotransferase) (Arabidopsis thaliana) SWISS-PROT:Q43295 1056 At2g14820 Dm phototropic-responsive NPH3 family protein, contains NPH3 family domain, Pfam:PF03000 1057 At2g14880 D2 SWIB complex BAF60b domain-containing protein, contains Pfam profile PF02201: BAF60b domain of the SWIB complex 1058 At2g14900 D1, Dm gibberellin-regulated family protein, similar to SP:P46690 Gibberellin-regulated protein 4 precursor {Arabidopsis thaliana} GASA4; contains Pfam profile PF02704: Gibberellin regulated protein 1059 At2g14910 D1, D2, Dm expressed protein 1060 At2g14960 D1 GH3.1__encodes a protein similar to IAA-amido synthases. Lines carrying an insertion in this gene are hypersensitive to auxin. 1061 At2g15000 D2 expressed protein 1062 At2g15020 D1, D2, Dm expressed protein, and genefinder 1063 At2g15090 D2, Dm fatty acid elongase, putative, similar to fatty acid elongase 1 (GI:881615) 1064 At2g15390 D1, D2, Dm FUT4_ATFUT4__xyloglucan fucosyltransferase, putative (FUT4), identical to SP:Q9SJP2 Probable fucosyltransferase 4 (EC 2.4.1.-) (AtFUT4) {Arabidopsis thaliana}; similar to SP:Q9SWH5 Galactoside 2-alpha-L-fucosyltransferase (EC 2.4.1.69) (Xyloglucan alpha-(1,2)- fucosyltransferase) (AtFUT1) {Arabidopsis thaliana} 1065 At2g15540 Dm transposable element gene 1066 At2g15580 D1, D2, Dm zinc finger (C3HC4-type RING finger) family protein, contains Pfam profile: PF00097 zinc finger, C3HC4 type (RING finger) 1067 At2g15620 D2 NIR1_ATHNIR_NIR__ferredoxin--nitrite reductase, putative, strong similarity to ferredoxin-- nitrite reductase (Nicotiana tabacum) GI:19893; contains Pfam profiles PF03460: Nitrite/Sulfite reductase ferredoxin-like half domain, PF01077: Nitrite and sulphite reductase 4Fe-4S domain 1068 At2g15630 Dm pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat 1069 At2g15670 Dm hypothetical protein 1070 At2g15830 D2 expressed protein 1071 At2g15880 D1, D2, Dm leucine-rich repeat family protein / extensin family protein, similar to extensin-like protein (Lycopersicon esculentum) gi:5917664:gb:AAD55979; contains leucine-rich repeats, Pfam:PF00560; contains proline rich extensin domains, INTERPRO:IPR002965 1072 At2g15960 D1, D2, Dm expressed protein 1073 At2g15970 D1, D2, Dm COR413-PM1_ATCOR413-PM1_FL3-5A3_WCOR413_WCOR413-LIKE__cold-acclimation protein, putative (FL3- 5A3), similar to cold acclimation WCOR413-like protein gamma form (Hordeum vulgare) gi:18449100:gb:AAL69988; similar to stress-regulated protein SAP1 (Xerophyta viscosa) gi:21360378:gb:AAM47505; identical to cDNA cold acclimation protein WCOR413-like protein alpha form GI:10121840, cold acclimation protein homolog (Arabidopsis thaliana) GI:11127595 1074 At2g16070 D1, D2, Dm expressed protein 1075 At2g16280 D1, D2, Dm very-long-chain fatty acid condensing enzyme, putative, similar to fatty acid condensing enzyme CUT1 GI:5001734 from (Arabidopsis thaliana) 1076 At2g16430 D1 PAP10__purple acid phosphatase (PAP10), identical to purple acid phosphatase (PAP10) GI:20257482 from (Arabidopsis thaliana) 1077 At2g16500 D1, D2, Dm ADC1_ARGDC_ARGDC1__arginine decarboxylase 1 (SPE1) (ARGDC), identical to SP:Q9SI64 Arginine decarboxylase 1 (EC 4.1.1.19) (ARGDC 1) (ADC 1) (ADC-O) {Arabidopsis thaliana} 1078 At2g16660 D1, D2, Dm nodulin family protein, similar to nodulin-like protein (Arabidopsis thaliana) GI:3329368, nodule-specific protein Nlj70 (Lotus japonicus) GI:3329366 1079 At2g16720 D1 MYB7_ATMYB7__myb family transcription factor, contains Pfam profile: PF00249 myb-like DNA- binding domain 1080 At2g16800 Dm high-affinity nickel-transport family protein, contains Pfam domain, PF03824: High-affinity nickel-transport protein 1081 At2g16830 D1, Dm a pseudogene whose sequence is similar to plasma membrane intrinsic protein 3 (PIP3) 1082 At2g16850 D1, D2, Dm PIP2;8_PIP3B__plasma membrane intrinsic protein, putative, very strong similarity to plasma membrane intrinsic protein (SIMIP) (Arabidopsis thaliana) GI:2306917 1083 At2g16890 D2, Dm UDP-glucoronosyl/UDP-glucosyl transferase family protein, contains Pfam profile: PF00201 UDP- glucoronosyl and UDP-glucosyl transferase 1084 At2g16990 D1, D2, Dm expressed protein 1085 At2g17050 Dm disease resistance protein (TIR-NBS-LRR class), putative, domain signature TIR-NBS-LRR exists, suggestive of a disease resistance protein. 1086 At2g17230 D2 phosphate-responsive 1 family protein, similar to phi-1 (phosphate-induced gene) (Nicotiana tabacum) GI:3759184; contains Pfam profile PF04674: Phosphate-induced protein 1 conserved region 1087 At2g17240 D2, Dm expressed protein 1088 At2g17250 D2 expressed protein, weak similarity to Ribosome biogenesis protein MAK21 (Swiss-Prot:Q12176) (Saccharomyces cerevisiae) 1089 At2g17310 Dm SON1__F-box family protein, contains F-box domain Pfam:PF00646 1090 At2g17330 D1, Dm putative obtusifoliol 14-alpha demethylase. Expressed pseudogene 1091 At2g17360 D1, D2, Dm 40S ribosomal protein S4 (RPS4A), contains ribosomal protein S4 signature from residues 8 to 22 1092 At2g17390 D2 ankyrin repeat family protein, contains ankyrin repeats, Pfam:PF00023 1093 At2g17420 D1, D2, Dm NTRA_ATNTRA_NTR2__similar to thioredoxin reductase 1 / NADPH-dependent thioredoxin reductase 1 (NTR1) [Arabidopsis thaliana] (TAIR:At4g35460.1); similar to NADPH-thioredoxin reductase [Triticum aestivum] (GB:CAD19162.1); contains InterPro domain Thioredoxin reductase (InterPro:IPR005982); contains InterPro domain Pyridine nucleotide-disulphide oxidoreductase, class I (InterPro:IPR001100); contains InterPro domain FAD-dependent pyridine nucleotide- disulphide oxidoreductase (InterPro:IPR001327); contains InterPro domain Pyridine nucleotide- disulphide oxidoreductase, class-II, active site (InterPro:IPR008255); contains InterPro domain Adrenodoxin reductase (InterPro:IPR000759); contains InterPro domain Pyridine nucleotide-disulphide oxidoreductase, class-II (InterPro:IPR000103) 1094 At2g17530 D2 protein kinase family protein, identical to SRPK2 (Arabidopsis thaliana) gi:9843645:emb:CAC03676; contains protein kinase domain, Pfam:PF00069 1095 At2g17650 D2, Dm AMP-dependent synthetase and ligase family protein, similar to AMP-binding protein GI:1903034 from (Brassica napus); contains Pfam AMP-binding domain PF00501; identical to cDNA adenosine monophosphate binding protein 2 AMPBP2 (AMPBP2) GI:20799712 1096 At2g17980 D2, Dm ATSLY1_SLY1__sec1 family protein, similar to SWISS-PROT:P22213 SLY1 protein (Saccharomyces cerevisiae); contains Pfam domain, PF00995: Sec1 family 1097 At2g17990 D2 expressed protein 1098 At2g18010 Dm auxin-responsive family protein, similar to auxin-induced protein TGSAUR22 (GI:10185820) (Tulipa gesnerian) ;similar to indole-3-acetic acid induced protein ARG7 (SP:P32295) (Phaseolus aureus) 1099 At2g18020 D1, D2, Dm EMB2296__60S ribosomal protein L8 (RPL8A) 1100 At2g18050 D1, D2, Dm HIS1-3__histone H1-3 (HIS1-3), similar to histone H1 (Lycopersicon pennellii) SWISS- PROT:P40267; identical to cDNA histone H1-3 (His1-3) GI:1809314, histone H1-3 (Arabidopsis thaliana) GI:1809305 1101 At2g18100 D1, Dm expressed protein 1102 At2g18230 D1, Dm inorganic pyrophosphatase (soluble) (PPA) / pyrophosphate phospho-hydrolase / PPase, nearly identical to SP:P21216 Soluble inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho- hydrolase) (PPase) {Arabidopsis thaliana} 1103 At2g18260 D2, Dm SYP112_ATSYP112__syntaxin-related protein, putative (SYP112), similar to SP:Q42374 Syntaxin- related protein KNOLLE (Syntaxin 111) (AtSYP111) {Arabidopsis thaliana} 1104 At2g18280 D1, D2, Dm tubby-like protein 2 (TULP2), identical to tubby-like protein 2 (GI:27372512) {Arabidopsis thaliana}; similar to phosphodiesterase (GI:467578) (Mus musculus); similar to Tubby related protein 2 (Tubby-like protein 2) (P4-6 protein) (Fragment) (SP:P46686) (Mus musculus); contains Pfam profile: PF01167: Tub family; contains Pfam PF00646: F-box domain 1105 At2g18290 D2, Dm anaphase-promoting complex, subunit 10 family / APC10 family, contains Pfam PF03256: Anaphase- promoting complex, subunit 10 (APC10) domain; similar to anaphase promoting complex subunit APC10 (GI:6463666) (Homo sapiens) 1106 At2g18400 Dm ribosomal protein L6 family protein 1107 At2g18440 D1, D2, Dm GUT15__expressed protein 1108 At2g18690 Dm expressed protein 1109 At2g18700 Dm ATTPS11_ATTPSB_TPS11__glycosyl transferase family 20 protein / trehalose-phosphatase family protein, similar to trehalose-6-phosphate synthase SL-TPS/P (Selaginella lepidophylla) GI:4100325; contains Pfam profiles PF00982: Glycosyltransferase family 20, PF02358: Trehalose- phosphatase 1110 At2g18900 D2 transducin family protein / WD-40 repeat family protein, contains 5 WD-40 repeats (PF00400); related to LACK protective antigen (GI:13625467) (Leishmania donovani) 1111 At2g18940 Dm pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile: PF01535 PPR repeat 1112 At2g19310 D1, D2, Dm expressed protein 1113 At2g19350 D2, Dm expressed protein 1114 At2g19480 D1, D2, Dm nucleosome assembly protein (NAP), putative, similar to nucleosome assembly protein 1 (Glycine max) GI:1161252; contains Pfam profile PF00956: Nucleosome assembly protein (NAP) 1115 At2g19520 D2, Dm FVE_ACG1_ATMSI4_MSI4_NFC04_NFC4__WD-40 repeat protein (MSI4), contains 6 (4 significant) WD-40 repeats (PF0400); identical to WD-40 repeat protein MSI4 (SP:O22607) (Arabidopsis thaliana)

1116 At2g19620 D1, Dm Ndr family protein, similar to SP:O23969 Pollen specific protein SF21 {Helianthus annuus}; contains Pfam profile PF03096: Ndr family 1117 At2g19680 Dm mitochondrial ATP synthase g subunit family protein, contains Pfam profile: PF04718 mitochondrial ATP synthase g subunit 1118 At2g19730 D1, D2, Dm 60S ribosomal protein L28 (RPL28A) 1119 At2g19740 D1, D2, Dm 60S ribosomal protein L31 (RPL31A) 1120 At2g19750 D1, D2, Dm 40S ribosomal protein S30 (RPS30A) 1121 At2g19760 D1, D2, Dm PRF1_PFN1__profilin 1 (PRO1) (PFN1) (PRF1) / allergen Ara t 8, identical to profilin 1 (Allergen Ara t 8) SP:Q42449 GI:1353770 from (Arabidopsis thaliana) 1122 At2g19780 D2, Dm leucine-rich repeat family protein / extensin family protein, contains leucine rich-repeat (LRR) domains Pfam:PF00560, INTERPRO:IPR001611; similar to leucine-rich repeat/extensin 1 (GI:13809918) (Arabidopsis thaliana); contains similarity to disease resistance protein (Lycopersicon esculentum) gi:3894383:gb:AAC78591 1123 At2g19810 D2, Dm zinc finger (CCCH-type) family protein, contains Pfam domain, PF00642: Zinc finger C-x8-C-x5- C-x3-H type (and similar) 1124 At2g19860 Dm ATHXK2__hexokinase 2 (HXK2), identical to hexokinase 2 (Arabidopsis thaliana) Swiss- Prot:P93834 1125 At2g19870 D2 tRNA/rRNA methyltransferase (SpoU) family protein, similar to SP:P25270 Ribose methyltransferase PET56 (EC 2.1.1.-) {Saccharomyces cerevisiae}; contains Pfam profile PF00588: SpoU rRNA Methylase (RNA methyltransferase, TrmH) family 1126 At2g20000 Dm HBT__cell division cycle family protein / CDC family protein, low similarity to SP:P30260:CC27_HUMAN Protein CDC27Hs (Cell division cycle protein 27 homolog) Homo sapiens; contains Pfam profile PF00515: TPR Domain 1127 At2g20070 D1 expressed protein, weak similarity to SP:O61705 Neurotoxin BmK-X precursor (BmK10) (Alpha- neurotoxin TX9) {Mesobuthus martensii} 1128 At2g20230 D2 expressed protein 1129 At2g20400 Dm myb family transcription factor, contains Pfam profile: PF00249 myb-like DNA-binding domain 1130 At2g20450 D1, D2, Dm 60S ribosomal protein L14 (RPL14A) 1131 At2g20530 Dm prohibitin, putative, similar to SP:P24142 Prohibitin (B-cell receptor associated protein 32) (BAP 32) {Rattus norvegicus}; contains Pfam profile PF01145: SPFH domain / Band 7 family 1132 At2g20670 D2, Dm expressed protein, contains Pfam profile PF04720: Protein of unknown function (DUF506) 1133 At2g20860 D2, Dm LIP1__lipoic acid synthase (LIP1), identical to gi:3928758 contains Pfam profile PF04055: radical SAM domain protein 1134 At2g20890 D1 THF1_PSB29__Chloroplast-localized Thylakoid formation1 gene product involved in vesicle- mediated formation of thylakoid membranes. Thf1 antisense lines contain abnormal chloroplasts early in leaf development (chloroplasts have loosely stacked thylakoid membranes). Expression was induced in the light and decreased under dark conditions. 1135 At2g20920 D1, D2, Dm expressed protein 1136 At2g20960 Dm PEARLI4__expressed protein, pEARLI 4 gene product (Arabidopsis thaliana) GI:871782 1137 At2g20990 D2 C2 domain-containing protein (sytA), similar to Ca2+-dependent lipid-binding protein (CLB1) GI:2789434 from (Lycopersicon esculentum) 1138 At2g21130 D1, D2, Dm peptidyl-prolyl cis-trans isomerase / cyclophilin (CYP2) / rotamase, identical to cyclophilin (Arabidopsis thaliana) gi:2443757:gb:AAB71402; similar to peptidyl-prolyl cis-trans isomerase, PPIase (cyclophilin, cyclosporin A-binding protein) (Arabidopsis thaliana) SWISS-PROT:P34790 1139 At2g21140 Dm ATPRP2__hydroxyproline-rich glycoprotein family protein, identical to proline-rich protein 2 (Arabidopsis thaliana) gi:7620011:gb:AAF64549 1140 At2g21170 D1 TIM__triosephosphate isomerase, chloroplast, putative, similar to Triosephosphate isomerase, chloroplast precursor: SP:P48496 from Spinacia oleracea, SP:P46225 from Secale cereale 1141 At2g21220 D1, Dm auxin-responsive protein, putative, similar to auxin-induced protein TGSAUR22 (GI:10185820) (Tulipa gesneriana) 1142 At2g21240 Dm expressed protein 1143 At2g21250 D1, D2 mannose 6-phosphate reductase (NADPH-dependent), putative, 6-phosphate reductase (Apium graveolens)(GI:1835701), NADP-dependent D-sorbitol-6-phosphate dehydrogenase (Malus domestica)(SP:P28475) 1144 At2g21280 D1, D2, Dm ATSULA_GC1__expressed protein, similar to YfhF (GI:2804536) (Bacillus subtilis) 1145 At2g21330 D1 fructose-bisphosphate aldolase, putative, strong similarity to plastidic fructose-bisphosphate aldolase (EC 4.1.2.13) from Nicotiana paniculata (NPALDP1) (GI:4827251), Oryza sativa, PIR2:T02057 (SP:Q40677) 1146 At2g21385 D1, D2, Dm expressed protein 1147 At2g21410 Dm vacuolar proton ATPase, putative, similar to vacuolar proton ATPase 100-kDa subunit from Dictyostelium discoideum P:1384136:gb:AAB49621 1148 At2g21560 Dm expressed protein, contains weak similarity to reticulocyte-binding protein 2 homolog A (Plasmodium falciparum) gi:9754767:gb:AAF98066 1149 At2g21590 D1, Dm APL4__glucose-1-phosphate adenylyltransferase large subunit, putative / ADP-glucose pyrophosphorylase, putative, strong similarity to SP:P55231 1150 At2g21620 D1, D2, Dm RD2__universal stress protein (USP) family protein / responsive to dessication protein (RD2), strong similarity to RD2 protein (Arabidopsis thaliana) GI:15320408; contains Pfam profile PF00582: universal stress protein family; identical to cDNA RD2 GI:15320407 1151 At2g21650 Dm myb family transcription factor, contains PFAM profile: PF00249 myb-like DNA-binding domain 1152 At2g21660 D2 ATGRP7__glycine-rich RNA-binding protein (GRP7), SP:Q03250 Glycine-rich RNA-binding protein 7 {Arabidopsis thaliana} 1153 At2g21720 D1 expressed protein, contains Pfam profile: PF04842 plant protein of unknown function (DUF639) 1154 At2g21790 D1, Dm R1__ribonucleoside-diphosphate reductase small chain, putative / ribonucleotide reductase, putative, similar to ribonucleotide reductase GI:4151068 from (Nicotiana tabacum) 1155 At2g21820 Dm expressed protein 1156 At2g21880 Dm Ras-related GTP-binding protein, putative, similar to Ras family GTP-binding protein SP:Q43463 from (Glycine max) 1157 At2g21900 D1, D2, Dm WRKY59_ATWRKY59__WRKY family transcription factor, contains Pfam profile: PF03106 WRKY DNA - binding domain 1158 At2g22040 D1, D2, Dm transducin family protein / WD-40 repeat family protein, similar to Pop3 (GI:3434986) (Schizosaccharomyces pombe); contains Pfam PF00400: WD domain, G-beta repeat (6 copies, 2 weak); 1159 At2g22080 D2, Dm expressed protein 1160 At2g22125 D1, D2, Dm similar to C2 domain-containing protein / armadillo/beta-catenin repeat family protein [Arabidopsis thaliana] (TAIR:At1g44120.1); similar to C2 domain, putative [Oryza sativa (japonica cultivar-group)] (GB:AAX95026.1); contains InterPro domain C2 domain (InterPro:IPR000008); contains InterPro domain Armadillo repeat (InterPro:IPR000225) 1161 At2g22170 D1, D2, Dm lipid-associated family protein, contains PLAT/LH2 (Polycystin-1, Lipoxygenase, Alpha- Toxin/Lipoxygenase homology) domain Pfam:PF01477 1162 At2g22190 D2 similar to trehalose-6-phosphate phosphatase, putative [Arabidopsis thaliana] (TAIR:At4g39770.1); similar to putative trehalose-phosphatase [Oryza sativa (japonica cultivar-group)] (GB:XP_482349.1); contains InterPro domain Trehalose-phosphatase (InterPro:IPR003337); contains InterPro domain HAD-superfamily hydrolase, subfamily IIB (InterPro:IPR006379) 1163 At2g22230 Dm beta-hydroxyacyl-ACP dehydratase, putative, similar to beta-hydroxyacyl-ACP dehydratase from Toxoplasma gondii (GI:3850997); contains Pfam profile PF01377 Thioester dehydratase 1164 At2g22240 D1, D2, Dm inositol-3-phosphate synthase isozyme 2 / myo-inositol-1-phosphate synthase 2 / MI-1-P synthase 2 / IPS 2, identical to SP:Q38862 Myo-inositol-1-phosphate synthase isozyme 2 (EC 5.5.1.4) (MI-1-P synthase 2) (IPS 2) {Arabidopsis thaliana} 1165 At2g22310 Dm ATUBP4__ubiquitin-specific protease 4 (UBP4), identical to GI:2347100 1166 At2g22400 D2 NOL1/NOP2/sun family protein, contains Pfam profile PF01189: NOL1/NOP2/sun family 1167 At2g22420 D1, Dm peroxidase 17 (PER17) (P17), identical to SP:Q9SJZ2 Peroxidase 17 precursor (EC 1.11.1.7) (Atperox P17) (ATP25a) {Arabidopsis thaliana} 1168 At2g22430 D1, D2, Dm ATHB6__homeobox-leucine zipper protein 6 (HB-6) / HD-ZIP transcription factor 6, identical to homeobox-leucine zipper protein ATHB-6 (HD-ZIP protein ATHB-6) (SP:P46668) (Arabidopsis thaliana) 1169 At2g22540 D2 SVP_AGL22__short vegetative phase protein (SVP), identical to cDNA short vegetative phase protein (SVP) GI:10944319; 1170 At2g22660 D1, D2, Dm similar to glycine-rich protein [Arabidopsis thaliana] (TAIR:At4g37900.1); similar to hypothetical protein [Sorghum bicolor] (GB:AAD27577.1); similar to pg1 [Hordeum vulgare] (GB:AAV65330.1) 1171 At2g22690 D2 expressed protein 1172 At2g22820 Dm expressed protein, prediced by genscan 1173 At2g22870 D2 EMB2001__expressed protein 1174 At2g22900 D1, Dm galactosyl transferase GMA12/MNN10 family protein, very low similarity to alpha-1,2- galactosyltransferase, Schizosaccharomyces pombe (SP:Q09174) 1175 At2g22970 D1, D2, Dm SCPL11__serine carboxypeptidase S10 family protein, similar to serine carboxypeptidase I precursor (SP:P37890) (Oryza sativa) 1176 At2g22980 D2, Dm SCPL13__similar to serine carboxypeptidase S10 family protein [Arabidopsis thaliana] (TAIR:At2g23000.1); similar to serine carboxypeptidase S10 family protein [Arabidopsis thaliana] (TAIR:At2g23010.2); similar to serine carboxypeptidase S10 family protein [Arabidopsis thaliana] (TAIR:At3g10450.1); similar to serine carboxypeptidase S10 family protein [Arabidopsis thaliana] (TAIR:At2g23010.1); similar to serine carboxypeptidase S10 family protein [Arabidopsis thaliana] (TAIR:At2g22920.2); similar to OSJNBb0051N19.2 [Oryza sativa (japonica cultivar-group)] (GB:XP_474646.1); contains InterPro domain Esterase/lipase/thioesterase (InterPro:IPR000379); contains InterPro domain Serine carboxypeptidase (S10) (InterPro:IPR001563) 1177 At2g23110 Dm expressed protein 1178 At2g23120 D1, D2, Dm expressed protein 1179 At2g23130 D1, D2, Dm AGP17_ATAGP17__arabinogalactan-protein (AGP17), identical to gi_11935086_gb_AAG41963 1180 At2g23250 Dm UDP-glucoronosyl/UDP-glucosyl transferase family protein, contains similarity to glucosyltransferases 1181 At2g23320 D2 WRKY15__WRKY family transcription factor, identical to WRKY DNA-binding protein 15 GI:13506742 from (Arabidopsis thaliana) 1182 At2g23330 Dm transposable element gene 1183 At2g23350 D1, D2, Dm PAB4__polyadenylate-binding protein, putative / PABP, putative.Member of the Class II family of PABP proteins. Highly and ubiquitously expressed. 1184 At2g23590 D1, D2, Dm hydrolase, alpha/beta fold family protein, similar to ethylene-induced esterase (Citrus sinensis) GI:14279437, polyneuridine aldehyde esterase (Rauvolfia serpentina) GI:6651393; contains Pfam profile PF00561: hydrolase, alpha/beta fold family 1185 At2g23600 D1, D2, Dm hydrolase, alpha/beta fold family protein, similar to ethylene-induced esterase (Citrus sinensis) GI:14279437, polyneuridine aldehyde esterase (Rauvolfia serpentina) GI:6651393; contains Pfam profile PF00561: hydrolase, alpha/beta fold family 1186 At2g23610 D1, D2, Dm esterase, putative, similar to ethylene-induced esterase (Citrus sinensis) GI:14279437, polyneuridine aldehyde esterase (Rauvolfia serpentina) GI:6651393; contains Pfam profile PF00561: hydrolase, alpha/beta fold family 1187 At2g23670 D1, D2, Dm expressed protein 1188 At2g23690 D2 expressed protein 1189 At2g23840 D2, Dm HNH endonuclease domain-containing protein, contains Pfam profile PF01844: HNH endonuclease 1190 At2g23930 D2, Dm small nuclear ribonucleoprotein G, putative / snRNP-G, putative / Sm protein G, putative, similar to small nuclear ribonucleoprotein G (snRNP-G, Sm protein G, Sm-G, SmG) (Homo sapiens) SWISS-PROT:Q15357 1191 At2g23980 Dm ATCNGC6_CNGC6__cyclic nucleotide-regulated ion channel / cyclic nucleotide-gated channel (CNGC6), identical to cyclic nucleotide and calmodulin-regulated ion channel (cngc6) GI:4581207 from (Arabidopsis thaliana) 1192 At2g24020 D1, Dm expressed protein, contains Pfam domain PF02575: Uncharacterized BCR, YbaB family COG0718 1193 At2g24040 D2, Dm hydrophobic protein, putative / low temperature and salt responsive protein, putative, similar to SP:Q9ZNQ7 Hydrophobic protein RCI2A (Low temperature and salt responsive protein LTI6A) {Arabidopsis thaliana}; contains Pfam profile PF01679: Uncharacterized protein family 1194 At2g24050 D2, Dm MIF4G domain-containing protein / MA3 domain-containing protein, similar to SP:Q03387 Eukaryotic initiation factor (iso)4F subunit P82-34 (eIF-(iso)4F P82-34) {Triticum aestivum}; contains Pfam profiles PF02854: MIF4G domain, PF02847: MA3 domain 1195 At2g24090 D1, Dm ribosomal protein L35 family protein, contains Pfam profile PF01632: ribosomal protein L35 1196 At2g24150 D2 expressed protein, contains Pfam profile PF03006: Uncharacterised protein family (Hly-III / UPF0073) 1197 At2g24180 D1, Dm CYP71B6__cytochrome P450 family protein 1198 At2g24200 D1, D2, Dm cytosol aminopeptidase, identical to cytosol aminopeptidase SP:P30184 from (Arabidopsis thaliana); contains Pfam profiles: PF00883 cytosol aminopeptidase family catalytic domain, PF02789: cytosol aminopeptidase family N-terminal domain 1199 At2g24270 D1, D2, Dm ALDH11A3__NADP-dependent glyceraldehyde-3-phosphate dehydrogenase, putative, similar to NADP- dependent glyceraldehyde-3-phosphate dehydrogenase (NON-phosphorylating glyceraldehyde 3- phosphate; glyceraldehyde-3-phosphate dehydrogenase (NADP+)) (Nicotiana plumbaginifolia) SWISS-PROT:P93338 1200 At2g24420 D1, D2, Dm DNA repair ATPase-related, contains 2 transmembrane domains; similar to DNA double-strand break repair rad50 ATPase. (Swiss-Prot:O33600) (Sulfolobus acidocaldarius) 1201 At2g24500 D2 FZF__zinc finger (C2H2 type) family protein, contains Pfam profile: PF00096 zinc finger, C2H2 type 1202 At2g24540 D2, Dm kelch repeat-containing F-box family protein, similar to SKP1 interacting partner 4 (Arabidopsis thaliana) GI:10716953; contains Pfam profiles PF01344: Kelch motif, PF00646: F- box domain 1203 At2g24570 D1 WRKY17_ATWRKY17__WRKY family transcription factor, identical to WRKY transcription factor 17 GI:15991743 from (Arabidopsis thaliana) 1204 At2g24940 D1, D2, Dm cytochrome b5 domain-containing protein, similar to SP:P70580 Membrane associated progesterone receptor component 1 {Rattus norvegicus}; contains Pfam profile PF00173: Heme/Steroid binding domain 1205 At2g25190 Dm expressed protein 1206 At2g25200 Dm expressed protein 1207 At2g25210 D2, Dm 60S ribosomal protein L39 (RPL39A) 1208 At2g25230 D2 MYB100__myb family transcription factor (MYB100), contains Pfam profile: PF00249 myb-like DNA- binding domain 1209 At2g25310 D2, Dm expressed protein 1210 At2g25450 D1, D2, Dm 2-oxoglutarate-dependent dioxygenase, putative, similar to 2A6 (GI:599622) and tomato ethylene synthesis regulatory protein E8 (SP:P10967) 1211 At2g25600 D2, Dm SPIK_AKT6__potassium channel protein, putative, similar to potassium channel (Lycopersicon esculentum) GI:8980432; member of the 1 pore, 6 transmembrane (1P/6TM- Shaker-type) K+ channel family, PMID:11500563; Shaker Pollen Inward K+ Channel (SPIK) PMID:11825875 1212 At2g25625 D1, D2, Dm expressed protein 1213 At2g25670 D1, Dm expressed protein 1214 At2g25790 Dm leucine-rich repeat transmembrane protein kinase, putative 1215 At2g25800 D1, Dm expressed protein 1216 At2g25830 Dm YebC-related, contains Pfam profile PF01709: Domain of unknown function; contains TIGRFAM TIGR01033: conserved hypothetical protein; similar to YebC (GI:5771432) (Legionella pneumophila) 1217 At2g25900 D2 ATCTH__zinc finger (CCCH-type) family protein, contains Pfam domain, PF00642: Zinc finger C- x8-C-x5-C-x3-H type (and similar) 1218 At2g25910 Dm 3`-5` exonuclease domain-containing protein / K homology domain-containing protein / KH domain-containing protein, contains Pfam profiles PF01612: 3`-5` exonuclease, PF00013: KH domain 1219 At2g25950 D2 expressed protein 1220 At2g26080 Dm glycine dehydrogenase (decarboxylating), putative / glycine decarboxylase, putative / glycine cleavage system P-protein, putative, strong similarity to SP:P26969 Glycine dehydrogenase (decarboxylating), mitochondrial precursor (EC 1.4.4.2) {Pisum sativum}; contains Pfam profile PF02347: Glycine cleavage system P-protein 1221 At2g26160 D1, Dm F-box family protein, contains F-box domain Pfam:PF00646 1222 At2g26210 Dm ankyrin repeat family protein, contains ankyrin repeats, Pfam:PF00023 1223 At2g26250 D2 FDH__beta-ketoacyl-CoA synthase family (FIDDLEHEAD) (FDH), identical to GB:AJ010713 (fiddlehead protein) 1224 At2g26290 Dm protein kinase, putative, similar to auxin-regulated dual specificity cytosolic kinase (Lycopersicon esculentum) gi:14484938:gb:AAK62821 1225 At2g26380 D1, Dm disease resistance protein-related / LRR protein-related, contains leucine rich-repeat domains Pfam:PF00560, INTERPRO:IPR001611; similar to Hcr2-2A (Lycopersicon pimpinellifolium) gi:3894389:gb:AAC78594 1226 At2g26430 Dm RCY1_ATRCY1__ania-6a type cyclin (RCY1), nearly identical to ania-6a type cyclin (Arabidopsis thaliana) GI:13924511 1227 At2g26500 D1, D2 cytochrome b6f complex subunit (petM), putative, nearly identical to cytochrome b6f complex subunit (GI:3090403) (Arabidopsis thaliana); alternative splice forms exist 1228 At2g26520 D1, D2, Dm expressed protein 1229 At2g26530 D1, Dm AR781__expressed protein 1230 At2g26570 D2 expressed protein, contains Pfam profile PF05701: Plant protein of unknown function (DUF827); weak similarity to merozoite surface protein 3 alpha (GI:27596802) (Plasmodium vivax)

1231 At2g26690 D2 nitrate transporter (NTP2), identical to nitrate transporter (ntp2) (Arabidopsis thaliana) GI:4490321 1232 At2g26740 D1 ATSEH__epoxide hydrolase, soluble (sEH), identical to ATsEH (Arabidopsis thaliana) GI:1109600

1233 At2g26800 D1, D2, Dm hydroxymethylglutaryl-CoA lyase, putative / 3-hydroxy-3-methylglutarate-CoA lyase, putative / HMG-CoA lyase, putative, similar to SP:P35915 Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4) (HMG-CoA lyase) {Gallus gallus}; contains Pfam profile PF00682: HMGL-like 1234 At2g26890 D1, D2, Dm GRV2__DNAJ heat shock N-terminal domain-containing protein, contains Pfam profile PF00226: DnaJ domain 1235 At2g27080 D2, Dm harpin-induced protein-related / HIN1-related / harpin-responsive protein-related, contains 1 transmembrane domain; similar to hin1 homolog (GI:13122296) (Arabidopsis thaliana); similar to hin1 (GI:22830759) (Nicotiana tabacum) 1236 At2g27290 D1, D2, Dm expressed protein 1237 At2g27380 D1, D2, Dm ATEPR1__proline-rich family protein, contains proline-rich extensin domains, INTERPRO:IPR002965 1238 At2g27410 D2 expressed protein, contains Pfam profile PF03754: Domain of unknown function (DUF313) 1239 At2g27530 D1, D2, Dm 60S ribosomal protein L10A (RPL10aB) 1240 At2g27550 D1 ATC__centroradialis protein, putative (CEN), strong similarity to SP:Q41261 CENTRORADIALIS protein {Antirrhinum majus}; contains Pfam profile PF01161: Phosphatidylethanolamine-binding protein 1241 At2g27710 D1, D2, Dm 60S acidic ribosomal protein P2 (RPP2B) 1242 At2g27730 D2 expressed protein, contains 1 transmembrane domain; similar to Unknown mitochondrial protein At2g27730 (Swiss-Prot:Q9ZUX4) (Arabidopsis thaliana) similar to F1F0-ATPase inhibitor protein (GI:5821432) (Oryza sativa) 1243 At2g27810 D2 xanthine/uracil permease family protein, contains Pfam profile: PF00860 permease family 1244 At2g27840 D1, D2, Dm HDT4_HDA13_HDT04__histone deacetylase-related / HD-related, similar to nucleolar histone deacetylase HD2-p39 (Zea mays) GI:2257756; contains non-consensus donor splice site AT at exon2 and acceptor splice site AC at exon3. 1245 At2g28000 D1, D2, Dm CPN60A_CH-CPN60A_SLP__RuBisCO subunit binding-protein alpha subunit, chloroplast / 60 kDa chaperonin alpha subunit / CPN-60 alpha, identical to SWISS-PROT:P21238- RuBisCO subunit binding-protein alpha subunit, chloroplast precursor (60 kDa chaperonin alpha subunit, CPN-60 alpha) (Arabidopsis thaliana) 1246 At2g28200 D1 similar to zinc finger (C2H2 type) family protein [Arabidopsis thaliana] (TAIR:At5g04390.1); similar to putative zinc finger protein [Pisum sativum] (GB:CAA60828.1); contains InterPro domain Zn-finger, C2H2 type (InterPro:IPR007087) 1247 At2g28210 Dm carbonic anhydrase family protein, similar to storage protein (dioscorin) (Dioscorea cayenensis) GI:433463; contains Pfam profile PF00194: Eukaryotic-type carbonic anhydrase 1248 At2g28305 Dm expressed protein, contains Pfam profile PF03641: decarboxylase family protein 1249 At2g28400 D2, Dm expressed protein, contains Pfam profile PF04520: Protein of unknown function, DUF584 1250 At2g28410 Dm expressed protein 1251 At2g28620 Dm kinesin motor protein-related 1252 At2g28720 D2, Dm histone H2B, putative, strong similarity to histone H2B Arabidopsis thaliana GI:2407802, Gossypium hirsutum SP:O22582; contains Pfam profile PF00125 Core histone H2A/H2B/H3/H4 1253 At2g28740 D1 HIS4__histone H4, identical to histone H4 from Lycopersicon esculentum GI:297150, Lolium temulentum SP:P02308, Acropora formosa GI:455652, Citrus jambhiri GI:16797797 1254 At2g28790 D2 osmotin-like protein, putative, similar to SP:Q41350 Osmotin-like protein precursor {Lycopersicon esculentum}; contains Pfam profile PF00314: Thaumatin family 1255 At2g28800 D2 ALB3_ABL3__chloroplast membrane protein (ALBINO3), Oxa1p homolog {PMID:11148275}; identical to chloroplast membrane protein ALBINO3 (Arabidopsis thaliana) GI:2209332 1256 At2g28840 D1, D2, Dm ankyrin repeat family protein, contains ankyrin repeats, Pfam:PF00023 1257 At2g28910 D1, D2, Dm CXIP4__CAX-interacting protein 4 (CAXIP4), contains Pfam domain PF00098: Zinc knuckle; identical to cDNA CAX-interacting protein 4 GI:27651998 1258 At2g28940 Dm protein kinase family protein, contains protein kinase domain, Pfam:PF00069 1259 At2g28950 D1, D2, Dm ATEXPA6_ATEXP6_ATHEXP ALPHA 1.8__expansin, putative (EXP6), similar to expansin GI:2828241 from (Brassica napus); contains Pfam profile PF01357: Pollen allergen 1260 At2g29070 Dm ubiquitin fusion degradation UFD1 family protein, similar to SP:P70362 Ubiquitin fusion degradation protein 1 homolog (UB fusion protein 1) {Mus musculus}; contains Pfam profile PF03152: Ubiquitin fusion degradation protein UFD1 1261 At2g29090 D2, Dm CYP707A2__cytochrome P450 family protein, similar to Cytochrome P450 88A3 (SP:O23051) (Arabidopsis thaliana); similar to taxane 13-alpha-hydroxylase (GI:17148242) (Taxus cuspidata). 1262 At2g29180 D1, Dm expressed protein 1263 At2g29300 D2, Dm tropinone reductase, putative / tropine dehydrogenase, putative, similar to tropinone reductase SP:P50165 from (Datura stramonium) 1264 At2g29310 D2 tropinone reductase, putative / tropine dehydrogenase, putative, similar to tropinone reductase SP:P50165 from (Datura stramonium) 1265 At2g29320 D2, Dm tropinone reductase, putative / tropine dehydrogenase, putative, similar to tropinone reductase SP:P50165 from (Datura stramonium) 1266 At2g29340 D2 short-chain dehydrogenase/reductase (SDR) family protein, similar to tropinone reductase-I GI:424160 from (Datura stramonium) 1267 At2g29370 Dm tropinone reductase, putative / tropine dehydrogenase, putative, similar to SP:P50162 Tropinone reductase-I (EC 1.1.1.206) (TR-I) (Tropine dehydrogenase) {Datura stramonium} 1268 At2g29400 D1, Dm TOPP1_PP1-AT__serine/threonine protein phosphatase PP1 isozyme 1 (TOPP1) / phosphoprotein phosphatase 1, identical to SP:P30366: Serine/threonine protein phosphatase PP1 isozyme 1 (EC 3.1.3.16) {Arabidopsis thaliana}, phosphoprotein phosphatase 1 GI:166572 (Arabidopsis thaliana) 1269 At2g29530 D2 TIM10__mitochondrial import inner membrane translocase (TIM10), identical to mitochondrial import inner membrane translocase subunit Tim10 (Arabidopsis thaliana) Swiss-Prot:Q9ZW33; contains Pfam domain, PF02953: Tim10/DDP family zinc finger 1270 At2g29550 D2, Dm TUB7__tubulin beta-7 chain (TUB7), identical to GB:M84704 SP:P29515 Tubulin beta-7 chain {Arabidopsis thaliana} 1271 At2g29560 D1, Dm enolase, putative, similar to enolase (Spinacia oleracea) gi:8919731:emb:CAB96173 1272 At2g29570 Dm PCNA2__proliferating cell nuclear antigen 2 (PCNA2), identical to SP:Q9ZW35 Proliferating cell nuclear antigen 2 (PCNA 2) {Arabidopsis thaliana}; nearly identical to SP:Q43124 Proliferating cell nuclear antigen (PCNA) {Brassica napus}; contains Pfam profiles PF00705: Proliferating cell nuclear antigen N-terminal domain, PF02747: Proliferating cell nuclear antigen C-terminal domain 1273 At2g29630 D1, D2, Dm thiamine biosynthesis family protein / thiC family protein, contains Pfam profile: PF01964 ThiC family 1274 At2g29650 D2 inorganic phosphate transporter, putative, similar to brain specific Na+-dependent inorganic phosphate cotransporter (Rattus norvegicus) GI:507415; contains Pfam profile PF00083: major facilitator superfamily protein 1275 At2g29700 D2, Dm ATPH1__pleckstrin homology (PH) domain-containing protein (PH1), identical to AtPH1 (Arabidopsis thaliana) GI:5926716; contains Pfam profile PF00169: PH domain 1276 At2g29760 Dm pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat 1277 At2g29950 D1, D2, Dm expressed protein, ; expression supported by MPSS 1278 At2g29980 D2 FAD3__omega-3 fatty acid desaturase, endoplasmic reticulum (FAD3), identical to SP:48623 1279 At2g30010 Dm expressed protein 1280 At2g30050 D1, Dm transducin family protein / WD-40 repeat family protein, similar to SEC13-related protein (SP:P55735) (Homo sapiens) 1281 At2g30200 D1, Dm expressed protein 1282 At2g30470 D1, D2, Dm HSI2__HSI2 is a member of a novel family of B3 domain proteins with a sequence similar to the ERF-associated amphiphilic repression (EAR) motif. It functions as an active repressor of the Spo minimal promoter (derived from a gene for sweet potato sporamin A1) through the EAR motif. It contains a plant-specific B3 DNA-binding domain. The Arabidopsis genome contains 42 genes with B3 domains which could be classified into three families that are represented by ABI3, ARF1 and RAV1. HSI2 belongs to the ABI3 family. It is expressed at similar levels in all organs. Treatment with 6% sucrose showed a slight increase in transcript levels after 24 h. No changes were observed after treatment with 50碌M ABA. It is localized in the nucleus via a nuclear localization sequence located in the fourth conserved region of the C-terminal B3 domain. 1283 At2g30490 D1, D2, Dm ATC4H_C4H_CYP73A5__trans-cinnamate 4-monooxygenase / cinnamic acid 4-hydroxylase (C4H) (CA4H) / cytochrome P450 73 (CYP73) (CYP73A5), identical to SP:P92994: Trans-cinnamate 4- monooxygenase (EC 1.14.13.11) (Cinnamic acid 4-hydroxylase) (CA4H) (C4H) (P450C4H) (Cytochrome P450 73). {Arabidopsis thaliana}; molecular marker C4H (GB:U71080) 1284 At2g30520 D1 RPT2__signal transducer of phototropic response (RPT2), identical to RPT2 (Arabidopsis thaliana) gi:6959488:gb:AAF33112 1285 At2g30570 D2 photosystem II reaction center W (PsbW) protein-related, similar to photosystem II reaction center W protein SP:Q41387 from (Spinacia oleracea) 1286 At2g30600 D1, D2, Dm BTB/POZ domain-containing protein, contains Pfam PF00651: BTB/POZ domain; contains Interpro IPR000210/ PS50097: BTBB/POZ domain; similar to MigA (GI:1841872) (Dictyostelium discoideum) 1287 At2g30620 D2 histone H1.2, nearly identical to SP:P26569 Histone H1.2 {Arabidopsis thaliana} 1288 At2g30695 D1, Dm expressed protein 1289 At2g30840 D2, Dm 2-oxoglutarate-dependent dioxygenase, putative, similar to 2A6 (GI:599622) and tomato ethylene synthesis regulatory protein E8 (SP:P10967) 1290 At2g30860 D1, D2, Dm ATGSTF9_ATGSTF7_GLUTTR__glutathione S-transferase, putative, identical to GB:Y12295 1291 At2g30870 D1, D2, Dm ATGSTF10_ATGSTF4_ERD13__glutathione S-transferase, putative, supported by cDNA GI:443698 GB:D17673 1292 At2g30930 D2, Dm expressed protein 1293 At2g30950 D2 VAR2_FTSH2__FtsH protease (VAR2), identical to zinc dependent protease VAR2 GI:7650138 from (Arabidopsis thaliana) 1294 At2g30970 D1, D2, Dm ASP1__aspartate aminotransferase, mitochondrial / transaminase A (ASP1), identical to SP:P46643 Aspartate aminotransferase, mitochondrial precursor (EC 2.6.1.1) (Transaminase A) {Arabidopsis thaliana} 1295 At2g31350 D1, D2, Dm GLX2-5__hydroxyacylglutathione hydrolase, putative / glyoxalase II, putative, similar to glyoxalase II isozyme (Arabidopsis thaliana) gi:2570338:gb:AAC49865 1296 At2g31360 D2, Dm ADS2__delta 9 desaturase (ADS2), identical to delta 9 acyl-lipid desaturase (ADS2) GI:2970036 from (Arabidopsis thaliana) 1297 At2g31380 D2 STH__zinc finger (B-box type) family protein / salt tolerance-like protein (STH), contains Pfam profile PF00643: B-box zinc finger; identical to cDNA B-box zinc finger protein STH GI:12698721, SP:Q9SID1 Salt tolerance-like protein (Arabidopsis thaliana) 1298 At2g31510 D1, D2, Dm IBR domain-containing protein / ARIADNE-like protein ARI7 (ARI7), identical to ARIADNE-like protein ARI7 (Arabidopsis thaliana) GI:29125028; contains similarity to Swiss-Prot:Q94981 ariadne-1 protein (Ari-1) (Drosophila melanogaster); contains Pfam profile PF01485: IBR domain

1299 At2g31570 D1, D2, Dm ATGPX2__glutathione peroxidase, putative 1300 At2g31610 D1, D2, Dm 40S ribosomal protein S3 (RPS3A) 1301 At2g31620 Dm receptor-like protein kinase-related, contains Pfam profile: PF01657 Domain of unknown function that is usually associated with protein kinase domain Pfam:PF00069; similar to receptor-like protein kinase 4 (GI:13506745) and receptor-like protein kinase 5 (GI:13506747) (Arabidopsis thaliana) 1302 At2g31690 D1, Dm lipase class 3 family protein, similar to DEFECTIVE IN ANTHER DEHISCENCE1 (Arabidopsis thaliana) GI:16215706; contains Pfam profile PF01764: Lipase 1303 At2g31750 Dm UDP-glucoronosyl/UDP-glucosyl transferase family protein, contains Pfam profile: PF00201 UDP- glucoronosyl and UDP-glucosyl transferase 1304 At2g31810 D2, Dm acetolactate synthase small subunit, putative, similar to gi:5931761 from Nicotiana plumbaginifolia 1305 At2g31840 Dm expressed protein 1306 At2g31960 D1, D2, Dm ATGSL03_ATGSL3_GSL03__glycosyl transferase family 48 protein, contains Pfam profile: PF02364 1,3-beta-glucan synthase; contains non-consensus splice aite AC at exon 33 1307 At2g32060 D1, D2, Dm 40S ribosomal protein S12 (RPS12C) 1308 At2g32090 D1, D2, Dm lactoylglutathione lyase family protein / glyoxalase I family protein, contains glyoxalase family protein domain, Pfam:PF00903 1309 At2g32100 D1, Dm ATOFP16_OFP16__ovate protein-related, contains TIGRFAM TIGR01568 : uncharacterized plant- specific domain TIGR01568 1310 At2g32150 D2 haloacid dehalogenase-like hydrolase family protein, contains InterPro accession IPR005834: Haloacid dehalogenase-like hydrolase 1311 At2g32170 D2, Dm expressed protein, ;supported by cDNA GI:20259498 1312 At2g32230 D1, D2, Dm pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat 1313 At2g32240 D2, Dm expressed protein, contains Pfam profile: PF04508 viral A-type inclusion protein repeat 1314 At2g32260 D2, Dm cholinephosphate cytidylyltransferase, putative / phosphorylcholine transferase, putative / CTP:phosphocholine cytidylyltransferase, putative, strong similarity to CTP:phosphocholine cytidylyltransferase (Brassica napus) GI:1418125; contains Pfam profile PF01467: Cytidylyltransferase 1315 At2g32490 D2 3`-5` exonuclease domain-containing protein, contains Pfam profile PF01612: 3`-5` exonuclease

1316 At2g32500 D1, Dm expressed protein 1317 At2g32650 D2, Dm expressed protein, contains Pfam PF05899: Protein of unknown function (DUF861) 1318 At2g32700 D1, Dm WD-40 repeat family protein, contains 7 WD-40 repeats ; similar to LEUNIG (GP:11141605)(Arabidopsis thaliana) 1319 At2g32710 D2 KRP4_ACK2_ICK7__kip-related protein 4 (KRP4) / cyclin-dependent kinase inhibitor 4 (ICK4), nearly identical to cyclin-dependent kinase inhibitor 4 (krp4) (Arabidopsis thaliana) GI:14422291 1320 At2g32730 Dm 26S proteasome regulatory subunit, putative, contains similarity to 26S proteasome regulatory subunit S1 SP:O88761, GI:3288594 from (Rattus norvegicus) 1321 At2g32800 D1, Dm protein kinase family protein, contains dual protein kinase domains, Pfam:PF00069 1322 At2g32870 D1, D2, Dm meprin and TRAF homology domain-containing protein / MATH domain-containing protein, similar to ubiquitin-specific protease 12 (Arabidopsis thaliana) GI:11993471; contains Pfam profile PF00917: MATH domain 1323 At2g32920 D2 ATPDIL2-3__Encodes a protein disulfide isomerase-like (PDIL) protein, a member of a multigene family within the thioredoxin (TRX) superfamily. 1324 At2g33030 D2, Dm leucine-rich repeat family protein, contains leucine rich-repeat (LRR) domains Pfam:PF00560, INTERPRO:IPR001611 1325 At2g33150 D1, D2, Dm PED1__acetyl-CoA C-acyltransferase, putative / 3-ketoacyl-CoA thiolase, putative, similar to 3-ketoacyl-CoA thiolase (E.C. 2.3.1.16) from (Arabidopsis thaliana) GI:2981616, (Cucumis sativus) GI:393707, (Cucurbita cv. Kurokawa Amakuri) GI:1694621; contains InterPro accession IPR002155: Thiolase 1326 At2g33180 D1 expressed protein 1327 At2g33310 Dm IAA13__auxin-responsive protein / indoleacetic acid-induced protein 13 (IAA13), identical to SP:Q38831 Auxin-responsive protein IAA13 (Indoleacetic acid-induced protein 13) {Arabidopsis thaliana} 1328 At2g33330 D1, D2, Dm 33 kDa secretory protein-related, contains Pfam PF01657: Domain of unknown function, duplicated in 33 KDa secretory proteins 1329 At2g33340 D1, Dm transducin family protein / WD-40 repeat family protein, contains 5 WD-40 repeats (PF00400); similar to cell cycle control protein cwf8 (SP:O14011) (Schizosaccharomyces pombe (Fission yeast)) 1330 At2g33370 D1, D2, Dm 60S ribosomal protein L23 (RPL23B) 1331 At2g33380 D1, D2, Dm RD20__calcium-binding RD20 protein (RD20), induced by abscisic acid during dehydration PMID:10965948; putative transmembrane channel protein PMID:10965948; identical to GI:10862968 (Arabidopsis thaliana); contains EF-hand domain 1332 At2g33430 D1, D2, Dm plastid developmental protein DAG, putative, similar to DAG protein, chloroplast precursor (Garden snapdragon) SWISS-PROT:Q38732 1333 At2g33590 D1, D2, Dm cinnamoyl-CoA reductase family, similar to cinnamoyl-CoA reductase from Pinus taeda (GI:17978649), Eucalyptus gunnii (GI:2058311) 1334 At2g33600 D1, Dm cinnamoyl-CoA reductase family, similar to cinnamoyl-CoA reductase from Pinus taeda (GI:17978649), Eucalyptus gunnii (GI:2058311) 1335 At2g33610 Dm ATSWI3B_CHB2__SWIRM domain-containing protein / DNA-binding family protein, contains similarity to SWI/SNF complex 170 KDa subunit (Homo sapiens) gi:1549241:gb:AAC50694; contains Pfam domain PF04433: SWIRM domain, PF00249: Myb-like DNA-binding domain 1336 At2g33770 D1, Dm ubiquitin-conjugating enzyme family protein, low similarity to ubiquitin-conjugating BIR- domain enzyme APOLLON (Homo sapiens) GI:8489831, ubiquitin-conjugating enzyme (Mus musculus) GI:3319990; contains Pfam profile PF00179: Ubiquitin-conjugating enzyme 1337 At2g33800 D2, Dm ribosomal protein S5 family protein, contains Pfam profiles PF03719: Ribosomal protein S5, C- terminal domain, PF00333: Ribosomal protein S5, N-terminal domain 1338 At2g33830 D2 dormancy/auxin associated family protein, contains Pfam profile: PF05564 dormancy/auxin associated protein 1339 At2g33850 Dm expressed protein, contains 1 transmembrane domain; similar to Protein E6 (Swiss-Prot:Q01197) (Gossypium hirsutum) 1340 At2g34080 D1 cysteine proteinase, putative, contains similarity to cysteine protease SPCP1 GI:13491750 from (Ipomoea batatas) 1341 At2g34260 D2 transducin family protein / WD-40 repeat family protein, similar to Vegetatible incompatibility protein HET-E-1 (SP:Q00808) {Podospora anserina} 1342 At2g34355 D1, Dm nodulin-related, contains 14 transmembrane domains; supported by tandem duplication of nodulin -related protein (TIGR_Ath1:At2g34350) (Arabidopsis thaliana) 1343 At2g34400 D1 pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat 1344 At2g34420 D2 LHB1B2_LHCB1.5__chlorophyll A-B binding protein / LHCII type I (LHB1B2), identical to GB:X64460 photosystem II type I chlorophyll a/b binding protein (Arabidopsis thaliana) GI:16364 1345 At2g34430 D1, Dm LHB1B1_LHCB1.4__chlorophyll A-B binding protein / LHCII type I (LHB1B1), identical to photosystem II type I chlorophyll a/b binding protein (Arabidopsis thaliana) GI:16366 1346 At2g34470 D2, Dm UREG_PSKF109__urease accessory protein (UREG), identical to urease accessory protein UREG GI:4324678 from (Arabidopsis thaliana); contains Pfam profile: PF01495 HypB/UreG nucleotide- binding domain 1347 At2g34480 D1, Dm 60S ribosomal protein L18A (RPL18aB) 1348 At2g34490 D2 CYP710A2__cytochrome P450 family protein, similar to Cytochrome P450 61 (C-22 sterol desaturase) (SP:P54781) {Saccharomyces cerevisiae}; contains Pfam profile: PF00067 cytochrome P450; supported by full-length cDNA: Ceres:158108. 1349 At2g34510 D1, D2, Dm expressed protein, contains Pfam profile PF04862: Protein of unknown function, DUF642 1350 At2g34640 D1, Dm expressed protein 1351 At2g34720 D1, D2, Dm CCAAT-binding transcription factor (CBF-B/NF-YA) family protein, contains Pfam profile: PF02045 CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B 1352 At2g34850 D1, D2, Dm NAD-dependent epimerase/dehydratase family protein, similar to UDP-galactose 4-epimerase from Cyamopsis tetragonoloba GI:3021357, Lactococcus lactis GI:3703056; contains Pfam profile PF01370 NAD dependent epimerase/dehydratase family 1353 At2g35040 D2 AICARFT/IMPCHase bienzyme family protein, similar to SP:P12048 Bifunctional purine biosynthesis protein purH (Includes: Phosphoribosylaminoimidazolecarboxamide formyltransferase (EC 2.1.2.3) (AICAR transformylase); IMP cyclohydrolase (EC 3.5.4.10) (Inosinicase) (IMP synthetase) (ATIC)) {Bacillus subtilis}; contains Pfam profiles PF01808: AICARFT/IMPCHase bienzyme, PF02142: MGS-like domain 1354 At2g35050 D2 protein kinase family protein, contains Pfam profile: PF00069 Eukaryotic protein kinase domain

1355 At2g35060 D1, Dm KUP11__potassium transporter family protein, similar to HAK2 (Hordeum vulgare) GI:7108599, potassium transporter HAK2p (Mesembryanthemum crystallinum) gi:14091471:gb:AAK53759; KUP/HAK/KT Transporter family member, PMID:11500563; contains Pfam profile PF02705: K+ potassium transporter 1356 At2g35070 D1, D2, Dm expressed protein 1357 At2g35090 D1, D2, Dm hypothetical protein 1358 At2g35210 D2 human Rev interacting-like family protein / hRIP family protein, similar to ARFGAP1 protein GI:7211442 from (Homo sapiens); contains InterPro accession IPR001164: Human Rev interacting- like protein (hRIP) 1359 At2g35410 D1, D2, Dm 33 kDa ribonucleoprotein, chloroplast, putative / RNA-binding protein cp33, putative, similar to SP:P19684 33 kDa ribonucleoprotein, chloroplast precursor {Nicotiana sylvestris}; contains InterPro entry IPR000504: RNA-binding region RNP-1 (RNA recognition motif) (RRM) 1360 At2g35605 D2 SWIB complex BAF60b domain-containing protein, contains Pfam profile PF02201: BAF60b domain of the SWIB complex 1361 At2g35680 D1, Dm dual specificity protein phosphatase family protein, contains Pfam profile: PF00782 dual specificity phosphatase, catalytic domain 1362 At2g35790 D2 expressed protein 1363 At2g35810 D1, D2, Dm expressed protein 1364 At2g35840 D1, D2, Dm sucrose-phosphatase 1 (SPP1), identical to sucrose-phosphatase (SPP1) (Arabidopsis thaliana) GI:11127757 1365 At2g35880 D2 expressed protein 1366 At2g35900 D1, D2, Dm expressed protein 1367 At2g35940 D1, D2, Dm BLH1__homeodomain-containing protein, contains `Homeobox` domain signature, Prosite:PS00027 1368 At2g36010 Dm E2F3_ATE2FA__E2F transcription factor-3 (E2F3), identical to E2F transcription factor-3 E2F3 (Arabidopsis thaliana) gi:10443853:gb:AAG17610 1369 At2g36060 Dm ubiquitin-conjugating enzyme family protein, similar to DNA-binding protein CROC-1B (Homo sapiens) GI:1066082; contains Pfam profile PF00179: Ubiquitin-conjugating enzyme 1370 At2g36170 D1, Dm ubiquitin extension protein 2 (UBQ2) / 60S ribosomal protein L40 (RPL40A), identical to GI:166930, GI:166931 1371 At2g36210 D2 auxin-responsive family protein, similar to auxin-induced protein SAUR-AC1 (GI:546362) (PIR:T06084) (Arabidopsis thaliana) 1372 At2g36390 D2, Dm SBE2.1__1,4-alpha-glucan branching enzyme / starch branching enzyme class II (SBE2-1), nearly identical to starch branching enzyme class II (Arabidopsis thaliana) GI:619939 1373 At2g36410 D2 expressed protein, contains Pfam profile PF04949: Family of unknown function (DUF662) 1374 At2g36780 Dm UDP-glucoronosyl/UDP-glucosyl transferase family protein, contains Pfam profile: PF00201 UDP- glucoronosyl and UDP-glucosyl transferase 1375 At2g36830 D1, D2, Dm GAMMA-TIP_GAMMA-TIP1_TIP1;1__major intrinsic family protein / MIP family protein, contains Pfam profile: MIP PF00230 1376 At2g36950 D2 heavy-metal-associated domain-containing protein, nearly identical to farnesylated protein ATFP2 (GI:4097545) Pfam profile PF00403: Heavy-metal-associated domain 1377 At2g36990 D1, D2, Dm SIGF_SIG6__RNA polymerase sigma subunit SigF (sigF) / sigma-like factor (SIG6), identical to RNA polymerase sigma subunit SigF (Arabidopsis thaliana) GI:7209640; contains Pfam profiles PF04545: Sigma-70, region 4, PF04539: Sigma-70 region 3, PF04542: Sigma-70 region 2; identical to cDNA partial mRNA for putative sigma-like transcription factor (sig6 gene) GI:6273429 1378 At2g37040 D2 PAL1__phenylalanine ammonia-lyase 1 (PAL1), nearly identical to SP:P35510 1379 At2g37110 D1, Dm expressed protein, contains Pfam profile PF04749: Protein of unknown function, DUF614 1380 At2g37130 D1, D2, Dm peroxidase 21 (PER21) (P21) (PRXR5), identical to SP:Q42580 Peroxidase 21 precursor (EC 1.11.1.7) (Atperox P21) (PRXR5) (ATP2a/ATP2b) {Arabidopsis thaliana} 1381 At2g37170 D1, D2, Dm PIP2B_PIP2;2__plasma membrane intrinsic protein 2B (PIP2B) / aquaporin PIP2.2 (PIP2.2), identical to SP:P43287 Plasma membrane intrinsic protein 2B {Arabidopsis thaliana} 1382 At2g37190 D1, D2, Dm 60S ribosomal protein L12 (RPL12A) 1383 At2g37220 D2 29 kDa ribonucleoprotein, chloroplast, putative / RNA-binding protein cp29, putative, similar to SP:Q43349 29 kDa ribonucleoprotein, chloroplast precursor (RNA-binding protein cp29) {Arabidopsis thaliana} 1384 At2g37240 D1, D2, Dm expressed protein, weak similarity to fmHP (GI:22902096) (Takifugu rubripes) 1385 At2g37270 D1, D2, Dm ATRPS5B__40S ribosomal protein S5 (RPS5A), identical to GP:3043428 1386 At2g37340 D1, D2, Dm RSZ33__splicing factor RSZ33 (RSZ33), nearly identical to splicing factor RSZ33 (Arabidopsis thaliana) GI:9843663; contains Pfam profiles PF00076: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain), PF00098: Zinc knuckle 1387 At2g37410 D1, Dm ATTIM17-2_TIM17__mitochondrial import inner membrane translocase (TIM17), nearly identical to SP:Q9SP35 Mitochondrial import inner membrane translocase subunit TIM17 {Arabidopsis thaliana}

1388 At2g37450 D1, D2, Dm nodulin MtN21 family protein, similar to MtN21 GI:2598575 (root nodule development) from (Medicago truncatula) 1389 At2g37470 Dm histone H2B, putative, strong similarity to histone H2B from Lycopersicon esculentum GI:3021483, GI:3021485, Capsicum annuum SP:O49118; contains Pfam profile PF00125 Core histone H2A/H2B/H3/H4 1390 At2g37550 D2, Dm ASP1__arabidopsis pde1 suppressor 1 protein (ASP1), identical to arabidopsis pde1 suppressor 1 (Asp1) from GI:4519792 (Arabidopsis thaliana); contains InterPro accession IPR001164: Human Rev interacting-like protein (hRIP) 1391 At2g37600 D2, Dm 60S ribosomal protein L36 (RPL36A) 1392 At2g37630 D1, Dm AS1_ATPHAN_MYB91__myb family transcription factor (MYB91), contains Pfam profile: PF00249 myb- like DNA-binding domain 1393 At2g37660 D1, D2, Dm expressed protein 1394 At2g37760 D1, D2, Dm aldo/keto reductase family protein, similar to chalcone reductase (Sesbania rostrata)(GI:2792155), and aldose reductase ALDRXV4 (Xerophyta viscosa)(GI:4539944), (Hordeum vulgare)(GI:728592) 1395 At2g37870 D2, Dm protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 1396 At2g37970 D1, D2, Dm SOUL heme-binding family protein, weak similarity to SOUL protein (Mus musculus) GI:4886906; contains Pfam profile PF04832: SOUL heme-binding protein 1397 At2g37990 D2, Dm ribosome biogenesis regulatory protein (RRS1) family protein, contains Pfam profile PF04939: Ribosome biogenesis regulatory protein (RRS1); similar to Ribosome biogenesis regulatory protein homolog (Swiss-Prot:Q15050) (Homo sapiens) 1398 At2g38000 D2 chaperone protein dnaJ-related, weak similarity to Chaperone protein dnaJ (Swiss-Prot:Q9ZFC5) (Methylovorus sp.) 1399 At2g38120 D1, D2, Dm AUX1_MAP1_PIR1_WAV5__amino acid permease, putative (AUX1), identical to AUX1 GI:1531758 from (Arabidopsis thaliana) 1400 At2g38140 D1, Dm PSRP4__chloroplast 30S ribosomal protein S31 (PSRP4) 1401 At2g38170 D2 CAX1_ATCAX1_RCI4__calcium exchanger (CAX1), identical to high affinity calcium antiporter CAX1 (Arabidopsis thaliana) gi:9256741:gb:AAB05913, except a possible frameshift at base 58008. Sequence has been confirmed with 5 sequencing reads.; Ca2+:Cation Antiporter (CaCA) Family member PMID:11500563 1402 At2g38230 D2 ATPDX1.1__Encodes a protein predicted to function in tandem with PDX2 to form glutamine amidotransferase complex with involved in vitamin B6 biosynthesis. 1403 At2g38290 D2 ATAMT2__ammonium transporter 2 (AMT2), identical to SP:Q9M6N7 Ammonium transporter 2 (AtAMT2) {Arabidopsis thaliana} 1404 At2g38310 Dm expressed protein, low similarity to early flowering protein 1 (Asparagus officinalis) GI:1572683, SP:P80889 Ribonuclease 1 (EC 3.1.-.-) {Panax ginseng} 1405 At2g38390 D2 peroxidase, putative, similar to peroxidase isozyme (Armoracia rusticana) gi:217934:dbj:BAA14144; identical to cDNA class III peroxidase ATP34, GI:17530563 1406 At2g38400 D1, Dm AGT3__alanine--glyoxylate aminotransferase, putative / beta-alanine-pyruvate aminotransferase, putative / AGT, putative, similar to SP:Q64565 Alanine--glyoxylate aminotransferase 2, mitochondrial precursor (EC 2.6.1.44) (AGT 2) (Beta-alanine-pyruvate aminotransferase) {Rattus norvegicus}; contains Pfam profile PF00202: aminotransferase, class III

1407 At2g38470 D1, Dm WRKY33_ATWRKY33__WRKY family transcription factor, contains Pfam profile: PF03106 WRKY DNA - binding domain; 1408 At2g38530 D1, D2, Dm LTP2_LP2__nonspecific lipid transfer protein 2 (LTP2), identical to nonspecific lipid-transfer protein 2 from Arabidopsis thaliana (SP:Q9S7I3); contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 1409 At2g38540 D1, Dm LP1_ATLTP1_LTP1_ATLTP1__nonspecific lipid transfer protein 1 (LTP1), identical to SP:Q42589 1410 At2g38610 Dm KH domain-containing protein 1411 At2g38650 Dm glycosyl transferase family 8 protein, contains Pfam profile: PF01501 glycosyl transferase family 8 1412 At2g38670 Dm ethanolamine-phosphate cytidylyltransferase, putative / phosphorylethanolamine transferase, putative / CTP:phosphoethanolamine cytidylyltransferase, putative, similar to SP:Q99447 Ethanolamine-phosphate cytidylyltransferase (EC 2.7.7.14) {Homo sapiens}; contains Pfam profile PF01467: Cytidylyltransferase 1413 At2g38740 D1, D2, Dm haloacid dehalogenase-like hydrolase family protein, similar to SP:P71447 Beta- phosphoglucomutase (EC 5.4.2.6) {Lactococcus lactis}; contains InterPro accession IPR005834: Haloacid dehalogenase-like hydrolase 1414 At2g38790 Dm expressed protein 1415 At2g38800 D2, Dm calmodulin-binding protein-related, contains similarity to potato calmodulin-binding protein PCBP GI:17933110 from (Solanum tuberosum) 1416 At2g38810 Dm histone H2A, putative, strong similarity to histone H2A.F/Z Arabidopsis thaliana GI:2407800; contains Pfam profile PF00125 Core histone H2A/H2B/H3/H4 1417 At2g38980 D1, D2, Dm pseudogene, similar to fiber protein Fb12 1418 At2g39010 Dm PIP2;6_PIP2E__aquaporin, putative, similar to plasma membrane aquaporin 2b GI:7209560 from (Raphanus sativus) 1419 At2g39050 D2, Dm hydroxyproline-rich glycoprotein family protein, contains QXW lectin repeat domain, Pfam:PF00652 1420 At2g39070 D1, Dm 1421 At2g39090 Dm tetratricopeptide repeat (TPR)-containing protein, low similarity to prediabetic NOD sera- reactive autoantigen (Mus musculus) GI:6670773, anaphase-promoting complex subunit 7 (Homo sapiens) GI:6180015; contains Pfam profile PF00515: TPR Domain 1422 At2g39100 D2, Dm zinc finger (C3HC4-type RING finger) family protein, contains Pfam profile: PF00097 zinc finger, C3HC4 type 1423 At2g39140 D1 pseudouridine synthase family protein 1424 At2g39190 D1, Dm ATATH8__ABC1 family protein, contains Pfam domain, PF03109: ABC1 family 1425 At2g39270 D2, Dm adenylate kinase family protein, contains Pfam profile: PF00406: adenylate kinase 1426 At2g39390 D1, D2, Dm 60S ribosomal protein L35 (RPL35B) 1427 At2g39520 D2, Dm expressed protein 1428 At2g39630 Dm glycosyl transferase family 2 protein, similar to dolichyl-phosphate beta-glucosyltransferase from Saccharomyces cerevisiae (SP:P40350); contains Pfam glycosyltransferase group 2 domain PF00535 1429 At2g39760 Dm ATBPM3__speckle-type POZ protein-related, contains Pfam PF00651 : BTB/POZ domain; contains Pfam PF00917: MATH domain; similar to Speckle-type POZ protein (SP:O43791) (Homo sapiens) 1430 At2g39800 D1, D2, Dm P5CS1_ATP5CS__delta 1-pyrroline-5-carboxylate synthetase A / P5CS A (P5CS1), identical to SP:P54887:P5C1_ARATH 1431 At2g39870 D1, D2, Dm expressed protein 1432 At2g39880 D2, Dm MYB25__myb family transcription factor (MYB25), contains Pfam profile: PF00249 myb-like DNA- binding domain 1433 At2g39940 D2, Dm COI1__coronatine-insensitive 1 / COI1 (FBL2), E3 ubiquitin ligase SCF complex F-box subunit; identical to LRR-containing F-box protein GI:3158394 from (Arabidopsis thaliana) 1434 At2g39950 Dm expressed protein 1435 At2g40060 Dm expressed protein 1436 At2g40270 Dm protein kinase family protein, contains Pfam domain, PF00069: Protein kinase domain 1437 At2g40290 D2, Dm eukaryotic translation initiation factor 2 subunit 1, putative / eIF-2A, putative / eIF-2- alpha, putative, similar to Swiss-Prot:P05198 eukaryotic translation initiation factor 2 subunit 1 (Eukaryotic translation initiation factor 2 alpha subunit) (eIF-2-alpha) (EIF- 2alpha) (EIF-2A) (Homo sapiens) 1438 At2g40300 D1, Dm ATFER4__ferritin, putative, similar to ferritin subunit cowpea2 precursor (Vigna unguiculata) GI:2970654; contains Pfam profile PF00210: Ferritin-like domain 1439 At2g40360 D2 transducin family protein / WD-40 repeat family protein, contains 4 WD-40 repeats (PF00400); similar to block of proliferation protein Bop1 (GI:1679772) (Mus musculus) 1440 At2g40400 D1, Dm expressed protein, similar to GI:7572912 (At3g56140)(Arabidopsis thaliana) 1441 At2g40430 D2 expressed protein, identical to Protein At2g40430 (Swiss-Prot:O22892) (Arabidopsis thaliana); similar to Glioma tumor suppressor candidate region gene 2 protein (p60) (Swiss-Prot:Q9NZM5) (Homo sapiens) 1442 At2g40460 Dm proton-dependent oligopeptide transport (POT) family protein, contains Pfam profile: PF00854 POT family 1443 At2g40490 D1, D2, Dm uroporphyrinogen decarboxylase, putative / UPD, putative, similar to uroporphyrinogen decarboxylase (chloroplast) from Nicotiana tabacum (SP:Q42967), Hordeum vulgare (SP:Q42855), Zea mays (SP:O81220); contains Pfam domain uroporphyrinogen decarboxylase (URO-D) PF01208 1444 At2g40510 D2, Dm 40S ribosomal protein S26 (RPS26A) 1445 At2g40590 D1, D2, Dm 40S ribosomal protein S26 (RPS26B) 1446 At2g40610 D1, D2, Dm ATEXPA8_ATEXP8_ATHEXP ALPHA 1.11_EXP8__expansin, putative (EXP8), similar to expansin 2 GI:7025493 from (Zinnia elegans); alpha-expansin gene family, PMID:11641069 1447 At2g40660 Dm tRNA-binding region domain-containing protein, similar to SP:Q12904 Multisynthetase complex auxiliary component p43 (Contains: Endothelial-monocyte activating polypeptide II (EMAP-II) (Small inducible cytokine subfamily E member 1)) {Homo sapiens}; contains Pfam profile PF01588: Putative tRNA binding domain 1448 At2g40670 D2 ARR16_RR16__two-component responsive regulator / response regulator 16 (ARR16), identical to response regulator 16 GI:11870067 from (Arabidopsis thaliana) 1449 At2g40830 D1, D2, Dm RHC1A__zinc finger (C3HC4-type RING finger) family protein, contains Pfam domain, PF00097: Zinc finger, C3HC4 type (RING finger) 1450 At2g40840 D2 DPE2__glycoside hydrolase family 77 protein, contains Pfam profiles PF02446: 4-alpha- glucanotransferase, PF00686: Starch binding domain; contains a non-consensus AT-AC intron between at intron 5 1451 At2g40880 D2, Dm FL3-27__cysteine protease inhibitor, putative / cystatin, putative (FL3-27), similar to PRLI- interacting factor M (Arabidopsis thaliana) GI:11139270, cysteine proteinase inhibitor (Brassica rapa) GI:762785; contains Pfam profile PF00031: Cystatin domain 1452 At2g40890 Dm CYP98A3_REF8__cytochrome P450 98A3, putative (CYP98A3), identical to Cytochrome P450 98A3 (SP:O22203) (Arabidopsis thaliana); similar to gi:17978651 from Pinus taeda 1453 At2g40900 D2, Dm nodulin MtN21 family protein, similar to MtN21 (Medicago truncatula) GI:2598575; contains Pfam profile PF00892: Integral membrane protein 1454 At2g41090 D1, D2, Dm calmodulin-like calcium-binding protein, 22 kDa (CaBP-22), identical to SP:P30187 22 kDa calmodulin-like calcium-binding protein (CABP-22) (Arabidopsis thaliana) 1455 At2g41100 D2, Dm TCH3_ATCAL5__touch-responsive protein / calmodulin-related protein 3, touch-induced (TCH3), identical to calmodulin-related protein 3, touch-induced SP:P25071 from (Arabidopsis thaliana)

1456 At2g41120 Dm expressed protein 1457 At2g41180 D2 sigA-binding protein-related, low similarity to SigA binding protein (Arabidopsis thaliana) GI:6980074; contains Pfam domain PF05678: VQ motif 1458 At2g41190 D2, Dm amino acid transporter family protein, low similarity to vesicular GABA transporter (Rattus norvegicus) GI:2587061; belongs to INTERPRO:IPR002422 amino acid/polyamine transporter, family II 1459 At2g41200 Dm expressed protein 1460 At2g41220 D1, D2, Dm GLU2__glutamate synthase, chloroplast (GLU2) / ferredoxin-dependent glutamate synthase (Fd- GOGAT 2), identical to SP:Q9T0P4 Ferredoxin-dependent glutamate synthase 2, chloroplast precursor (EC 1.4.7.1) (Fd-GOGAT 2) {Arabidopsis thaliana} 1461 At2g41410 D1, D2, Dm calmodulin, putative, identical to SP:P30188 Calmodulin-like protein {Arabidopsis thaliana} 1462 At2g41470 D1, D2, Dm embryo-specific protein-related, similar to embryo-specific protein 3 (ATS3) (Arabidopsis thaliana) GI:3335171 1463 At2g41500 Dm WD-40 repeat family protein / small nuclear ribonucleoprotein Prp4p-related, similar to U4/U6 small nuclear ribonucleoprotein hPrp4 (GP:2708305) {Homo sapiens}; contains Pfam PF00400: WD domain, G-beta repeat (7 copies):19877698:gb:AU238529.1:AU238529 1464 At2g41560 D2 ACA4__calcium-transporting ATPase 4, plasma membrane-type / Ca2+-ATPase, isoform 4 (ACA4), identical to SP:O22218 Calcium-transporting ATPase 4, plasma membrane-type (EC 3.6.3.8) (Ca(2+)-ATPase isoform 4) {Arabidopsis thaliana} Belongs to plant 2B ATPase聮s with an N- terminal autoinhibitor. 1465 At2g41650 D2 expressed protein 1466 At2g41680 D1, Dm thioredoxin reductase, putative / NADPH-dependent thioredoxin reductase, putative, The last 2 exons encode thioredoxin. There is an EST match to exons 5-7, and the distance between exon 7 and exon 8 is only 90bp. It is unlikely this is two separate genes, but more likely a hybrid protein. 1467 At2g41730 Dm expressed protein 1468 At2g41750 Dm DTW domain-containing protein, contains Pfam domain, PF03942: DTW domain 1469 At2g41870 D2 remorin family protein, contains Pfam domain, PF03763: Remorin, C-terminal region 1470 At2g41900 D1, D2, Dm zinc finger (CCCH-type) family protein, contains Pfam domain, PF00642: Zinc finger C-x8-C-x5- C-x3-H type (and similar) and Pfam domain, PF00023: Ankyrin repeat 1471 At2g41950 D2, Dm expressed protein 1472 At2g42100 D2 actin, putative, very strong similarity to SP:P53496 Actin 11 {Arabidopsis thaliana}, SP:P53493 Actin 3 {Arabidopsis thaliana}; contains Pfam profile PF00022: Actin 1473 At2g42160 Dm zinc finger (ubiquitin-hydrolase) domain-containing protein, similar to BRCA1-associated protein 2 (Homo sapiens) GI:3252872; contains Pfam profile PF02148: Zn-finger in ubiquitin- hydrolases and other protein 1474 At2g42220 D1, Dm rhodanese-like domain-containing protein, contains rhodanese-like domain PF:00581 1475 At2g42300 D2 basic helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain 1476 At2g42350 D2, Dm zinc finger (C3HC4-type RING finger) family protein, contains Pfam domain, PF00097: Zinc finger, C3HC4 type (RING finger) 1477 At2g42380 D1, D2, Dm bZIP transcription factor family protein 1478 At2g42490 D2 copper amine oxidase, putative, similar to copper methylamine oxidase precursor (MAOXII) (Arthrobacter sp.) SWISS-PROT:Q07123 1479 At2g42500 D2, Dm PP2A-3_EP7_PP2A-4__serine/threonine protein phosphatase PP2A-3 catalytic subunit (PP2A3), identical to SP:Q07100 Serine/threonine protein phosphatase PP2A-3 catalytic subunit (EC 3.1.3.16) {Arabidopsis thaliana}; contains Pfam profile PF00149: Ser/Thr protein phosphatase 1480 At2g42530 D2, Dm cold-responsive protein / cold-regulated protein (cor15b), nearly identical to cold-regulated gene cor15b (Arabidopsis thaliana) GI:456016; contains Pfam profile PF02987: Late embryogenesis abundant protein 1481 At2g42570 Dm expressed protein 1482 At2g42580 D1, D2, Dm tetratricopeptide repeat (TPR)-containing protein, contains Pfam profile PF00515 TPR Domain 1483 At2g42590 D1, D2, Dm GRF9_GF14 MU__14-3-3 protein GF14 mu (GRF9), identical to GF14 mu GI:3551052, SP:Q96299 from (Arabidopsis thaliana) 1484 At2g42600 D1, Dm ATPPC2__phosphoenolpyruvate carboxylase, putative / PEP carboxylase, putative (PPC2), strong similarity to phosphoenolpyruvate carboxylase (Brassica napus) GI:507808; contains Pfam profile PF00311: phosphoenolpyruvate carboxylase 1485 At2g42610 D1, Dm expressed protein, contains Pfam profile PF04852: Protein of unknown function (DUF640) 1486 At2g42680 Dm ATMBF1A_MBF1A__ethylene-responsive transcriptional coactivator, putative, similar to ethylene- responsive transcriptional coactivator (Lycopersicon esculentum) gi:5669634:gb:AAD46402

1487 At2g42690 D2, Dm lipase, putative, similar to lipase (Dianthus caryophyllus) GI:4103627; contains Pfam profile PF01764: Lipase 1488 At2g42750 D2 DNAJ heat shock N-terminal domain-containing protein, low similarity to GFA2 (Arabidopsis thaliana) GI:21429604; contains Pfam profile PF00226: DnaJ domain 1489 At2g42760 D2 expressed protein 1490 At2g42790 D1, D2, Dm CSY3__citrate synthase, glyoxysomal, putative, strong similarity to SP:P49299 Citrate synthase, glyoxysomal precursor {Cucurbita maxima}; contains Pfam profile PF00285: Citrate synthase 1491 At2g42800 D1, Dm leucine-rich repeat family protein, contains leucine rich-repeat domains Pfam:PF00560, INTERPRO:IPR001611; and grail 1492 At2g42870 D2 expressed protein 1493 At2g43010 D2 PIF4_SRL2__phytochrome-interacting factor 4 (PIF4) / basic helix-loop-helix protein 9 (bHLH9) / short under red-light 2 (SRL2), identical to SP:Q8W2F3 Phytochrome-interacting factor 4 (Basic helix-loop-helix protein 9) (bHLH9) (Short under red-light 2) {Arabidopsis thaliana}; supporting cDNA gi:18026965:gb:AF251694.1:AF251694 1494 At2g43020 D1, D2, Dm amine oxidase family protein, similar to polyamine oxidase SP:O64411 (Zea mays); contains Pfam profile PF01593 amine oxidase, flavin-containing 1495 At2g43030 D1, D2, Dm ribosomal protein L3 family protein, contains Pfam profile PF00297: ribosomal protein L3 1496 At2g43090 D1, Dm aconitase C-terminal domain-containing protein, contains Pfam profile PF00694: Aconitase C- terminal domain 1497 At2g43320 D1, Dm expressed protein 1498 At2g43360 D1, D2, Dm BIO2_BIOB__biotin synthase (BioB) (BIO2), identical to SP:P54967 Pfam profile PF04055: radical SAM domain protein 1499 At2g43460 D1, D2, Dm 60S ribosomal protein L38 (RPL38A) 1500 At2g43510 D2 ATTI1__Encodes a defensin-like (DEFL) family protein. 1501 At2g43540 D2, Dm expressed protein 1502 At2g43560 D1, D2, Dm immunophilin / FKBP-type peptidyl-prolyl cis-trans isomerase family protein, identical to Probable FKBP-type peptidyl-prolyl cis-trans isomerase 2, chloroplast precursor (Ppiase) (Rotamase) (SP:O22870)(Arabidopsis thaliana); contains Pfam PF00254: peptidyl-prolyl cis-trans isomerase, FKBP-type 1503 At2g43590 D1, Dm chitinase, putative, similar to basic endochitinase CHB4 precursor SP:Q06209 from (Brassica napus) 1504 At2g43620 Dm chitinase, putative, similar to basic endochitinase CHB4 precursor SP:Q06209 from (Brassica napus) 1505 At2g43650 D2 Sas10/U3 ribonucleoprotein (Utp) family protein, contains Pfam profile PF04000: Sas10/Utp3 family; contains Prosite PS00761: Signal peptidases I signature 3; weak similarity to PEBP2 beta-binding protein / charged amino acid rich leucine zipper factor-1 (GI:12061569) (Mus musculus) 1506 At2g43680 D2 calmodulin-binding family protein, similar to SF16 protein (Helianthus annuus) GI:560150; contains Pfam profile PF00612: IQ calmodulin-binding motif 1507 At2g43710 D1 SSI2_FAB2__acyl-(acyl-carrier-protein) desaturase / stearoyl-ACP desaturase (SSI2), identical to gi:15149310; contains Pfam profile PF03405: Fatty acid desaturase; identical to cDNA stearoyl ACP desaturase (SSI2), SSI2-FAB2 allele, GI:15149309 1508 At2g43820 D2 UDP-glucoronosyl/UDP-glucosyl transferase family protein, contains Pfam profile: PF00201 UDP- glucoronosyl and UDP-glucosyl transferase 1509 At2g43910 D2 thiol methyltransferase, putative, similar to thiol methyltransferase 1 GI:14583119 from (Brassica oleracea) 1510 At2g44040 D1, Dm dihydrodipicolinate reductase family protein, weak similarity to SP:Q52419 Dihydrodipicolinate reductase (EC 1.3.1.26) (DHPR) {Pseudomonas syringae} ; contains Pfam profiles PF01113: Dihydrodipicolinate reductase N-terminus, PF05173: Dihydrodipicolinate reductase C-terminus

1511 At2g44050 Dm COS1__6,7-dimethyl-8-ribityllumazine synthase / DMRL synthase / lumazine synthase / riboflavin synthase, identical to 6,7-dimethyl-8-ribityllumazine synthase, chloroplast (precursor) SP:O80575 from (Arabidopsis thaliana) 1512 At2g44060 D1, D2, Dm late embryogenesis abundant family protein / LEA family protein, similar to ethylene- responsive late embryogenesis-like protein (Lycopersicon esculentum) GI:1684830; contains Pfam profile PF03168: Late embryogenesis abundant protein 1513 At2g44100 Dm Rab GDP dissociation inhibitor (GDI1), identical to GDP dissociation inhibitor (Arabidopsis thaliana) GI:1655424 1514 At2g44120 D2, Dm 60S ribosomal protein L7 (RPL7C) 1515 At2g44140 D1, D2, Dm autophagy 4a (APG4a), identical to autophagy 4a (Arabidopsis thaliana) gi:19912143:dbj:BAB88383 1516 At2g44210 D1, Dm expressed protein, Pfam profile PF03080: Arabidopsis proteins of unknown function 1517 At2g44300 D2 lipid transfer protein-related, low similarity to lipid transfer protein Picea abies GI:2627141; contains Pfam profile: PF00234: Protease inhibitor/seed storage/LTP family 1518 At2g44500 D2 expressed protein, contains Pfam PF03138: Plant protein family. The function of this family of plant proteins is unknown; previously annotated as `axi 1 protein from Nicotiana tabacum - related` based on similarity to axi 1 protein (GB:X80301) (GI:559920) from (Nicotiana tabacum), which, due to scienitific fraud was retracted. Retraction in: Schell J. EMBO J 1999 May 17;18(10):2908. PMID:10400497. 1519 At2g44610 D2 RAB6__Ras-related GTP-binding protein, putative, similar to GTP-binding protein GI:623586 from (Nicotiana tabacum) ; contains an ADP-ribosylation factors family signature for proteins involved in protein trafficking 1520 At2g44620 D1, Dm mtACP-1__acyl carrier protein, mitochondrial / ACP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit, identical to SP:P53665 Acyl carrier protein, mitochondrial precursor (ACP) (NADH- ubiquinone oxidoreductase 9.6 kDa subunit) (MtACP-1) {Arabidopsis thaliana}; identical to cDNA acyl carrier protein precursor GI:468265 1521 At2g44640 D2, Dm expressed protein 1522 At2g44650 D1, Dm CHL-CPN10_CPN10__chloroplast chaperonin 10 (cpn10), identical to chloroplast chaperonin 10 GI:14041813 from (Arabidopsis thaliana) 1523 At2g44860 D2, Dm 60S ribosomal protein L24, putative 1524 At2g44880 Dm pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat 1525 At2g44920 D1, Dm thylakoid lumenal 15 kDa protein, chloroplast, identical to SP:O22160 Thylakoid lumenal 15 kDa protein, chloroplast precursor (p15) {Arabidopsis thaliana}; contains 8 pentapeptide repeats

1526 At2g45070 D1, Dm SEC61 BETA__sec61beta family protein, similar to SP:P52870 Protein transport protein SEC61 beta 1 subunit {Saccharomyces cerevisiae}; contains Pfam profile PF03911: Sec61beta family 1527 At2g45110 Dm ATEXPB4_ATHEXP BETA 1.1_EXPB4__beta-expansin, putative (EXPB4), similar to beta-expansin GI:16517013 from (Oryza sativa); beta-expansin gene family, PMID:11641069 1528 At2g45180 D1, D2, Dm protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, similar to 14 kDa polypeptide (Catharanthus roseus) GI:407410; contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 1529 At2g45190 Dm AFO_FIL_YAB1_FIL_AFO_YAB1_AFO_FIL__axial regulator YABBY1 (YABBY1) / abnormal floral organs protein (AFO) / filamentous flower protein (FIL), identical to YABBY1 (Arabidopsis thaliana) GI:4928749, abnormal floral organs protein (AFO) (Arabidopsis thaliana) GI:4322477; supporting cDNA gi:4322476:gb:AF087015.1:AF087015 1530 At2g45310 D2 GAE4__NAD-dependent epimerase/dehydratase family protein, similar to nucleotide sugar epimerase from Vibrio vulnificus GI:3093975 (PID:g3093975), WbnF (Escherichia coli) GI:5739472, CAPI protein {Staphylococcus aureus} SP:P39858; contains Pfam profile PF01370 NAD dependent epimerase/dehydratase family 1531 At2g45370 D1, Dm 1532 At2g45440 D2 DHDPS2__dihydrodipicolinate synthase 2 (DHDPS2), identical to dihydrodipicolinate synthase 2 (DHDPS2) (Arabidopsis thaliana) GI:11066382 1533 At2g45470 D2, Dm FLA8__fasciclin-like arabinogalactan-protein (FLA8) 1534 At2g45500 Dm similar to spastin ATPase, putative [Arabidopsis thaliana] (TAIR:At3g27120.1); similar to Tobacco mosaic virus helicase domain-binding protein [Nicotiana tabacum] (GB:AAL25088.1); contains InterPro domain AAA ATPase (InterPro:IPR003593); contains InterPro domain AAA ATPase, central region (InterPro:IPR003959) 1535 At2g45510 Dm CYP704A2__cytochrome P450, putative 1536 At2g45570 D2 CYP76C2__cytochrome P450 76C2, putative (CYP76C2) (YLS6), identical to SP:O64637 Cytochrome P450 76C2 (EC 1.14.-.-) {Arabidopsis thaliana}, cDNA YLS6 mRNA for cytochrome P450 (CYP76C2), partial cds GI:13122289 1537 At2g45600 D1, D2, Dm expressed protein, low similarity to PrMC3 (Pinus radiata) GI:5487873 1538 At2g45640 Dm sin3 associated polypeptide p18 family protein, similar to Sin3 associated polypeptide p18 (2HOR0202) (Swiss-Prot:O00422) (Homo sapiens) 1539 At2g45660 D2, Dm AGL20_SOC1__MADS-box protein (AGL20) 1540 At2g45670 D1, D2, Dm calcineurin B subunit-related, contains Pfam PF00036: EF hand domain and Prosite PS00018: EF- hand calcium-binding domain; contains Pfam profile PF01553: Acyltransferase; weak similarity to Calcineurin B subunit isoform 2 (Protein phosphatase 2B regulatory subunit 2) (Protein phosphatase 3 regulatory subunit B alpha isoform 2) (Swiss-Prot:Q63811) (Mus musculus)

1541 At2g45710 D2 40S ribosomal protein S27 (RPS27A) 1542 At2g45790 D1, D2, Dm eukaryotic phosphomannomutase family protein, contains Pfam profile: PF03332 eukaryotic phosphomannomutase 1543 At2g45810 Dm DEAD/DEAH box helicase, putative 1544 At2g45820 D2, Dm DNA-binding protein, putative, identical to DNA-binding protein gi:601843:gb:AAA57124 (Arabidopsis thaliana); contains Pfam domain, PF03766: Remorin, N-terminal region; contains Pfam domain, PF03763: Remorin, C-terminal region 1545 At2g45860 D2, Dm expressed protein 1546 At2g45890 Dm ATROPGEF4__Encodes a member of KPP-like gene family, homolog of KPP (kinase partner protein) gene in tomato. Also a member of the RopGEF (guanine nucleotide exchange factor) family, containing the novel PRONE domain (plant-specific Rop nucleotide exchanger), which is exclusively active towards members of the Rop subfamily. 1547 At2g45950 D2, Dm ASK20__SKP1 family protein, similar to glycoprotein FP21 SP:P52285 from (Dictyostelium discoideum); contains Pfam profile PF01466: Skp1 family, dimerisation domain 1548 At2g45980 D1, Dm expressed protein 1549 At2g45990 D2 expressed protein 1550 At2g46100 D2, Dm expressed protein 1551 At2g46270 Dm GBF3__G-box binding factor 3 (GBF3), identical to G-box binding factor 3 (GBF3) SP:P42776 from (Arabidopsis thaliana); contains Pfam profile: PF00170 bZIP transcription factor 1552 At2g46330 D1, D2, Dm AGP16__arabinogalactan-protein (AGP16), identical to gi:10880509:gb:AAG24284 1553 At2g46390 D2 expressed protein 1554 At2g46550 D2, Dm expressed protein 1555 At2g46610 D1, Dm arginine/serine-rich splicing factor, putative, similar to SP:P92964 Arginine/serine-rich splicing factor RSP31 {Arabidopsis thaliana} 1556 At2g46630 Dm unknown protein 1557 At2g46650 D1, D2, Dm B5 #1__cytochrome b5, putative, similar to cytochome b5 GI:2695711 from (Olea europaea) 1558 At2g46680 D2, Dm ATHB-7_ATHB7__homeobox-leucine zipper protein 7 (HB-7) / HD-ZIP transcription factor 7, identical to homeobox-leucine zipper protein ATHB-7 (HD-ZIP protein ATHB-7) (SP:P46897) (Arabidopsis thaliana); 1559 At2g46690 D1, D2, Dm auxin-responsive family protein, similar to indole-3-acetic acid induced protein ARG7 (SP:P32295) (Phaseolus aureus) 1560 At2g46740 D2, Dm FAD-binding domain-containing protein, strong similarity to At1g32300, At5g56490, At2g46750, At2g46760; contains PF01565: FAD binding domain 1561 At2g46800 D1, D2, Dm ZAT_ATMTP1_MTP1_ZAT1__zinc transporter (ZAT), identical to zinc transporter ZAT (Arabidopsis thaliana) gi:4206640:gb:AAD11757; member of the cation diffusion facilitator (CDF) family, or cation efflux (CE) family, PMID:11500563 1562 At2g46830 D2, Dm CCA1__myb-related transcription factor (CCA1), identical to myb-related transcription factor (CCA1) GI:4090569 from (Arabidopsis thaliana) 1563 At2g46910 D1, D2, Dm plastid-lipid associated protein PAP / fibrillin family protein, contains Pfam profile PF04755: PAP_fibrillin 1564 At2g47180 D2, Dm galactinol synthase, putative, similar to galactinol synthase, isoform GolS-1 GI:5608497 from (Ajuga reptans) 1565 At2g47240 D2, Dm long-chain-fatty-acid--CoA ligase family protein / long-chain acyl-CoA synthetase family protein, similar to GI:1617270 (MF7P) and gi:1617628 (MF45P) from (Brassica napus) ; contains Pfam AMP-binding enzyme domain PF00501 1566 At2g47380 D2 cytochrome c oxidase subunit Vc family protein / COX5C family protein, contains Pfam profile: PF05799 cytochrome c oxidase subunit Vc (COX5C) 1567 At2g47390 D1 expressed protein 1568 At2g47440 D1, D2, Dm DNAJ heat shock N-terminal domain-containing protein, contains Pfam profiles PF00226: DnaJ domain, PF00515: TPR Domain; similar to GP:2104534:AF001308 (T10M13.11) 1569 At2g47510 D2 FUM1__fumarate hydratase, putative / fumarase, putative, similar to SP:P55250 Fumarate hydratase, mitochondrial precursor (EC 4.2.1.2) (Fumarase) {Rhizopus oryzae}; contains Pfam profile PF00206: Lyase 1570 At2g47600 D1, D2, Dm ATMHX_ATMHX1_MHX1__magnesium/proton exchanger (MHX1), identical to magnesium/proton exchanger AtMHX (Arabidopsis thaliana) gi:6492237:gb:AAF14229; Ca2+:Cation Antiporter (CaCA) Family member PMID:11500563 1571 At2g47610 D1, D2, Dm 60S ribosomal protein L7A (RPL7aA) 1572 At2g47710 D1, D2, Dm universal stress protein (USP) family protein, similar to ER6 protein (Lycopersicon esculentum) GI:5669654; contains Pfam profile PF00582: universal stress protein family 1573 At2g47770 D1, D2, Dm benzodiazepine receptor-related, contains weak similarity to Peripheral-type benzodiazepine receptor (PBR) (PKBS) (Mitochondrial benzodiazepine receptor) (Swiss-Prot:P30536) (Homo sapiens) 1574 At2g47810 D1 histone-like transcription factor (CBF/NF-Y) family protein, contains Pfam PF00808 : Histone- like transcription factor (CBF/NF-Y) and archaeal histone; similar to LEC1-like protein (GI:22536010) (Phaseolus coccineus) 1575 At2g47880 D2 glutaredoxin family protein, contains INTERPRO Domain IPR002109, Glutaredoxin (thioltransferase) 1576 At2g47930 D2 hydroxyproline-rich glycoprotein family protein, contains proline-rich extensin domains, INTERPRO:IPR002965 1577 At2g47940 D1, Dm DEGP2__DegP2 protease (DEGP2), identical to DegP2 protease GI:13172275 from (Arabidopsis thaliana); identical to cDNA DegP2 protease (DEGP2) nuclear gene for chloroplast product GI:13172274 1578 At2g48020 Dm sugar transporter, putative, similar to ERD6 protein {Arabidopsis thaliana} GI:3123712, sugar- porter family proteins 1 and 2 (Arabidopsis thaliana) GI:14585699, GI:14585701; contains Pfam profile PF00083: major facilitator superfamily protein 1579 At2g48070 Dm expressed protein 1580 At2g48100 Dm exonuclease family protein, contains Pfam domain PF00929: exonuclease 1581 At2g48140 D1 protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, similar to pEARLI 1 (Accession No. L43080): an Arabidopsis member of a conserved gene family (PGF95-099), Plant Physiol. 109 (4), 1497 (1995); contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 1582 At3g01090 D1, D2, Dm AKIN10__Snf1-related protein kinase (KIN10) (SKIN10), identical to Snf1-related protein kinase, KIN10 SP:Q38997 from (Arabidopsis thaliana) 1583 At3g01100 Dm HYP1_ATHYP1__early-responsive to dehydration protein-related / ERD protein-related, low similarity to ERD4 protein (early-responsive to dehydration stress) (Arabidopsis thaliana) GI:15375406; contains Pfam profile PF02714: Domain of unknown function DUF221 1584 At3g01140 D2, Dm MYB106__similar to myb family transcription factor [Arabidopsis thaliana] (TAIR:At5g15310.1); similar to protein 1 [Petunia x hybrida] (GB:CAA78386.1); contains InterPro domain Myb DNA- binding domain (InterPro:IPR001005) 1585 At3g01150 D2, Dm PTB__polypyrimidine tract-binding protein, putative / heterogeneous nuclear ribonucleoprotein, putative, similar to Polypyrimidine tract-binding protein 1 (PTB) (Heterogeneous nuclear ribonucleoprotein I) (hnRNP I) from {Sus scrofa} SP:Q29099, {Mus musculus} SP:P17225; contains InterPro entry IPR000504: RNA-binding region RNP-1 (RNA recognition motif) (RRM)

1586 At3g01290 D1, D2, Dm band 7 family protein, similar to hypersensitive-induced response protein (Zea mays) GI:7716470; contains Pfam profile PF01145: SPFH domain / Band 7 family 1587 At3g01330 Dm DEL3_E2FF_E2L2__transcription factor, putative / E2F-like repressor E2L2 (E2L2), identical to E2F-like repressor E2L2 (Arabidopsis thaliana) GI:20502506 1588 At3g01450 D2 expressed protein 1589 At3g01470 D1, D2, Dm ATHB-1_ATHB1_HAT5_HD-ZIP-1__homeobox-leucine zipper protein 5 (HAT5) / HD-ZIP protein 5 / HD- ZIP protein (HB-1), identical to homeobox-leucine zipper protein HAT5 (HD-ZIP protein 5) (HD- ZIP protein ATHB-1) GB:Q02283 (Arabidopsis thaliana) 1590 At3g01480 D1, Dm peptidyl-prolyl cis-trans isomerase, putative / cyclophilin, putative / rotamase, putative, similar to peptidyl-prolyl cis-trans isomerase, chloroplast precursor (40 kDa thylakoid lumen PPIase, 40 kDa thylakoid lumen rotamase) (Spinacia oleracea) SWISS-PROT:O49939 1591 At3g01500 D1, Dm CA1__carbonic anhydrase 1, chloroplast / carbonate dehydratase 1 (CA1), nearly identical to SP:P27140 Carbonic anhydrase, chloroplast precursor (EC 4.2.1.1) (Carbonate dehydratase) {Arabidopsis thaliana} 1592 At3g01520 D1, D2, Dm universal stress protein (USP) family protein, similar to ER6 protein (GI:5669654) (Lycopersicon esculentum); contains Pfam profile PF00582: universal stress protein family 1593 At3g01540 D2, Dm DRH1_ATDRH1__DEAD box RNA helicase (DRH1), identical to RNA helicase DRH1 GB:BAA28347 GI:3149952 (Arabidopsis thaliana); contains Pfam profiles PF00270: DEAD/DEAH box helicase, PF00271: Helicase conserved C-terminal domain 1594 At3g01770 Dm DNA-binding bromodomain-containing protein, contains bromodomain, INTERPRO:IPR001487 1595 At3g01910 D1, D2, Dm SOX__sulfite oxidase, putative, similar to sulfite oxidase GB:3212610 SP:P07850 (Gallus gallus), Moco containing protein (Oryza sativa (japonica cultivar-group)) GI:22759584; contains Pfam profiles: PF00174: Oxidoreductase molybdopterin binding domain and PF03404: Mo- co oxidoreductase dimerisation domain 1596 At3g02000 D2, Dm ROXY1__glutaredoxin family protein, contains INTERPRO Domain IPR002109, Glutaredoxin (thioltransferase) 1597 At3g02020 D1, D2, Dm aspartate kinase, lysine-sensitive, putative, similar to aspartate kinase gi:2257743 (Arabidopsis thaliana) 1598 At3g02080 D2, Dm 40S ribosomal protein S19 (RPS19A), similar to 40S ribosomal protein S19 GB:P40978 (Oryza sativa) 1599 At3g02170 D1, D2, Dm expressed protein 1600 At3g02180 D1 SP1L__expressed protein 1601 At3g02190 D1, D2, Dm 60S ribosomal protein L39 (RPL39B), similar to ribosomal protein L39 GB:P51424 (Arabidopsis thaliana) 1602 At3g02230 Dm RGP1_ATRGP_ATRGP1__reversibly glycosylated polypeptide-1 (RGP1), identical to reversibly glycosylated polypeptide-1 (AtRGP) (Arabidopsis thaliana) GI:2317729 1603 At3g02300 D2, Dm regulator of chromosome condensation (RCC1) family protein, weak similarity to UVB-resistance protein UVR8 (Arabidopsis thaliana) GI:5478530; contains Pfam profile PF00415: Regulator of chromosome condensation (RCC1) 1604 At3g02360 D1, D2, Dm 6-phosphogluconate dehydrogenase family protein, contains Pfam profiles: PF00393 6- phosphogluconate dehydrogenase C-terminal domain, PF03446 NAD binding domain of 6- phosphogluconate ;similar to 6-phosphogluconate dehydrogenase GB:BAA22812 GI:2529229 (Glycine max) 1605 At3g02480 D1, D2, Dm ABA-responsive protein-related, similar to ABA-inducible protein (Fagus sylvatica) GI:3901016, cold-induced protein kin1 (Brassica napus) GI:167146 1606 At3g02555 D2 expressed protein 1607 At3g02560 D1, D2, Dm 40S ribosomal protein S7 (RPS7B), similar to ribosomal protein S7 GB:AAD26256 from (Secale cereale) 1608 At3g02570 D2, Dm phosphomannose isomerase type I family protein, contains Pfam profile: PF01238 phosphomannose isomerase type I 1609 At3g02640 D1 expressed protein 1610 At3g02660 Dm tRNA synthetase class I (W and Y) family protein, similar to SP:P00952 Tyrosyl-tRNA synthetase (EC 6.1.1.1) (Tyrosine--tRNA ligase) (TyrRS) {Bacillus stearothermophilus}; contains Pfam profiles PF00579: tRNA synthetases class I (W and Y), PF01479: S4 domain 1611 At3g02730 D2 TRXF1__thioredoxin, putative, similar to SP:P29450 Thioredoxin F-type, chloroplast precursor (TRX-F) {Pisum sativum}; contains Pfam profile: PF00085 Thioredoxin 1612 At3g02770 Dm dimethylmenaquinone methyltransferase family protein, similar to bacterial S- adenosylmethionine:2-demethylmenaquinone methyltransferases; contains Pfam profile PF03737: Dimethylmenaquinone methyltransferase 1613 At3g02790 Dm zinc finger (C2H2 type) family protein, contains Pfam profile: PF00096 zinc finger, C2H2 type 1614 At3g02870 D1, Dm inositol-1(or 4)-monophosphatase, putative / inositol monophosphatase, putative / IMPase, putative, similar to SP:P54928 Inositol-1(or 4)-monophosphatase 3 (EC 3.1.3.25) (IMPase 3) (IMP 3) (Inositol monophosphatase 3) {Lycopersicon esculentum}; contains Pfam profile PF00459: Inositol monophosphatase family 1615 At3g02880 D2, Dm leucine-rich repeat transmembrane protein kinase, putative, contains Pfam profiles: PF00069 Eukaryotic protein kinase domain, PF00560 Leucine Rich Repeat (5 copies) 1616 At3g02900 D1, Dm expressed protein 1617 At3g02910 D1, D2, Dm expressed protein, contains Pfam domain PF03674: Uncharacterised protein family (UPF0131) 1618 At3g02940 D2, Dm MYB107__myb family transcription factor (MYB107), contains Pfam profile: PF00249 Myb-like DNA- binding domain 1619 At3g03000 D2 calmodulin, putative, similar to calmodulin SP:P04352 from (Chlamydomonas reinhardtii); contains Pfam profile: PF00036 EF hand (4 copies) 1620 At3g03150 D1, D2, Dm expressed protein 1621 At3g03170 D2, Dm expressed protein 1622 At3g03200 Dm ANAC045__no apical meristem (NAM) family protein, similar to NAC2 (GI:6456751) {Arabidopsis thaliana} 1623 At3g03270 D1, D2, Dm universal stress protein (USP) family protein / early nodulin ENOD18 family protein, contains Pfam profile PF00582: universal stress protein family; similar to early nodulin ENOD18 (GI:11602747) (Vicia faba) 1624 At3g03330 D2 short-chain dehydrogenase/reductase (SDR) family protein, contains INTERPRO family IPR002198 Short-chain dehydrogenase/reductase (SDR) superfamily 1625 At3g03470 D1, D2, Dm CYP89A9__cytochrome P450, putative, similar to cytochrome P450 89A2 GB:Q42602 (Arabidopsis thaliana) 1626 At3g03480 D1, Dm transferase family protein, similar to hypersensitivity-related gene GB:CAA64636 (Nicotiana tabacum); contains Pfam transferase family domain PF00248 1627 At3g03630 D2 CS26__cysteine synthase, chloroplast, putative / O-acetylserine (thiol)-lyase, putative / O- acetylserine sulfhydrylase, putative, identical to SP:O22682 Probable cysteine synthase, chloroplast precursor {Arabidopsis thaliana}, similar to SP:P31300 Cysteine synthase, chloroplast precursor {Capsicum annuum} 1628 At3g03670 D2, Dm peroxidase, putative, similar to peroxidase GB:CAA66966 (Arabidopsis thaliana) 1629 At3g03790 Dm ankyrin repeat family protein / regulator of chromosome condensation (RCC1) family protein, similar to hect domain and RLD 2 GB:NP_004658 (Homo sapiens); contains Pfam PF00415: Regulator of chromosome condensation (RCC1); contains Pfam PF00023: Ankyrin repeat; similar to rjs (GI:3414809) (Mus musculus); similar to HERC2 (GI:4079809) (Homo sapiens) 1630 At3g03820 D1, D2, Dm auxin-responsive protein, putative, similar to auxin-inducible SAUR (Small Auxin Up RNAs) (GI:3043536) (Raphanus sativus) 1631 At3g03830 D1 auxin-responsive protein, putative, similar to auxin-inducible SAUR (Small Auxin Up RNAs) (GI:3043536) (Raphanus sativus) 1632 At3g03870 D1, D2, Dm expressed protein, predicted using genefinder 1633 At3g03890 D1, Dm expressed protein 1634 At3g03920 D2 Gar1 RNA-binding region family protein, contains Pfam profile PF04410: Gar1 protein RNA binding region 1635 At3g04090 D1 SIP1;1_SIP1A__major intrinsic family protein / MIP family protein, contains Pfam profile: MIP PF00230 1636 At3g04160 D1 expressed protein, ; expression supported by MPSS 1637 At3g04210 D1, D2, Dm disease resistance protein (TIR-NBS class), putative, domain signature TIR-NBS exists, suggestive of a disease resistance protein. 1638 At3g04240 D1, D2, Dm SEC__O-linked N-acetyl glucosamine transferase, putative, similar to O-GlcNAc transferase, Homo sapiens (SP:O15294), Rattus norvegicus (SP:P56558); contains Pfam profile PF00515: TPR Domain; identical to cDNA GI:18139886 1639 At3g04260 D2 SAP domain-containing protein, contains Pfam domain PF02037: SAP domain 1640 At3g04290 D1, D2, Dm GDSL-motif lipase/hydrolase family protein, similar to family II lipases EXL3 GI:15054386, EXL1 GI:15054382, EXL2 GI:15054384 from (Arabidopsis thaliana); contains Pfam profile: lipase/acylhydrolase with GDSL-like motif 1641 At3g04350 D1, Dm expressed protein 1642 At3g04470 D2 similar to ankyrin repeat family protein [Arabidopsis thaliana] (TAIR:At1g04780.1); similar to hypothetical protein [Oryza sativa (japonica cultivar-group)] (GB:XP_477804.1); contains InterPro domain Ankyrin (InterPro:IPR002110) 1643 At3g04630 Dm WDL1__expressed protein 1644 At3g04650 D1, D2, Dm expressed protein 1645 At3g04720 D1 PR4_HEL_PR-4__hevein-like protein (HEL), identical to SP:P43082 Hevein-like protein precursor {Arabidopsis thaliana}; similar to SP:P09762 Wound-induced protein WIN2 precursor {Solanum tuberosum}; contains Pfam profile PF00187: Chitin recognition protein 1646 At3g04760 Dm pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat 1647 At3g04770 D2 RPSAB_P40_AP40_RP40_RPSAA__40S ribosomal protein SA (RPSaB), identical to p40 protein homolog GB:AAB67866 (Arabidopsis thaliana); similar to 40S ribosomal protein SA (P40) GB:O65751 (Cicer arietinum) 1648 At3g04790 D1, D2, Dm ribose 5-phosphate isomerase-related, similar to ribose-5-phosphate isomerase GI:18654317 from (Spinacia oleracea) 1649 At3g04840 D1, D2, Dm 40S ribosomal protein S3A (RPS3aA), similar to 40S ribosomal protein S3A (S phase specific protein GBIS289) GB:P49396 (Brassica rapa) 1650 At3g04910 D1, D2, Dm WNK1_ZIK4__protein kinase family protein, contains protein kinase domain, Pfam:PF00069 1651 At3g04920 D2, Dm 40S ribosomal protein S24 (RPS24A), similar to ribosomal protein S19 GB:445612 (Solanum tuberosum) and similar to ribosomal protein S24 GB:4506703 (Homo sapiens) 1652 At3g05020 D1, Dm ACP1_ACP__acyl carrier protein 1, chloroplast (ACP-1), identical to SP:P11829 Acyl carrier protein 1, chloroplast precursor (ACP) {Arabidopsis thaliana} 1653 At3g05030 Dm NHX2_ATNHX2__sodium proton exchanger, putative (NHX2), similar to sodium proton exchanger Nhx1 GB:AAD16946 (Arabidopsis thaliana); Member of The Monovalent Cation:Proton Antiporter (CPA1) Family, PMID:11500563 1654 At3g05060 D2, Dm SAR DNA-binding protein, putative, strong similarity to SAR DNA-binding protein-1 (Pisum sativum) GI:3132696; contains Pfam profile PF01798: Putative snoRNA binding domain; encodes NOP58-like protein 1655 At3g05100 Dm expressed protein 1656 At3g05140 Dm protein kinase family protein, contains protein kinase domain, Pfam:PF00069 1657 At3g05160 D1, D2, Dm sugar transporter, putative, similar to sugar-porter family proteins 1 and 2 (Arabidopsis thaliana) GI:14585699, GI:14585701; contains Pfam profile PF00083: major facilitator superfamily protein 1658 At3g05165 D1, Dm sugar transporter, putative, similar to sugar-porter family proteins 1 and 2 (Arabidopsis thaliana) GI:14585699, GI:14585701; contains Pfam profile PF00083: major facilitator superfamily protein 1659 At3g05220 D2 heavy-metal-associated domain-containing protein, similar to farnesylated protein 1 (GI:23304411) {Hordeum vulgare subsp. spontaneum}; contains Pfam profile PF00403: Heavy-metal- associated domain 1660 At3g05330 Dm cyclin family, low similarity to microtubule-binding protein TANGLED1 (Zea mays) GI:11228986; contains Pfam profile PF00134: Cyclin, N-terminal domain 1661 At3g05560 D1, D2, Dm 60S ribosomal protein L22-2 (RPL22B), identical to 60S ribosomal protein L22-2 SP:Q9M9W1 from (Arabidopsis thaliana) 1662 At3g05590 D1, D2, Dm RPL18__60S ribosomal protein L18 (RPL18B), similar to GB:P42791 1663 At3g05600 Dm epoxide hydrolase, putative, similar to epoxide hydrolase from (Glycine max) GI:2764806, (Arabidopsis thaliana) GI:1109600; contains Pfam profile PF00561: hydrolase, alpha/beta fold family 1664 At3g05640 D1, D2, Dm protein phosphatase 2C, putative / PP2C, putative, similar to protein phosphatase-2C GB:AAC36699 from (Mesembryanthemum crystallinum) 1665 At3g05730 D1, Dm Encodes a defensin-like (DEFL) family protein. 1666 At3g05880 D1, D2, Dm RCI2A__hydrophobic protein (RCI2A) / low temperature and salt responsive protein (LTI6A), identical to SP:Q9ZNQ7 Hydrophobic protein RCI2A (Low temperature and salt responsive protein LTI6A) {Arabidopsis thaliana} 1667 At3g05910 D1, D2, Dm pectinacetylesterase, putative, similar to pectinacetylesterase precursor GI:1431629 from (Vigna radiata) 1668 At3g06100 Dm major intrinsic family protein / MIP family protein, contains Pfam profile: PF00230 major intrinsic protein; contains non-consensus TT acceptor splice site at exon 4 1669 At3g06130 D2, Dm heavy-metal-associated domain-containing protein, contains Pfam heavy metal associated domain PF00403 1670 At3g06170 D1 TMS membrane family protein / tumour differentially expressed (TDE) family protein, contains Pfam domain, PF03348: TMS membrane protein/tumour differentially expressed protein (TDE) 1671 At3g06250 D2 far-red impaired responsive protein, putative, similar to far-red impaired response protein FAR1 (Arabidopsis thaliana) gi:5764395:gb:AAD51282; contains Pfam:PF03101 domain: FAR1 family

1672 At3g06320 D2 ribosomal protein L33 family protein, similar to 50S ribosomal protein L33 GB:Q9ZC89 (Rickettsia prowazekii) 1673 At3g06380 Dm F-box family protein / tubby family protein, similar to phosphodiesterase (GI:467578) (Mus musculus); similar to C-terminal half of tubby protein (A mutation in the tub gene causes maturity-onset obesity, insulin resistance, and sensory deficits) (GB:P50586) (GI:6730158)(Mus musculus); contains Pfam PF00646: F-box domain and Pfam PF01167: Tub family; similar to Tubby protein homolog (Swiss-Prot:O88808) (Rattus norvegicus) 1674 At3g06420 D2, Dm autophagy 8h (APG8h), identical to autophagy 8h (Arabidopsis thaliana) GI:19912165; contains Pfam profile PF02991: Microtubule associated protein 1A/1B, light chain 3; supporting cDNA gi:19912164:dbj:AB073182.1: 1675 At3g06510 D2, Dm SFR2__glycosyl hydrolase family 1 protein, similar to Beta-galactosidase (SP:P22498) (Sulfolobus solfataricus}; almost identical to beta-glucosidase GB:AAF23823 GI:6685165 from (Arabidopsis thaliana) 1676 At3g06530 D2 BAP28-related, similar to Protein BAP28 (Swiss-Prot:Q9H583) (Homo sapiens) 1677 At3g06650 D1 ACLB-1__ATP-citrate synthase, putative / ATP-citrate (pro-S-)-lyase, putative / citrate cleavage enzyme, putative, strong similarity to ATP:citrate lyase (Capsicum annuum) GI:13160653; contains Pfam profiles PF00549: CoA-ligase, PF02629: CoA binding domain 1678 At3g06680 D1, D2, Dm 60S ribosomal protein L29 (RPL29B), similar to 60S ribosomal protein L29 GB:P25886 from (Rattus norvegicus) 1679 At3g06690 D2 acyl-CoA oxidase family, similar to acyl-CoA oxidase (Arabidopsis thaliana) GI:8515709, acyl- CoA oxidase ACX3 (Arabidopsis thaliana) GI:8163758; contains Pfam profile PF01756: Acyl-CoA oxidase 1680 At3g06700 D1, D2, Dm 60S ribosomal protein L29 (RPL29A), similar to ribosomal protein L29 GI:7959366 (Panax ginseng) 1681 At3g06730 D2, Dm thioredoxin family protein, contains Pfam profile: PF00085 Thioredoxin 1682 At3g06770 D1, D2, Dm glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family protein, weak similarity to polygalacturonase (Persea americana) GI:166951; contains PF00295: Glycosyl hydrolases family 28 (polygalacturonases) 1683 At3g06860 D1, D2, Dm MFP2_ATMPF2__fatty acid multifunctional protein (MFP2), identical to fatty acid multifunctional protein (AtMFP2) GB:AF123254 (gi:4337027) (Arabidopsis thaliana) (fatty acid beta-oxidation); contains Pfam profiles PF02737 (3-hydroxyacyl-CoA dehydrogenase, NAD binding domain), PF00378 (enoyl-CoA hydratase/isomerase family protein), PF00725 (3-hydroxyacyl-CoA dehydrogenase) 1684 At3g06930 D2 protein arginine N-methyltransferase family protein, similar to protein arginine methyltransferase (Mus musculus) GI:5257221 1685 At3g06980 D1, D2, Dm DEAD/DEAH box helicase, putative, contains Pfam profile: PF00270 DEAD/DEAH box helicase 1686 At3g07010 D1, D2, Dm pectate lyase family protein, similar to pectate lyase GP:14531296 from (Fragaria x ananassa)

1687 At3g07050 D2 GTP-binding family protein, contains Pfam domain, PF01926: GTPase of unknown function 1688 At3g07100 D1 protein transport protein Sec24, putative, similar to protein transport protein Sec24A (SEC24- related protein) (Homo sapiens) SWISS-PROT:O95486 1689 At3g07110 D1, D2, Dm 60S ribosomal protein L13A (RPL13aA), similar to ribosomal protein L13A GB:O49885 (Lupinus luteus) 1690 At3g07190 D2 expressed protein 1691 At3g07310 D1, D2, Dm expressed protein 1692 At3g07350 D2 expressed protein, contains Pfam profile PF04720: Protein of unknown function (DUF506) 1693 At3g07360 D1, D2, Dm armadillo/beta-catenin repeat family protein / U-box domain-containing protein, contains Pfam domain, PF00514: Armadillo/beta-catenin-like repeats and Pfam, PF04564: U-box domain 1694 At3g07430 D1, D2, Dm EMB1990__YGGT family protein, contains Pfam profile PF02325: YGGT family (unknown function) 1695 At3g07460 D1, D2, Dm expressed protein, contains Pfam profile PF04398: Protein of unknown function, DUF538 1696 At3g07470 D1, D2, Dm expressed protein, contains Pfam profile PF04398: Protein of unknown function, DUF538 1697 At3g07540 Dm formin homology 2 domain-containing protein / FH2 domain-containing protein, contains formin homology 2 domain, Pfam:PF02181 1698 At3g07560 D1 glycine-rich protein 1699 At3g07680 D1, Dm emp24/gp25L/p24 family protein, similar to SP:Q15363 Cop-coated vesicle membrane protein p24 precursor (p24A) {Homo sapiens}; contains Pfam profile PF01105: emp24/gp25L/p24 family 1700 At3g07700 D1, D2, Dm ABC1 family protein, contains Pfam domain, PF03109: ABC1 family 1701 At3g07770 D2 heat shock protein-related, strong similarity to heat-shock protein (Secale cereale) GI:556673; contains Pfam profiles PF02518: ATPase, histidine kinase-, DNA gyrase B-, and HSP90-like domain protein, PF00183: Hsp90 protein 1702 At3g07910 D2 expressed protein 1703 At3g08000 D2, Dm RNA-binding protein, putative, similar to RNA-binding protein from (Nicotiana tabacum) GI:15822703, (Nicotiana sylvestris) GI:624925; contains Pfam profile: PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 1704 At3g08580 D1, Dm AAC1__ADP, ATP carrier protein 1, mitochondrial / ADP/ATP translocase 1 / adenine nucleotide translocator 1 (ANT1), identical to SWISS-PROT:P31167 ADP,ATP carrier protein 1 (Adenine nucleotide translocator 1) (Arabidopsis thaliana) 1705 At3g08590 D1, D2, Dm 2,3-biphosphoglycerate-independent phosphoglycerate mutase, putative / phosphoglyceromutase, putative, strong similarity to SP:Q42908 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.1) (Phosphoglyceromutase) {Mesembryanthemum crystallinum}; contains Pfam profile PF01676: Metalloenzyme superfamily 1706 At3g08610 D2 expressed protein 1707 At3g08700 D1, D2, Dm ubiquitin-conjugating enzyme, putative, strong similar to ubiquitin-conjugating enzymes E2-17 from (Arabidopsis thaliana) SP:P35134, SP:P35132, SP:P35133; contains Pfam profile PF00179: Ubiquitin-conjugating enzyme 1708 At3g08740 D1, Dm elongation factor P (EF-P) family protein, similar to SP:P33398 Elongation factor P (EF-P) {Escherichia coli O157:H7}; contains Pfam profile PF01132: Elongation factor P (EF-P) 1709 At3g08910 Dm DNAJ heat shock protein, putative, similar to SP:P25685 DnaJ homolog subfamily B member 1 (Heat shock 40 kDa protein 1) {Homo sapiens}; contains Pfam profile PF00226: DnaJ domain 1710 At3g08920 D1, Dm rhodanese-like domain-containing protein, contains rhodanese-like domain PF:00581 1711 At3g08950 D2, Dm electron transport SCO1/SenC family protein, similar to SP:P23833 SCO1 protein, mitochondrial precursor {Saccharomyces cerevisiae}; contains Pfam profile PF02630: SCO1/SenC 1712 At3g08970 D1 DNAJ heat shock N-terminal domain-containing protein, low similarity to PIR:A47079:A47079 heat shock protein dnaJ - Lactococcus lactis; contains Pfam profile PF00226 DnaJ domain 1713 At3g09200 D1, D2, Dm 60S acidic ribosomal protein P0 (RPP0B), similar to putative 60S acidic ribosomal protein P0 GB:P50346 (Glycine max) 1714 At3g09210 D1, D2, Dm KOW domain-containing transcription factor family protein, ; est match 1715 At3g09350 D2, Dm armadillo/beta-catenin repeat family protein, contains Pfam profile: PF00514 armadillo/beta- catenin-like repeat 1716 At3g09390 D1, D2, Dm MT2A_ATMT-1_ATMT-K_MT2__metallothionein protein, putative (MT2A), identical to Swiss- Prot:P25860 metallothionein-like protein 2A (MT-2A) (MT-K) (MT-1G) (Arabidopsis thaliana) 1717 At3g09440 D1, D2, Dm heat shock cognate 70 kDa protein 3 (HSC70-3) (HSP70-3), identical to SP:O65719 Heat shock cognate 70 kDa protein 3 (Hsc70.3) {Arabidopsis thaliana} 1718 At3g09450 D2, Dm expressed protein 1719 At3g09480 D1, Dm histone H2B, putative, similar to histone from Arabidopsis thaliana GI:2407802, Gossypium hirsutum SP:O22582, H2B-3 GB:CAA12231 from (Lycopersicon esculentum); contains Pfam profile PF00125 Core histone H2A/H2B/H3/H4 1720 At3g09580 D1, Dm amine oxidase family protein, low similarity to SP:P28553 Phytoene dehydrogenase, chloroplast precursor (Phytoene desaturase) from Glycine max; contains Pfam profile PF01593 amine oxidase, flavin-containing 1721 At3g09630 D1, Dm 60S ribosomal protein L4/L1 (RPL4A), strong similarity to 60S ribosomal protein L1 GB:P49691 1722 At3g09680 D1, Dm 40S ribosomal protein S23 (RPS23A), similar to 40S ribosomal protein S23 (S12) GB:P46297 from (Fragaria x ananassa) 1723 At3g09770 D1, D2, Dm zinc finger (C3HC4-type RING finger) family protein, contains Pfam domain, PF00097: Zinc finger, C3HC4 type (RING finger) 1724 At3g09840 D1, D2, Dm CDC48_ATCDC48_CDC48A__cell division cycle protein 48 (CDC48A) (CDC48), identical to SP:P54609 Cell division cycle protein 48 homolog {Arabidopsis thaliana} 1725 At3g10020 D1, D2, Dm expressed protein 1726 At3g10060 D1 immunophilin, putative / FKBP-type peptidyl-prolyl cis-trans isomerase, putative, Pfam:PF-254: FKBP-type peptidyl-prolyl cis-trans isomerases 1727 At3g10080 D1 germin-like protein, putative, similar to germin-like protein 2 (Oryza sativa) GI:2655287 1728 At3g10090 D1, D2, Dm 40S ribosomal protein S28 (RPS28A), similar to ribosomal protein S28 GB:P34789 (Arabidopsis thaliana) 1729 At3g10120 D2 expressed protein 1730 At3g10130 D2, Dm SOUL heme-binding family protein, weak similarity to heme-binding protein (Homo sapiens) GI:4886908; contains Pfam profile PF04832: SOUL heme-binding protein 1731 At3g10250 D2, Dm expressed protein 1732 At3g10270 D1, D2, Dm Protein targeting to mitochondria is influenced by UTR sequences. 1733 At3g10340 D2, Dm phenylalanine ammonia-lyase, putative, similar to phenylalanine ammonia-lyase GB:S48726 (Petroselinum crispum) 1734 At3g10410 D1, D2, Dm SCPL49__serine carboxypeptidase III, putative, similar to serine carboxypeptidase III from Oryza sativa SP:P37891, Matricaria chamomilla GI:6960455, Hordeum vulgare SP:P21529, Triticum aestivum SP:P11515; contains Pfam profile PF0450 serine carboxypeptidase 1735 At3g10520 D1, D2, Dm AHB2_ARATH GLB2_GLB2_NSHB2__non-symbiotic hemoglobin 2 (HB2) (GLB2), identical to SP:O24521 Non-symbiotic hemoglobin 2 (Hb2) (ARAth GLB2) {Arabidopsis thaliana} 1736 At3g10530 D2 transducin family protein / WD-40 repeat family protein, contains 2 WD-40 repeats (PF00400); BING4 (gi:3811380) {Mus musculus); similar to hypothetical protein GB:P40055 (Saccharomyces cerevisiae) 1737 At3g10610 D1, D2, Dm 40S ribosomal protein S17 (RPS17C), similar to 40S ribosomal protein S17 GB:AAD50774 (Lycopersicon esculentum) 1738 At3g10720 Dm pectinesterase, putative, contains similarity to pectinesterase from Vitis vinifera GI:15081598, Prunus persica SP:Q43062; contains Pfam profile PF01095 pectinesterase 1739 At3g10730 D2 sad1/unc-84-like 2 family protein, contains 1 transmembrane domain; similar to Sad1 unc-84 domain protein 2 (GI:6538749) (Homo sapiens); similar to Sad1/unc-84-like protein 2 (Fragment) (Swiss-Prot:Q9UH99) (Homo sapiens) 1740 At3g10770 D1, D2, Dm expressed protein 1741 At3g10800 Dm bZIP transcription factor family protein, contains Pfam profile: PF00170 bZIP transcription factor; contains similarity to TGACG-sequence specific DNA-binding protein TGA-1B (HSBF) GB:P14233 (Nicotiana tabacum) 1742 At3g10940 D2, Dm protein phosphatase-related, similar to protein phosphatase PTPKIS1 protein (GI:11595504) (Arabidopsis thaliana) 1743 At3g10950 D1, D2, Dm 60S ribosomal protein L37a (RPL37aB), similar to putative 60S ribosomal protein L37a GB:AAD28753 (Gossypium hirsutum) 1744 At3g10970 D2, Dm haloacid dehalogenase-like hydrolase family protein, low similarity to genetic modifier (Zea mays) GI:10444400; contains InterPro accession IPR005834: Haloacid dehalogenase-like hydrolase

1745 At3g10980 D2 SAG20_ATWI-12_WI12__expressed protein 1746 At3g11250 D1, Dm 60S acidic ribosomal protein P0 (RPP0C), similar to 60S acidic ribosomal protein P0 GI:2088654 (Arabidopsis thaliana) 1747 At3g11320 D2 similar to phosphate translocator-related [Arabidopsis thaliana] (TAIR:At5g05820.1); similar to Putative phosphate/phosphoenolpyruvate translocator protein [Oryza sativa (japonica cultivar-group)] (GB:XP_470662.1) 1748 At3g11410 D1, D2, Dm protein phosphatase 2C, putative / PP2C, putative, identical to protein phosphatase 2C (PP2C) GB:P49598 (Arabidopsis thaliana); contains Pfam profile PF00481: Protein phosphatase 2C; identical to cDNA protein phosphatase 2C GI:633027 1749 At3g11420 D1, D2, Dm fringe-related protein, similar to hypothetical protein GB:AAC23643 (Arabidopsis thaliana) + weak similarity to Fringe (Schistocerca gregaria)(GI:6573138);Fringe encodes an extracellular protein that regulates Notch signalling. 1750 At3g11450 D2 DNAJ heat shock N-terminal domain-containing protein / cell division protein-related, similar to GlsA (Volvox carteri f. nagariensis) GI:4633129; contains Pfam profiles PF00226 DnaJ domain, PF00249 Myb-like DNA-binding domain 1751 At3g11560 D2 expressed protein 1752 At3g11670 D1, Dm DGD1__digalactosyldiacylglycerol synthase 1 (DGD1) / MGDG:MGDG galactosyltransferase / galactolipid galactosyltransferase, identical to digalactosyldiacylglycerol synthase (DGD1) GI:5354158 (Arabidopsis thaliana) 1753 At3g11690 D1, D2, Dm expressed protein 1754 At3g11700 D1, D2, Dm beta-Ig-H3 domain-containing protein / fasciclin domain-containing protein, contains Pfam profile PF02469: Fasciclin domain 1755 At3g11710 D2, Dm lysyl-tRNA synthetase, putative / lysine--tRNA ligase, putative, similar to SP:Q43776 Lysyl- tRNA synthetase (EC 6.1.1.6) (Lysine--tRNA ligase) {Lycopersicon esculentum}; contains Pfam profile PF00152: tRNA synthetases class II (D, K and N) 1756 At3g11730 Dm ATFP8__Ras-related GTP-binding protein, putative, similar to Rab1-like small GTP-binding protein GI:4096662 from (Petunia x hybrida) 1757 At3g11830 D2 chaperonin, putative, similar to SWISS-PROT:P80313 T-complex protein 1, eta subunit (TCP-1- eta) (Mus musculus); contains Pfam:PF00118 domain, TCP-1/cpn60 chaperonin family 1758 At3g11910 Dm ubiquitin-specific protease, putative, strong similarity to ubiquitin-specific protease 12 (UBP12) (Arabidopsis thaliana) GI:11993471; contains Pfam profiles PF00443: Ubiquitin carboxyl-terminal hydrolase, PF00917: MATH domain 1759 At3g11930 D1 universal stress protein (USP) family protein, similar to ER6 protein GB:AAD46412 GI:5669654 from (Lycopersicon esculentum); contains Pfam profile PF00582: universal stress protein family

1760 At3g11940 D1, Dm ATRPS5A_AML1__40S ribosomal protein S5 (RPS5B), similar to 40S ribosomal protein S5 GB:AAC98068 GI:4056502 from (Arabidopsis thaliana) 1761 At3g12110 D1, D2, Dm ACT11__actin 11 (ACT11), identical to SP:P53496 Actin 11 {Arabidopsis thaliana} 1762 At3g12120 D2, Dm FAD2__omega-6 fatty acid desaturase, endoplasmic reticulum (FAD2) / delta-12 desaturase, identical to omega-6 fatty acid desaturase, endoplasmic reticulum (FAD2) SP:P46313 (Arabidopsis thaliana (Mouse-ear cress)) (Plant Cell 6:147-158(1994)) 1763 At3g12145 D1, D2, Dm FLR1_FLOR1__polygalacturonase inhibitor, putative / leucine-rich repeat protein (FLR1), similar to Swiss-Prot:Q05091 polygalacturonase inhibitor precursor (Polygalacturonase- inhibiting protein) (Pyrus communis); identical to leucine-rich repeat protein FLR1 (FLR1) cDNA NCBI_gi:7637422; contains Pfam domain PF00560 Leucine Rich Repeat 1764 At3g12210 D1, Dm expressed protein 1765 At3g12270 D2 protein arginine N-methyltransferase family protein, similar to protein arginine N- methyltransferase 3 from {Rattus norvegicus} SP:O70467, {Homo sapiens} SP:O60678 1766 At3g12320 D2 expressed protein 1767 At3g12360 D2 ankyrin repeat family protein, contains ankyrin repeat domains, Pfam:PF00023 1768 At3g12490 D1, D2, Dm similar to cysteine protease inhibitor, putative / cystatin, putative [Arabidopsis thaliana] (TAIR:At5g05110.1); similar to cysteine protease inhibitor CPI-1 [Brassica oleracea] (GB:AAL59842.1); contains InterPro domain Cystatin C/M (InterPro:IPR003243); contains InterPro domain Cysteine protease inhibitor (InterPro:IPR000010) 1769 At3g12570 Dm expressed protein 1770 At3g12580 D1, D2, Dm HSP70__heat shock protein 70, putative / HSP70, putative, strong similarity to heat shock protein GI:425194 (Spinacia oleracea) 1771 At3g12600 D1, Dm ATNUDT16__MutT/nudix family protein, contains Pfam profile PF00293: NUDIX domain 1772 At3g12610 D1, D2, Dm DRT100__DNA-damage-repair/toleration protein, putative (DRT100), similar to DNA-damage- repair/toleration protein DRT100 (Precursor) SWISS-PROT:Q00874, NCBI_gi:5701788; contains multiple LRR repeats Pfam profile: PF00560 1773 At3g12630 D2 zinc finger (AN1-like) family protein, contains Pfam domain, PF01428: AN1-like Zinc finger 1774 At3g12850 D2 COP9 signalosome complex-related / CSN complex-related, low similarity to SP:P45432 COP9 signalosome complex subunit 1 (CSN complex subunit 1) (COP11 protein) (FUSCA protein FUS6) {Arabidopsis thaliana} 1775 At3g12930 D1, D2, Dm expressed protein, contains Pfam domain PF02410: Domain of unknown function DUF143 1776 At3g12960 Dm expressed protein, similar to seed maturation protein PM28 GB:AAD30427 from (Glycine max) 1777 At3g13070 D2, Dm CBS domain-containing protein / transporter associated domain-containing protein, similar to SP:Q54318 Hemolysin C (Serpulina hyodysenteriae) {Treponema hyodysenteriae}; contains Pfam profiles PF00571: CBS domain, PF03471: Transporter associated domain, PF01595: Domain of unknown function 1778 At3g13080 D2 EST2_ATMRP3_MRP3__ABC transporter family protein, almost identical to MRP-like ABC transporter GI:2316016 from (Arabidopsis thaliana); contains Pfam profile: PF00005 ABC transporter

1779 At3g13120 D1, D2, Dm 30S ribosomal protein S10, chloroplast, putative, similar to 30S ribosomal protein S10 GB:P02364 (Escherichia coli) (est matches suggest the N-terminal extension) 1780 At3g13140 D2, Dm hydroxyproline-rich glycoprotein family protein 1781 At3g13180 D1, Dm NOL1/NOP2/sun family protein / antitermination NusB domain-containing protein, low similarity to SP:P36929 SUN protein (FMU protein) {Escherichia coli}; contains Pfam profiles PF01189: NOL1/NOP2/sun family, PF01029: NusB family 1782 At3g13230 D2 expressed protein 1783 At3g13270 D2 expressed protein, contains similarity to replication protein A1 1784 At3g13340 D2, Dm WD-40 repeat family protein, contains Pfam profile: PF00400 WD domain, G-beta repeat (3 copies, 1 significant); similar to Trp-Asp repeat protein (PIR:T40094) (Schizosaccharomyces) 1785 At3g13470 D1, D2, Dm chaperonin, putative, similar SWISS-PROT:P21240- RuBisCO subunit binding-protein beta subunit, chloroplast precursor (60 kDa chaperonin beta subunit, CPN-60 beta) (Arabidopsis thaliana); contains Pfam:PF00118 domain, TCP-1/cpn60 chaperonin family 1786 At3g13520 D2, Dm AGP12__arabinogalactan-protein (AGP12), identical to gi:10880501:gb:AAG24280 1787 At3g13560 D2, Dm glycosyl hydrolase family 17 protein, similar to beta-1,3-glucanase GI:15150341 from (Camellia sinensis) 1788 At3g13670 D2 protein kinase family protein, contains Pfam domains, PF00069: Protein kinase domain 1789 At3g13672 D1, D2, Dm seven in absentia (SINA) family protein, low similarity to SP:P21461 Developmental protein seven in absentia {Drosophila melanogaster}; contains Pfam profile PF03145: Seven in absentia protein family 1790 At3g13720 D2, Dm prenylated rab acceptor (PRA1) family protein, contains Pfam profile PF03208: Prenylated rab acceptor (PRA1) 1791 At3g13750 D1, D2, Dm BGAL1__beta-galactosidase, putative / lactase, putative, similar to beta-galactosidase precursor SP:P48980 from (Lycopersicon esculentum) 1792 At3g13920 Dm EIF4A1_RH4_TIF4A1_EIF4A-2__eukaryotic translation initiation factor 4A-1 / eIF-4A-1, eIF-4A-1 gi:15293046, gi:15450485; contains Pfam profile PF00270: DEAD/DEAH box helicase; contains Pfam profile PF00271: Helicase conserved C-terminal domain 1793 At3g13930 D1, D2, Dm dihydrolipoamide S-acetyltransferase, putative, similar to dihydrolipoamide S- acetyltransferase (Zea mays) GI:5669871; contains Pfam profiles PF00198: 2-oxo acid dehydrogenases acyltransferase (catalytic domain), PF00364: Biotin-requiring enzyme, PF02817: e3 binding domain 1794 At3g13970 Dm autophagy 12b (APG12b), identical to autophagy 12b (Arabidopsis thaliana), gi:19912171:dbj:BAB88397 1795 At3g14110 D1, Dm FLU__tetratricopeptide repeat (TPR)-containing protein, contains Pfam profile PF00515: TPR Domain 1796 At3g14150 D2 (S)-2-hydroxy-acid oxidase, peroxisomal, putative / glycolate oxidase, putative / short chain alpha-hydroxy acid oxidase, putative, similar to (S)-2-hydroxy-acid oxidase, peroxisomal (Glycolate oxidase, GOX) (Short chain alpha-hydroxy acid oxidase) (Spinacia oleracea) SWISS- PROT:P05414 1797 At3g14220 D1 GDSL-motif lipase/hydrolase family protein, similar to myrosinase-associated proteins GI:1769968, GI:1769970 from (Brassica napus); contains InterPro Entry IPR001087 Lipolytic enzyme, G-D-S-L family; contains 1 predicted transmembrane domain; 1798 At3g14230 Dm RAP2.2__encodes a member of the ERF (ethylene response factor) subfamily B-2 of ERF/AP2 transcription factor family (RAP2.2). The protein contains one AP2 domain. There are 5 members in this subfamily including RAP2.2 AND RAP2.12. 1799 At3g14240 D1, Dm subtilase family protein, contains similarity to SBT1 GI:1771160 from (Lycopersicon esculentum) 1800 At3g14280 D2, Dm expressed protein 1801 At3g14310 D1, D2, Dm ATPME3__pectinesterase family protein, contains Pfam profiles: PF01095 pectinesterase, PF04043 plant invertase/pectin methylesterase inhibitor ;similar to pectin methylesterase GB:Q42534 from (Arabidopsis thaliana) 1802 At3g14360 D1, Dm lipase class 3 family protein, low similarity to Chain A, Lipase Ii From Rhizopus Niveus GI:1942798; contains Pfam profile PF01764: Lipase 1803 At3g14415 D1 (S)-2-hydroxy-acid oxidase, peroxisomal, putative / glycolate oxidase, putative / short chain alpha-hydroxy acid oxidase, putative, similar to (S)-2-hydroxy-acid oxidase, peroxisomal (Glycolate oxidase, GOX) (Short chain alpha-hydroxy acid oxidase) (Spinacia oleracea) SWISS- PROT:P05414 1804 At3g14420 Dm (S)-2-hydroxy-acid oxidase, peroxisomal, putative / glycolate oxidase, putative / short chain alpha-hydroxy acid oxidase, putative, similar to (S)-2-hydroxy-acid oxidase, peroxisomal (Glycolate oxidase, GOX) (Short chain alpha-hydroxy acid oxidase) (Spinacia oleracea) SWISS- PROT:P05414 1805 At3g14430 D1, D2, Dm expressed protein 1806 At3g14440 D2, Dm NCED3_ATNCED3_STO1__9-cis-epoxycarotenoid dioxygenase, putative / neoxanthin cleavage enzyme, putative / carotenoid cleavage dioxygenase, putative, similar to 9-cis-epoxycarotenoid dioxygenase GB:AAF26356 (GI:6715257)(Phaseolus vulgaris) 1807 At3g14560 D1, D2, Dm expressed protein 1808 At3g14640 D2, Dm CYP72A10__cytochrome P450, putative, similar to GB:Q05047 from (Catharanthus roseus) 1809 At3g14650 Dm CYP72A11__cytochrome P450, putative, similar to GB:Q05047 from (Catharanthus roseus) 1810 At3g14690 D1, Dm CYP72A15__cytochrome P450, putative, similar to GB:Q05047 from (Catharanthus roseus) 1811 At3g14750 D1 expressed protein, weak similarity to Septation ring formation regulator (Swiss-Prot:O34894) (Bacillus subtilis) 1812 At3g14840 D1, D2, Dm leucine-rich repeat family protein / protein kinase family protein, contains Pfam domains PF00560: Leucine Rich Repeat and PF00069: Protein kinase domain; contains 2 predicted transmembrane domains 1813 At3g14850 D1 expressed protein, similar to expressed protein [Arabidopsis thaliana] (TAIR:At1g29050.1); similar to unknown protein [Oryza sativa (japonica cultivar-group)] (GB:BAD73054.1); similar to unknown protein [Oryza sativa (japonica cultivar-group)] (GB:BAD73055.1); contains InterPro domain Protein of unknown function DUF231 (InterPro:IPR004253) 1814 At3g14900 Dm expressed protein 1815 At3g14930 D1, Dm uroporphyrinogen decarboxylase, putative / UPD, putative, similar to uroporphyrinogen decarboxylase (chloroplast) from Nicotiana tabacum (SP:Q42967), Hordeum vulgare (SP:Q42855), Zea mays (SP:O81220); contains Pfam domain uroporphyrinogen decarboxylase (URO-D) PF01208 1816 At3g14940 D2 ATPPC3_PPCK1__phosphoenolpyruvate carboxylase, putative / PEP carboxylase, putative, strong similarity to SP:P29196 Phosphoenolpyruvate carboxylase (EC 4.1.1.31) (PEPCASE) {Solanum tuberosum}; contains Pfam profile PF00311: phosphoenolpyruvate carboxylase 1817 At3g15020 D1, Dm malate dehydrogenase (NAD), mitochondrial, putative, similar to mitochondrial NAD-dependent malate dehydrogenase GB:CAA10320 SP:Q9ZP06 (Arabidopsis thaliana); contains InterPro entry IPR001236: Lactate/malate dehydrogenase 1818 At3g15210 D2, Dm ATERF4_ATERF-4_ERF4_RAP2.5__Encodes a member of the ERF (ethylene response factor) subfamily B-1 of ERF/AP2 transcription factor family (ATERF-4). The protein contains one AP2 domain. Acts as a negative regulator of JA-responsive defense gene expression and resistance to the necrotrophic fungal pathogen Fusarium oxysporum and antagonizes JA inhibition of root elongation. 1819 At3g15290 D2 3-hydroxybutyryl-CoA dehydrogenase, putative, similar to S(+)-beta-hydroxybutyryl CoA dehydrogenase (3-hydroxybutyryl-CoA dehydrogenase) (Paracoccus denitrificans) GI:12003356; contains Pfam profiles PF02737: 3-hydroxyacyl-CoA dehydrogenase NAD binding, PF00725: 3- hydroxyacyl-CoA dehydrogenase C-terminal 1820 At3g15350 D1, D2, Dm glycosyltransferase family 14 protein / core-2/I-branching enzyme family protein, contains Pfam profile: PF02485 Core-2/I-Branching enzyme 1821 At3g15353 Dm MT3__metallothionein protein, putative 1822 At3g15360 D2 ATHM4__thioredoxin M-type 4, chloroplast (TRX-M4), nearly identical to SP:Q9SEU6 Thioredoxin M-type 4, chloroplast precursor (TRX-M4) {Arabidopsis thaliana} 1823 At3g15450 D1, D2, Dm expressed protein, similar to auxin down-regulated protein ARG10 (Vigna radiata) GI:2970051, wali7 (aluminum-induced protein) (Triticum aestivum) GI:451193 1824 At3g15480 D2, Dm expressed protein 1825 At3g15530 D1, Dm expressed protein 1826 At3g15630 D1, D2, Dm expressed protein 1827 At3g15640 D1, Dm cytochrome c oxidase family protein, contains Pfam domain, PF01215: Cytochrome c oxidase subunit Vb 1828 At3g15660 Dm glutaredoxin family protein, contains Pfam profile PF00462: Glutaredoxin 1829 At3g15680 D2 zinc finger (Ran-binding) family protein, contains Pfam domain, PF00641: Zn-finger in Ran binding protein and others 1830 At3g15730 D1, D2, Dm PLDALPHA1_PLD__phospholipase D alpha 1 / PLD alpha 1 (PLDALPHA1) (PLD1) / choline phosphatase 1, identical to SP:Q38882 Phospholipase D alpha 1 (EC 3.1.4.4) (AtPLDalpha1) (PLD alpha 1) (Choline phosphatase 1) (Phosphatidylcholine-hydrolyzing phospholipase D 1) (PLDalpha) (Arabidopsis thaliana) 1831 At3g15780 D1, D2, Dm expressed protein 1832 At3g15790 D1, D2, Dm MBD11__methyl-CpG-binding domain-containing protein, contains Pfam profile PF01429: Methyl-CpG binding domain 1833 At3g15850 D1, D2, Dm FAD5_ADS3_FADB_JB67__fatty acid desaturase family protein, similar to delta 9 acyl-lipid desaturase (ADS1) GI:2970034 from (Arabidopsis thaliana) 1834 At3g16000 D1, Dm MFP1__matrix-localized MAR DNA-binding protein-related, similar to matrix-localized MAR DNA binding protein MFP1 GI:1771158 from (Lycopersicon esculentum) 1835 At3g16080 D1, Dm 60S ribosomal protein L37 (RPL37C), similar to ribosomal protein L37 GB:BAA04888 from (Homo sapiens) 1836 At3g16110 D1, Dm ATPDIL1-6__Encodes a protein disulfide isomerase-like (PDIL) protein, a member of a multigene family within the thioredoxin (TRX) superfamily. 1837 At3g16190 D1, D2, Dm isochorismatase hydrolase family protein, low similarity to SP:P32400 N-carbamoylsarcosine amidase (EC 3.5.1.59) (N-carbamoylsarcosine amidohydrolase) {Arthrobacter sp}; contains Pfam profile PF00857: isochorismatase family protein 1838 At3g16240 D1, D2, Dm DELTA-TIP_AQP1_ATTIP2;1_DELTA-TIP1_TIP2;1__delta tonoplast integral protein (delta-TIP), identical to delta tonoplast integral protein (delta-TIP) (GI:9279707)(GB:U39485) (Arabidopsis thaliana) (Plant Cell 8 (4), 587-599 (1996)) 1839 At3g16250 D1, D2, Dm ferredoxin-related, contains Pfam profile: PF00111 2Fe-2S iron-sulfur cluster binding domains

1840 At3g16270 D2, Dm expressed protein, gene model 1841 At3g16360 Dm AHP4__phosphotransfer family protein, similar to two-component phosphorelay mediators ATHP1 (GI:4156241), ATHP3 (GI:4156245) (Arabidopsis thaliana), histidine-containing phosphotransfer protein (Catharanthus roseus) GI:13774348 1842 At3g16370 D1, D2, Dm GDSL-motif lipase/hydrolase family protein, similar to family II lipases EXL3 GI:15054386, EXL1 GI:15054382, EXL2 GI:15054384 from (Arabidopsis thaliana); contains Pfam profile: PF00657 Lipase Acylhydrolase with GDSL-like motif 1843 At3g16390 D1, D2, Dm jacalin lectin family protein, similar to myrosinase-binding protein homolog (Arabidopsis thaliana) GI:2997767, epithiospecifier (Arabidopsis thaliana) GI:16118845; contains Pfam profiles PF01419 jacalin-like lectin family, PF01344 Kelch motif 1844 At3g16400 D1, D2, Dm ATMLP-470__jacalin lectin family protein, similar to myrosinase-binding protein homolog (Arabidopsis thaliana) GI:2997767, epithiospecifier (Arabidopsis thaliana) GI:16118845; contains Pfam profiles PF01419 jacalin-like lectin family, PF01344 Kelch motif 1845 At3g16480 D1, D2, Dm MPPALPHA__mitochondrial processing peptidase alpha subunit, putative, similar to mitochondrial processing peptidase alpha subunit, mitochondrial precursor, Alpha-MPP (Ubiquinol-cytochrome C reductase subunit II) (Potato) SWISS-PROT:P29677 1846 At3g16520 D2 UDP-glucoronosyl/UDP-glucosyl transferase family protein, contains Pfam profile: PF00201 UDP- glucoronosyl and UDP-glucosyl transferase 1847 At3g16570 D1, Dm RALFL23__rapid alkalinization factor (RALF) family protein, similar to RALF precursor (Nicotiana tabacum) GI:16566316 1848 At3g16640 D2, Dm TCTP__translationally controlled tumor family protein, similar to translationally controlled tumor protein GB:AAD10032 from (Hevea brasiliensis) 1849 At3g16770 D1, Dm ATEBP_RAP2.3__Encodes a member of the ERF (ethylene response factor) subfamily B-2 of the plant specific ERF/AP2 transcription factor family (RAP2.3). The protein contains one AP2 domain. There are 5 members in this subfamily including RAP2.2 AND RAP2.12.It is localized to the nucleus and acts as a transcriptional activator through the GCC-box. It has been identified as a suppressor of Bax-induced cell death by functional screening in yeast and can also suppress Bax-induced cell death in tobacco plants. Overexpression of this gene in tobacco BY-2 cells confers resistance to H2O2 and heat stresses. Overexpression in Arabidopsis causes upregulation of PDF1.2 and GST6. It is part of the ethylene signaling pathway and is predicted to act downstream of EIN2 and CTR1, but not under EIN3. 1850 At3g16850 D1, Dm glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family protein, weak similarity to SP:P05117 Polygalacturonase 2A precursor (EC 3.2.1.15) (Pectinase) {Lycopersicon esculentum}; contains PF00295: Glycosyl hydrolases family 28 1851 At3g16870 D2 zinc finger (GATA type) family protein, contains Pfam profile:PF00320 GATA:GATA zinc finger 1852 At3g16940 Dm calmodulin-binding protein, similar to anther ethylene-upregulated protein ER1 GI:11612392 from (Nicotiana tabacum); contains Pfam profile: PF00612 IQ calmodulin-binding motif (3 copies) 1853 At3g16990 D1, D2, Dm TENA/THI-4 family protein, contains Pfam profile: PF03070 TENA/THI-4 family 1854 At3g17000 D1, D2, Dm ubiquitin-conjugating enzyme, putative, similar to Non-Canonical UBiquitin Conjugating Enzyme 1 (NCUBE1) from (Gallus gallus) GI:7362937, (Mus musculus) GI:7363050, (Homo sapiens) GI:7362973; contains Pfam profile PF00179: Ubiquitin-conjugating enzyme 1855 At3g17050 D2 transposable element gene 1856 At3g17070 D1, Dm peroxidase, putative, similar to peroxidase GB:AAD37376 (Glycine max) 1857 At3g17100 D2 expressed protein 1858 At3g17160 Dm expressed protein 1859 At3g17170 D1, D2, Dm RFC3__ribosomal protein S6 family protein (RFC3), annotation temporarily based on supporting cDNA gi:15620809:dbj:AB057424.1:; contains TIGRfam TIGR00166 and Pfam PF01250 profiles ribosomal protein S6. 1860 At3g17310 Dm methyltransferase family protein, similar to cytosine methyltransferase (GI:7658293) (Arabidopsis thaliana) 1861 At3g17390 D1, D2, Dm MTO3_SAMS3__S-adenosylmethionine synthetase, putative, similar to S-adenosylmethionine synthetase 2 (Methionine adenosyltransferase 2, AdoMet synthetase 2) (Catharanthus roseus) SWISS-PROT:Q96552 1862 At3g17465 D2 RPL3P__ribosomal protein L3 family protein 1863 At3g17520 D1, D2, Dm late embryogenesis abundant domain-containing protein / LEA domain-containing protein, low similarity to PIR:S04045:S04045 embryonic abundant protein D-29 (Gossypium hirsutum); contains Pfam profile PF02987: Late embryogenesis abundant protein 1864 At3g17790 D1, D2, Dm ATPAP17_PAP17_ATACP5__acid phosphatase type 5 (ACP5), contains Pfam profile: PF00149 calcineurin-like phosphoesterase; nearly identical to acid phosphatase type 5 (GI:10278031) (Arabidopsis thaliana) 1865 At3g17800 D1, D2, Dm expressed protein 1866 At3g17810 D1, D2, Dm dihydroorotate dehydrogenase family protein / dihydroorotate oxidase family protein, low similarity to SP:Q12882 Dihydropyrimidine dehydrogenase (NADP+) precursor (EC 1.3.1.2) (DPD) (DHPDHase) (Dihydrouracil dehydrogenase) (Dihydrothymine dehydrogenase) {Homo sapiens}; contains Pfam profile PF01180: Dihydroorotate dehydrogenase 1867 At3g17840 D1, Dm RLK902__leucine-rich repeat transmembrane protein kinase, putative, similar to receptor kinase GB:AAA33715 from (Petunia integrifolia) 1868 At3g17930 D1, D2, Dm expressed protein 1869 At3g17940 Dm aldose 1-epimerase family protein, similar to ALDOSE 1-EPIMERASE PRECURSOR GB:P05149 (SP:P05149) from (Acinetobacter calcoaceticus); contains Pfam profile PF01263 Aldose 1- epimerase 1870 At3g17970 D2 chloroplast outer membrane translocon subunit, putative, similar to Toc64 (Pisum sativum) GI:7453538; contains Pfam profile PF00515 TPR Domain 1871 At3g18010 D2 similar to homeobox-leucine zipper transcription factor family protein [Arabidopsis thaliana] (TAIR:At2g01500.1); similar to homeodomain transcription factor [Zea mays] (GB:CAD60454.1); contains InterPro domain Homeobox (InterPro:IPR001356) 1872 At3g18060 Dm transducin family protein / WD-40 repeat family protein, similar to 66 kDa stress protein (SP:P90587) (Physarum polycephalum (Slime mold)); similar to WDR1 protein GB:AAD05042 (Gallus gallus) (Genomics 56 (1), 59-69 (1999)); contains 11 WD-40 repeats (PF00400) 1873 At3g18080 D1, Dm glycosyl hydrolase family 1 protein, contains Pfam PF00232 : Glycosyl hydrolase family 1 domain; TIGRFAM TIGR01233: 6-phospho-beta-galactosidase; similar to beta-glucosidase BGQ60 precursor GB:A57512 (Hordeum vulgare); similar to beta-mannosidase enzyme (GI:17226270) (Lycopersicon esculentum) 1874 At3g18130 D1, D2, Dm guanine nucleotide-binding family protein / activated protein kinase C receptor (RACK1), identical to guanine nucleotide-binding protein; activated protein kinase C receptor; RACK1 (GI:9294068) {Arabidopsis thaliana}; contains Pfam profile: PF00400 WD domain, G-beta repeat (7 copies) 1875 At3g18140 Dm transducin family protein / WD-40 repeat family protein, contains 6 WD-40 repeats (PF00400); similar to Pop3 (GP:3434986) (Schizosaccharomyces pombe) 1876 At3g18190 D2 chaperonin, putative, similar to SWISS-PROT:P50991- T-complex protein 1, delta subunit (TCP-1- delta) (Homo sapiens); contains Pfam:PF00118 domain, TCP-1/cpn60 chaperonin family 1877 At3g18280 D1, D2, Dm protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, similar to TED4 (Zinnia elegans) GI:493721; contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 1878 At3g18330 Dm F-box family protein, contains Pfam PF00646: F-box domain; contains TIGRFAM TIGR01640: F-box protein interaction domain 1879 At3g18490 D2, Dm aspartyl protease family protein, contains Pfam domain, PF00026: eukaryotic aspartyl protease

1880 At3g18680 D1, D2, Dm aspartate/glutamate/uridylate kinase family protein, similar to UMP-kinase GB:CAB38122 gi:4468612 from (Lactococcus lactis) ; contains Pfam profile PF00696: Amino acid kinase family

1881 At3g18710 Dm U-box domain-containing protein, similar to immediate-early fungal elicitor protein CMPG1 (Petroselinum crispum) GI:14582200; contains Pfam profile PF04564: U-box domain 1882 At3g18740 D2, Dm 60S ribosomal protein L30 (RPL30C), similar to 60S RIBOSOMAL PROTEIN L30 GB:O49884 from (Lupinus luteus) 1883 At3g18773 D2 zinc finger (C3HC4-type RING finger) family protein, contains Pfam profile: PF00097 zinc finger, C3HC4 type (RING finger) 1884 At3g18800 D1 expressed protein 1885 At3g18830 Dm ATPLT5__This gene encodes a plasma membrane-localized polyol/cyclitol/monosaccharide-H+- symporter. The AtPLT5 symporter is able to catalyze the energy-dependent membrane passage of a wide range of linear polyols (three to six carbon backbone), of cyclic polyols (myo-inositol), and of numerous monosaccharides, including pyranose ring-forming and furanose ring-forming hexoses and pentoses. This gene belongs to a monosaccharide transporter-like (MST-like) superfamily. 1886 At3g18890 D1, Dm expressed protein, similar to UV-B and ozone similarly regulated protein 1 UOS1 (Pisum sativum) GI:20339364 1887 At3g19000 D2 oxidoreductase, 2OG-Fe(II) oxygenase family protein, similar to SP:P24397 Hyoscyamine 6- dioxygenase (EC 1.14.11.11) (Hyoscyamine 6-beta- hydroxylase) {Hyoscyamus niger}, SP:Q05965 Naringenin,2-oxoglutarate 3-dioxygenase (EC 1.14.11.9) (Flavonone- 3-hydroxylase) (F3H) (FHT) {Matthiola incana}; contains Pfam profile PF03171: oxidoreductase, 2OG-Fe(II) oxygenase family

1888 At3g19290 D1, D2, Dm ABF4_AREB2__ABA-responsive element-binding protein 2 (AREB2), almost identical (one amino acid) to GB:AAF27182 from (Arabidopsis thaliana); contains Pfam profile PF00170:bZIP transcription factor; identical to cDNA abscisic acid responsive elements-binding factor (ABRE) mRNA, partial cds GI:6739282 1889 At3g19320 Dm leucine-rich repeat family protein, contains leucine-rich repeats, Pfam:PF00560; 1890 At3g19380 D2 U-box domain-containing protein, contains similarity to immediate-early fungal elicitor protein CMPG1 GI:14582200 (Petroselinum crispum); contains Pfam profile PF04564: U-box domain

1891 At3g19460 D2 reticulon family protein (RTNLB11), weak similarity to neuroendocrine-specific protein C (Homo sapiens) GI:307311; identical to cDNA RTNLB11 GI:32331878 1892 At3g19500 D1, D2, Dm ethylene-responsive protein -related, contains similarity to ethylene-inducible ER33 protein (Lycopersicon esculentum) gi:5669656:gb:AAD46413 1893 At3g19520 D1 expressed protein, contains Pfam profile PF04776: Protein of unknown function (DUF626) 1894 At3g19580 D2 AZF2__zinc finger (C2H2 type) protein 2 (AZF2), identical to Cys2/His2-type zinc finger protein 2 (Arabidopsis thaliana) gi:6009885:dbj:BAA85107 1895 At3g19640 D1, Dm magnesium transporter CorA-like family protein (MRS2-3), low similarity to SP:Q01926 RNA splicing protein MRS2, mitochondrial precursor {Saccharomyces cerevisiae}; contains Pfam profile PF01544: CorA-like Mg2+ transporter protein 1896 At3g19710 D1, D2, Dm branched-chain amino acid aminotransferase, putative / branched-chain amino acid transaminase, putative (BCAT4), similar to branched-chain amino acid transaminase 6 (Arabidopsis thaliana) GI:13810195; contains Pfam profile: PF01063 aminotransferase class IV 1897 At3g19820 D1, D2, Dm DWF1_CBB1_DIM_DIM1_DW1_EVE1__cell elongation protein / DWARF1 / DIMINUTO (DIM), identical to GB:S71189 (SP:Q39085) from (Arabidopsis thaliana); contains Pfam FAD binding domain PF01565 1898 At3g19830 Dm C2 domain-containing protein, low similarity to GLUT4 vesicle protein (Rattus norvegicus) GI:4193489; contains Pfam profile PF00168: C2 domain 1899 At3g19850 D2 phototropic-responsive NPH3 family protein, contains NPH3 family domain, Pfam:PF03000 1900 At3g19930 D2 STP4__sugar transport protein (STP4), identical to GB:S25009 GI:16524 from (Arabidopsis thaliana) 1901 At3g19940 D1 sugar transporter, putative, similar to sugar transport protein (Arabidopsis thaliana) GI:16524; contains Pfam profile PF00083: major facilitator superfamily protein 1902 At3g19960 D2 ATATM_ATM1__myosin (ATM), nearly identical to myosin (Arabidopsis thaliana) GI:6491702; similar to myosin GI:6491702 from (Arabidopsis thaliana) ;contains Pfam profiles: PF00063: myosin head (motor domain), PF00612: IQ calmodulin-binding motif; identical to cDNA myosin (ATM) GI:297068 1903 At3g20050 D2, Dm ATTCP-1__T-complex protein 1 alpha subunit / TCP-1-alpha / chaperonin (CCT1), identical to SWISS-PROT:P28769- T-complex protein 1, alpha subunit (TCP-1-alpha) (Arabidopsis thaliana) 1904 At3g20100 D1, Dm CYP705A19__cytochrome P450 family protein, similar to Cytochrome P450 93A3 (P450 CP5) (SP:O81973) (Glycine max); contains Pfam profile: PF00067 cytochrome P450; supported by full- length cDNA: Ceres:149380. 1905 At3g20120 D1 CYP705A21__cytochrome P450 family protein, contains Pfam profile: PF00067 cytochrome P450 1906 At3g20200 Dm protein kinase family protein, contains protein kinase domain, Pfam:PF00069 1907 At3g20230 D1, Dm 50S ribosomal protein L18 family, similar to ribosomal protein L18 (GI:29342325) (Enterococcus faecalis V583); similar to 50S ribosomal protein L18 (Swiss-Prot:O24704) (Synechococcus sp.)

1908 At3g20250 D1, Dm pumilio/Puf RNA-binding domain-containing protein, contains Pfam profile: PF00806 Pumilio- family RNA binding domains (aka PUM-HD, Pumilio homology domain) (8 copies at C-terminus) 1909 At3g20390 D1 endoribonuclease L-PSP family protein, contains Pfam domain PF01042: Endoribonuclease L-PSP 1910 At3g20470 D2 glycine-rich protein 5, encodes a glycine-rich protein that is expressed more abundantly in immature seed pods than in stems and leaves. Expression is not detected in roots or flowers 1911 At3g20580 D1, Dm phytochelatin synthetase-related, contains Pfam PF04833: Phytochelatin synthetase-like conserved region; supporting cDNA gi:26452232:dbj:AK118605.1: 1912 At3g20670 D1, Dm histone H2A, putative, strong similarity to histone H2A GB:AAF64418 GI:7595337 from Arabidopsis thaliana, Triticum aestivum GI:536892; contains Pfam profile PF00125 Core histone H2A/H2B/H3/H4 1913 At3g20710 D2 F-box protein-related, contains weak hit to TIGRFAM TIGR01640 : F-box protein interaction domain; contains weak hit to Pfam PF00646: F-box domain 1914 At3g20750 D1 zinc finger (GATA type) family protein 1915 At3g20940 D1, D2, Dm CYP705A28_CYP705A30_CYP705A31P__cytochrome P450 family protein, similar to Cytochrome P450 93A3 (P450 CP5) (SP:O81973) (Glycine max); similar to cytochrome P450 (SP:H71417) (Arabidopsis thaliana) 1916 At3g21175 Dm ZML1__zinc finger (GATA type) family protein, similar to zinc finger protein ZIM gi:8918533 from (Arabidopsis thaliana); contains Pfam PF00320: GATA zinc finger 1917 At3g21180 D2, Dm ACA9_ATACA9__calcium-transporting ATPase, plasma membrane-type, putative / Ca2+-ATPase, putative (ACA9), identical to SP:Q9LU41 Potential calcium-transporting ATPase 9, plasma membrane-type (EC 3.6.3.8) (Ca(2+)-ATPase isoform 9) {Arabidopsis thaliana} 1918 At3g21200 D1, D2, Dm expressed protein 1919 At3g21300 D2, Dm RNA methyltransferase family protein, contains TIGRfam TIGR00479: RNA methyltransferase, TrmA family 1920 At3g21400 Dm expressed protein 1921 At3g21510 D2, Dm AHP1_ATHP3__two-component phosphorelay mediator 3 (HP3), identical to ATHP3 (Arabidopsis thaliana) GI:4156245 1922 At3g21530 D1, D2, Dm endonuclease/exonuclease/phosphatase family protein, contains Pfam profile PF03372: Endonuclease/Exonuclease/phosphatase family 1923 At3g21540 D2 transducin family protein / WD-40 repeat family protein, contains Pfam profile: PF00400 WD domain, G-beta repeat (10 copies); similar to WD-repeat protein 3 (SP:Q9UNX4) (Homo sapiens) 1924 At3g21640 D1, Dm TWD1_UCU2__FKBP-type peptidyl-prolyl cis-trans isomerase family protein, similar to rof1 (Arabidopsis thaliana) GI:1354207; contains Pfam profile: PF00254 FKBP-type peptidyl-prolyl cis-trans isomerases 1925 At3g21670 D1, D2, Dm nitrate transporter (NTP3), nearly identical to nitrate transporter (Arabidopsis thaliana) GI:4490323; contains Pfam profile: PF00854 POT family 1926 At3g21840 Dm ASK7__E3 ubiquitin ligase SCF complex subunit SKP1/ASK1 (At7), putative, E3 ubiquitin ligase; similar to Skp1 homolog GI:3068809, UIP2 GI:3719211 from (Arabidopsis thaliana) 1927 At3g22060 D1, Dm contains Pfam profile: PF01657 Domain of unknown function that is usually associated with protein kinase domain Pfam:PF00069, however this protein does not have the protein kinase domain 1928 At3g22120 D2, Dm CWLP__protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, similar to SP:Q00451:PRF1_LYCES 36.4 kDa proline-rich protein Lycopersicon esculentum, proline-rich cell wall protein (Medicago sativa) GI:3818416; contains Pfam profile PF00234 Protease inhibitor/seed storage/LTP family 1929 At3g22140 D1, Dm 1930 At3g22200 D1, D2, Dm POP2_GABA-T__4-aminobutyrate aminotransferase / gamma-amino-N-butyrate transaminase / GABA transaminase / beta-alanine--oxoglutarate aminotransferase, identical to gamma-aminobutyrate transaminase subunit precursor (Arabidopsis thaliana) (EC 2.6.1.19) GI:14030435; contains Pfam profile PF00202: aminotransferase, class III; identical to cDNA gamma-aminobutyrate transaminase subunit precursor, nuclear gene for mitochondrial product GI:14030434 1931 At3g22230 D2, Dm 60S ribosomal protein L27 (RPL27B), similar to 60S RIBOSOMAL PROTEIN L27 GB:P41101 from (Solanum tuberosum) 1932 At3g22231 D1, D2, Dm PCC1__expressed protein 1933 At3g22240 D1, D2, Dm expressed protein 1934 At3g22310 D2 DEAD box RNA helicase, putative (RH9), similar to RNA helicases GI:3775995, GI:3775987 (Arabidopsis thaliana); contains Pfam profiles PF00270: DEAD/DEAH box helicase, PF00271: Helicase conserved C-terminal domain 1935 At3g22370 D2 AOX1A__alternative oxidase 1a, mitochondrial (AOX1A), identical to GB:Q39219 (SP:Q39219) from (Arabidopsis thaliana) 1936 At3g22380 D1, D2, Dm expressed protein 1937 At3g22410 Dm expressed protein 1938 At3g22420 D1, D2, Dm WNK2_ZIK3__protein kinase family protein, contains protein kinase domain, Pfam:PF00069 1939 At3g22460 D2 cysteine synthase, putative / O-acetylserine (thiol)-lyase, putative / O-acetylserine sulfhydrylase, putative, nearly identical over 185 amino acids to SP:P47998 Cysteine synthase (EC 4.2.99.8) (O-acetylserine sulfhydrylase) (O-acetylserine (Thiol)-lyase) {Arabidopsis thaliana} 1940 At3g22480 D2 prefoldin-related KE2 family protein, similar to Swiss-Prot:Q9UHV9 prefoldin subunit 2 (Protein HSPC231) (Homo sapiens); contains Pfam domain, PF01920: KE2 family protein 1941 At3g22560 Dm GCN5-related N-acetyltransferase (GNAT) family protein, contains Pfam profile:PF00583 Acetyltransf:Acetyltransferase (GNAT) family 1942 At3g22660 D2 rRNA processing protein-related, contains weak similarity to rRNA processing protein EBP2 (EBNA1-binding protein homolog) (Swiss-Prot:P36049) (Saccharomyces cerevisiae) 1943 At3g22740 D1, Dm HMT3__homocysteine S-methyltransferase 3 (HMT-3), identical to homocysteine S- methyltransferase HMT-3 (Arabidopsis thaliana) GI:9966515; similar to homocysteine S- methyltransferase AtHMT-2 (GI:6685163) (Arabidopsis thaliana); similar to selenocysteine methyltransferase GB:P56707 from (Astragalus bisulcatus) 1944 At3g22840 D1, Dm ELIP1_ELIP_ELIP2__chlorophyll A-B binding family protein / early light-induced protein (ELIP), identical to early light-induced protein; ELIP (Arabidopsis thaliana) GI:1872544; contains Pfam profile: PF00504 chlorophyll A-B binding protein; identical to cDNA early light-induced protein GI:1872543 1945 At3g22850 D2, Dm expressed protein, similar to auxin down-regulated protein ARG10 (Vigna radiata) GI:2970051, wali7 (aluminum-induced protein) (Triticum aestivum) GI:451193 1946 At3g23000 D1, D2, Dm CIPK7_ATSR2_ATSRPK1_PKS7__CBL-interacting protein kinase 7 (CIPK7), identical to CBL- interacting protein kinase 7 (Arabidopsis thaliana) gi:13249113:gb:AAK16682; contains Pfam profiles PF00069: Protein kinase domain and PF03822: NAF domain; identical to cDNA CBL- interacting protein kinase 7 (CIPK7) GI:13249112 1947 At3g23050 D1, D2, Dm IAA7_AXR2__auxin-responsive protein / indoleacetic acid-induced protein 7 (IAA7), identical to SP:Q38825:AXI7_ARATH Auxin-responsive protein IAA7 (Indoleacetic acid-induced protein 7) 1948 At3g23070 D2 expressed protein, contains Pfam domain, PF04581: Protein of unknown function (DUF578) 1949 At3g23080 D1 expressed protein, weak similarity to SP:Q9UKL6 Phosphatidylcholine transfer protein (PC-TP) {Homo sapiens} 1950 At3g23100 D1, D2, Dm XRCC4__double strand break repair protein, putative (XRCC4), identical to cDNA putative double strand break repair protein (XRCC4) GI:9800642 1951 At3g23140 Dm zinc finger (C2H2 type) family protein, contains Pfam profile: PF00096 zinc finger, C2H2 type

1952 At3g23390 D1, D2, Dm 60S ribosomal protein L36a/L44 (RPL36aA), similar to ribosomal protein L41 GB:AAA34366 from (Candida maltosa) 1953 At3g23490 D1, D2, Dm CYN__cyanate lyase family, contains Pfam profile: PF02560 cyanate lyase C-terminal domain 1954 At3g23530 Dm cyclopropane fatty acid synthase, putative / CPA-FA synthase, putative, similar to cyclopropane synthase (Sterculia foetida) GI:21069167; contains Pfam profiles PF02353: Cyclopropane-fatty-acyl-phospholipid synthase, PF01593: amine oxidase, flavin-containing 1955 At3g23600 D1, D2, Dm dienelactone hydrolase family protein, similar to SP:Q9ZT66 Endo-1,3;1,4-beta-D-glucanase precursor (EC 3.2.1.-) {Zea mays}; contains Pfam profile: PF01738 Dienelactone hydrolase family 1956 At3g23620 D2 brix domain-containing protein, contains Pfam domain, PF04427: Brix domain 1957 At3g23660 D2, Dm transport protein, putative, similar to Swiss-Prot:Q15436 protein transport protein Sec23A (Homo sapiens) 1958 At3g23700 D1, D2, Dm S1 RNA-binding domain-containing protein, contains Pfam domain, PF00575: S1 RNA binding domain

1959 At3g23750 D2 leucine-rich repeat family protein / protein kinase family protein, contains Pfam domains PF00560: Leucine Rich Repeat and PF00069: Protein kinase domain 1960 At3g23830 D2 glycine-rich RNA-binding protein, putative, similar to Glycine-rich RNA-binding protein 2, mitochondrial precursor (AtGRP2) (Swiss-Prot:Q9SVM8) (Arabidopsis thaliana); contains Pfam profile: PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 1961 At3g23940 D1, D2, Dm dehydratase family, contains Pfam profile: PF00920 dehydratase family 1962 At3g24030 D1, Dm hydroxyethylthiazole kinase family protein, contains Pfam profile: PF02110 hydroxyethylthiazole kinase family 1963 At3g24050 D2 GATA transcription factor 1 (GATA-1), identical to GATA transcription factor 1 (AtGATA-1) GB:Y13648 (Arabidopsis thaliana) 1964 At3g24190 D2, Dm ABC1 family protein, contains Pfam domain, PF03109: ABC1 family 1965 At3g24250 D2, Dm glycine-rich protein 1966 At3g24270 D1, Dm expressed protein 1967 At3g24420 D1, Dm hydrolase, alpha/beta fold family protein, low similarity to 3-oxoadipate enol-lactone hydrolase (Pseudomonas sp. B13) GI:17736948, B-ketoadipate enol-lactone hydrolase (Bradyrhizobium japonicum) GI:2239060; contains Pfam profile:PF00561 abhydrolase:alpha/beta hydrolase fold 1968 At3g24430 D1, Dm HCF101__expressed protein, contains Pfam profile PF01883: Domain of unknown function 1969 At3g24460 D2, Dm TMS membrane family protein / tumour differentially expressed (TDE) family protein, contains Pfam domain, PF03348: TMS membrane protein/tumour differentially expressed protein (TDE) 1970 At3g24480 D1, D2, Dm leucine-rich repeat family protein / extensin family protein, similar to extensin-like protein (Lycopersicon esculentum) gi:5917664:gb:AAD55979; contains leucine-rich repeats, Pfam:PF00560; contains proline rich extensin domains, INTERPRO:IPR002965 1971 At3g24500 D1, D2, Dm ATMBF1C_MBF1C__ethylene-responsive transcriptional coactivator, putative, similar to ethylene- responsive transcriptional coactivator (Lycopersicon esculentum) gi:5669634:gb:AAD46402

1972 At3g24520 D1, D2, Dm AT-HSFC1_HSFC1__heat shock transcription factor family protein, contains Pfam profile: PF00447 HSF-type DNA-binding domain 1973 At3g24550 D2, Dm protein kinase family protein, contains Pfam domain PF00069: Protein kinase domain 1974 At3g24810 D2 KRP5_ICK3__kip-related protein 5 (KRP5) / cyclin-dependent kinase inhibitor 5 (ICK5), identical to cyclin-dependent kinase inhibitor 5 (krp5) (Arabidopsis thaliana) GI:14422293 1975 At3g24820 D2 BSD domain-containing protein, contains Pfam profile PF03909: BSD domain 1976 At3g24830 D1, Dm 60S ribosomal protein L13A (RPL13aB), similar to 60S RIBOSOMAL PROTEIN L13A GB:P35427 from (Rattus norvegicus) 1977 At3g25020 D1 disease resistance family protein, contains leucine rich-repeat (LRR) domains Pfam:PF00560, INTERPRO:IPR001611; similar to Hcr2-0B (Lycopersicon esculentum) gi:3894387:gb:AAC78593 1978 At3g25480 D1 rhodanese-like domain-containing protein, contains Rhodanese-like domain PF:00581 1979 At3g25500 D1, D2, Dm AFH1_AHF1_FH1__formin homology 2 domain-containing protein / FH2 domain-containing protein, contains formin homology 2 domain, Pfam:PF02181 1980 At3g25520 D2, Dm ATL5__60S ribosomal protein L5, similar to 60S ribosomal protein L5 GB:P49625 from (Oryza sativa) 1981 At3g25530 D2 6-phosphogluconate dehydrogenase NAD-binding domain-containing protein, low similarity to SP:P23523 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) (Tartronate semialdehyde reductase) {Escherichia coli}; contains Pfam profile PF03446: NAD binding domain of 6- phosphogluconate dehydrogenase; supporting cDNA gi:15375067:gb:AY044183.1: 1982 At3g25660 D1, Dm glutamyl-tRNA(Gln) amidotransferase, putative, similar to SP:O06491 Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.-) {Bacillus subtilis}; contains Pfam profile PF01425: Amidase 1983 At3g25800 D1 PDF1_PR65_PR 65__serine/threonine protein phosphatase 2A (PP2A) 65 KDa regulatory subunit A, identical to protein phosphatase 2A 65 kDa regulatory subunit (pDF1) GI:683502 from (Arabidopsis thaliana) 1984 At3g25860 D1, D2, Dm LTA2_PLE2__dihydrolipoamide S-acetyltransferase (LTA2), identical to dihydrolipoamide S- acetyltransferase (LTA2) (Arabidopsis thaliana) GI:5881963 1985 At3g25870 D2 expressed protein 1986 At3g25920 D1, Dm RPL15__50S ribosomal protein L15, chloroplast (CL15), identical to GB:P25873 from (Arabidopsis thaliana) 1987 At3g25980 Dm mitotic spindle checkpoint protein, putative (MAD2), identical to Swiss-Prot:Q9LU93 mitotic spindle checkpoint protein MAD2 (Arabidopsis thaliana) 1988 At3g26060 D1, Dm peroxiredoxin Q, putative, similar to peroxiredoxin Q (Sedum lineare) GI:6899842; contains Pfam profile: PF00578 AhpC/TSA (alkyl hydroperoxide reductase and thiol-specific antioxidant) family 1989 At3g26070 D1, D2, Dm plastid-lipid associated protein PAP / fibrillin family protein, contains Pfam profile PF04755: PAP_fibrillin 1990 At3g26080 D1, Dm plastid-lipid associated protein PAP / fibrillin family protein, low similarity to Plastid- lipid-Associated Protein (Nicotiana tabacum) GI:2632088; contains Pfam profile PF04755: PAP_fibrillin 1991 At3g26130 Dm glycosyl hydrolase family 5 protein / cellulase family protein, contains Pfam profile: PF00150 cellulase (glycosyl hydrolase family 5) 1992 At3g26210 D1, Dm CYP71B23__cytochrome P450 71B23, putative (CYP71B23), Identical to Cytochrome P450 71B23 (SP:Q9LTM0)(Arabidopsis thaliana);contains Pfam profile: PF00067 cytochrome P450 1993 At3g26280 D1, D2, Dm CYP71B4__cytochrome P450 family protein, identical to cytochrome P450 monooxygenase (CYP71B4) GB:D78603 (Arabidopsis thaliana) (Plant Mol. Biol. 37 (1), 39-52 (1998)) 1994 At3g26290 D1, D2, Dm CYP71B26__cytochrome P450 71B26, putative (CYP71B26), identical to cytochrome P450 71B26 (SP:Q9LTL0) (Arabidopsis thaliana); contains Pfam profile: PF00067 cytochrome P450 1995 At3g26450 D1, D2, Dm major latex protein-related / MLP-related, low similarity to major latex protein {Papaver somniferum}(GI:294060) ; contains Pfam profile PF00407: Pathogenesis-related protein Bet v I family 1996 At3g26460 D2, Dm major latex protein-related / MLP-related, low similarity to major latex protein {Papaver somniferum}(GI:294060) contains Pfam profile PF00407: Pathogenesis-related protein Bet v I family 1997 At3g26510 D1, D2, Dm similar to octicosapeptide/Phox/Bem1p (PB1) domain-containing protein [Arabidopsis thaliana] (TAIR:At1g70640.1); similar to PB1 domain, putative [Oryza sativa (japonica cultivar-group)] (GB:AAX96261.1); contains InterPro domain Octicosapeptide/Phox/Bem1p (InterPro:IPR000270) 1998 At3g26520 D1, D2, Dm TIP2_GAMMA-TIP2_SITIP_TIP1;2__tonoplast intrinsic protein, putative, similar to tonoplast intrinsic protein GI:5081419 from (Brassica napus) 1999 At3g26570 D1, Dm PHT2;1_ORF02__phosphate transporter family protein, contains Pfam profile: PF01384 phosphate transporter family 2000 At3g26580 D1, D2, Dm expressed protein 2001 At3g26700 Dm protein kinase family protein, contains protein kinase domain, Pfam:PF00069 2002 At3g26710 D1, D2, Dm expressed protein 2003 At3g26740 Dm CCL__light responsive protein-related, similar to light regulated protein precursor SP:Q03200 (Oryza sativa) (Plant Mol. Biol. 22 (1), 165-170 (1993)), ccr protein GB:S52663 (Citrus X paradisi) (Plant Mol. Biol. 26 (1), 165-173 (1994)) 2004 At3g27160 D1, Dm GHS1__ribosomal protein S21 family protein, contains Pfam profile: PF01165 ribosomal protein S21 2005 At3g27230 D2, Dm expressed protein 2006 At3g27270 D2 expressed protein 2007 At3g27280 D2 prohibitin, putative, strong similarity to prohibitin (Arabidopsis thaliana) GI:1946331; contains Pfam profile PF01145: SPFH domain / Band 7 family 2008 At3g27360 D1, Dm histone H3, identical to histone H3 from Zea mays SP:P05203, Medicago sativa GI:166384, Encephalartos altensteinii SP:P08903, Pisum sativum SP:P02300; contains Pfam profile PF00125 Core histone H2A/H2B/H3/H4 2009 At3g27740 D1, D2, Dm CARA__carbamoyl-phosphate synthase (glutamine-hydrolyzing) (CARA) / glutamine-dependent carbamoyl-phosphate synthase small subunit, identical to carbamoyl phosphate synthetase small subunit GI:2462781 (Arabidopsis thaliana) 2010 At3g27770 D1, D2, Dm expressed protein 2011 At3g27820 D1, D2, Dm ATMDAR4__monodehydroascorbate reductase, putative, similar to cytosolic monodehydroascorbate reductase GB:BAA77214 (Oryza sativa) 2012 At3g27830 D1, D2, Dm RPL12-A_RPL12__50S ribosomal protein L12-1, chloroplast (CL12-A), identical to ribosomal protein L12 GB:X68046 (Arabidopsis thaliana) (J. Biol. Chem. 269 (10), 7330-7336 (1994)) 2013 At3g27850 D1, D2, Dm RPL12-C__50S ribosomal protein L12-3, chloroplast (CL12-C), identical to ribosomal protein L12 GB:X68046 (Arabidopsis thaliana) (J. Biol. Chem. 269 (10), 7330-7336 (1994)) 2014 At3g27925 D2, Dm DEGP__DegP protease, putative, SP:022609; almost identical to DegP protease precursor GB:AF028842 from (Arabidopsis thaliana) (J. Biol. Chem. 273 (12), 7094-7098 (1998)) 2015 At3g28007 D1, D2, Dm nodulin MtN3 family protein, contains Pfam PF03083 MtN3/saliva family; similar to LIM7 GI:431154 (induced in meiotic prophase in lily microsporocytes) from (Lilium longiflorum) 2016 At3g28040 D2, Dm leucine-rich repeat transmembrane protein kinase, putative, contains Pfam profiles: PF00560 leucine rich repeat, PF00069 eukaryotic protein kinase domain 2017 At3g28070 D2 nodulin MtN21 family protein, similar to MtN21 (Medicago truncatula) GI:2598575 2018 At3g28100 D2, Dm nodulin MtN21 family protein, similar to MtN21 (Medicago truncatula) GI:2598575 2019 At3g28180 D1, D2, Dm ATCSLC04_ATCSLC4_CSLC04__glycosyl transferase family 2 protein, similar to beta-(1-3)-glucosyl transferase GB:AAC62210 GI:3687658 from (Bradyrhizobium japonicum), cellulose synthase from Agrobacterium tumeficiens (gi:710492) and Agrobacterium radiobacter (gi:710493); contains Pfam glycosyl transferase, group 2 family protein domain PF00535 2020 At3g28200 D2, Dm peroxidase, putative, similar to peroxidase ATP26a GB:CAA72487 GI:1890317 (Arabidopsis thaliana) 2021 At3g28270 D1, D2, Dm expressed protein, similar to At14a protein (GI:11994571 and GI:11994573) (Arabidopsis thaliana) 2022 At3g28420 D1, D2, Dm expressed protein 2023 At3g28520 D2 AAA-type ATPase family protein, contains Pfam profile: ATPase family PF00004 2024 At3g28650 D1, Dm DC1 domain-containing protein, similar to hypothetical protein GI:4204272 from (Arabidopsis thaliana) contains weak PHD zinc finger motifs contains weak PHD zinc finger motifs DC1 domain, a divergent protein kinase C domain of unknown function. 2025 At3g28715 D1 H+-transporting two-sector ATPase, putative, similar to SP:P54641 Vacuolar ATP synthase subunit d (EC 3.6.3.14) (Vacuolar proton pump d subunit) (V-ATPase 41 KDa accessory protein) {Dictyostelium discoideum}; contains Pfam profile PF01992: ATP synthase (C/AC39) subunit 2026 At3g28830 D2, Dm expressed protein 2027 At3g28860 D1, D2, Dm ATMDR1_ATMDR1_ATMDR11_PGP19__Belongs to the family of ATP-binding cassette (ABC) transporters. Also known as AtMDR11 and PGP19. Possibly regulates auxin-dependent responses by influencing basipetal auxin transport in the root. Acts upstream of phyA in regulating hypocotyl elongation and gravitropic response. Exerts nonredundant, partially overlapping functions with the ABC transporter encoded by AtPGP1. 2028 At3g28920 D2 zinc finger homeobox family protein / ZF-HD homeobox family protein, contains Pfam PF04770: ZF-HD protein dimerisation region; contains Pfam TIGR01566: ZF-HD homeobox protein Cys/His- rich domain; contains TIGRFAM TIGR01565: homeobox domain, ZF-HD class; similar to ZF-HD homeobox protein (GI:13277220) (Flaveria bidentis) 2029 At3g28930 D1, Dm AIG2__avrRpt2-induced AIG2 protein (AIG2), identical to SP:P54121 AIG2 protein (avrRpt2- induced gene) {Arabidopsis thaliana} 2030 At3g29130 D2, Dm expressed protein, ; expression supported by MPSS 2031 At3g29160 D2 AKIN11__Snf1-related protein kinase (KIN11), identical to protein kinase AKin11 GI:1729444 from (Arabidopsis thaliana) 2032 At3g29170 Dm expressed protein, contains Pfam PF05915: Eukaryotic protein of unknown function (DUF872) 2033 At3g29180 Dm expressed protein 2034 At3g29185 D1, D2, Dm similar to WRKY11 [Oryza sativa (japonica cultivar-group)] (GB:AAQ20911.1) 2035 At3g29220 D2 hypothetical protein 2036 At3g29240 D2 expressed protein, similar to At1g33780 (Arabidopsis thaliana); contains Pfam profile PF02622: Uncharacterized ACR, COG1678 2037 At3g29320 D2 glucan phosphorylase, putative, similar to alpha-glucan phosphorylase, L isozyme 1 precursor GB:P04045 from (Solanum tuberosum) (J. Biochem. 106 (4), 691-695 (1989)) 2038 At3g29330 D2 expressed protein 2039 At3g29360 D2 UDP-glucose 6-dehydrogenase, putative, very strong similarity to SP:Q96558 UDP-glucose 6- dehydrogenase (EC 1.1.1.22) (UDP-Glc dehydrogenase) (UDP-GlcDH) (UDPGDH) {Glycine max}; contains Pfam profiles PF03721: UDP-glucose/GDP-mannose dehydrogenase family NAD binding domain, PF00984: UDP-glucose/GDP-mannose dehydrogenase family central domain, PF03720: UDP- glucose/GDP-mannose dehydrogenase family UDP binding domain 2040 At3g29575 D1, D2, Dm expressed protein 2041 At3g29612 Dm transposable element gene 2042 At3g29670 D1, Dm transferase family protein, similar to anthocyanin 5-aromatic acyltransferase from Gentiana triflora GI:4185599, malonyl CoA:anthocyanin 5-O-glucoside-6```-O-malonyltransferase from Perilla frutescens GI:17980232, Salvia splendens GI:17980234; contains Pfam profile PF02458 transferase family 2043 At3g30390 D1, D2, Dm amino acid transporter family protein, low similarity to neuronal glutamine transporter (Rattus norvegicus) GI:6978016; belongs to INTERPRO:IPR002422 amino acid/polyamine transporter, family II 2044 At3g30415 Dm pseudogene, putative urophorphyrin III methylase 2045 At3g30775 D2, Dm ERD5_ATPDH_ATPOX_AT-POX_PRO1__proline oxidase, mitochondrial / osmotic stress-responsive proline dehydrogenase (POX) (PRO1) (ERD5), nearly identical to SP:P92983 Proline oxidase, mitochondrial precursor (EC 1.5.3.-) (Osmotic stress- induced proline dehydrogenase) (Arabidopsis thaliana); identical to cDNA proline oxidase precursor GI:1817543 2046 At3g32130 Dm hypothetical protein 2047 At3g32240 Dm transposable element gene 2048 At3g41979 D2 5SrRNA 2049 At3g42050 D2 vacuolar ATP synthase subunit H family protein, identical to probable vacuolar ATP synthase subunit H (EC 3.6.3.14)(V-ATPase H subunit) (Vacuolar proton pump H subunit) (Vacuolar proton pump subunit SFD) SP:Q9LX65 from (Arabidopsis thaliana); contains Pfam PF03224: V-ATPase subunit H 2050 At3g42060 D2 myosin heavy chain-related 2051 At3g42130 D2 glycine-rich protein 2052 At3g42680 Dm expressed protein 2053 At3g42810 Dm hypothetical protein, hypothetical proteins - Arabidopsis thaliana 2054 At3g43250 D1 cell cycle control protein-related, contains similarity to Swiss-Prot:Q9P7C5 cell cycle control protein cwf16 (Schizosaccharomyces pombe) 2055 At3g43460 D1, Dm hypothetical protein 2056 At3g43520 Dm expressed protein, contains Pfam profile PF03647: Uncharacterised protein family (UPF0136) 2057 At3g43600 D1, Dm AAO2__aldehyde oxidase, putative, identical to gi: 3172025; identical to cDNA putative aldehyde oxidase (AO3) mRNA, partial cds GI:2792303 2058 At3g43720 D1, D2, Dm protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 2059 At3g43740 D2, Dm leucine-rich repeat family protein, contains leucine rich-repeat (LRR) domains Pfam:PF00560, INTERPRO:IPR001611; contains similarity to somatic embryogenesis receptor-like kinase 2 (Arabidopsis thaliana) gi:14573457:gb:AAK68073 2060 At3g43750 D2 zinc finger (C3HC4-type RING finger) family protein, contains a zinc finger, C3HC4 type (RING finger), signature, PROSITE:PS00518 2061 At3g43810 D1, Dm CAM7__calmodulin-7 (CAM7), almost identical to calmodulin GI:16227 from (Arabidopsis thaliana), SP:P59220 Calmodulin-7 {Arabidopsis thaliana} 2062 At3g43980 D2, Dm 40S ribosomal protein S29 (RPS29A), ribosomal protein S29, rat, PIR:S30298 2063 At3g44000 Dm transposable element gene 2064 At3g44010 D1, D2, Dm 40S ribosomal protein S29 (RPS29B), ribosomal protein S29, rat, PIR:S30298 2065 At3g44100 D1, D2, Dm MD-2-related lipid recognition domain-containing protein / ML domain-containing protein, contains Pfam profile PF02221: ML domain 2066 At3g44140 Dm expressed protein 2067 At3g44280 Dm expressed protein 2068 At3g44300 D2 NIT2__nitrilase 2 (NIT2), identical to SP:P32962 Nitrilase 2 (EC 3.5.5.1) {Arabidopsis thaliana} 2069 At3g44310 D2, Dm ATNIT1_NIT1__The protein undergoes thiolation following treatment with the oxidant tert- butylhydroperoxide. 2070 At3g44430 Dm expressed protein 2071 At3g44450 D1, D2, Dm expressed protein 2072 At3g44590 D2 60S acidic ribosomal protein P2 (RPP2D), acidic ribosomal protein P2, maize, PIR:S54179 2073 At3g44670 D2 disease resistance protein RPP1-Ws(A,C)-like (TIR-NBS-LRR class), putative, domain signature TIR-NBS-LRR exists, suggestive of a disease resistance protein. Closest Col-0 homolog to both RPP1 Ws-A and RPP1 Ws-C 2074 At3g44750 D2, Dm HD2A_ATHD2A_HDA3_HDT1__histone deacetylase, putative (HD2A), contains Pfam domain, PF00096: Zinc finger, C2H2 type; identical to cDNA putative histone deacetylase (HD2A) GI:11066134 2075 At3g44860 D1, D2, Dm S-adenosyl-L-methionine:carboxyl methyltransferase family protein, similar to defense-related protein cjs1 (Brassica carinata)(GI:14009292)(Mol Plant Pathol (2001) 2(3):159-169) 2076 At3g44870 D2, Dm S-adenosyl-L-methionine:carboxyl methyltransferase family protein, similar to defense-related protein cjs1 (Brassica carinata)(GI:14009292)(Mol Plant Pathol (2001) 2(3):159-169) 2077 At3g44880 D1, D2, Dm ACD1_LLS1__Rieske (2Fe-2S) domain-containing protein, similar to lethal leaf-spot 1 from Zea mays (gi:1935909); contains Pfam PF00355 Rieske (2Fe-2S) domain 2078 At3g44890 D1, Dm RPL9_RP19__50S ribosomal protein L9, chloroplast (CL9), contains Pfam profile PF03948: Ribosomal protein L9, C-terminal domain; contains Pfam profile PF01281: ribosomal protein L9, N-terminal domain; contains TIGRfam profile TIGR00158: ribosomal protein L9 2079 At3g44950 D2 glycine-rich protein 2080 At3g45030 D1, D2, Dm 40S ribosomal protein S20 (RPS20A), 40S ribsomomal proteinS20, Arabidopsis thaliana, pir:T12992 2081 At3g45050 D2, Dm expressed protein 2082 At3g45060 Dm ATNRT2.6__high-affinity nitrate transporter, putative, similar to trans-membrane nitrate transporter protein AtNRT2:1 (Arabidopsis thaliana) GI:3747058, high-affinity nitrate transporter ACH1 (Arabidopsis thaliana) GI:3608362 2083 At3g45070 Dm sulfotransferase family protein, similar to steroid sulfotransferase 3 (Brassica napus) GI:3420008, steroid sulfotransferase 1 (Brassica napus) GI:3420004; contains Pfam profile PF00685: Sulfotransferase domain 2084 At3g45140 Dm LOX2_ATLOX2__lipoxygenase (LOX2), identical to SP:P38418 2085 At3g45160 D1, Dm expressed protein 2086 At3g45190 Dm SIT4 phosphatase-associated family protein, contains Pfam profile: PF04499 SIT4 phosphatase- associated protein 2087 At3g45260 Dm zinc finger (C2H2 type) family protein, contains Pfam domain, PF00096: Zinc finger, C2H2 type

2088 At3g45320 Dm hypothetical protein 2089 At3g45600 D2, Dm senescence-associated family protein, similar to senescence-associated protein 5 (Hemerocallis hybrid cultivar) gi:3551954:gb:AAC34855 2090 At3g45650 D2 proton-dependent oligopeptide transport (POT) family protein, contains Pfam profile: PF00854 POT family 2091 At3g45780 D1 PHOT1_JK224_NPH1_RPT1__protein kinase / nonphototropic hypocotyl protein 1 (NPH1) / phototropin, identical to SP:O48963 Nonphototropic hypocotyl protein 1 (EC 2.7.1.37) (Phototropin) {Arabidopsis thaliana}, cDNA nonphototropic hypocotyl 1 (NPH1) GI:2832240; contains Pfam profiles PF00069:Protein kinase domain and PF00785:PAC motif 2092 At3g45980 D1 histone H2B, identical to histone H2B Arabidopsis thaliana GI:2407802; contains Pfam profile PF00125 Core histone H2A/H2B/H3/H4 2093 At3g46000 D2 ADF2__actin-depolymerizing factor, putative (ADF2), strong similarity to SP:Q9ZSK3 Actin- depolymerizing factor 4 (ADF-4) (AtADF4) {Arabidopsis thaliana}; contains Pfam profile PF00241: Cofilin/tropomyosin-type actin-binding protein 2094 At3g46100 D2 ATHRS1__histidyl-tRNA synthetase / histidine--tRNA ligase, identical to histidyl-tRNA synthetase (Arabidopsis thaliana) GI:3659909 2095 At3g46170 D1, Dm short-chain dehydrogenase/reductase (SDR) family protein, contains similarity to 3-oxoacyl- (acyl-carrier protein) reductase SP:P51831 from (Bacillus subtilis) 2096 At3g46230 D1, D2, Dm ATHSP17.4__17.4 kDa class I heat shock protein (HSP17.4-CI), identical to 17.4 kDa class I heat shock protein SP:P19036 from (Arabidopsis thaliana) 2097 At3g46260 Dm protein kinase-related, contains low similarity to light repressible receptor protein kinase (Arabidopsis thaliana) gi:1321686:emb:CAA66376 2098 At3g46290 D1, Dm protein kinase, putative, similar to receptor-like protein kinase (Catharanthus roseus) gi:1644291:emb:CAA97692 2099 At3g46320 D1, Dm histone H4, nearly identical to histone H4 (Arabidopsis thaliana) GI:166740 2100 At3g46380 D1, D2, Dm expressed protein 2101 At3g46450 Dm SEC14 cytosolic factor family protein / phosphoglyceride transfer family protein, contains Pfam PF00650 : CRAL/TRIO domain; similar to polyphosphoinositide binding protein Ssh1p (GI::2739044) {Glycine max} 2102 At3g46550 Dm SOS5__fasciclin-like arabinogalactan family protein, similar to fasciclin-like arabinogalactan protein FLA8 (Arabidopsis thaliana) gi:10880493:gb:AAG24276 2103 At3g46740 D1, D2, Dm TOC75-III__chloroplast outer envelope protein, putative, similar to chloroplastic outer envelope membrane protein (OEP75) (Pisum sativum) GI:633607; contains Pfam profile PF01103: outer membrane protein, OMP85 family 2104 At3g46940 D2, Dm deoxyuridine 5`-triphosphate nucleotidohydrolase family, contains Pfam profile: PF00692 deoxyuridine 5`-triphosphate nucleotidohydrolase 2105 At3g46970 D2 ATPHS2_PHS2__Encodes a cytosolic alpha-glucan phosphorylase. 2106 At3g47020 D1, Dm F-box family protein, contains F-box domain Pfam:PF00646 2107 At3g47070 D1, Dm expressed protein 2108 At3g47080 Dm expressed protein 2109 At3g47290 Dm phosphoinositide-specific phospholipase C family protein, similar to phosphoinositide-specific phospholipase C (Nicotiana rustica) GI:1771381, 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase (Nicotiana rustica) GI:2765140; contains Pfam profiles PF00168: C2 domain, PF00388: Phosphatidylinositol-specific phospholipase C, X domain 2110 At3g47370 D2, Dm 40S ribosomal protein S20 (RPS20B), 40S RIBOSOMAL PROTEIN S20 - ARABIDOPSIS THALIANA,PID:g1350956 2111 At3g47420 D1, D2, Dm glycerol-3-phosphate transporter, putative / glycerol 3-phosphate permease, putative, similar to cAMP inducible 2 protein (Mus musculus) GI:4580997, glycerol-3-phosphate transporter (glycerol 3-phosphate permease) (Homo sapiens) GI:7543982; contains Pfam profile PF00083: major facilitator superfamily protein 2112 At3g47470 D2 CAB4_LHCA4__chlorophyll A-B binding protein 4, chloroplast / LHCI type III CAB-4 (CAB4), identical to SP:P27521 Chlorophyll A-B binding protein 4, chloroplast precursor (LHCI type III CAB-4) (LHCP) {Arabidopsis thaliana} 2113 At3g47500 D2 CDF3__Dof-type zinc finger domain-containing protein, identical to H-protein promoter binding factor-2a GI:3386546 from (Arabidopsis thaliana). Interacts with LKP2 and FKF1, but its overexpression does not change flowering time under short or long day conditions. 2114 At3g47520 D1, D2, Dm MDH__malate dehydrogenase (NAD), chloroplast (MDH), identical to chloroplast NAD-malate dehydrogenase (Arabidopsis thaliana) GI:3256066; contains InterPro entry IPR001236: Lactate/malate dehydrogenase; contains Pfam profiles PF00056: lactate/malate dehydrogenase, NAD binding domain and PF02866: lactate/malate dehydrogenase, alpha/beta C-terminal domain 2115 At3g47560 D1, Dm esterase/lipase/thioesterase family protein, low similarity to cinnamoyl ester hydrolase CinI (Butyrivibrio fibrisolvens) GI:1622732; contains Interpro entry IPR000379 2116 At3g47600 D2, Dm MYB94__myb family transcription factor (MYB94), contains Pfam profile: PF00249 myb-like DNA- binding domain; identical to cDNA putative transcription factor (MYB94) GI:3941527 2117 At3g47650 D1, Dm bundle-sheath defective protein 2 family / bsd2 family, similar to bundle sheath defective protein 2 (Zea mays) GI:4732091 2118 At3g47800 D1, D2, Dm aldose 1-epimerase family protein, similar to ALDOSE 1-EPIMERASE PRECURSOR GB:P05149 (SP:P05149) from (Acinetobacter calcoaceticus); contains Pfam profile PF01263 Aldose 1- epimerase 2119 At3g47810 D1, Dm calcineurin-like phosphoesterase family protein, contains Pfam profile: PF00149 calcineurin- like phosphoesterase 2120 At3g47833 D2 expressed protein 2121 At3g47860 D1 apolipoprotein D-related, contains weak similarity to Apolipoprotein D precursor (ApoD) (Swiss-Prot:P51910) (Mus musculus) 2122 At3g47930 Dm ATGLDH__L-galactono-1,4-lactone dehydrogenase, putative, strong similarity to L-galactono-1,4- lactone dehydrogenase, Brassica oleracea, Z97060 (gi:2760543), and gi:3986289 from Ipomea batatas 2123 At3g48000 D1, D2, Dm ALDH2B4_ALDH2__aldehyde dehydrogenase (ALDH2), identical to aldehyde dehydrogenase (Arabidopsis thaliana) GI:8574427; similar to mitochondrial aldehyde dehydrogenase (Arabidopsis thaliana) gi:19850249:gb:AAL99612; identical to cDNA aldehyde dehydrogenase AtALDH2a GI:20530140 2124 At3g48020 D1, D2, Dm expressed protein 2125 At3g48100 D2, Dm ARR2_ARR5_ATRR2_IBC6__two-component responsive regulator / response regulator 5 (ARR5) / response reactor 2 (RR2), identical to responce reactor2 (AtRR2) (Arabidopsis thaliana) GI:3273198, response regulator 5 (ARR5) (Arabidopsis thaliana) GI:3953599; contains Pfam profile: PF00072 response regulator receiver domain 2126 At3g48160 D1, Dm DEL1_E2FE_E2L3__transcription factor, putative / E2F-like repressor E2L3 (E2L3), identical to E2F-like repressor E2L3 (Arabidopsis thaliana) GI:20502508 2127 At3g48170 Dm ALDH10A9__betaine-aldehyde dehydrogenase, putative, similar to betaine-aldehyde dehydrogenase, chloroplast precursor (BADH) (Arabidopsis thaliana) SWISS-PROT:Q9S795 2128 At3g48200 Dm expressed protein 2129 At3g48220 D1, D2, Dm expressed protein 2130 At3g48240 D2, Dm octicosapeptide/Phox/Bem1p (PB1) domain-containing protein, contains Pfam profile PF00564: PB1 domain 2131 At3g48360 D2, Dm speckle-type POZ protein-related, contains Pfam PF00651 : BTB/POZ domain; similar to Speckle- type POZ protein (SP:O43791) (Homo sapiens) 2132 At3g48500 D2 PDE312__expressed protein 2133 At3g48570 D1, D2, Dm protein transport protein SEC61 gamma subunit, putative, similar to Swiss-Prot:Q19967 protein transport protein SEC61 gamma subunit (Caenorhabditis elegans) 2134 At3g48610 Dm phosphoesterase family protein, low similarity to SP:P95246 Phospholipase C 2 precursor (EC 3.1.4.3) {Mycobacterium tuberculosis}; contains Pfam profile PF04185: Phosphoesterase family 2135 At3g48680 D1 bacterial transferase hexapeptide repeat-containing protein, contains Pfam profile PF00132: Bacterial transferase hexapeptide (four repeats); ferripyochelin binding protein - Methanobacterium thermoautotrophicum, EMBL:AE000918.1 2136 At3g48690 D1, D2, Dm expressed protein, similar to PrMC3 (Pinus radiata) GI:5487873 2137 At3g48720 D1, D2, Dm transferase family protein, similar to hypersensitivity-related hsr201 protein - Nicotiana tabacum,PIR2:T03274; contains Pfam transferase family domain PF00248 2138 At3g48730 D1, D2, Dm glutamate-1-semialdehyde 2,1-aminomutase 2 (GSA 2) / glutamate-1-semialdehyde aminotransferase 2 (GSA-AT 2), identical to GSA2 (SP:Q42522) 2139 At3g48740 D1, Dm nodulin MtN3 family protein, similar to MtN3 GI:1619602 (root nodule development) from (Medicago truncatula) 2140 At3g48750 D1, Dm CDKA;1_CDC2A_CDC2AAT_CDK2__A-type cyclin-dependent kinase. Together with its specific inhibitor, the Kip-related protein, KRP2 they regulate the mitosis-to-endocycle transition during leaf development. 2141 At3g48850 Dm mitochondrial phosphate transporter, putative, similar to mitochondrial phosphate transporter GI:3318617 from (Arabidopsis thaliana) 2142 At3g48890 D2, Dm ATMP2__cytochrome b5 domain-containing protein, similar to SP:O00264 Membrane associated progesterone receptor component (mPR) {Homo sapiens}; contains Pfam profile PF00173: Heme/Steroid binding domain 2143 At3g48930 D1, Dm EMB1080__40S ribosomal protein S11 (RPS11A) 2144 At3g49010 D1, D2, Dm ATBBC1_BBC1_RSU2__60S ribosomal protein L13 (RPL13B) / breast basic conserved protein 1- related (BBC1) 2145 At3g49040 D2, Dm F-box family protein, contains F-box domain Pfam:PF00646 2146 At3g49120 D1, D2, Dm PRXCB__peroxidase, putative, identical to peroxidase (Arabidopsis thaliana) gi:405611:emb:CAA50677 2147 At3g49240 D2 EMB1796__pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat 2148 At3g49260 D1, Dm calmodulin-binding family protein, low similarity to SF16 protein (Helianthus annuus) GI:560150; contains Pfam profile PF00612: IQ calmodulin-binding motif 2149 At3g49490 D2, Dm expressed protein 2150 At3g49560 D1, D2, Dm mitochondrial import inner membrane translocase subunit Tim17/Tim22/Tim23 family protein, contains Pfam PF02466: Mitochondrial import inner membrane translocase subunit Tim17 2151 At3g49630 Dm 2-oxoacid-dependent oxidase, putative, strong similarity to partial cds of 2-oxoacid-dependent oxidase (din11) from GI:10834554 (Arabidopsis thaliana) 2152 At3g49670 D2, Dm leucine-rich repeat transmembrane protein kinase, putative, CLAVATA1 receptor kinase, Arabidopsis thaliana, EMBL:ATU96879 2153 At3g49720 D2 expressed protein 2154 At3g49910 D2, Dm 60S ribosomal protein L26 (RPL26A), 60S RIBOSOMAL PROTEIN L26, Brassica rapa, EMBL:BRD495 2155 At3g49960 D2 peroxidase, putative, identical to peroxidase ATP21a (Arabidopsis thaliana) gi:1546696:emb:CAA67339 2156 At3g50000 D2, Dm CKA2__casein kinase II alpha chain 2, identical to casein kinase II, alpha chain 2 (CK II) (Arabidopsis thaliana) SWISS-PROT:Q08466 2157 At3g50080 D2 VFB2__F-box family protein (FBL16), contains similarity to SKP1 interacting partner 2 GI:10716949 from (Arabidopsis thaliana); contains Pfam profile: PF00646 F-box domain 2158 At3g50290 Dm HXXXD-type acyl-transferase family protein; FUNCTIONS IN: transferase activity, transferring acyl groups other than amino-acyl groups; 2159 At3g50340 D1, D2, Dm expressed protein, predicted protein, Arabidopsis thaliana 2160 At3g50410 D2, Dm OBP1__Dof-type zinc finger domain-containing protein 2161 At3g50440 Dm similar to esterase, putative [Arabidopsis thaliana] (TAIR:At2g23620.1); similar to methyl jasmonate esterase [Solanum tuberosum] (GB:AAV87151.1); contains InterPro domain Esterase/lipase/thioesterase (InterPro:IPR000379); contains InterPro domain Alpha/beta hydrolase fold (InterPro:IPR000073) 2162 At3g50480 D2 HR4__broad-spectrum mildew resistance RPW8 family protein, contains Pfam PF05659: Arabidopsis broad-spectrum mildew resistance protein RPW8 2163 At3g50690 D1 leucine-rich repeat family protein 2164 At3g50700 D2 zinc finger (C2H2 type) family protein, contains Pfam domain, PF00096: Zinc finger, C2H2 type

2165 At3g50760 D2, Dm similar to glycosyl transferase family 8 protein [Arabidopsis thaliana] (TAIR:At1g19300.1); similar to putative Avr9/Cf-9 rapidly elicited protein 231 [Oryza sativa (japonica cultivar- group)] (GB:BAD45664.1); contains InterPro domain Glycosyl transferase, family 8 (InterPro:IPR002495) 2166 At3g50830 D2, Dm COR413-PM2_ATCOR413-PM2__stress-responsive protein, putative, similar to cold acclimation WCOR413-like protein gamma form (Hordeum vulgare) gi:18449100:gb:AAL69988; similar to stress- regulated protein SAP1 (Xerophyta viscosa) gi:21360378:gb:AAM47505; identical to cDNA cold acclimation protein WCOR413-like protein beta form GI:10121842 2167 At3g50840 D1, D2, Dm phototropic-responsive NPH3 family protein, contains NPH3 family domain, Pfam:PF03000 2168 At3g50910 D2, Dm expressed protein 2169 At3g50970 D1, D2, Dm XERO2__dehydrin xero2 (XERO2) / low-temperature-induced protein LTI30 (LTI30), identical to dehydrin Xero 2 (Low-temperature-induced protein LTI30) (Arabidopsis thaliana) SWISS- PROT:P42758 2170 At3g50990 D2, Dm similar to peroxidase 72 (PER72) (P72) (PRXR8) [Arabidopsis thaliana] (TAIR:At5g66390.1); similar to putative peroxidase [Oryza sativa (japonica cultivar-group)] (GB:NP_918204.1); contains InterPro domain Haem peroxidase (InterPro:IPR002016); contains InterPro domain Plant peroxidase (InterPro:IPR000823) 2171 At3g51000 D1, D2, Dm epoxide hydrolase, putative, similar to epoxide hydrolase (Glycine max) GI:2764806; contains Pfam profile PF00561: hydrolase, alpha/beta fold family 2172 At3g51030 D1, D2, Dm ATTRX H1_ATTRX1__| Symbol: ATTRX H1 | thioredoxin H-type 1 (TRX-H-1), identical to SP:P29448 Thioredoxin H-type 1 (TRX-H-1) {Arabidopsis thaliana} | chr3:18961981-18962984 REVERSE | Aliases: F24M12.70, THIOREDOXIN H1, ATTRX H1 2173 At3g51130 D2 expressed protein, contains Pfam PF03676: Uncharacterised protein family (UPF0183) 2174 At3g51240 D1, Dm F3H_TT6__naringenin 3-dioxygenase / flavanone 3-hydroxylase (F3H), identical to GI:3790548 2175 At3g51270 D1 RIO1 family protein, contains Pfam profile PF01163: RIO1 family 2176 At3g51470 Dm protein phosphatase 2C, putative / PP2C, putative, protein phosphatase-2C, Mesembryanthemum crystallinum, EMBL:AF075580 2177 At3g51510 D2, Dm expressed protein 2178 At3g51600 D2 LTP5__nonspecific lipid transfer protein 5 (LTP5), identical to SP:Q9XFS7 Nonspecific lipid- transfer protein 5 (LTP 5) {Arabidopsis thaliana} 2179 At3g51630 Dm WNK5_ZIK1__protein kinase family protein, contains Pfam profile: PF00069 protein kinase domain

2180 At3g51660 Dm macrophage migration inhibitory factor family protein / MIF family protein, contains Pfam profile: PF01187 Macrophage migration inhibitory factor family(MIF) 2181 At3g51730 D1, D2, Dm saposin B domain-containing protein, contains Pfam profiles: PF00026 eukaryotic aspartyl protease, PF03489 surfactant protein B, PF05184 saposin-like type B, region 1 2182 At3g51750 D2 expressed protein 2183 At3g51800 D1, D2, Dm ATG2__metallopeptidase M24 family protein, similar to SP:P50580 Proliferation-associated protein 2G4 {Mus musculus}; contains Pfam profile PF00557: metallopeptidase family M24 2184 At3g51830 D1, Dm ATG5__phosphoinositide phosphatase family protein, contains similarity to phosphoinositide phosphatase SAC1 (Rattus norvegicus) gi:11095248:gb:AAG29810; contains Pfam domain, PF02383: SacI homology domain ; Contains nonconsensus AT/AA splice site at intron 7 2185 At3g51895 D1, D2, Dm SULTR3;1_AST12_ATST1__sulfate transporter (ST1), identical to sulfate transporter (Arabidopsis thaliana) GI:2285885 2186 At3g51920 D2 CAM9__calmodulin-9 (CAM9), identical to calmodulin 9 GI:5825602 from (Arabidopsis thaliana); contains Pfam profile PF00036: EF hand 2187 At3g51930 Dm transducin family protein / WD-40 repeat family protein, contains 7 WD-40 repeats (PF00400); myosin heavy chain kinase B (SP:P90648)(GI:1903458) (Dictyostelium discoideum) 2188 At3g52070 D2 expressed protein 2189 At3g52100 D2, Dm PHD finger family protein, contains Pfam profile PF00628: PHD-finger 2190 At3g52130 D1, D2, Dm protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, similar to cysteine-rich 5B protein - Lycopersicon esculentum, PIR2:S39552 (GI:415833); contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 2191 At3g52155 D1 expressed protein 2192 At3g52180 D1, D2, Dm protein tyrosine phosphatase/kinase interaction sequence protein (PTPKIS1), identical to PTPKIS1 protein (Arabidopsis thaliana) GI:11595504; contains Pfam profile PF00782: Dual specificity phosphatase, catalytic domain 2193 At3g52230 D2, Dm expressed protein 2194 At3g52340 D1, Dm SPP2__sucrose-phosphatase 2 (SPP2), identical to sucrose-phosphatase (SPP2) (Arabidopsis thaliana) GI:13811669; supporting cDNA gi:13811668:gb:AF356816.1:AF356816 2195 At3g52360 D1, D2, Dm expressed protein 2196 At3g52380 D1, D2, Dm PDE322_CP33__33 kDa ribonucleoprotein, chloroplast, putative / RNA-binding protein cp33, putative, similar to chloroplast RNA-binding protein (cp33) GB:BAA06523 (Arabidopsis thaliana) (Plant Mol. Biol. 27 (3), 529-539 (1995)); contains InterPro entry IPR000504: RNA-binding region RNP-1 (RNA recognition motif) (RRM) 2197 At3g52500 D1, D2, Dm aspartyl protease family protein, contains Pfam PF00026: eukaryotic aspartyl protease 2198 At3g52580 D1, Dm 40S ribosomal protein S14 (RPS14C), ribosomal protein S14 -Zea mays,PIR2:A30097 2199 At3g52590 D1 EMB2167_UBQ1__ubiquitin extension protein 1 (UBQ1) / 60S ribosomal protein L40 (RPL40B), identical to GI:166929, GI:166930 2200 At3g52800 D1, D2, Dm zinc finger (AN1-like) family protein, contains Pfam domain, PF01428: AN1-like Zinc finger 2201 At3g52840 Dm beta-galactosidase, putative / lactase, putative, similar to beta-galactosidase precursor GI:3869280 from (Carica papaya) 2202 At3g52850 D2, Dm ATELP1_ATELP_BP-80_VSR-1__vacuolar sorting receptor, putative, nearly identical to vacuolar sorting receptor homolog (GP:1737218) (Arabidopsis thaliana) 2203 At3g52880 D1, D2, Dm ATMDAR1__monodehydroascorbate reductase, putative, monodehydroascorbate reductase (NADH), Lycoperison esculentum, PIR:T06407 2204 At3g52890 D1 KIPK__protein kinase (KIPK), identical to protein kinase KIPK (KCBP-interacting protein kinase) (Arabidopsis thaliana) gi:7716430:gb:AAF68383 2205 At3g52930 D1, D2, Dm fructose-bisphosphate aldolase, putative, similar to SP:O65735:ALF_CICAR Fructose-bisphosphate aldolase, cytoplasmic isozyme {Cicer arietinum}, cytosolic aldolase (Fragaria x ananassa) GI:10645188; contains Pfam profile PF00274 Fructose-bisphosphate aldolase class-I 2206 At3g52940 D1, D2, Dm FK_ELL1_HYD2__C-14 sterol reductase / delta(14)-sterol reductase / FACKEL (FK), identical to gi:9082182 2207 At3g52960 Dm peroxiredoxin type 2, putative, similar to type 2 peroxiredoxin (Brassica rapa subsp. pekinensis) GI:4928472; contains Pfam profile: PF00578 AhpC/TSA (alkyl hydroperoxide reductase and thiol-specific antioxidant) family 2208 At3g53020 D2 RPL24B_STV1_RPL24_RPL24B__Regulated by TCP20. 2209 At3g53200 D2 myb family transcription factor (MYB27), similar to myb-related DNA-binding protein GI:6467223 from (Arabidopsis thaliana); contains PFAM profile: myb DNA binding domain PF00249

2210 At3g53220 D2 thioredoxin family protein, low similarity to SP:P29451 Thioredoxin (Rhesus macaque) {Macaca mulatta}; contains Pfam profile: PF00085 Thioredoxin 2211 At3g53280 D1, Dm CYP71B5__cytochrome P450 71B5 (CYP71B5), Identical to Cytochrome P450 71B5 (SP:O65784) (Arabidopsis thaliana) 2212 At3g53410 Dm zinc finger (C3HC4-type RING finger) family protein, contains Pfam domain: PF00097: Zinc finger, C3HC4 type (RING finger) 2213 At3g53420 D1, Dm PIP2A_PIP2_PIP2;1__plasma membrane intrinsic protein 2A (PIP2A) / aquaporin PIP2.1 (PIP2.1), identical to plasma membrane intrinsic protein 2A SP: P43286 from (Arabidopsis thaliana) 2214 At3g53430 D1, D2, Dm 60S ribosomal protein L12 (RPL12B), 60S RIBOSOMAL PROTEIN L12, Prunus armeniaca, SWISSPROT:RL12_PRUAR 2215 At3g53460 D1, D2, Dm CP29__29 kDa ribonucleoprotein, chloroplast / RNA-binding protein cp 29, nearly identical to SP:Q43349 29 kDa ribonucleoprotein, chloroplast precursor (RNA-binding protein cp29) {Arabidopsis thaliana} 2216 At3g53470 D2 expressed protein, ribosomal protein S25, cytosolic, Arabidopsis thaliana, PIR:T08568 2217 At3g53500 D2 RSZ32__zinc knuckle (CCHC-type) family protein, contains Pfam domain PF00098: Zinc knuckle 2218 At3g53560 D2 chloroplast lumen common family protein 2219 At3g53580 D1, D2, Dm diaminopimelate epimerase family protein, contains Pfam profile PF01678: Diaminopimelate epimerase 2220 At3g53650 D1, Dm histone H2B, putative, similar to histone H2B from Lycopersicon esculentum, PIR:T06389 GI:3021483, Gossypium hirsutum SP:O22582, Capsicum annuum SP:O49118; contains Pfam profile PF00125 Core histone H2A/H2B/H3/H4 2221 At3g53710 D2, Dm ARF GAP-like zinc finger-containing protein ZIGA2 (ZIGA2), nearly identical to ARF GAP-like zinc finger-containing protein ZIGA2 from GI:10441356 (Arabidopsis thaliana); contains InterPro accession IPR001164: Human Rev interacting-like protein (hRIP) 2222 At3g53750 D1, Dm ACT3__actin 3 (ACT3), identical to SP:P53493 Actin 3 {Arabidopsis thaliana}; supported by full-length cDNA: Ceres: 19581. 2223 At3g53870 D1, D2, Dm 40S ribosomal protein S3 (RPS3B), ribosomal protein S3a - Xenopus laevis, PIR:R3XL3A 2224 At3g53890 D1, D2, Dm 40S ribosomal protein S21 (RPS21B), ribosomal protein S21, cytosolic - Oryza sativa, PIR:S38357 2225 At3g53900 D1, Dm uracil phosphoribosyltransferase, putative / UMP pyrophosphorylase, putative / UPRTase, putative, similar to SP:P50926 Uracil phosphoribosyltransferase (EC 2.4.2.9) (UMP pyrophosphorylase) (UPRTase) {Lactococcus lactis}; contains Pfam profile PF00156: Phosphoribosyl transferase domain 2226 At3g53920 D2 SIGC_SIG3__RNA polymerase sigma subunit SigC (sigC) / sigma factor 3 (SIG3), identical to sigma factor SigC (Arabidopsis thaliana) GI:5478585, sigma factor 3 (SIG3) (Arabidopsis thaliana) GI:2353175, plastid RNA polymerase sigma-subunit (Arabidopsis thaliana) GI:2398853; contains Pfam profiles PF04545: Sigma-70, region 4, PF04539: Sigma-70 region 3, PF04542: Sigma-70 region 2 2227 At3g53970 D1, Dm proteasome inhibitor-related, similar to proteasome inhibitor PI31 subunit (hPI31) SP:Q92530 from (Homo sapiens) 2228 At3g53980 D1, D2, Dm protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 2229 At3g53990 D1, D2, Dm universal stress protein (USP) family protein, contains Pfam PF00582: universal stress protein family 2230 At3g54050 D1, Dm fructose-1,6-bisphosphatase, putative / D-fructose-1,6-bisphosphate 1-phosphohydrolase, putative / FBPase, putative, strong similarity to fructose-1,6-bisphosphatase (Brassica napus) GI:289367; identical to SP:P25851 Fructose-1,6-bisphosphatase, chloroplast precursor (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase) (FBPase) {Arabidopsis thaliana}; contains Pfam profile PF00316: fructose-1,6-bisphosphatase 2231 At3g54090 D2 pfkB-type carbohydrate kinase family protein, contains Pfam profile: PF00294 pfkB family carbohydrate kinase 2232 At3g54110 D2 ATPUMP1_PUMP_UCP_UCP2__plant uncoupling mitochondrial protein (PUMP), identical to plant uncoupling mitochondrial protein (Arabidopsis thaliana) GI:3115108 2233 At3g54140 D2, Dm proton-dependent oligopeptide transport (POT) family protein, contains Pfam profile: PF00854 POT family 2234 At3g54210 D1, Dm ribosomal protein L17 family protein, contains Pfam profile: PF01196 ribosomal protein L17 2235 At3g54340 D2 AP3__floral homeotic protein APETALA3 (AP3) 2236 At3g54360 D2, Dm expressed protein, DNA-binding Mel-18 protein, Homo sapiens, PIR:JN0717 2237 At3g54400 D1, D2, Dm aspartyl protease family protein, contains Pfam profile: PF00026 eukaryotic aspartyl protease 2238 At3g54470 D2 uridine 5`-monophosphate synthase / UMP synthase (PYRE-F) (UMPS), identical to SP:Q42586 Uridine 5`-monophosphate synthase (UMP synthase) (Includes: Orotate phosphoribosyltransferase (EC 2.4.2.10) (OPRtase); Orotidine 5`- phosphate decarboxylase (EC 4.1.1.23) (OMPdecase)) {Arabidopsis thaliana} 2239 At3g54500 D2 expressed protein 2240 At3g54590 D1, D2, Dm ATHRGP1__proline-rich extensin-like family protein, contains proline-rich extensin domains, INTERPRO:IPR002965 2241 At3g54660 D1, D2, Dm GR_EMB2360__gluthatione reductase, chloroplast, nearly identical to SP:P42770 Glutathione reductase, chloroplast precursor (EC 1.8.1.7) (GR) (GRASE) {Arabidopsis thaliana}; identical to cDNA glutathione reductase GI:451197 2242 At3g54750 D2, Dm expressed protein 2243 At3g54810 D2 zinc finger (GATA type) family protein, GATA transcription factor 3, Arabidopsis thaliana, Y13650 2244 At3g54840 D2 ARA6__Rab GTPase (ARA6), identical to small GTPase Ara6 (Arabidopsis thaliana) GI:13160603 2245 At3g54920 D1, D2, Dm PMR6__pectate lyase, putative / powdery mildew susceptibility protein (PMR6), identical to powdery mildew susceptibility protein (Arabidopsis thaliana) GI:22506901; similar to pectate lyase 2 GP:6606534 from (Musa acuminata) 2246 At3g55010 D2, Dm phosphoribosylformylglycinamidine cyclo-ligase, chloroplast / phosphoribosyl-aminoimidazole synthetase / AIR synthase (PUR5), identical to phosphoribosylformylglycinamidine cyclo-ligase, chloroplast precursor SP:Q05728 from (Arabidopsis thaliana); contains Pfam profiles: PF02769 AIR synthase related protein, C-terminal domain, PF00586 AIR synthase related protein, N- terminal domain 2247 At3g55020 Dm RabGAP/TBC domain-containing protein, low similarity to SP:Q9BXI6 EBP50-PDZ interactor of 64 kDa (EPI64 protein) {Homo sapiens}; contains Pfam profile PF00566: TBC domain 2248 At3g55030 Dm phosphatidylglycerolphosphate synthase, putative, similar to phosphatidylglycerolphosphate synthase GI:13365519 from (Arabidopsis thaliana); contains non-consensus CG acceptor splice site at exon 4 2249 At3g55070 D1, Dm expressed protein 2250 At3g55170 D1, D2, Dm 60S ribosomal protein L35 (RPL35C), various ribosomal L35 proteins 2251 At3g55250 Dm expressed protein, predicted pectate-lyase, Arabidopsis thaliana, PIR:T06728 2252 At3g55280 D1, D2, Dm 60S ribosomal protein L23A (RPL23aB), various ribosomal L23a proteins 2253 At3g55290 D1, Dm short-chain dehydrogenase/reductase (SDR) family protein, contains similarity to 3-oxoacyl- (acyl-carrier protein) reductase SP:P51831 from (Bacillus subtilis) 2254 At3g55330 D2, Dm photosystem II reaction center PsbP family protein, contains Pfam profile PF01789: PsbP 2255 At3g55360 D2 CER10_ECR__Enoyl-CoA reductase (ECA) is involved in all very long chain fatty acids (VLCFA) elongation reactions that are required for cuticular wax, storage lipid and sphingolipid metabolism. The protein is located in the ER, but in contrast to its yeast homolog TSC13 is not particularly enriched in the nuclear envelope-vacuole junction. Mutants in this gene show abnormal organ morphology and stem glossiness. Cells in all tissues are only about 1/3 of the size of wild type cells. The morphological changes are most likely to result from the reduction in the VLCFA content of sphingolipids. Mutants also show abnormalities in the endocytic membrane organization and transport. 2256 At3g55400 D1, Dm methionyl-tRNA synthetase / methionine--tRNA ligase / MetRS (cpMetRS), identical to methionyl- tRNA synthetase MEtRS (Arabidopsis thaliana) GI:2266985 2257 At3g55460 Dm SCL30__SC35-like splicing factor, 30 kD (SCL30), nearly identical to SC35-like splicing factor SCL30, 30 kD (Arabidopsis thaliana) GI:9843657; Serine/arginine-rich protein/putative splicing factor, Arabidopdis thaliana, EMBL:AF099940; contains Pfam profile PF00076: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 2258 At3g55600 Dm expressed protein, predicted proteins, Arabidopsis thaliana 2259 At3g55605 D1 mitochondrial glycoprotein family protein / MAM33 family protein, low similarity to SUAPRGA1 (Emericella nidulans) GI:6562379; contains Pfam profile PF02330: Mitochondrial glycoprotein 2260 At3g55610 D1, D2, Dm delta 1-pyrroline-5-carboxylate synthetase B / P5CS B (P5CS2), identical to SP:P54888 2261 At3g55620 D2 EMB1624__eukaryotic translation initiation factor 6, putative / eIF-6, putative, similar to SP:O55135 Eukaryotic translation initiation factor 6 (eIF-6) (B4 integrin interactor) {Mus musculus}; contains Pfam profile PF01912: eIF-6 family 2262 At3g55770 D1 LIM domain-containing protein, similar to pollen specific LIM domain protein 1b (Nicotiana tabacum) GI:6467905, PGPS/D1 (Petunia x hybrida) GI:4105772; contains Pfam profile PF00412: LIM domain 2263 At3g55800 D1, Dm SBPASE__Encodes the chloroplast enzyme sedoheptulose-1,7-bisphosphatase (SBPase), involved in the carbon reduction of the Calvin cycle. Increase in SBPase activity in transgenic lines accumulate up to 50% more sucrose and starch than wild-type. 2264 At3g55840 D2, Dm expressed protein 2265 At3g55900 D2 F-box family protein, putative protein, Arabidopsis thaliana ; similar to SKP1 interacting partner 2 (SKIP2) TIGR_Ath1:At5g67250 2266 At3g55980 D1, D2 zinc finger (CCCH-type) family protein, contains Pfam domain, PF00642: Zinc finger C-x8-C-x5- C-x3-H type (and similar) and Pfam domain, PF00023: Ankyrin repeat 2267 At3g56010 D1 expressed protein 2268 At3g56050 D2, Dm protein kinase family protein, contains Pfam domain, PF00069: Protein kinase domain 2269 At3g56070 D2 ROC2__peptidyl-prolyl cis-trans isomerase, putative / cyclophilin, putative / rotamase, putative, similar to peptidyl-prolyl cis-trans isomerase, PPIase (cyclophilin, cyclosporin A- binding protein) (Catharanthus roseus) SWISS-PROT:Q39613 2270 At3g56080 D2, Dm dehydration-responsive protein-related, similar to early-responsive to dehydration stress ERD3 protein (Arabidopsis thaliana) GI:15320410; contains Pfam profile PF03141: Putative methyltransferase 2271 At3g56150 D1, D2, Dm EIF3C_ATEIF3C-1_ATTIF3C1_EIF3C-1_TIF3C1__eukaryotic translation initiation factor 3 subunit 8 / eIF3 p110 / eIF3c / p105 (TIF3C1), nearly identical to SP:O49160 Eukaryotic translation initiation factor 3 subunit 8 (eIF3 p110) (eIF3c) (p105) {Arabidopsis thaliana} 2272 At3g56240 D1, D2, Dm CCH_ATX1_COPPER CHAPERONE__copper homeostasis factor / copper chaperone (CCH) (ATX1), identical to gi:3168840 Pfam profile PF00403: Heavy-metal-associated domain 2273 At3g56290 D1, D2, Dm expressed protein 2274 At3g56310 D1, D2, Dm alpha-galactosidase, putative / melibiase, putative / alpha-D-galactoside galactohydrolase, putative, similar to alpha-galactosidase SP:Q42656 from (Coffea arabica) 2275 At3g56340 D1, D2, Dm 40S ribosomal protein S26 (RPS26C), several 40S ribosomal protein S26 2276 At3g56360 D1, D2, Dm expressed protein, unknown protein 110K5.12 - Sorghum bicolor, TREMBL:AF124045_5 2277 At3g56370 Dm leucine-rich repeat transmembrane protein kinase, putative, leucine-rich receptor-like protein kinase - Malus domestica, EMBL:AF053127 2278 At3g56400 D2 WRKY70_ATWRKY70__WRKY family transcription factor, DNA-binding protein 4 WRKY4 - Nicotiana tabacum, EMBL:AF193771 2279 At3g56450 D2 ALPHA-SNAP1__alpha-soluble NSF attachment protein 1 / alpha-SNAP1 (ASNAP1), identical to alpha-soluble NSF attachment protein 1 (Alpha-SNAP1) (N- ethylmaleimide-sensitive factor attachment protein, alpha 1) (Swiss-Prot:Q9LXZ5) (Arabidopsis thaliana) 2280 At3g56650 D1, Dm thylakoid lumenal 20 kDa protein, SP:Q9LXX5; PMID:11719511; F22K20.16 - Arabidopsis thaliana, EMBL:AC002291; 2281 At3g56680 Dm expressed protein 2282 At3g56770 D2 basic helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain 2283 At3g56800 D2 CAM3_ACAM-3__calmodulin-2/3/5 (CAM3), identical to calmodulin GI:474183 from (Arabidopsis thaliana); almost identical to calmodulin-2/3/5 SP:P25069 (Arabidopsis thaliana) 2284 At3g56820 D1, D2, Dm expressed protein 2285 At3g56860 D2, Dm UBP1 interacting protein 2a (UBA2a), identical to UBP1 interacting protein 2a (Arabidopsis thaliana) GI:19682816; contains InterPro entry IPR000504: RNA-binding region RNP-1 (RNA recognition motif) (RRM) 2286 At3g56910 D1, D2, Dm expressed protein 2287 At3g57020 D1, D2, Dm strictosidine synthase family protein, similar to strictosidine synthase (Rauvolfia serpentina)(SP:P15324) 2288 At3g57150 D2, Dm NAP57__dyskerin, putative / nucleolar protein NAP57, putative, similar to SP:P40615 Dyskerin (Nucleolar protein NAP57) {Rattus norvegicus}; contains Pfam profiles PF01509: TruB family pseudouridylate synthase (N terminal domain), PF01472: PUA domain; supporting cDNA gi:8901185:gb:AF234984.2:AF234984 2289 At3g57180 Dm expressed protein 2290 At3g57330 D1, D2, Dm calcium-transporting ATPase, plasma membrane-type, putative / Ca2+-ATPase, putative (ACA11), identical to SP:Q9M2L4:ACAB_ARATH Potential calcium-transporting ATPase 11, plasma membrane- type (EC 3.6.3.8) (Ca(2+)-ATPase isoform 11) {Arabidopsis thaliana}; strong similarity to calmodulin-stimulated calcium-ATPase (Brassica oleracea) GI:1805654 Belongs to plant 2B ATPase 聮s with an N-terminal autoinhibitor. 2291 At3g57340 D2, Dm DNAJ heat shock N-terminal domain-containing protein, similar to SP:Q9QYI4 DnaJ homolog subfamily B member 12 Mus musculus; contains Pfam profile PF00226 DnaJ domain 2292 At3g57410 D1, D2, Dm VLN3__villin 3 (VLN3), nearly identical to villin 3 (VLN3) (Arabidopsis thaliana) GI:3415117 2293 At3g57450 D2 expressed protein 2294 At3g57520 D1, D2, Dm alkaline alpha galactosidase, putative, similar to alkaline alpha galactosidase II (Cucumis melo) GI:29838631; contains Pfam profile PF05691: Raffinose synthase or seed imbibition protein Sip1 2295 At3g57540 D2, Dm remorin family protein, contains Pfam domain, PF03763: Remorin, C-terminal region 2296 At3g57550 D1, D2, Dm AGK2_GK-2__guanylate kinase 2 (GK-2), identical to guanylate kinase (GK-2) (Arabidopsis thaliana) gi:7861798:gb:AAF70409 2297 At3g57560 D1 aspartate/glutamate/uridylate kinase family protein, similar to acetylglutamate kinase from Porphyra purpurea (SP:P31595), Campylobacter jejuni (GI:6650364) contains Pfam profile PF00696: Amino acid kinase family 2298 At3g57680 D1, Dm peptidase S41 family protein, similar to PSII D1 protein processing enzyme (GI::7268527) (Arabidopsis thaliana); similar to SP:Q55669 Carboxyl-terminal processing protease precursor (Photosystem II D1 protein processing peptidase) (EC 3.4.21.102) (strain PCC 6803) {Synechocystis sp.}; contains Pfam profile PF03572: Peptidase family S41B 2299 At3g57810 D1, D2, Dm expressed protein, similar to expressed protein [Arabidopsis thaliana] (TAIR:At2g38025.1); similar to hypothetical protein Haso02002274 [Haemophilus somnus 2336] (GB:ZP_00133718.2); contains InterPro domain OTU-like cysteine protease (InterPro:IPR003323) 2300 At3g57930 D2 expressed protein 2301 At3g57940 D2 expressed protein, contains Pfam profile PF05127: Putative ATPase (DUF699) 2302 At3g58020 D1 DNAJ heat shock N-terminal domain-containing protein, contains Pfam profile PF00226 DnaJ domain 2303 At3g58070 Dm zinc finger (C2H2 type) family protein, contains Pfam domain, PF00096: Zinc finger, C2H2 type

2304 At3g58120 D1, Dm bZIP transcription factor family protein, contains Pfam profile: PF00170 bZIP transcription factor ;supported by cDNA gi:15100054:gb:AF401300.1:AF401300 2305 At3g58490 D2, Dm phosphatidic acid phosphatase family protein / PAP2 family protein, similar to sphingosine-1- phosphate phosphohydrolase from (Mus musculus) GI:9623190, (Homo sapiens) GI:23345324; contains Pfam profile PF01569: PAP2 superfamily 2306 At3g58500 D1, Dm PP2A-3_EP7__serine/threonine protein phosphatase PP2A-4 catalytic subunit (PP2A4), identical to SP:P48578 Serine/threonine protein phosphatase PP2A-4 catalytic subunit (EC 3.1.3.16) (Protein phosphatase 2A isoform 4) {Arabidopsis thaliana}; contains Pfam profile PF00149: Ser/Thr protein phosphatase 2307 At3g58560 D2 endonuclease/exonuclease/phosphatase family protein, similar to SP:P31384 Glucose-repressible alcohol dehydrogenase transcriptional effector (Carbon catabolite repressor protein 4) {Saccharomyces cerevisiae}; contains Pfam profile PF03372: Endonuclease/Exonuclease/phosphatase family 2308 At3g58610 D1, D2, Dm ketol-acid reductoisomerase, identical to ketol-acid reductoisomerase, chloroplast precursor (EC 1.1.1.86) (Acetohydroxy-acid reductoisomerase) (Alpha-keto-beta-hydroxylacil reductoisomerase) (Swiss-Prot:Q05758) (Arabidopsis thaliana) 2309 At3g58660 D2, Dm 60S ribosomal protein-related, contains weak similarity to 60S ribosomal protein L10A (CSA-19) (NEDD-6) (Swiss-Prot:P53026) (Mus musculus) 2310 At3g58680 D1, D2, Dm ATMBF1B_MBF1B__ethylene-responsive transcriptional coactivator, putative, similar to ethylene- responsive transcriptional coactivator (Lycopersicon esculentum) gi:5669634:gb:AAD46402

2311 At3g58730 D1, D2, Dm vacuolar ATP synthase subunit D (VATD) / V-ATPase D subunit / vacuolar proton pump D subunit (VATPD), identical to Vacuolar ATP synthase subunit D (EC 3.6.3.14) (V-ATPase D subunit) (Vacuolar proton pump D subunit) (Swiss-Prot:Q9XGM1) (Arabidopsis thaliana) 2312 At3g58780 Dm AGL1_SHP1_AGL1__agamous-like MADS box protein AGL1 / shatterproof 1 (AGL1) (SHP1), identical to SP:P29381 Agamous-like MADS box protein AGL1 (Protein Shatterproof 1) {Arabidopsis thaliana} 2313 At3g58940 Dm F-box family protein, contains F-box domain Pfam:PF00646 2314 At3g59040 D1, D2, Dm pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat 2315 At3g59090 Dm expressed protein 2316 At3g59210 D2 F-box family protein, contains F-box domain Pfam:PF00646 2317 At3g59270 D2, Dm syntaxin-related family protein, contains a novel domain similar to F-box that is shared among other proteins in Arabidopsis; similar to proteins At1g56610, At3g54160, At1g47920 (syntaxin SYP81), At5g41830, At3g44180, At1g48390, At3g59270 (Arabidopsis thaliana) 2318 At3g59280 D1, Dm TXR1__signaling molecule-related, contains similarity to mitochondria-associated granulocyte macrophage CSF signaling molecule, mitochondrial precursor (CGI-136) (Mus musculus) SWISS- PROT:Q9CQV1 2319 At3g59400 D1 GUN4__expressed protein 2320 At3g59540 D1, D2, Dm 60S ribosomal protein L38 (RPL38B), 60S RIBOSOMAL PROTEIN L38 - Lycopersicon esculentum, EMBL:X69979 2321 At3g59660 D2 C2 domain-containing protein / GRAM domain-containing protein, low similarity to GLUT4 vesicle protein (Rattus norvegicus) GI:4193489; contains Pfam profiles PF00168: C2 domain, PF02893: GRAM domain 2322 At3g59910 D2 expressed protein 2323 At3g59920 Dm ATGDI2__Rab GDP dissociation inhibitor (GDI2), identical to Rab GDP dissociation inhibitor AtGDI2 (Arabidopsis thaliana) GI:2446981 2324 At3g59980 D1 tRNA-binding region domain-containing protein, similar to SP:O54873 Multisynthetase complex auxiliary component p43 (Contains: Endothelial-monocyte activating polypeptide II (EMAP-II) (Small inducible cytokine subfamily E member 1)) {Cricetulus griseus}; contains Pfam profile PF01588: Putative tRNA binding domain 2325 At3g60130 Dm glycosyl hydrolase family 1 protein / beta-glucosidase, putative (YLS1), contains Pfam PF00232 : Glycosyl hydrolase family 1 domain; TIGRFAM TIGR01233: 6-phospho-beta-galactosidase; similar to amygdalin hydrolase isoform AH I precursor (GI:16757966) (Prunus serotina); identical to cDNA YLS1 mRNA for beta-glucosidase, partial cds GI:13122279 2326 At3g60260 Dm phagocytosis and cell motility protein ELMO1-related, contains weak similarity to ELMO1 (Mus musculus) gi:16118551:gb:AAL14464 2327 At3g60300 D1, D2, Dm RWD domain-containing protein, contains weak similarity to RING finger protein 25 (RING finger protein AO7) (Swiss-Prot:Q9QZR0) (Mus musculus) 2328 At3g60320 D2, Dm P9L__expressed protein, contains Pfam profiles: PF04782: protein of unknown function (DUF632), PF04783: protein of unknown function (DUF630) 2329 At3g60340 D1 palmitoyl protein thioesterase family protein, palmitoyl-protein thioesterase precursor, Mus musculus, EMBL:AF071025 2330 At3g60420 D1, Dm expressed protein 2331 At3g60640 D2 autophagy 8g (APG8g), identical to autophagy 8g (Arabidopsis thaliana) GI:19912163; contains Pfam profile PF02991: Microtubule associated protein 1A/1B, light chain 3; supporting cDNA gi:19912162:dbj:AB073181.1: 2332 At3g60690 D1, D2, Dm auxin-responsive family protein, similar to auxin-induced protein SAUR-AC1 (GP:546362) (PIR:T06084)(Arabidopsis thaliana) PIR:T06084 2333 At3g60770 D1, D2, Dm 40S ribosomal protein S13 (RPS13A), AtRPS13A mRNA for cytoplasmic ribosomal protein S13, Arabidopsis thaliana,AB031739 2334 At3g60840 Dm microtubule associated protein (MAP65/ASE1) family protein, low similarity to protein regulating cytokinesis 1 (PRC1) (Homo sapiens) GI:2865521; contains Pfam profile PF03999: Microtubule associated protein (MAP65/ASE1 family) 2335 At3g61000 D2 2336 At3g61020 D2 pseudogene, similar to P0034A04.28, several hypothetical proteins 2337 At3g61110 D2, Dm ARS27A_ARS__40S ribosomal protein S27 (ARS27A), identical to cDNA ribosomal protein S27 (ARS27A) GI:4193381 2338 At3g61200 D1, D2, Dm thioesterase family protein, contains Pfam profile PF03061: thioesterase family protein 2339 At3g61220 D1, D2, Dm short-chain dehydrogenase/reductase (SDR) family protein, similar to carbonyl reductase GI:1049108 from (Mus musculus) 2340 At3g61240 D2, Dm DEAD/DEAH box helicase, putative (RH12), identical to cDNA DEAD box RNA helicase, RH12 GI:3776000 2341 At3g61260 Dm DNA-binding family protein / remorin family protein, similar to DNA-binding protein gi:601843 (Arabidopsis thaliana), remorin (Solanum tuberosum) GI:1881585; contains Pfam profiles PF03763: Remorin C-terminal region, PF03766: Remorin N-terminal region 2342 At3g61310 D1, Dm DNA-binding family protein, contains a AT hook motif (DNA binding motifs with a preference for A/T rich regions), Pfam:PF02178 2343 At3g61400 Dm 2-oxoglutarate-dependent dioxygenase, putative, similar to 2A6 (GI:599622) and tomato ethylene synthesis regulatory protein E8 (SP:P10967); 1-aminocyclopropane-1-carboxylate oxidase homolog - Arabidopsis thaliana, PIR:S59548 2344 At3g61410 D1 similar to protein kinase family protein / U-box domain-containing protein [Arabidopsis thaliana] (TAIR:At2g45910.1); similar to putative protein kinase [Oryza sativa (japonica cultivar-group)] (GB:AAP51741.1) 2345 At3g61440 Dm ARATH;BSAS3;1_ATCYSC1__encodes a cysteine synthase isomer. The isomer is however less effective in cysteine biosynthesis. It is involved in beta-cyanoalanine biosynthesis, a intermediate of cyanide detoxification pathway. 2346 At3g61460 D1, D2, Dm BRH1__zinc finger (C3HC4-type RING finger) family protein (BRH1), identical to BRH1 RING finger protein (Arabidopsis thaliana) GI:4689366; identical to cDNA BRH1 RING finger protein, GI:4689365 2347 At3g61470 D1, Dm LHCA2__chlorophyll A-B binding protein (LHCA2), identical to Lhca2 protein (Arabidopsis thaliana) GI:4741940; similar to chlorophyll A-B binding protein, chloroplast (Precursor) SP:P13869 from (Petunia hybrida); contains Pfam profile: PF00504 chlorophyll A-B binding protein 2348 At3g61560 Dm reticulon family protein (RTNLB6), contains Pfam profile PF02453: Reticulon 2349 At3g61600 D2, Dm ATPOB1__BTB/POZ domain-containing protein, contains Pfam PF00651: BTB/POZ domain; contains Interpro IPR000210/ PS50097: BTBB/POZ domain; similar to POZ/BTB containing-protein AtPOB1 (GI:12006855) (Arabidopsis thaliana); similar to actinfilin (GI:21667852) (Rattus norvegicus)

2350 At3g61640 D1, D2, Dm AGP20__arabinogalactan-protein (AGP20) 2351 At3g61710 D1, Dm autophagy protein Apg6 family, contains weak similarity to Beclin 1 (Coiled-coil myosin-like BCL2-interacting protein) (Protein GT197) (Swiss-Prot:Q14457) (Homo sapiens); contains Pfam profile PF04111: Autophagy protein Apg6 2352 At3g61770 D2 expressed protein, contains Pfam domain, PF02681: Uncharacterized BCR, COG1963 2353 At3g61820 D2 aspartyl protease family protein, contains Pfam domain, PF00026: eukaryotic aspartyl protease

2354 At3g61870 D1, Dm expressed protein, hypothetical protein - Synechocystis sp. (strain PCC 6803), PIR:S75899 2355 At3g61890 D1, D2, Dm ATHB-12_ATHB12__homeobox-leucine zipper protein 12 (HB-12) / HD-ZIP transcription factor 12, identical to homeobox-leucine zipper protein ATHB-12 (GI:6899887) (Arabidopsis thaliana) 2356 At3g62020 D2, Dm GLP10__germin-like protein (GLP10), identical to germin-like protein subfamily 2 member 4 (SP:Q9M263) 2357 At3g62030 D1, Dm ROC4__peptidyl-prolyl cis-trans isomerase, chloroplast / cyclophilin / rotamase / cyclosporin A-binding protein (ROC4), identical to peptidyl-prolyl cis-trans isomerase, chloroplast precursor, PPIase (cyclophilin, cyclosporin A-binding protein) (Arabidopsis thaliana) SWISS- PROT:P34791; identical to cDNA nuclear-encoded chloroplast stromal cyclophilin (ROC4) GI:405130 2358 At3g62090 D2 PIL2_PIF6__basic helix-loop-helix (bHLH) protein, putative, very strong similarity to PIF3 like basic Helix Loop Helix protein 2 (PIL2) (Arabidopsis thaliana) GI:22535494 2359 At3g62110 D1, D2, Dm glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family protein, weak similarity to polygalacturonase (Lycopersicon esculentum) GI:4325090; contains PF00295: Glycosyl hydrolases family 28 2360 At3g62120 D1, D2, Dm tRNA synthetase class II (G, H, P and S) family protein, similar to SP:P07814 Bifunctional aminoacyl-tRNA synthetase (Includes: Glutamyl-tRNA synthetase (EC 6.1.1.17) (Glutamate--tRNA ligase); Prolyl-tRNA synthetase (EC 6.1.1.15) (Proline--tRNA ligase)) {Homo sapiens}; contains Pfam profiles PF00587: tRNA synthetase class II core domain (G, H, P, S and T), PF03129: Anticodon binding domain 2361 At3g62190 D2 DNAJ heat shock N-terminal domain-containing protein, similar to SP:P39101 CAJ1 protein Saccharomyces cerevisiae; contains Pfam profile PF00226 DnaJ domain 2362 At3g62250 D1, D2, Dm ubiquitin extension protein 5 (UBQ5) / 40S ribosomal protein S27A (RPS27aC), identical to GI:166933, GI:166934 2363 At3g62490 D1 expressed protein, hypothetical proteins - Arabidopsis thaliana 2364 At3g62530 D1, D2, Dm PBS lyase HEAT-like repeat-containing protein, contains Pfam profile: PF03130 PBS lyase HEAT- like repeat 2365 At3g62550 D1, D2, Dm universal stress protein (USP) family protein, similar to ER6 protein (Lycopersicon esculentum) GI:5669654; contains Pfam profile PF00582: universal stress protein family 2366 At3g62650 D2, Dm expressed protein, putative mitochondrial carrier protein At2g47490 - Arabidopsis thaliana, EMBL:AC002535 2367 At3g62700 D1, D2, Dm ATMRP10__glutathione-conjugate transporter, putative, similar to glutathione-conjugate transporter AtMRP4 GI:2959767 from (Arabidopsis thaliana) 2368 At3g62720 D2 galactosyl transferase GMA12/MNN10 family protein, low similarity to alpha-1,2- galactosyltransferase, Schizosaccharomyces pombe (SP:Q09174) 2369 At3g62870 D1, D2, Dm 60S ribosomal protein L7A (RPL7aB), 60S RIBOSOMAL PROTEIN L7A - Oryza sativa, SWISSPROT:RL7A_ORYSA 2370 At3g62930 D2 glutaredoxin family protein, contains glutaredoxin domain, INTERPRO:IPR002109 2371 At3g63000 D1, Dm NPL4 family protein, contains Pfam domain, PF05021: NPL4 family 2372 At3g63120 Dm cyclin family protein, similar to cyclin 2 (Trypanosoma brucei) GI:7339572, cyclin 6 (Trypanosoma cruzi) GI:12005317; contains Pfam profile PF00134: Cyclin, N-terminal domain 2373 At3g63130 Dm RANGAP1__RAN GTPase activating protein 1 (RanGAP1), contains Pfam PF00560: Leucine Rich Repeat domains; identical to RAN GTPase activating protein 1 (GI:6708466)(Arabidopsis thaliana)

2374 At3g63140 Dm mRNA-binding protein, putative, similar to mRNA binding protein precursor (GI:26453355) (Lycopersicon esculentum) 2375 At3g63160 D1, D2, Dm expressed protein 2376 At3g63190 D1, Dm ribosome recycling factor, chloroplast, putative / ribosome releasing factor, chloroplast, putative, similar to SP:P82231 Ribosome recycling factor, chloroplast precursor (Ribosome releasing factor, chloroplast) (RRF) (CpFrr) (RRFHCP) {Spinacia oleracea}; contains Pfam profile PF01765: ribosome recycling factor 2377 At3g63210 D1, Dm MARD1__expressed protein, identical to senescence-associated protein SAG102 (GI::22331931) (Arabidopsis thaliana) (unpublished); contains Pfam profile PF04570: Protein of unknown function (DUF581) 2378 At3g63490 D1, Dm ribosomal protein L1 family protein, ribosomal protein L1, S.oleracea, EMBL:SORPL1 2379 At4g00050 D1, Dm basic helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain 2380 At4g00100 D1, Dm ATRPS13A_PFL2_RPS13__40S ribosomal protein S13 (RPS13A), similar to ribosomal protein S13; PF00312 (View Sanger Pfam): ribosomal protein S15; identical to cDNA AtRPS13A mRNA for cytoplasmic ribosomal protein S13 GI:6521011 2381 At4g00180 Dm YAB3__axial regulator YABBY3 (YABBY3), identical to YABBY3 (Arabidopsis thaliana) GI:4928753 2382 At4g00300 D1, D2, Dm fringe-related protein, + weak similarity to Fringe (Schistocerca gregaria)(GI:6573138);Fringe encodes an extracellular protein that regulates Notch signalling.

2383 At4g00310 Dm expressed protein 2384 At4g00330 D2, Dm CRCK2__protein kinase family protein, contains protein kinase domain, Pfam:PF00069 2385 At4g00355 D1, D2, Dm similar to expressed protein [Arabidopsis thaliana] (TAIR:At2g45980.1); similar to OSJNBa0019G23.5 [Oryza sativa (japonica cultivar-group)] (GB:XP_474580.1) 2386 At4g00370 D1, D2, Dm ANTR2__sugar transporter family protein, contains Pfam profile PF00083: major facilitator superfamily protein 2387 At4g00400 D2, Dm phospholipid/glycerol acyltransferase family protein 2388 At4g00510 D1, Dm cyclic nucleotide-binding domain-containing protein, contains Pfam profile: PF00027 cyclic nucleotide-binding domain 2389 At4g00720 D1 shaggy-related protein kinase theta / ASK-theta (ASK8), identical to shaggy-related protein kinase theta (ASK-theta) (Arabidopsis thaliana) SWISS-PROT:Q96287 2390 At4g00755 D1, D2, Dm F-box family protein, ; similar to SKP1 interacting partner 2 (SKIP2) TIGR_Ath1:At5g67250 2391 At4g00780 D2 meprin and TRAF homology domain-containing protein / MATH domain-containing protein, contains Pfam profile PF00917: MATH domain 2392 At4g00860 Dm ATOZI1__stress-related ozone-induced protein (OZI1) / stress-related ozone-responsive protein, identical to stress-related ozone-induced protein AtOZI1 (mRNA corresponding to this gene accumulates in response to ozone stress and pathogen (bacterial) infection); putative pathogenesis-related protein (GI:790583) (Arabidopsis thaliana) 2393 At4g00880 D1 auxin-responsive family protein, similar to small auxin up RNA (GI:546362) {Arabidopsis thaliana} 2394 At4g00970 D1, Dm protein kinase family protein, contains Pfam domain PF00069: Protein kinase domain 2395 At4g01026 D1, D2, Dm expressed protein 2396 At4g01060 D2, Dm myb family transcription factor, contains PFAM profile: PF00249 myb-like DNA binding domain 2397 At4g01070 D1, D2, Dm the glycosyltransferase (UGT72B1) is involved in metabolizing xenobiotica (chloroaniline and chlorophenole). Comparison between wild type and knock-out mutant demonstrates the central role of this gene for metabolizing chloroaniline but significantly less for chlorophenole. The glucosyltransferase preferred UDP-xylose over UDP-glucose indicating its (additional) functioning as a xylosyltransferase in planta 2398 At4g01140 D2, Dm expressed protein 2399 At4g01310 D1, D2, Dm ribosomal protein L5 family protein, contains Pfam profiles PF00673: ribosomal L5P family C- terminus, PF00281: ribosomal protein L5 2400 At4g01330 D2, Dm protein kinase family protein, contains protein kinase domain, Pfam:PF00069; contains serine/threonine protein kinase domain, INTERPRO:IPR002290 2401 At4g01370 D2 ATMPK4_MPK4__mitogen-activated protein kinase, putative / MAPK, putative (MPK4), identical to mitogen-activated protein kinase homolog (AtMPK4)(Arabidopsis thaliana) SWISS-PROT:Q39024; PMID:12119167 2402 At4g01470 D1, D2, Dm GAMMA-TIP3_TIP1;3__major intrinsic family protein / MIP family protein, contains Pfam profile: MIP PF00230 2403 At4g01550 D2 ANAC069__no apical meristem (NAM) family protein, similar to NAC1 (GI:7716952) {Medicago truncatula}; contains Pfam PF02365 : No apical meristem (NAM) protein 2404 At4g01610 D1, D2, Dm cathepsin B-like cysteine protease, putative, similar to cathepsin B-like cysteine proteinase GI:609175 from (Nicotiana rustica); contains an unusually short, 5nt exon 2405 At4g01690 D1, Dm PPOX__protoporphyrinogen oxidase (PPOX), identical to SP:P55826 2406 At4g01820 D2 MDR3_PGP3__multidrug resistance P-glycoprotein, putative, similar to multidrug-resistant protein CjMDR1 GI:14715462 from (Coptis japonica) 2407 At4g01850 D2 S-adenosylmethionine synthetase 2 (SAM2), identical to S-adenosylmethionine synthetase 2 (Methionine adenosyltransferase 2, AdoMet synthetase 2) (Arabidopsis thaliana) SWISS- PROT:P17562 2408 At4g01940 D1, D2, Dm NFU1_ATCNFU1__nitrogen fixation NifU-like family protein, similar to apricot NifU homolog partial CDS, GenBank accession number U95179; contains Pfam profile: PF01106 NifU-like domain

2409 At4g01950 D2 ATGPAT3_GPAT3__Encodes a member of a family of proteins with glycerol-3-phosphate acyltransferase activity. 2410 At4g02050 D1, D2, Dm sugar transporter, putative, similar to SP:Q10710 Sugar carrier protein A {Ricinus communis}, glucose transporter (Saccharum hybrid cultivar H65-7052) GI:347855; contains Pfam profile PF00083: major facilitator superfamily protein 2411 At4g02060 D1, Dm PRL_MCM7__prolifera protein (PRL) / DNA replication licensing factor Mcm7 (MCM7), identical to DNA replication licensing factor Mcm7 SP:P43299 PROLIFERA protein {Arabidopsis thaliana}; contains Pfam profile PF00493: MCM2/3/5 family 2412 At4g02230 Dm 60S ribosomal protein L19 (RPL19C), similar to L19 from several species 2413 At4g02280 D1, D2, Dm sucrose synthase, putative / sucrose-UDP glucosyltransferase, putative, strong similarity to sucrose synthase GI:6682841 from (Citrus unshiu) 2414 At4g02290 D1, D2, Dm glycosyl hydrolase family 9 protein, similar to endo-1,4-beta glucanase; ATCEL2 GI:3132891 from (Arabidopsis thaliana) 2415 At4g02360 D1, D2, Dm expressed protein, contains Pfam profile PF04398: Protein of unknown function, DUF538 2416 At4g02380 D1, D2, Dm SAG21__late embryogenesis abundant 3 family protein / LEA3 family protein, similar to several small proteins (~100 aa) that are induced by heat, auxin, ethylene and wounding such as Phaseolus aureus indole-3-acetic acid induced protein ARG (SW:32292); contains Pfam profile PF03242: Late embryogenesis abundant protein 2417 At4g02430 D2 pre-mRNA splicing factor, putative / SR1 protein, putative, strong similarity to SP:O22315 Pre-mRNA splicing factor SF2 (SR1 protein) {Arabidopsis thaliana}; cDNA NCBI_gi:15810292 supports a truncated version while protein evidence supports a longer model. 2418 At4g02510 D1, Dm TOC159_ATTOC159_PPI2_TOC160_TOC86__chloroplast outer membrane protein, putative, similar to chloroplast protein import component Toc159 (Pisum sativum) GI:8489806, chloroplast outer envelope protein 86 (Pisum sativum) GI:599958, GTP-binding protein (Pisum sativum) GI:576509 2419 At4g02520 D2, Dm ATGSTF2_ATPM24_ATPM24.1_GST2__glutathione S-transferase, putative 2420 At4g02530 D1, Dm chloroplast thylakoid lumen protein, SP:022773 ;TL16_ARATH 2421 At4g02700 D1, D2, Dm AST77_SULTR3;2__sulfate transporter, identical to sulfate transporter (Arabidopsis thaliana) GI:2130944 2422 At4g02790 D2 GTP-binding family protein, contains Pfam domain, PF01926: GTPase of unknown function 2423 At4g02820 D1, Dm pentatricopeptide (PPR) repeat-containing protein, low similarity to DNA-binding protein (Triticum aestivum) GI:6958202; contains Pfam profile PF01535: PPR repeat 2424 At4g02850 Dm phenazine biosynthesis PhzC/PhzF family protein, contains Pfam profile: PF02567 phenazine biosynthesis-like protein 2425 At4g02890 Dm UBQ14__polyubiquitin (UBQ14), identical to GI:166795; similar to N. sylvestris hexameric polyubiquitin, GenBank accession number M74101 2426 At4g02930 D2 elongation factor Tu, putative / EF-Tu, putative, similar to mitochondrial elongation factor Tu (Arabidopsis thaliana) gi:1149571:emb:CAA61511 2427 At4g02940 Dm oxidoreductase, 2OG-Fe(II) oxygenase family protein, similar to A. thaliana hypothetical protein T13L16.2, GenBank accession number 2708738; contains Pfam domain PF03171 2OG-Fe(II) oxygenase superfamily 2428 At4g03110 D2, Dm RNA-binding protein, putative, similar to Etr-1 (Danio rerio) GI:7670536, BRUNO-like 6 RNA- binding protein (Homo sapiens) GI:15341327, CUG-BP and ETR-3 like factor 3 (Homo sapiens) GI:12746392; contains InterPro entry IPR000504: RNA-binding region RNP-1 (RNA recognition motif) (RRM) 2429 At4g03190 Dm GRH1_ATGER1_ATGRH1__F-box family protein (FBL18), almost identical to GRR1-like protein 1 GI:12658970 from (Arabidopsis thaliana); similar to leucine-rich repeats containing F-box protein FBL3 (GI:5919219) (Homo sapiens); similar to F-box protein FBL2 (GI:6063090) (Homo sapiens) 2430 At4g03200 D1, Dm expressed protein, contains Pfam PF03190: Protein of unknown function, DUF255 2431 At4g03210 D1, D2, Dm XTH9__xyloglucan:xyloglucosyl transferase, putative / xyloglucan endotransglycosylase, putative / endo-xyloglucan transferase, putative, contains similarity to xyloglucan endo- transglycosylase-like protein (XET-1) GI:5070246 from (Medicago truncatula) 2432 At4g03220 D2, Dm F-box family protein, ; similar to SKP1 interacting partner 2 (SKIP2) TIGR_Ath1:At5g67250 2433 At4g03380 D1, Dm expressed protein 2434 At4g03390 D2 leucine-rich repeat transmembrane protein kinase, putative, similar to Z. mays leucine-rich repeat transmembrane protein kinase LRRTPK 1, GenBank accession number AF023164 2435 At4g03400 D2 DFL2_GH3-10__auxin-responsive GH3 family protein, similar to auxin-responsive GH3 product (Glycine max) GI:18591; contains Pfam profile PF03321: GH3 auxin-responsive promoter 2436 At4g03560 D1, Dm ATTPC1_ATCCH1_TPC1__two-pore calcium channel (TPC1), identical to two-pore calcium channel (TPC1) (Arabidopsis thaliana) gi:14041819:dbj:BAB55460 2437 At4g03820 Dm expressed protein 2438 At4g03960 Dm tyrosine specific protein phosphatase family protein, contains tyrosine specific protein phosphatases active site, PROSITE:PS00383 2439 At4g04020 D1, Dm plastid-lipid associated protein PAP, putative / fibrillin, putative, strong similarity to plastid-lipid associated proteins PAP1 GI:14248554, PAP2 GI:14248556 from (Brassica rapa), fibrillin (Brassica napus) GI:4139097; contains Pfam profile PF04755: PAP_fibrillin 2440 At4g04040 Dm pyrophosphate--fructose-6-phosphate 1-phosphotransferase beta subunit, putative / pyrophosphate-dependent 6-phosphofructose-1-kinase, putative, strong similarity to SP:Q41141 Pyrophosphate--fructose 6-phosphate 1-phosphotransferase beta subunit (EC 2.7.1.90) (PFP) (6- phosphofructokinase, pyrophosphate-dependent) (Pyrophosphate-dependent 6-phosphofructose-1- kinase) (PPI-PFK) {Ricinus communis} 2441 At4g04570 Dm protein kinase family protein, contains Pfam domain PF00069: Protein kinase domain 2442 At4g04620 D1, Dm autophagy 8b (APG8b), identical to autophagy 8b (Arabidopsis thaliana) GI:19912153; contains Pfam profile PF02991: Microtubule associated protein 1A/1B, light chain 3 2443 At4g04720 D2, Dm CPK21__calcium-dependent protein kinase, putative / CDPK, putative, similar to calcium- dependent protein kinase(CDPK) (Carrot) SWISS-PROT:P28582 2444 At4g04770 D2 ATABC1_ATNAP1_LAF6__ATP-binding-cassette transporter (ABC1), Identical to the protein described in PMID:11156608 and note that sequence was not deposited into GenBank by the authors. 2445 At4g04840 D1, D2, Dm methionine sulfoxide reductase domain-containing protein / SeIR domain-containing protein, low similarity to pilin-like transcription factor (Homo sapiens) GI:5059062; contains Pfam profile PF01641: SelR domain 2446 At4g04955 D2 ATALN__Encodes an allantoinase which is involved in allantoin degradation and assimilation. Gene expression was induced when allantoin was added to the medium. The insertion mutant, ataln m2-1, did not grow well on the MS medium where allantoin, instead of ammonium nitrate, was supplied. 2447 At4g05070 D2, Dm expressed protein 2448 At4g05160 D1, Dm Encodes a peroxisomal protein involved in the activation of fatty acids through esterification with CoA. At4g05160 preferentially activates fatty acids with medium chain length (C6:0 and C7:0) as well as even-numbered long-chain fatty acids (C14:0, C16:0 and C18:0). At4g05160 was also able to catalyze the conversion of OPC-6:0 to its CoA ester and is therefore thought to be involved in the peroxisomal β-oxidation steps of jasmonic acid biosynthesis.

2449 At4g05390 D2, Dm ferredoxin--NADP(+) reductase, putative / adrenodoxin reductase, putative, strong similarity to SP:P41345 Ferredoxin--NADP reductase, root isozyme, chloroplast precursor (EC 1.18.1.2) (FNR) {Oryza sativa}, ferredoxin-NADP reductase precursor (Zea mays) GI:500751 2450 At4g05530 D2 short-chain dehydrogenase/reductase (SDR) family protein, similar to peroxisomal short-chain alcohol dehydrogenase GI:4105190 from (Homo sapiens) 2451 At4g07685 D2 transposable element gene 2452 At4g07840 Dm transposable element gene 2453 At4g08150 D2, Dm KNAT1_BP_BP1__homeobox protein knotted-1 like 1 (KNAT1), identical to homeobox protein knotted-1 like 1 (KNAT1) SP:P46639 from (Arabidopsis thaliana) 2454 At4g08230 Dm glycine-rich protein 2455 At4g08380 D1, D2, Dm proline-rich extensin-like family protein, contains proline-rich extensin domains, INTERPRO:IPR002965 2456 At4g08390 D1, Dm L-ascorbate peroxidase, stromal (sAPX), identical to stromal ascorbate peroxidase (Arabidopsis thaliana) gi:1419388:emb:CAA67425 2457 At4g08400 D1, D2, Dm proline-rich extensin-like family protein, contains proline-rich extensin domains, INTERPRO:IPR002965 2458 At4g08455 D1, D2, Dm BTB/POZ domain-containing protein, Interpro IPR000210/ PS50097: BTBB/POZ domain; similar to POZ 56 protein (GI:17483747) (Mus musculus) 2459 At4g08540 D2 expressed protein 2460 At4g08570 D1, D2, Dm heavy-metal-associated domain-containing protein / copper chaperone (CCH)-related, low similarity to copper homeostasis factor (GI:3168840)(PMID:9701579); similar to farnesylated proteins GMFP7 (Glycine max)(GI:4097573) and ATFP7 (GI:4097555); contains heavy-metal- associated domain PF00403 2461 At4g08750 Dm RNA recognition motif (RRM)-containing protein, contains Pfam domain PF00076: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 2462 At4g08850 D1 leucine-rich repeat family protein / protein kinase family protein, contains Pfam domains PF00560: Leucine Rich Repeat and PF00069: Protein kinase domain 2463 At4g08870 D2 arginase, putative, similar to Swiss-Prot:P46637 arginase (EC 3.5.3.1) (Arabidopsis thaliana)

2464 At4g08900 Dm arginase, identical to Swiss-Prot:P46637 arginase (EC 3.5.3.1) (Arabidopsis thaliana) 2465 At4g08940 D2, Dm expressed protein 2466 At4g08950 D2, Dm phosphate-responsive protein, putative (EXO), similar to phi-1 (phosphate-induced gene) (Nicotiana tabacum) GI:3759184; contains Pfam profile PF04674: Phosphate-induced protein 1 conserved region 2467 At4g08980 D1, Dm F-box family protein (FBW2), contains similarity to N7 protein GI:3273101 from (Medicago truncatula) 2468 At4g09040 D1, D2, Dm RNA recognition motif (RRM)-containing protein, low similarity to enhancer binding protein-1; EBP1 (Entamoeba histolytica) GI:8163877, SP:P19682 28 kDa ribonucleoprotein, chloroplast precursor (28RNP) {Nicotiana sylvestris}; contains InterPro entry IPR000504: RNA-binding region RNP-1 (RNA recognition motif) (RRM) 2469 At4g09160 D1, D2, Dm SEC14 cytosolic factor family protein / phosphoglyceride transfer family protein, similar to polyphosphoinositide binding protein Ssh1p (GI:2739044) {Glycine max}; similar to polyphosphoinositide binding protein Ssh2, Glycine max, gb:T05953; contains Pfam PF00650 : CRAL/TRIO domain; contains Pfam PF03765 : CRAL/TRIO, N-terminus 2470 At4g09320 D1, D2, Dm NDPK1__nucleoside diphosphate kinase 1 (NDK1), identical to identical to Nucleoside diphosphate kinase I (NDK I) (NDP kinase I) (NDPK I) (SP:P39207) (Arabidopsis thaliana); contains Pfam PF00334 : Nucleoside diphosphate kinase domain; 2471 At4g09400 D1, Dm expressed protein, similar to At3g45350, At2g14330 2472 At4g09480 D2 transposable element gene 2473 At4g09600 Dm GASA3__gibberellin-regulated protein 3 (GASA3) / gibberellin-responsive protein 3, identical to SP:P46687 Gibberellin-regulated protein 3 precursor {Arabidopsis thaliana} 2474 At4g09650 D2, Dm ATP synthase delta chain, chloroplast, putative / H(+)-transporting two-sector ATPase, delta (OSCP) subunit, putative, similar to SP:P32980 ATP synthase delta chain, chloroplast precursor (EC 3.6.3.14) {Nicotiana tabacum}; contains Pfam profile PF00213: ATP synthase F1, delta subunit 2475 At4g09730 D2 DEAD/DEAH box helicase, putative, RNA helicase -Mus musculus,PIR2:I84741 2476 At4g09750 D1, D2, Dm short-chain dehydrogenase/reductase (SDR) family protein, similar to androgen-regulated short- chain dehydrogenase/reductase 1 GI:9622124 from (Homo sapiens) 2477 At4g09830 D1, Dm expressed protein 2478 At4g09890 D1, D2, Dm expressed protein 2479 At4g09900 Dm hydrolase, alpha/beta fold family protein, similar to ethylene-induced esterase (Citrus sinensis) GI:14279437, polyneuridine aldehyde esterase (Rauvolfia serpentina) GI:6651393, SP:Q40708 PIR7A protein {Oryza sativa}; contains Pfam profile PF00561: hydrolase, alpha/beta fold family 2480 At4g09980 D1, Dm EMB1691__methyltransferase MT-A70 family protein, low similarity to SP:P25583 Karyogamy protein KAR4 {Saccharomyces cerevisiae}, (N6-adenosine)-methyltransferase (Mus musculus) GI:10179948; contains Pfam profile PF05063: MT-A70 (S-adenosylmethionine-binding subunit of human mRNA:m6A methyl-transferase (MTase)) 2481 At4g10000 D2 expressed protein 2482 At4g10050 D1, Dm hydrolase, alpha/beta fold family protein, similar to protein phosphatase methylesterase-1 (Homo sapiens) GI:5533003; contains Pfam profile PF00561: hydrolase, alpha/beta fold family 2483 At4g10060 D1 expressed protein, contains Pfam domain PF04685: Protein of unknown function, DUF608 2484 At4g10100 D2 CNX7_SIR5__molybdenum cofactor synthesis family protein, similar to Molybdenum cofactor synthesis protein 2 small subunit (Molybdopterin- synthase small subunit) (MOCS2A) (MOCO1-A) (Swiss-Prot:O96033) (Homo sapiens); contains TIGRFAM TIGR01682: molybdopterin converting factor, subunit 1; sir loss-of-function mutants are resistant to sirtinol, a modulator of auxin signaling. 2485 At4g10480 D1, D2, Dm nascent polypeptide associated complex alpha chain protein, putative / alpha-NAC, putative, similar to alpha-NAC, non-muscle form (Mus musculus) GI:1666690; contains Pfam profiles PF01849: NAC domain, PF00627: UBA/TS-N domain 2486 At4g10540 D1, Dm subtilase family protein, contains similarity to subtilase; SP1 GI:9957714 from (Oryza sativa)

2487 At4g10640 D1 calmodulin-binding family protein, contains IQ calmodulin-binding motif, Pfam:PF00612 2488 At4g10680 Dm transcription factor IIB (TFIIB) family protein, contains Pfam profile: PF00382 transcription factor TFIIB repeat 2489 At4g10840 D1, D2, Dm kinesin light chain-related, low similarity to kinesin light chain (Plectonema boryanum) GI:2645229; contains Pfam profile PF00515 TPR Domain 2490 At4g10940 D2 PHD finger family protein, contains Pfam profile: PF00097 zinc finger, C3HC4 type 2491 At4g10960 Dm UDP-glucose 4-epimerase, putative / UDP-galactose 4-epimerase, putative / Galactowaldenase, putative, similar to UDP-galactose 4-epimerase from Arabidopsis thaliana SP:Q42605, Cyamopsis tetragonoloba GI:3021357 (AJ005082) 2492 At4g11010 D1, Dm NDPK3__nucleoside diphosphate kinase 3, mitochondrial (NDK3), identical to Nucleoside diphosphate kinase III, mitochondrial precursor (NDK III) (NDP kinase III) (NDPK III) (SP:O49203) (Arabidopsis thaliana); contains Pfam PF00334 : Nucleoside diphosphate kinase domain; 2493 At4g11100 D2 expressed protein 2494 At4g11130 Dm RDR2__RNA-dependent RNA polymerase, putative, similar to RNA-directed RNA polymerase (Lycopersicon esculentum) gi:4038592:emb:CAA71421 2495 At4g11480 D1, Dm protein kinase family protein, contains Pfam PF00069: Protein kinase domain 2496 At4g11570 D1, D2, Dm haloacid dehalogenase-like hydrolase family protein, similar to genetic modifier (Zea mays) GI:10444400; contains InterPro accession IPR005834: Haloacid dehalogenase-like hydrolase 2497 At4g11600 D1, D2, Dm ATGPX6_LSC803_PHGPX__glutathione peroxidase, putative 2498 At4g11820 Dm BAP1_MVA1__hydroxymethylglutaryl-CoA synthase / HMG-CoA synthase / 3-hydroxy-3-methylglutaryl coenzyme A synthase, identical to Hydroxymethylglutaryl-CoA synthase (EC 4.1.3.5) (HMG-CoA synthase) (3-hydroxy-3-methylglutaryl coenzyme A synthase) (Swiss-Prot:P54873) (Arabidopsis thaliana) 2499 At4g11960 D2 expressed protein, hypothetical protein F7H19.70 - Arabidopsis thaliana, PID:e1310057 2500 At4g12000 Dm expressed protein 2501 At4g12300 D2 CYP706A4__cytochrome P450 family protein, flavonoid 3`,5`-hydroxylase - Campanula medium, PID:d1003951 2502 At4g12320 Dm CYP706A6__cytochrome P450, putative, Similar to P450 monooxygenase (gi:14334057) (Gossypium arboreum) 2503 At4g12400 D1, Dm stress-inducible protein, putative, similar to sti (stress inducible protein) (Glycine max) GI:872116; contains Pfam profile PF00515 TPR Domain 2504 At4g12420 D1, D2, Dm SKU5__multi-copper oxidase, putative (SKU5), identical to multi-copper oxidase-related protein (SKU5)(GI:18158154) (Arabidopsis thaliana); similar to pollen-specific protein precursor - common tobacco, PIR2:S22495; contains Pfam profile: PF00394 Multicopper oxidase 2505 At4g12460 D1, Dm oxysterol-binding family protein, similar to SP:P22059 Oxysterol-binding protein 1 {Homo sapiens}; contains Pfam profiles PF00169: PH domain, PF01237: Oxysterol-binding protein 2506 At4g12470 D2, Dm protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, similar to pEARLI 1 (Accession No. L43080): an Arabidopsis member of a conserved gene family (PGF95-099), Plant Physiol. 109 (4), 1497 (1995); contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 2507 At4g12480 D1, Dm PEARLI 1 1__protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, identical to pEARLI 1 (Accession No. L43080): an Arabidopsis member of a conserved gene family (PGF95-099), Plant Physiol. 109 (4), 1497 (1995); contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 2508 At4g12490 D2, Dm protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, similar to pEARLI 1 (Accession No. L43080): an Arabidopsis member of a conserved gene family (PGF95-099), Plant Physiol. 109 (4), 1497 (1995); contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 2509 At4g12600 D2, Dm ribosomal protein L7Ae/L30e/S12e/Gadd45 family protein, Similar to NHP2/L7Ae family proteins, see SWISSPROT:P32495 and PMID:2063628. 2510 At4g12650 D2 endomembrane protein 70, putative, TM4 family; 2511 At4g12730 D1, D2, Dm FLA2__fasciclin-like arabinogalactan-protein (FLA2), identical to gi_13377778_gb_AAK20858 2512 At4g12800 D1 photosystem I reaction center subunit XI, chloroplast (PSI-L) / PSI subunit V, identical to Photosystem I reaction center subunit XI, chloroplast precursor (PSI-L) (PSI subunit V) (Swiss-Prot:Q9SUI4) (Arabidopsis thaliana); contains Pfam profile PF02605: photosystem I reaction center subunit XI; contains 2 transmembrane domains 2513 At4g12830 D1, Dm hydrolase, alpha/beta fold family protein, low similarity to haloalkane dehalogenase from (Mycobacterium avium subsp. avium) GI:14422311, (Pseudomonas pavonaceae) GI:6689030; contains Pfam profile PF00561: hydrolase, alpha/beta fold family 2514 At4g12980 D1, D2, Dm auxin-responsive protein, putative, similar to auxin-induced protein AIR12 GI:11357190 (Arabidopsis thaliana) 2515 At4g13010 D1, D2, Dm oxidoreductase, zinc-binding dehydrogenase family protein, low similarity to probable NADP- dependent oxidoreductase (zeta-crystallin homolog) P1 (SP:Q39172)(gi:886428) and P2 (SP:Q39173)(gi:886430); contains Pfam profile PF00107: oxidoreductase, zinc-binding dehydrogenase family 2516 At4g13030 D2, Dm expressed protein 2517 At4g13150 D2 expressed protein 2518 At4g13170 D2 60S ribosomal protein L13A (RPL13aC), ribosomal protein L13a -Lupinus luteus,PID:e1237871 2519 At4g13220 D1, Dm expressed protein 2520 At4g13270 Dm expressed protein 2521 At4g13340 D2 leucine-rich repeat family protein / extensin family protein, similar to extensin-like protein (Lycopersicon esculentum) gi:5917664:gb:AAD55979; contains leucine-rich repeats, Pfam:PF00560; contains proline rich extensin domains, INTERPRO:IPR002965 2522 At4g13390 D1 proline-rich extensin-like family protein, contains proline-rich extensin domains, INTERPRO:IPR002965 2523 At4g13510 D1, Dm AMT1_ATAMT1__ammonium transporter 1, member 1 (AMT1.1), identical to SP:P54144 High affinity ammonium transporter (AtAMT1;1) {Arabidopsis thaliana} 2524 At4g13520 D2 expressed protein 2525 At4g13530 D1, D2, Dm expressed protein, predicted protein, Arabidopsis thaliana 2526 At4g13770 D2 CYP83A1_REF2__cytochrome P450 family protein 2527 At4g13830 D1, D2, Dm J20__DNAJ heat shock N-terminal domain-containing protein (J20), identical to DnaJ-like protein (Arabidopsis thaliana) GI:6691127; similar to SP:Q05646 Chaperone protein dnaJ Erysipelothrix rhusiopathiae, J11 protein (Arabidopsis thaliana) GI:9843641; contains Pfam profile PF00226 DnaJ domain 2528 At4g13850 D2 ATGRP2__glycine-rich RNA-binding protein (GRP2), glycine-rich RNA binding protein 2 AtGRP2 (Arabidopsis thaliana) GI:2826811 2529 At4g13930 D1, D2, Dm SHM4__glycine hydroxymethyltransferase, putative / serine hydroxymethyltransferase, putative / serine/threonine aldolase, putative, similar to serine hydroxymethyltransferase (Chlamydomonas reinhardtii) GI:17066746; contains Pfam profile PF00464: serine hydroxymethyltransferase

2530 At4g13960 D2, Dm F-box family protein, contains F-box domain Pfam:PF00646 2531 At4g13970 Dm similar to SWIM zinc finger family protein [Arabidopsis thaliana] (TAIR:At1g60560.1); similar to SWIM zinc finger family protein-like [Oryza sativa (japonica cultivar-group)] (GB:BAD36475.1); contains InterPro domain SWIM Zn-finger (InterPro:IPR007527) 2532 At4g14010 D2, Dm RALFL32__rapid alkalinization factor (RALF) family protein, similar to RALF precursor (Nicotiana tabacum) GI:16566316 2533 At4g14020 D1, D2, Dm rapid alkalinization factor (RALF) family protein 2534 At4g14040 D1, Dm selenium-binding protein, putative, contains Pfam profile PF05694: 56kDa selenium binding protein (SBP56); similar to Putative selenium-binding protein (Swiss-Prot:O23264) (Arabidopsis thaliana); similar to selenium binding protein (GI:15485232) (Arabidopsis thaliana)

2535 At4g14090 D2, Dm UDP-glucoronosyl/UDP-glucosyl transferase family protein, contains Pfam profile: PF00201 UDP- glucoronosyl and UDP-glucosyl transferase ;similar to UDP-glucose:anthocyanin 5-O- glucosyltransferase GI:4115563 from (Verbena x hybrida) 2536 At4g14270 D1, D2, Dm Protein containing PAM2 motif which mediates interaction with the PABC domain of polyadenyl binding proteins. 2537 At4g14320 D1, D2, Dm 60S ribosomal protein L36a/L44 (RPL36aB) 2538 At4g14360 D1, Dm dehydration-responsive protein-related, similar to early-responsive to dehydration stress ERD3 protein (Arabidopsis thaliana) GI:15320410; contains Pfam profile PF03141: Putative methyltransferase 2539 At4g14385 Dm expressed protein 2540 At4g14400 Dm ACD6__ankyrin repeat family protein, contains ankyrin repeats, Pfam domain PF00023 2541 At4g14420 D2 lesion inducing protein-related, similar to ORF, able to induce HR-like lesions (Nicotiana tabacum) gi:1762945:gb:AAC49975 2542 At4g14500 Dm expressed protein, weak similarity to SP:Q9UKL6 Phosphatidylcholine transfer protein (PC-TP) {Homo sapiens} 2543 At4g14540 D2 CCAAT-box binding transcription factor subunit B (NF-YB) (HAP3 ) (AHAP3) family, contains Pfam PF00808 : Histone-like transcription factor (CBF/NF-Y) and archaeal histone; similar to LEC1- like protein (GI:22536010) (Phaseolus coccineus) 2544 At4g14550 D1, D2, Dm IAA14_SLR__auxin-responsive AUX/IAA family protein, identical to IAA14 (GI:972931) (Arabidopsis thaliana); similar to SP:Q38825 Auxin-responsive protein IAA7 (Indoleacetic acid- induced protein 7) {Arabidopsis thaliana} 2545 At4g14560 D1, D2, Dm IAA1__auxin-responsive protein / indoleacetic acid-induced protein 1 (IAA1), identical to SP:P49677 Auxin-responsive protein IAA1 (Indoleacetic acid-induced protein 1) {Arabidopsis thaliana} 2546 At4g14610 D1, D2, Dm pseudogene, disease resistance protein (CC-NBS-LRR class), putative, domain signature CC-NBS- LRR exists, suggestive of a disease resistance protein. 2547 At4g14690 D1, D2, Dm ELIP1_ELIP_ELIP2__chlorophyll A-B binding family protein / early light-induced protein, putative, strong similarity to early light-induced protein; ELIP (Arabidopsis thaliana) GI:1872544; contains Pfam profile: PF00504 chlorophyll A-B binding protein 2548 At4g14710 D1, D2, Dm iron-deficiency-responsive protein, putative, strong similarity to iron-deficiency induced gene (Hordeum vulgare) GI:14522834; contains Pfam profile PF03079: ARD/ARD` family 2549 At4g14800 D2 PBD2__20S proteasome beta subunit D2 (PBD2) (PRCGA), identical to SP:O24633 Proteasome subunit beta type 2-2 (EC 3.4.25.1) (20S proteasome alpha subunit D2) {Arabidopsis thaliana}, cDNA proteasome subunit prcga GI:2511571 2550 At4g14860 D2 ATOFP11__ovate family protein, 58% similar to ovate protein (GI:23429649) (Lycopersicon esculentum); contains TIGRFAM TIGR01568 : uncharacterized plant-specific domain TIGR01568 2551 At4g14870 D1, Dm expressed protein 2552 At4g14880 D2 OASA1_CYTACS1__cysteine synthase / O-acetylserine (thiol)-lyase / O-acetylserine sulfhydrylase (OAS1), nearly identical to SP:P47998 Cysteine synthase (EC 4.2.99.8) (O-acetylserine sulfhydrylase) (O-acetylserine (Thiol)-lyase) {Arabidopsis thaliana}; identical to cDNA O- acetylserine lyase (At.OAS.5-8) GI:6983573 2553 At4g14890 Dm ferredoxin family protein, similar to SP:P00252 Ferredoxin I from Nostoc muscorum, SP:P00248 Ferredoxin from Mastigocladus laminosus, SP:P00244 Ferredoxin I from Aphanizomenon flos-aquae; contains Pfam profile PF00111 2Fe-2S iron-sulfur cluster binding domain 2554 At4g14960 D1, D2, Dm TUA6__tubulin alpha-6 chain (TUA6), nearly identical to SP:P29511 Tubulin alpha-6 chain {Arabidopsis thaliana} 2555 At4g15000 D1, D2, Dm 60S ribosomal protein L27 (RPL27C) 2556 At4g15110 D1 CYP97B3__cytochrome P450 97B3, putative (CYP97B3), identical to Cytochrome P450 97B3 (SP:O23365) (Arabidopsis thaliana) 2557 At4g15150 D2, Dm glycine-rich protein 2558 At4g15475 D2, Dm F-box family protein (FBL4), 99.7% identical to F-box protein family, AtFBL4 (GP:21536497) (Arabidopsis thaliana); similar to grr1 GI:2407790 from (Glycine max) 2559 At4g15490 D2, Dm UDP-glucoronosyl/UDP-glucosyl transferase family protein, contains Pfam profile: PF00201 UDP- glucoronosyl and UDP-glucosyl transferase ;simalr to UDP-glucose:sinapate glucosyltransferase GI:9794913 from (Brassica napus) 2560 At4g15530 D1, D2, Dm similar to pyruvate,orthophosphate dikinase [Flaveria brownii] (GB:CAA55784.1); similar to pyruvate,orthophosphate dikinase [Mesembryanthemum crystallinum] (GB:CAA55143.1); similar to cold stable pyruvate, orthophosphate dikinase (GB:AAA86940.1); similar to pyruvate, phosphate dikinase (EC 2.7.9.1) precursor, chloroplast - Flaveria brownii (GB:S56649); similar to pyruvate,orthophosphate dikinase [Flaveria pringlei] (GB:CAA53223.1); contains InterPro domain Pyruvate phosphate dikinase, PEP/pyruvate-binding (InterPro:IPR002192); contains InterPro domain PEP-utilizing enzyme (InterPro:IPR000121); contains InterPro domain PEP-utilising enzyme, mobile region (InterPro:IPR008279) 2561 At4g15545 D2 expressed protein 2562 At4g15630 D2 integral membrane family protein, contains TIGRFAM TIGR01569 : plant integral membrane protein TIGR01569; contains Pfam PF04535 : Domain of unknown function (DUF588) 2563 At4g15650 D1, Dm protein kinase-related, contains weak similarity to protein kinase (Dictyostelium discoideum) gi:551446:emb:CAA86053 2564 At4g15660 D2, Dm glutaredoxin family protein, contains INTERPRO Domain IPR002109, Glutaredoxin (thioltransferase) 2565 At4g15670 D2, Dm glutaredoxin family protein, contains INTERPRO Domain IPR002109, Glutaredoxin (thioltransferase) 2566 At4g15680 D1, D2, Dm glutaredoxin family protein, contains INTERPRO Domain IPR002109, Glutaredoxin (thioltransferase) 2567 At4g15700 D1, D2, Dm glutaredoxin family protein, contains INTERPRO Domain IPR002109, Glutaredoxin (thioltransferase) 2568 At4g15760 Dm monooxygenase, putative (MO1), similar to GI:3426062 2569 At4g15770 D2 60S ribosome subunit biogenesis protein, putative, contains similarity to 60S ribosome subunit biogenesis protein NIP7 (Swiss-Prot:Q08962) (Saccharomyces cerevisiae) 2570 At4g15780 Dm ATVAMP724_VAMP724__synaptobrevin-related family protein, similar to Vesicle-associated membrane protein 722 (AtVAMP722) Synaptobrevin-related protein 1 (SP:P47192) {Arabidopsis thaliana} 2571 At4g15800 D2 RALFL33__rapid alkalinization factor (RALF) family protein, similar to RALF precursor (Nicotiana tabacum) GI:16566316 2572 At4g15910 D1, D2, Dm ATDI21_DI21__drought-responsive protein / drought-induced protein (Di21), identical to GI:469112; contains PF03242 Late embryogenesis abundant protein domain 2573 At4g16110 D1 ARR2_ARR5_ATRR2_IBC6__two-component responsive regulator family protein / response regulator family protein, similar to ARR2 protein GI:4210451 from (Arabidopsis thaliana); contains Pfam profile: PF00072 response regulator receiver domain 2574 At4g16143 D2 importin alpha-2, putative (IMPA-2), similar to importin alpha 2 (Capsicum annuum) GI:13752562; contains Pfam profiles PF01749: Importin beta binding domain, PF00514: Armadillo/beta-catenin-like repeat; non-consensus GG donor splice site at exon 1 and 6; CT acceptor splice site at exon 2 2575 At4g16155 D1, Dm dihydrolipoamide dehydrogenase 2, plastidic / lipoamide dehydrogenase 2 (PTLPD2), identical to plastidic lipoamide dehydrogenase from Arabidopsis thaliana (gi:7159284) 2576 At4g16190 D1, D2, Dm cysteine proteinase, putative, contains similarity to papain-like cysteine proteinase isoform I GI:7381219 from (Ipomoea batatas) 2577 At4g16330 D2, Dm oxidoreductase, 2OG-Fe(II) oxygenase family protein, similar to flavonone-3-hydroxylase (naringenin,2-oxoglutarate 3-dioxygenase) from Malus domestica (SP:Q06942), Pyrus communis (GI:20269881); contains Pfam domain PF03171, 2OG-Fe(II) oxygenase superfamily 2578 At4g16390 D1, D2, Dm chloroplastic RNA-binding protein P67, putative, nearly identical to 67kD chloroplastic RNA- binding protein, P67 (Arabidopsis thaliana) GI:9755842 2579 At4g16450 D1 expressed protein 2580 At4g16500 D1, Dm cysteine protease inhibitor family protein / cystatin family protein, similar to SP:Q06445 Cysteine proteinase inhibitor (Cystatin) {Vigna unguiculata}; contains Pfam profile PF00031: Cystatin domain 2581 At4g16520 D2, Dm autophagy 8f (APG8f), identical to autophagy 8f (Arabidopsis thaliana) GI:19912161; contains Pfam profile PF02991: Microtubule associated protein 1A/1B, light chain 3 2582 At4g16590 D2, Dm ATCSLA01_ATCSLA1_CSLA01__glucosyltransferase-related, low similarity to beta-(1-3)-glucosyl transferase (Bradyrhizobium japonicum) GI:3687658 2583 At4g16720 D1, D2, Dm 60S ribosomal protein L15 (RPL15A) 2584 At4g16830 D1 nuclear RNA-binding protein (RGGA), identical to nuclear RNA binding protein GI:6492264 from (Arabidopsis thaliana) 2585 At4g16880 D1, Dm disease resistance protein-related, contains weak similarity to disease resistance protein RPP4 (Arabidopsis thaliana) gi:20270890:gb:AAM18462 2586 At4g16990 D1, D2, Dm similar to disease resistance protein (TIR-NBS-LRR class), putative [Arabidopsis thaliana] (TAIR:At5g51630.1); similar to disease resistance-like protein 9 [Brassica rapa] (GB:AAV88086.1); similar to nematode resistance-like protein [Solanum tuberosum] (GB:AAP44393.1); contains InterPro domain NB-ARC domain (InterPro:IPR002182); contains InterPro domain TIR domain (InterPro:IPR000157); contains InterPro domain Disease resistance protein (InterPro:IPR000767) 2587 At4g17030 D2, Dm ATEXLB1_AT-EXPR_ATEXPR1_ATHEXP BETA 3.1_EXPR__expansin-related, identical to SWISS-PROT:O23547 expansin-related protein 1 precursor (At-EXPR1)(Arabidopsis thaliana); related to expansins, http://www.bio.psu.edu/expansins/ 2588 At4g17050 D1, D2, Dm expressed protein 2589 At4g17090 D1, D2, Dm CT-BMY_BMY8__beta-amylase (CT-BMY) / 1,4-alpha-D-glucan maltohydrolase, identical to beta- amylase enzyme GI:6065749 from (Arabidopsis thaliana) 2590 At4g17110 D1 expressed protein, ; expression supported by MPSS 2591 At4g17230 D2 scarecrow-like transcription factor 13 (SCL13) 2592 At4g17520 D1, D2, Dm nuclear RNA-binding protein, putative, similar to nuclear RNA binding protein GI:6492264 from (Arabidopsis thaliana) 2593 At4g17530 D2, Dm RAB1C__Ras-related GTP-binding protein, putative, very strong similarity to RAB1C (Lotus corniculatus var. japonicus) GI:1370166; contains Pfam profile PF00071: Ras family 2594 At4g17560 D1, Dm ribosomal protein L19 family protein, similar to plastid ribosomal protein L19 precursor (Spinacia oleracea) gi:7582403:gb:AAF64312 2595 At4g17600 D1, D2, Dm LIL3:1__lil3 protein, identical to Lil3 protein (Arabidopsis thaliana) gi:4741966:gb:AAD28780

2596 At4g17780 D1, Dm MYB39__F-box family protein, contains F-box domain Pfam:PF00646 2597 At4g17800 D2, Dm DNA-binding protein-related, contains Pfam domain PF03479: Domain of unknown function (DUF296), found in AT-hook motifs Pfam:PF02178 2598 At4g17840 Dm expressed protein 2599 At4g17920 Dm zinc finger (C3HC4-type RING finger) family protein, similar to RING-H2 zinc finger protein ATL6 (Arabidopsis thaliana) GI:4928403; contains Pfam profile PF00097: Zinc finger, C3HC4 type (RING finger) 2600 At4g18040 D2 EIF4E_AT.EIF4E1_CUM1_LSP1__eukaryotic translation initiation factor 4E 1 / eIF-4E1 / mRNA cap- binding protein 1 (EIF4E1), identical to SP:O23252 Eukaryotic translation initiation factor 4E (eIF-4E) (eIF4E) (mRNA cap-binding protein) (eIF-4F 25 kDa subunit) (eIF-4F P26 subunit) {Arabidopsis thaliana} 2601 At4g18110 D2 zinc finger (C3HC4-type RING finger) family protein, contains Pfam profile: PF00097 zinc finger, C3HC4 type (RING finger) 2602 At4g18130 D1, Dm PHYE__phytochrome E (PHYE), identical to SP:P42498 Phytochrome E {Arabidopsis thaliana} 2603 At4g18200 D2, Dm 2604 At4g18280 D1, D2, Dm glycine-rich cell wall protein-related, glycine-rich protein 1.0 precursor, Phaseolus vulgaris, PIR1:S01821 2605 At4g18440 D1, D2, Dm adenylosuccinate lyase, putative / adenylosuccinase, putative, similar to SP:P25739 Adenylosuccinate lyase (EC 4.3.2.2) (Adenylosuccinase) {Escherichia coli}; contains Pfam profile PF00206: Lyase 2606 At4g18500 Dm expressed protein 2607 At4g18680 Dm hypothetical protein, weak similarity to tumor-related protein (Nicotiana glauca x Nicotiana langsdorffii) GI:688423 2608 At4g18730 D2 RPL16B__60S ribosomal protein L11 (RPL11C) 2609 At4g18800 Dm Ras-related GTP-binding family protein, similar to ras-related GTP binding protein RIC2 SP:P40393 from (Oryza sativa); contains Pfam profile: PF00071 Ras family 2610 At4g18880 D1 AT-HSFA4A_HSFA4A__heat shock transcription factor 21 (HSF21), identical to heat shock transcription factor 21 (Arabidopsis thaliana) GI:3399765; contains Pfam profile: PF00447 HSF- type DNA-binding domain 2611 At4g18930 Dm cyclic phosphodiesterase, identical to cyclic phosphodiesterase (Arabidopsis thaliana) gi:2065013:emb:CAA72363 2612 At4g18970 D1, D2, Dm GDSL-motif lipase/hydrolase family protein, similar to family II lipases EXL3 GI:15054386, EXL1 GI:15054382, EXL2 GI:15054384 from (Arabidopsis thaliana); contains Pfam profile PF00657: GDSL-like Lipase/Acylhydrolase 2613 At4g19090 Dm hypothetical protein, contains Pfam domain, PF04578: Protein of unknown function, DUF594 2614 At4g19120 D2, Dm early-responsive to dehydration stress protein (ERD3), identical to ERD3 protein (Arabidopsis thaliana) GI:15320410; contains Pfam profile PF03141: Putative methyltransferase; identical to cDNA ERD3 GI:15320409 2615 At4g19130 D1, D2, Dm replication protein-related, similar to replication protein A 70kDa (Oryza sativa) GI:13536993; contains Pfam profile PF00098: Zinc knuckle 2616 At4g19160 D2 expressed protein 2617 At4g19210 Dm ATRLI2__RNase L inhibitor protein, putative, similar to 68 kDa protein HP68 GI:16755057 from (Triticum aestivum) 2618 At4g19270 D2 expressed protein 2619 At4g19390 D1, D2, Dm expressed protein 2620 At4g19410 D1, D2, Dm pectinacetylesterase, putative, similar to pectinacetylesterase precursor GI:1431629 from (Vigna radiata) 2621 At4g19500 D1, Dm disease resistance protein (TIR-NBS-LRR class), putative, domain signature TIR-NBS-LRR exists, suggestive of a disease resistance protein. A false intron was added between exons 2 and 3 to circumvent a frameshift caused by a sequencing error, as per Blake Meyers ([email protected]) 2622 At4g19530 D2, Dm disease resistance protein (TIR-NBS-LRR class), putative, domain signature TIR-NBS-LRR exists, suggestive of a disease resistance protein. 2623 At4g19710 Dm AK-HSDH_AK-HSDH II__bifunctional aspartate kinase/homoserine dehydrogenase, putative / AK- HSDH, putative, similar to gb:X71364 (PIR:S46497) aspartate kinase / homoserine dehydrogenase from Arabidopsis thaliana 2624 At4g19780 D2 transposable element gene 2625 At4g19810 D2 glycosyl hydrolase family 18 protein, similar to chitinase/lysozyme GI:467689 from (Nicotiana tabacum) 2626 At4g19840 D1, D2, Dm ATPP2-A1__lectin-related, similar to PP2 lectin polypeptide (Cucurbita maxima) GI:410437 2627 At4g19860 D1, D2, Dm lecithin:cholesterol acyltransferase family protein / LACT family protein, similar to lysosomal phospholipase A2 (Mus musculus) GI:18699602; contains Pfam profile PF02450: Lecithin:cholesterol acyltransferase (phosphatidylcholine-sterol acyltransferase) 2628 At4g20020 D2 expressed protein 2629 At4g20110 D1, D2, Dm vacuolar sorting receptor, putative, similar to BP-80 vacuolar sorting receptor (Pisum sativum) GI:1737222; identical to vacuolar sorting receptor-like protein (GI:2827665) (Arabidopsis thaliana) 2630 At4g20260 D2 DREPP plasma membrane polypeptide family protein, contains Pfam profile: PF05558 DREPP plasma membrane polypeptide 2631 At4g20310 D1, Dm similar to PREDICTED: similar to Membrane-bound transcription factor site 2 protease (S2P endopeptidase) (Site-2 protease) (Sterol-regulatory element-binding proteins intramembrane protease) [Gallus gallus] (GB:XP_425566.1); similar to membrane-bound transcription factor protease, site 2 [Mus musculus] (GB:NP_758511.1); contains InterPro domain Mammalian sterol- regulatory element binding protein (SREBP) site 2 protease (InterPro:IPR001193) 2632 At4g20330 D2, Dm transcription initiation factor-related, contains weak similarity to Transcription initiation factor IIE, beta subunit (TFIIE-beta) (Swiss-Prot:P29084) (Homo sapiens) 2633 At4g20420 D1, D2, Dm tapetum-specific protein-related, similar to SaTAP 35 (Sinapis alba) GI:408108 2634 At4g20760 D1, Dm short-chain dehydrogenase/reductase (SDR) family protein, contains Pfam profile: PF00106 short chain dehydrogenase 2635 At4g20850 D2, Dm TPP2__subtilase family protein, contains similarity to Tripeptidyl-peptidase II (EC 3.4.14.10) (TPP-II) (Tripeptidyl aminopeptidase) (Swiss-Prot:P29144) (Homo sapiens) 2636 At4g20890 D2, Dm TUB9__tubulin beta-9 chain (TUB9), nearly identical to SP:P29517 Tubulin beta-9 chain {Arabidopsis thaliana} 2637 At4g21110 D1, Dm G10 family protein, contains Pfam profile: PF01125 G10 protein 2638 At4g21150 Dm ribophorin II (RPN2) family protein, contains Pfam domain PF05817: Ribophorin II (RPN2) 2639 At4g21210 D1, Dm expressed protein, contains Pfam domain PF03618: Domain of unknown function (DUF299) 2640 At4g21280 D1, D2, Dm oxygen-evolving enhancer protein 3, chloroplast, putative (PSBQ1) (PSBQ), identical to SP:Q9XFT3 Oxygen-evolving enhancer protein 3-1, chloroplast precursor (OEE3) (16 kDa subunit of oxygen evolving system of photosystem II) (OEC 16 kDa subunit) {Arabidopsis thaliana}; similar to SP:P12301 Oxygen-evolving enhancer protein 3, chloroplast precursor (OEE3) (16 kDa subunit of oxygen evolving system of photosystem II) (OEC 16 kDa subunit) {Spinacia oleracea}; contains Pfam profile PF05757: Oxygen evolving enhancer protein 3 (PsbQ) 2641 At4g21510 Dm F-box family protein, contains Pfam PF00646: F-box domain; similar to SKP1 interacting partner 2 (SKIP2) TIGR_Ath1:At5g67250 2642 At4g21560 D1, Dm vacuolar protein sorting-associated protein 28 family protein / VPS28 family protein, contains similarity to Swiss-Prot:Q02767 vacuolar protein sorting-associated protein VPS28 (Saccharomyces cerevisiae) 2643 At4g21570 D1, D2, Dm expressed protein, contains Pfam profile PF03619: Domain of unknown function 2644 At4g21580 D2 oxidoreductase, zinc-binding dehydrogenase family protein, Pig3 Homo sapiens, PID:G2754812; contains Pfam zinc-binding dehydrogenase domain PF00107 2645 At4g21620 D2 glycine-rich protein 2646 At4g21640 D1, D2, Dm subtilase family protein, similar to subtilase SP1 (Oryza sativa) GI:9957714 2647 At4g21650 D1, D2, Dm subtilase family protein, contains Pfam domain, PF00082: Subtilase family; contains Pfam domain, PF02225: protease associated (PA) domain 2648 At4g21680 Dm proton-dependent oligopeptide transport (POT) family protein, contains Pfam profile: PF00854 POT family 2649 At4g21800 Dm ATP-binding family protein, contains Pfam domain, PF03029: Conserved hypothetical ATP binding protein 2650 At4g21870 D2 26.5 kDa class P-related heat shock protein (HSP26.5-P), contains Pfam profile: PF00011 Hsp20/alpha crystallin family: identified in Scharf, K-D., et al,Cell Stress & Chaperones (2001) 6: 225-237. 2651 At4g21930 D2, Dm expressed protein, contains Pfam profile PF04520: Protein of unknown function, DUF584 2652 At4g21960 D1, D2, Dm PRXR1__peroxidase 42 (PER42) (P42) (PRXR1), identical to SP:Q9SB81 Peroxidase 42 precursor (EC 1.11.1.7) (Atperox P42) (PRXR1) (ATP1a/ATP1b) {Arabidopsis thaliana} 2653 At4g21980 D1, D2, Dm APG8A_ATG8A__autophagy 8a (APG8a), identical to autophagy 8a (Arabidopsis thaliana) GI:19912151; contains Pfam profile PF02991: Microtubule associated protein 1A/1B, light chain 3 2654 At4g22010 D1, D2, Dm SKS4__multi-copper oxidase type I family protein, similar to pollen-specific BP10 protein (SP:Q00624)(Brassica napus); contains Pfam profile: PF00394 Multicopper oxidase 2655 At4g22020 D2, Dm pseudogene, hypothetical protein, similar to uncharacterized glycine-rich protein (GI:7269047) {Arabidopsis thaliana} 2656 At4g22200 D1, Dm AKT2_AKT3__potassium channel protein 2 (AKT2) (AKT3), identical to potassium channel (Arabidopsis thaliana) gi:1100898:gb:AAA97865; Note: also identical to AKT3 (Arabidopsis thaliana) gi:1172218:gb:AAA96153, which is a truncated version of AKT2, PMID:10852932; member of the 1 pore, 6 transmembrane (1P/6TM- Shaker-type) K+ channel family, PMID:11500563; identical to cDNA inward-rectifying K+ channel (AKT3) GI:1172219 2657 At4g22220 D1, Dm ISU1_ATISU1__iron-sulfur cluster assembly complex protein, putative, similar to iron-sulfur cluster assembly complex ISCU1 (GI:11545705) (Homo sapiens); nifU protein homolog YPL135w (GI:15619823) (Saccharomyces cerevisiae) PIR2:S69049 2658 At4g22240 D1, D2, Dm plastid-lipid associated protein PAP, putative, similar to plastid-lipid associated proteins PAP2 (Brassica rapa) GI:14248550 GI:14248556; contains Pfam profile PF04755: PAP_fibrillin 2659 At4g22260 D1, Dm IM_IM1__alternative oxidase, putative / immutans protein (IM), identical to IMMUTANS from Arabidopsis thaliana (gi:4138855); contains Pfam profile PF01786 alternative oxidase 2660 At4g22490 D1, Dm protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 2661 At4g22500 D2 2662 At4g22610 D2 protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 2663 At4g22670 Dm tetratricopeptide repeat (TPR)-containing protein, similar to Hsc70-interacting protein (Hip) from {Homo sapiens} SP:P50502, {Rattus norvegicus} SP:P50503; contains Pfam profile PF00515: tetratricopeptide repeat (TPR) domain 2664 At4g22720 D2 glycoprotease M22 family protein, similar to sialylglycoprotease (Haemophilus ducreyi) GI:6942294; contains Pfam profile PF00814: Glycoprotease family 2665 At4g22740 Dm glycine-rich protein 2666 At4g22880 D2, Dm LDOX_ANS_TDS4_TT18__leucoanthocyanidin dioxygenase, putative / anthocyanidin synthase, putative, similar to SP:P51091 (Malus domestica); contains PF03171 2OG-Fe(II) oxygenase superfamily 2667 At4g22950 D2 AGL19_GL19__MADS-box protein (AGL19), MADS-box protein AGL14, Arabidopsis thaliana, gb:U20184

2668 At4g23050 D2 protein kinase, putative, similar to MAP3K delta-1 protein kinase (Arabidopsis thaliana) gi:2253010:emb:CAA74591; contains Pfam PF00069 Protein kinase domain and PF00989 PAS domain 2669 At4g23430 Dm short-chain dehydrogenase/reductase (SDR) family protein, contains INTERPRO family IPR002198 Short-chain dehydrogenase/reductase (SDR) superfamily; contains Pfam PF00106: oxidoreductase, short chain dehydrogenase/reductase family 2670 At4g23500 D1, Dm glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family protein, weak similarity to SP:P27644 Polygalacturonase (EC 3.2.1.15) (Pectinase) {Agrobacterium tumefaciens}; contains PF00295: Glycosyl hydrolases family 28 2671 At4g23560 D2 glycosyl hydrolase family 9 protein, similar to cellulase GI:1039431 from (Phaseolus vulgaris)

2672 At4g23600 Dm CORI3_JR2__coronatine-responsive tyrosine aminotransferase / tyrosine transaminase, similar to nicotianamine aminotransferase from Hordeum vulgare (GI:6498122, GI:6469087); contains Pfam profile PF00155 aminotransferase, classes I and II; identical to cDNA coronatine-regulated tyrosine aminotransferase (F9D16.70) GI:15076852 2673 At4g23630 D1, D2, Dm reticulon family protein (RTNLB1), weak similarity to Nogo-C protein (Rattus norvegicus) GI:6822251; contains Pfam profile PF02453: Reticulon 2674 At4g23670 D1, D2, Dm major latex protein-related / MLP-related, low similarity to major latex protein {Papaver somniferum}(GI:294060) contains Pfam profile PF00407: Pathogenesis-related protein Bet v I family 2675 At4g23680 D1, D2, Dm major latex protein-related / MLP-related, low similarity to major latex protein {Papaver somniferum}(GI:294060) ; contains Pfam profile PF00407: Pathogenesis-related protein Bet v I family 2676 At4g23710 D2 vacuolar ATP synthase subunit G 2 (VATG2) / V-ATPase G subunit 2 (VAG2) / vacuolar proton pump G subunit 2, identical to Swiss-Prot:O82629 vacuolar ATP synthase subunit G 2 (V-ATPase G subunit 2, Vacuolar proton pump G subunit 2) (Arabidopsis thaliana) 2677 At4g23820 D1, D2, Dm glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family protein, weak similarity to polygalacturonase PG1 (Glycine max) GI:5669846; contains PF00295: Glycosyl hydrolases family 28 2678 At4g23870 D1, D2, Dm expressed protein, predicted proteins, Arabidopsis thaliana 2679 At4g23880 Dm expressed protein 2680 At4g23900 D2 nucleoside diphosphate kinase 4 (NDK4), contains Pfam PF00334 : Nucleoside diphosphate kinase domain; identical to nucleoside diphosphate kinase 4 (GI:11990430) (Arabidopsis thaliana)

2681 At4g24190 D2, Dm SHD__shepherd protein (SHD) / clavata formation protein, putative, nearly identical to SHEPHERD (Arabidopsis thaliana) GI:19570872; contains Pfam profiles PF02518: ATPase, histidine kinase-, DNA gyrase B-, and HSP90-like domain protein, PF00183: Hsp90 protein 2682 At4g24220 D1, Dm VEP1_AWI31__expressed protein, protein induced upon wounding - Arabidopsis thaliana, PID:e257749 2683 At4g24290 Dm expressed protein 2684 At4g24350 D1, Dm phosphorylase family protein, contains Pfam PF01048: Phosphorylase family 2685 At4g24520 D1, Dm ATR1_AR1__NADPH-cytochrome p450 reductase, putative / NADPH-ferrihemoprotein reductase, putative, similar to NADPH-ferrihemoprotein reductase NADPH-cytochrome P450 oxydoreductase isoform 1 (Populus balsamifera subsp. trichocarpa x Populus deltoides) GI:13183562, SP:P37116 NADPH-cytochrome P450 reductase (EC 1.6.2.4) (CPR) (Vigna radiata) {Phaseolus aureus}

2686 At4g24590 D2, Dm expressed protein 2687 At4g24660 D2, Dm zinc finger homeobox family protein / ZF-HD homeobox family protein, hypothetical protein T8K22.16, Arabidopsis thalianachromosome II BAC T8K22, PATX:G3184285 2688 At4g24690 D1, Dm ubiquitin-associated (UBA)/TS-N domain-containing protein / octicosapeptide/Phox/Bemp1 (PB1) domain-containing protein, contains Pfam profiles PF00627: Ubiquitin-associated (UBA)/TS-N domain, PF00569: Zinc finger ZZ type domain, PF00564: PB1 domain 2689 At4g24750 D1, D2, Dm similar to rhodanese-like domain-containing protein [Arabidopsis thaliana] (TAIR:At3g08920.1); similar to rhodanese family protein-like [Oryza sativa (japonica cultivar-group)] (GB:XP_450481.1); contains InterPro domain Rhodanese-like (InterPro:IPR001763)

2690 At4g24770 D2, Dm RBP31_ATRBP31_ATRBP33_CP31__31 kDa ribonucleoprotein, chloroplast, putative / RNA-binding protein RNP-T, putative / RNA-binding protein 1/2/3, putative / RNA-binding protein cp31, putative, similar to SP:Q04836 31 kDa ribonucleoprotein, chloroplast precursor (RNA-binding protein RNP-T) (RNA-binding protein 1/2/3) (AtRBP33) (RNA-binding protein cp31) {Arabidopsis thaliana}; contains InterPro entry IPR000504: RNA-binding region RNP-1 (RNA recognition motif) (RRM) 2691 At4g24780 D1, Dm pectate lyase family protein, similar to pectate lyase GP:14289169 from (Salix gilgiana) 2692 At4g24930 D1, Dm thylakoid lumenal 17.9 kDa protein, chloroplast, SP:Q9SW33;GI:17369630;PMID:11719511; similar to expressed protein gi:12321169 {Oryza sativa} 2693 At4g25000 D2 AMY1_AMY1_ATAMY1__alpha-amylase, putative / 1,4-alpha-D-glucan glucanohydrolase, putative, similar to alpha-amylase from Vigna mungo SP:P17859, Ipomoea nil GI:21670851; contains Pfam profile PF00128: Alpha amylase, catalytic domain. Predicted to be secreted protein based on signalP prediction. Involved in starch mobilization. 2694 At4g25030 D2, Dm expressed protein 2695 At4g25050 D1, D2, Dm ACP4__acyl carrier family protein / ACP family protein, similar to Acyl carrier protein, chloroplast precursor from {Spinacia oleracea} SP:P23235, {Casuarina glauca} SP:P93092; contains InterPro accession IPR003881: Isochorismatase 2696 At4g25080 D1, Dm magnesium-protoporphyrin O-methyltransferase, putative / magnesium-protoporphyrin IX methyltransferase, putative, similar to SP:Q55467 Magnesium-protoporphyrin O-methyltransferase (EC 2.1.1.1) (Magnesium-protoporphyrin IX methyltransferase) {Synechocystis sp.}

2697 At4g25100 D1, D2, Dm FSD1__superoxide dismutase (Fe), chloroplast (SODB) / iron superoxide dismutase (FSD1), identical to Fe-superoxide dismutase (Arabidopsis thaliana) gi:166700:gb:AAA32791; supported by cDNA, Ceres:32935 2698 At4g25260 D1 invertase/pectin methylesterase inhibitor family protein, low similarity to pectinesterase from Phaseolus vulgaris SP:Q43111, Lycopersicon esculentum SP:Q43143, Arabidopsis thaliana SP:Q42534; contains Pfam profile PF04043: Plant invertase/pectin methylesterase inhibitor 2699 At4g25340 D2 immunophilin-related / FKBP-type peptidyl-prolyl cis-trans isomerase-related, immunophilin FKBP46 - Spodoptera frugiperda (fall armyworm),PIR2:A55320 2700 At4g25400 D2 basix helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain 2701 At4g25420 D1, Dm ATGA20OX1_GA20OX1_GA5_ATGA20OX1__gibberellin 20-oxidase, identical to GI:1109695 2702 At4g25570 D2 ACYB-2__cytochrome B561 family protein, contains Pfam domain, PF03188: Cytochrome b561 2703 At4g25580 D2, Dm stress-responsive protein-related, contains weak similarity to Low-temperature-induced 65 kDa protein (Desiccation-responsive protein 29B) (Swiss-Prot:Q04980) (Arabidopsis thaliana) 2704 At4g25630 D2, Dm FIB2_ATFIB2_U60.2f__fibrillarin 2 (FIB2), identical to fibrillarin 2 GI:9965655 from (Arabidopsis thaliana) 2705 At4g25640 D1 MATE efflux family protein, similar to ripening regulated protein DDTFR18 (Lycopersicon esculentum) GI:12231296; contains Pfam profile PF01554: Uncharacterized membrane protein family 2706 At4g25650 D1, D2, Dm Rieske (2Fe-2S) domain-containing protein, similar to cell death suppressor protein lls1 from Zea mays (gi:1935909), Rieske iron-sulfur protein Tic55 from Pisum sativum (gi:2764524); contains Pfam PF00355 Rieske (2Fe-2S) domain 2707 At4g25670 D1, D2, Dm expressed protein 2708 At4g25730 D2 FtsJ-like methyltransferase family protein, contains Pfam profile: PF01728 FtsJ-like methyltransferase 2709 At4g25740 Dm 40S ribosomal protein S10 (RPS10A), 40S ribosomal protein S10 - Lumbricus rubellus, PID:e1329701 2710 At4g25770 Dm expressed protein 2711 At4g25780 Dm pathogenesis-related protein, putative, similar to gene PR-1 protein - Medicago truncatula, SP:Q40374; contains Pfam profile PF00188: SCP-like extracellular protein 2712 At4g25890 D2 60S acidic ribosomal protein P3 (RPP3A), acidic ribosomal protein P3a - maize, PIR2:T02037 2713 At4g26060 D2, Dm expressed protein 2714 At4g26080 D1, D2, Dm ABI1__protein phosphatase 2C ABI1 / PP2C ABI1 / abscisic acid-insensitive 1 (ABI1), nearly identical to SP:P49597 Protein phosphatase 2C ABI1 (EC 3.1.3.16) (PP2C) (Abscisic acid- insensitive 1) {Arabidopsis thaliana} 2715 At4g26110 D2 nucleosome assembly protein (NAP), putative, similar to nucleosome assembly protein 1 (Glycine max) GI:1161252; contains Pfam profile PF00956: Nucleosome assembly protein (NAP) 2716 At4g26130 D1, Dm expressed protein 2717 At4g26230 D1, D2, Dm 60S ribosomal protein L31 (RPL31B), ribosomal protein L31, Nicotiana glutinosa, U23784 2718 At4g26300 D2 EMB1027__arginyl-tRNA synthetase, putative / arginine--tRNA ligase, putative, similar to SP:P37880 Arginyl-tRNA synthetase (EC 6.1.1.19) (Arginine--tRNA ligase) (ArgRS) {Cricetulus longicaudatus}; contains Pfam profiles PF00750: arginyl-tRNA synthetase, PF03485: arginyl-tRNA synthetase N-terminal domain 2719 At4g26370 D1, D2, Dm antitermination NusB domain-containing protein, contains Pfam profile: PF01029 NusB family 2720 At4g26380 D1 DC1 domain-containing protein, contains Pfam profile PF03107: DC1 domain 2721 At4g26510 D2 uracil phosphoribosyltransferase / UMP pyrophosphorylase (UPT1), nearly identical to SP:O65583 Uracil phosphoribosyltransferase (EC 2.4.2.9) (UMP pyrophosphorylase) (UPRTase) {Arabidopsis thaliana} 2722 At4g26520 D2 fructose-bisphosphate aldolase, cytoplasmic, identical to SP:P22197 Fructose-bisphosphate aldolase, cytoplasmic isozyme (EC 4.1.2.13) {Arabidopsis thaliana} 2723 At4g26530 D2 fructose-bisphosphate aldolase, putative, strong similarity to SP:P22197 Fructose-bisphosphate aldolase, cytoplasmic isozyme (EC 4.1.2.13) {Arabidopsis thaliana} 2724 At4g26620 D1, Dm sucrase-related 2725 At4g26670 D2 mitochondrial import inner membrane translocase subunit Tim17/Tim22/Tim23 family protein, weak similarity to SP:Q9Z0V8 Mitochondrial import inner membrane translocase subunit TIM17 A {Mus musculus}; contains Pfam profile PF02466: Mitochondrial import inner membrane translocase subunit Tim17 2726 At4g26690 D1, D2, Dm glycerophosphoryl diester phosphodiesterase family protein, weak similarity to glycerophosphodiester phosphodiesterase (Borrelia hermsii) GI:1399038; contains Pfam profile PF03009: Glycerophosphoryl diester phosphodiesterase family 2727 At4g26780 D2 AR192__co-chaperone grpE family protein, similar to chaperone GrpE type 2 (Nicotiana tabacum) GI:3851640; contains Pfam profile PF01025: co-chaperone GrpE 2728 At4g26850 D1, D2, Dm VTC2__expressed protein 2729 At4g26900 Dm AT-HF_HISHF__imidazole glycerol phosphate synthase hisHF, chloroplast / IGP synthase / ImGPP synthase / IGPS, identical to SP:Q9SZ30 Imidazole glycerol phosphate synthase hisHF, chloroplast precursor (IGP synthase) {Arabidopsis thaliana} 2730 At4g27120 D2 expressed protein 2731 At4g27130 D1, D2, Dm eukaryotic translation initiation factor SUI1, putative, similar to SP:P32911 Protein translation factor SUI1 {Saccharomyces cerevisiae}; contains Pfam profile PF01253: Translation initiation factor SUI1 2732 At4g27240 D2, Dm zinc finger (C2H2 type) family protein, contains zinc finger, C2H2 type, domain, PROSITE:PS00028 2733 At4g27330 D1, Dm SPL_NZZ__sporocyteless (SPL), identical to sporocyteless SPL (MADS-box related protein) (Arabidopsis thaliana) gi:5566240:gb:AAD45344 2734 At4g27380 Dm expressed protein 2735 At4g27390 D1, Dm expressed protein, hypothetical protein, Synechocystis sp., PIR2:S77328 2736 At4g27410 D2, Dm ANAC072_RD26__no apical meristem (NAM) family protein (RD26), contains Pfam PF02365: No apical meristem (NAM) domain; Arabidopsis thaliana nap gene,PID:e1234813; identical to cDNA RD26 mRNA for NAM-like protein GI:15375403 2737 At4g27440 D1 PORB__protochlorophyllide reductase B, chloroplast / PCR B / NADPH-protochlorophyllide oxidoreductase B (PORB), identical to SP:P21218 protochlorophyllide reductase B, chloroplast precursor (EC 1.3.1.33) (PCR B) (NADPH-protochlorophyllide oxidoreductase B) (POR B) (Arabidopsis thaliana) 2738 At4g27450 D2, Dm expressed protein, similar to auxin down-regulated protein ARG10 (Vigna radiata) GI:2970051, wali7 (aluminum-induced protein) (Triticum aestivum) GI:451193 2739 At4g27500 D1, Dm PPI1__expressed protein, non-consensus GA donor splice site at exon 6 2740 At4g27530 D2, Dm expressed protein 2741 At4g27560 D1, Dm glycosyltransferase family protein, contains Pfam profile: PF00201 UDP-glucoronosyl and UDP- glucosyl transferase 2742 At4g27600 D1, D2, Dm pfkB-type carbohydrate kinase family protein, contains Pfam profile: PF00294 pfkB family carbohydrate kinase 2743 At4g27720 D2, Dm expressed protein, contains Pfam PF05631: Protein of unknown function (DUF791) 2744 At4g27800 D1, D2, Dm protein phosphatase 2C PPH1 / PP2C PPH1 (PPH1), identical to SP:P49599:P2C3_ARATH Protein phosphatase 2C PPH1 (EC 3.1.3.16) (PP2C) {Arabidopsis thaliana}; similar to protein phosphatase-2C; PP2C (GI:3643090) (Mesembryanthemum crystallinum) 2745 At4g27820 D2, Dm glycosyl hydrolase family 1 protein, contains Pfam PF00232 : Glycosyl hydrolase family 1 domain; TIGRFAM TIGR01233: 6-phospho-beta-galactosidase; similar to hydroxyisourate hydrolase (GI:19569603) (Glycine max) 2746 At4g27830 Dm glycosyl hydrolase family 1 protein, contains Pfam PF00232 : Glycosyl hydrolase family 1 domain; TIGRFAM TIGR01233: 6-phospho-beta-galactosidase; similar to hydroxyisourate hydrolase (GI:19569603) (Glycine max) 2747 At4g27990 D2, Dm YGGT family protein, contains Pfam profile PF02325: YGGT family (unknown function) 2748 At4g28210 Dm EMB1923__expressed protein 2749 At4g28240 D1, D2, Dm wound-responsive protein-related, wound-induced protein - tomato (fragment), PIR2:S19773 2750 At4g28260 D2, Dm expressed protein 2751 At4g28420 Dm aminotransferase, putative, tsimilar to nicotianamine aminotransferase from Hordeum vulgare (GI:6498122, GI:6469087); contains Pfam profile PF00155 aminotransferase, classes I and II 2752 At4g28430 D2, Dm reticulon family protein, contains Pfam profile PF02453: Reticulon 2753 At4g28660 D1, D2, Dm photosystem II reaction centre W (PsbW) family protein, contains Pfam profile: PF03912 photosystem II reaction centre W protein, PsbW 2754 At4g28750 D2 PSAE1__photosystem I reaction center subunit IV, chloroplast, putative / PSI-E, putative (PSAE1), identical to SP:Q9S831; similar to SP:P12354 Photosystem I reaction center subunit IV, chloroplast precursor (PSI-E) {Spinacia oleracea}; contains Pfam profile PF02427: Photosystem I reaction centre subunit IV / PsaE 2755 At4g28780 D1, D2, Dm GDSL-motif lipase/hydrolase family protein, similar to family II lipase EXL3 (GI:15054386), EXL1 (GI:15054382), EXL2 (GI:15054384) (Arabidopsis thaliana); contains Pfam profile PF00657: Lipase/Acylhydrolase with GDSL-like motif 2756 At4g29010 D2, Dm AIM1__abnormal inflorescence meristem 1 / fatty acid multifunctional protein (AIM1), identical to gi:4337025; contains Pfam profiles PF02737 (3-hydroxyacyl-CoA dehydrogenase, NAD binding domain), PF00378 (enoyl-CoA hydratase/isomerase family protein), PF00725 (3-hydroxyacyl-CoA dehydrogenase) 2757 At4g29040 D1, Dm RPT2A__26S proteasome AAA-ATPase subunit (RPT2a), almost identical to 26S proteasome AAA- ATPase subunit RPT2a (GI:6652880) {Arabidopsis thaliana}; Drosophila melanogaster 26S proteasome subunit 4 ATPase, PID:g1066065 2758 At4g29060 D1, D2, Dm EMB2726__elongation factor Ts family protein, similar to SP:P35019 Elongation factor Ts (EF- Ts) {Galdieria sulphuraria}; contains Pfam profiles PF00627: UBA/TS-N domain, PF00889: Elongation factor TS, PF00575: S1 RNA binding domain 2759 At4g29070 D1, D2, Dm expressed protein 2760 At4g29090 D2 reverse transcriptase, putative / RNA-dependent DNA polymerase, putative, similar to reverse transcriptase (Arabidopsis thaliana) GI:976278; contains Pfam profile PF00075: RNase H 2761 At4g29130 Dm ATHXK1_GIN2_HXK1__hexokinase 1 (HXK1), identical to hexokinase 1 (Arabidopsis thaliana) Swiss- Prot:Q42525 2762 At4g29160 D1, Dm SNF7 family protein, contains Pfam domain, PF03357: SNF7 family 2763 At4g29190 D1, D2, Dm zinc finger (CCCH-type) family protein, contains Pfam domain, PF00642: Zinc finger C-x8-C-x5- C-x3-H type (and similar) 2764 At4g29250 D2 transferase family protein, low similarity to CER2 Arabidopsis thaliana GI:1213594, anthocyanin 5-aromatic acyltransferase Gentiana triflora GI:4185599; contains Pfam profile PF02458 transferase family 2765 At4g29310 D1, D2, Dm expressed protein 2766 At4g29370 D2, Dm kelch repeat-containing F-box family protein, contains F-box domain Pfam:PF00646 and Kelch motif Pfam:PF01344 2767 At4g29470 D2, Dm phospholipase A2, putative, similar to secretory low molecular weight phospholipase A2 gamma (Arabidopsis thaliana) GI:26006457; contains INTERPRO domain IPR001211 phospholipase A2 2768 At4g29510 D2 protein arginine N-methyltransferase, putative, similar to protein arginine N- methyltransferase 1-variant 2 (Homo sapiens) GI:7453575 2769 At4g29670 Dm thioredoxin family protein, contains Pfam profile PF00085: Thioredoxin 2770 At4g29680 D2, Dm type I phosphodiesterase/nucleotide pyrophosphatase family protein, similar to SP:P06802 Ectonucleotide pyrophosphatase/phosphodiesterase 1 (Plasma-cell membrane glycoprotein PC-1) (Includes: Alkaline phosphodiesterase I (EC 3.1.4.1); Nucleotide pyrophosphatase (EC 3.6.1.9) {Mus musculus}; contains Pfam profile PF01663: Type I phosphodiesterase / nucleotide pyrophosphatase 2771 At4g29820 Dm expressed protein 2772 At4g30100 Dm tRNA-splicing endonuclease positive effector-related, contains similarity to SEN1, a positive effector of tRNA-splicing endonuclease (Saccharomyces cerevisiae) gi:172574:gb:AAB63976

2773 At4g30190 D1, D2, Dm AHA2_PMA2__ATPase 2, plasma membrane-type, putative / proton pump 2, putative / proton- exporting ATPase, putative, strong similarity to SP:P19456 ATPase 2, plasma membrane-type (EC 3.6.3.6) (Proton pump 2) {Arabidopsis thaliana}; contains InterPro accession IPR001757: ATPase, E1-E2 type; contains Pfam profile PF00690: Cation transporter/ATPase, N-terminus 2774 At4g30210 D1, Dm ATR2_AR2__NADPH-cytochrome p450 reductase, putative / NADPH-ferrihemoprotein reductase, putative, similar to NADPH-cytochrome P450 oxydoreductase from (Populus balsamifera subsp. trichocarpa x Populus deltoides) GI:13183564, GI:13183566 2775 At4g30260 D2 integral membrane Yip1 family protein, contains Pfam domain, PF04893: Yip1 domain 2776 At4g30270 D2, Dm MERI5B_BRU1_MERI-5__MERI-5 protein (MERI-5) (MERI5B) / endo-xyloglucan transferase / xyloglucan endo-1,4-beta-D-glucanase (SEN4), identical to endo-xyloglucan transferase gi:944810, SP:P24806 MERI-5 protein precursor (Endo-xyloglucan transferase) (Xyloglucan endo- 1,4-beta-D-glucanase) {Arabidopsis thaliana} 2777 At4g30280 D2 ATXTH18__putative xyloglucan endotransglycosylase/hydrolase, expressed in the mature or basal regions of both the main and lateral roots, but not in the tip of these roots where cell division occurs. 2778 At4g30290 Dm ATXTH19__putative xyloglucan endotransglycosylase/hydrolase, expressed throughout both the main and the lateral root, with intensive expression at the dividing and elongating regions. Is expressed in lateral root primordia but expression ceases after lateral root begins to grow. 2779 At4g30330 D1, Dm small nuclear ribonucleoprotein E, putative / snRNP-E, putative / Sm protein E, putative, similar to SWISS-PROT:P08578 small nuclear ribonucleoprotein E (snRNP-E) (Sm protein E, Sm-E, SmE) (Chicken) 2780 At4g30450 D1, D2, Dm glycine-rich protein 2781 At4g30460 D1, D2, Dm glycine-rich protein 2782 At4g30470 D1, Dm cinnamoyl-CoA reductase-related, similar to cinnamoyl-CoA reductase from Pinus taeda (GI:17978649), Saccharum officinarum (GI:3341511) 2783 At4g30490 D1, D2, Dm AFG1-like ATPase family protein, contains Pfam profile: PF03969 AFG1-like ATPase 2784 At4g30530 D1, Dm defense-related protein, putative, strong similarity to defense-related protein (Brassica carinata) GI:14009290; contains Pfam profile PF00117: glutamine amidotransferase class-I 2785 At4g30620 D1, D2, Dm expressed protein, contains Pfam domain PF02575: Uncharacterized BCR, YbaB family COG0718; contains similarity to complex interacting protein 9 (CIP9) GI: 32892212 2786 At4g30630 D2, Dm expressed protein 2787 At4g30650 D2 hydrophobic protein, putative / low temperature and salt responsive protein, putative, similar to SP:Q9ZNQ7 Hydrophobic protein RCI2A (Low temperature and salt responsive protein LTI6A) {Arabidopsis thaliana}; contains Pfam profile PF01679: Uncharacterized protein family 2788 At4g30660 D2, Dm hydrophobic protein, putative / low temperature and salt responsive protein, putative, similar to SP:Q9ZNQ7 Hydrophobic protein RCI2A (Low temperature and salt responsive protein LTI6A) {Arabidopsis thaliana}; contains Pfam profile PF01679: Uncharacterized protein family 2789 At4g30670 D2, Dm expressed protein 2790 At4g30760 D1, Dm expressed protein, contains Pfam profile PF04396: Protein of unknown function, DUF537 2791 At4g30825 Dm pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat 2792 At4g30960 D1, D2, Dm CIPK6__CBL-interacting protein kinase 6 (CIPK6), identical to CBL-interacting protein kinase 6 (Arabidopsis thaliana) gi:9280634:gb:AAF86505 2793 At4g31000 D1, D2, Dm calmodulin-binding protein, similar to calmodulin-binding protein TCB60 GI:1698548 from (Nicotiana tabacum); contains non-consensus donor splice site AT at exon 4; supported by cDNA gi:17065559 2794 At4g31040 D2 proton extrusion protein-related, contains weak similarity to Proton extrusion protein pcxA (Swiss-Prot:P75028) (Synechocystis sp.) 2795 At4g31120 D2 Skb1 methyltransferase family protein, contains Pfam profile: PF05185 Skb1 methyltransferase 2796 At4g31130 D2 expressed protein 2797 At4g31210 D2 DNA topoisomerase family protein, similar to DNA Topoisomerase I (SP:Q9X3X7) {Zymomonas mobilis} 2798 At4g31290 D1, Dm ChaC-like family protein, contains Pfam profile: PF04752 ChaC-like protein 2799 At4g31310 D2 avirulence-responsive protein-related / avirulence induced gene (AIG) protein-related, similar to SP:P54121 AIG2 protein {Arabidopsis thaliana} 2800 At4g31450 D2 zinc finger (C3HC4-type RING finger) family protein, similar to Pfam domain, PF00097: Zinc finger, C3HC4 type (RING finger) 2801 At4g31530 D2 expressed protein 2802 At4g31550 D1, Dm WRKY11_ATWRKY11__WRKY family transcription factor, contains Pfam profile: PF03106 2803 At4g31700 D1, D2, Dm RPS6__40S ribosomal protein S6 (RPS6A), ribosomal protein S6, Arabidopsis thaliana, PID:g2662469 2804 At4g31790 D2 diphthine synthase, putative (DPH5), similar to Diphthine synthase (Diphtamide biosynthesis methyltransferase) (DPH5) (SP:P32469) (Saccharomyces cerevisiae); similar to CGI-30 protein (GI:4680699) (Homo sapiens); similar to methyltransferase DPH5, Saccharomyces cerevisiae, PIR2:S30890; contains Pfam PF00590 : Tetrapyrrole (Corrin/Porphyrin) Methylases domain; contains TIGRFAMS TIGR00522 : diphthine synthase 2805 At4g31800 D2 WRKY18__WRKY family transcription factor 2806 At4g31860 D1, D2, Dm protein phosphatase 2C, putative / PP2C, putative, protein phosphatase 2C, Schizosaccharomyces pombe, PIR2:S54297 2807 At4g31880 Dm expressed protein 2808 At4g31910 D1 transferase family protein, low similarity to anthranilate N- hydroxycinnamoyl/benzoyltransferase Dianthus caryophyllus GI:3288180, 10-deacetylbaccatin III- 10-O-acetyl transferase Taxus cuspidata GI:6746554; contains Pfam profile PF02458 transferase family 2809 At4g31985 D1, D2, Dm 60S ribosomal protein L39 (RPL39C) 2810 At4g31990 Dm ASP5_AAT3_ATAAT1__aspartate aminotransferase, chloroplast / transaminase A (ASP5) (AAT1), nearly identical to SP:P46248 Aspartate aminotransferase, chloroplast precursor (EC 2.6.1.1) (Transaminase A) {Arabidopsis thaliana} 2811 At4g32020 D2, Dm expressed protein, NuLL 2812 At4g32150 D1, D2, Dm VAMP7C_ATVAMP711_VAMP711__synaptobrevin family protein, similar to Synaptobrevin-like protein 1 (SP:P51809) (Homo sapiens) 2813 At4g32210 D1, D2, Dm Encodes one of the membrane anchor subunits of the mitochondrial respiratory complex II. The protein is encoded by the nuclear genome but is imported into the mitochondrion. There are two genes that encode this protein, the other is SDH3-1. 2814 At4g32520 D2 glycine hydroxymethyltransferase, putative / serine hydroxymethyltransferase, putative / serine/threonine aldolase, putative, similar to serine hydroxymethyltransferase (Chlamydomonas reinhardtii) GI:17066746; contains Pfam profile PF00464: serine hydroxymethyltransferase

2815 At4g32570 D2, Dm expressed protein 2816 At4g32590 D2 ferredoxin-related, contains Pfam profile: PF00111 2Fe-2S iron-sulfur cluster binding domain 2817 At4g32600 Dm zinc finger (C3HC4-type RING finger) family protein, low similarity to RING finger protein 38 (Homo sapiens) GI:21666412; contains Pfam profile PF00097: Zinc finger, C3HC4 type (RING finger) 2818 At4g32640 Dm sec23/sec24 transport protein-related 2819 At4g32770 D1, D2, Dm VTE1_ATSDX1__tocopherol cyclase, chloroplast / vitamin E deficient 1 (VTE1) / sucrose export defective 1 (SXD1), identical to SP:Q94FY7 Tocopherol cyclase, chloroplast precursor (Vitamin E deficient 1) (Sucrose export defective 1) {Arabidopsis thaliana} 2820 At4g32850 D1, Dm nPAP__nucleotidyltransferase family protein, contains Pfam profiles: PF01909 nucleotidyltransferase domain, PF04926 poly(A) polymerase predicted RNA binding domain 2821 At4g32890 D2, Dm zinc finger (GATA type) family protein, GATA transcription factor 3, Arabidopsis thaliana, gb:Y13650 2822 At4g32900 D2, Dm expressed protein 2823 At4g32910 D1 expressed protein 2824 At4g32915 D1 expressed protein 2825 At4g32920 D1, D2, Dm glycine-rich protein 2826 At4g32940 D1, D2, Dm GAMMA-VPE_GAMMAVPE__vacuolar processing enzyme gamma / gamma-VPE, nearly identical to SP:Q39119 Vacuolar processing enzyme, gamma-isozyme precursor (EC 3.4.22.-) (Gamma-VPE) {Arabidopsis thaliana} 2827 At4g33010 D1, D2, Dm glycine dehydrogenase (decarboxylating), putative / glycine decarboxylase, putative / glycine cleavage system P-protein, putative, strong similarity to SP:P49361 Glycine dehydrogenase (decarboxylating) A, mitochondrial precursor (EC 1.4.4.2) {Flaveria pringlei}; contains Pfam profile PF02347: Glycine cleavage system P-protein 2828 At4g33030 D1, Dm SQD1__UDP-sulfoquinovose synthase / sulfite:UDP-glucose sulfotransferase / sulfolipid biosynthesis protein (SQD1), identical to gi:2736155 2829 At4g33090 D2, Dm APM1_ATAPM1__aminopeptidase M, similar to SP:Q11011 Puromycin-sensitive aminopeptidase (EC 3.4.11.-) (PSA) {Mus musculus}; contains Pfam profile PF01433: Peptidase family M1 2830 At4g33110 D1 coclaurine N-methyltransferase, putative, similar to coclaurine N-methyltransferase (Coptis japonica) GI:16754879; contains Pfam profile PF02353: Cyclopropane-fatty-acyl-phospholipid synthase 2831 At4g33150 D1, D2, Dm LKR_SDH__lysine-ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzyme, identical to lysine-ketoglutarate reductase/saccharopine dehydrogenase GI:2052508 from (Arabidopsis thaliana) 2832 At4g33270 D1, Dm CDC20.1__WD-40 repeat family protein, contains 6 WD-40 repeats (PF00400); WD-repeat protein - Daucus carota,PID:g2253631 2833 At4g33300 D2 ADR1-L1__disease resistance protein (CC-NBS-LRR class), putative, domain signature CC-NBS-LRR exists, suggestive of a disease resistance protein. 2834 At4g33350 D2, Dm chloroplast inner membrane import protein Tic22, putative, similar to Tic22 (Pisum sativum) gi:3769671:gb:AAC64606 2835 At4g33550 D1, D2, Dm similar to protease inhibitor/seed storage/lipid transfer protein (LTP) family protein [Arabidopsis thaliana] (TAIR:At4g30880.1); similar to seed specific protein Bn15D18B [Brassica napus] (GB:AAP37971.1); contains InterPro domain Plant lipid transfer/seed storage/trypsin- alpha amylase inhibitor (InterPro:IPR003612) 2836 At4g33630 D2 expressed protein 2837 At4g33666 D2 expressed protein 2838 At4g33680 D1, Dm AGD2__aminotransferase class I and II family protein, low similarity to Aromatic Aminotransferase from Pyrococcus horikoshii GP:14278621; contains Pfam profile PF00155 aminotransferase, classes I and II 2839 At4g33710 D2 pathogenesis-related protein, putative, similar to PR-1a protein (Nicotiana tabacum) GI:19944; contains Pfam profile PF00188: SCP-like extracellular protein 2840 At4g33720 D2 pathogenesis-related protein, putative, similar to SP:P33154 Pathogenesis-related protein 1 precursor (PR-1) {Arabidopsis thaliana}; contains Pfam profile PF00188: SCP-like extracellular protein 2841 At4g33865 D2, Dm 40S ribosomal protein S29 (RPS29C) 2842 At4g33905 Dm peroxisomal membrane protein 22 kDa, putative, similar to 22 kDa peroxisomal membrane protein PMP22 (Mus musculus) gi:10954089:gb:AAG25724 2843 At4g33970 D2 leucine-rich repeat family protein / extensin family protein, similar to extensin-like protein (Lycopersicon esculentum) gi:5917664:gb:AAD55979; contains leucine-rich repeats, Pfam:PF00560; contains proline rich extensin domains, INTERPRO:IPR002965 2844 At4g34000 D1, D2, Dm ABF3_DPBF5__ABA-responsive element-binding protein / abscisic acid responsive elements-binding factor (ABRE) / ABA-responsive elements-binding factor (ABF3), identical to abscisic acid responsive elements-binding factor (ABF3) GI:6739280 from (Arabidopsis thaliana); identical to cDNA abscisic acid responsive elements-binding factor (ABRE) mRNA, complete cds GI:6739279

2845 At4g34050 D1, D2, Dm caffeoyl-CoA 3-O-methyltransferase, putative, nearly identical to GI:2960356 (Populus balsamifera subsp. trichocarpa), GI:684942 (Medicago sativa subsp. sativa) isoform contains a GT-TG intron which removes an internal segment of the protein. 2846 At4g34070 D1 expressed protein 2847 At4g34180 D1, D2, Dm cyclase family protein, contains Pfam profile: PF04199 putative cyclase 2848 At4g34215 Dm expressed protein 2849 At4g34230 D1, D2, Dm ATCAD5_CAD5_CAD-5__cinnamyl-alcohol dehydrogenase, putative, similar to cinnamyl alcohol dehydrogenase, Nicotiana tabacum (SP:P30359), Populus deltoides, PATCHX:G288753 2850 At4g34240 D1, Dm ALDH3I1_ALDH3__aldehyde dehydrogenase (ALDH3), similar to aldehyde dehydrogenase (Arabidopsis thaliana) gi:17065876:emb:CAC84903; contains Pfam profile PF00171: aldehyde dehydrogenase (NAD) family protein; identical to cDNA aldehyde dehydrogenase (ALDH3 gene) GI:17065875, aldehyde dehydrogenase (Arabidopsis thaliana) GI:17065876 2851 At4g34260 D2 expressed protein 2852 At4g34370 D2 IBR domain-containing protein, similar to SP:Q94981 Ariadne-1 protein (Ari-1) {Drosophila melanogaster}; contains Pfam profile PF01485: IBR domain 2853 At4g34410 D2 encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 18 members in this subfamily including ATERF-1, ATERF-2, AND ATERF-5. 2854 At4g34440 D2 protein kinase family protein, contains Pfam domain, PF00069: Protein kinase domain 2855 At4g34450 D2 coatomer gamma-2 subunit, putative / gamma-2 coat protein, putative / gamma-2 COP, putative, similar to SP:Q9UBF2 Coatomer gamma-2 subunit (Gamma-2 coat protein) (Gamma-2 COP) {Homo sapiens}; contains Pfam profile: PF01602 Adaptin N terminal region 2856 At4g34530 D1, Dm basic helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain 2857 At4g34620 D1, Dm SSR16__ribosomal protein S16 family protein, ribosomal protein S16, Neurospora crassa, PIR2:A29927 2858 At4g34630 D1, D2, Dm expressed protein 2859 At4g34640 D2 SQS1_ERG9__farnesyl-diphosphate farnesyltransferase 1 / squalene synthase 1 (SQS1), identical to SP:P53799 Farnesyl-diphosphate farnesyltransferase (EC 2.5.1.21) (Squalene synthetase) (SQS) (SS) (FPP:FPP farnesyltransferase) {Arabidopsis thaliana}; non-consensus GC donor splice site at exon 3, squalene synthase 2 (SQS2), Arabidopsis thaliana 2860 At4g34760 D1, D2, Dm auxin-responsive family protein, auxin-induced protein X15, Glycine max, PIR2:JQ1097 2861 At4g34770 D2 auxin-responsive family protein, similar to auxin-induced protein X10A (SP:P33080) (Glycine max); small auxin up-regulated RNA, Malus domestica, gb:Z93766 2862 At4g34790 D2, Dm auxin-responsive family protein, similar to auxin-induced protein X10A (SP:P33080) (Glycine max.) PIR:JQ1099 2863 At4g34830 D2, Dm pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat 2864 At4g34860 D2, Dm beta-fructofuranosidase, putative / invertase, putative / saccharase, putative / beta- fructosidase, putative, similar to neutral invertase (Daucus carota) GI:4200165; contains Pfam profile PF04853: Plant neutral invertase 2865 At4g34990 D2 myb family transcription factor (MYB32), similar to myb DNA-binding protein GI:19052 from (Hordeum vulgare) 2866 At4g35020 D2 ARAC3_ATROP6_RHO1PS_ROP6__Encodes a Rho-like GTPase; Rho-like GTP binding protein. 2867 At4g35090 D1, D2, Dm CAT2__catalase 2, identical to catalase 2 SP:P25819, GI:17865693 from (Arabidopsis thaliana) 2868 At4g35100 D1, D2, Dm PIP3_PIP2;7_PIP3A_SIMIP__plasma membrane intrinsic protein (SIMIP), nearly identical to plasma membrane intrinsic protein (Arabidopsis thaliana) GI:2306917 2869 At4g35140 Dm transducin family protein / WD-40 repeat family protein, contains 6 (3 significant) WD-40 repeats; similar to PC326 protein (GI:200241) (PIR2:S37694) (Mus musculus); Human (H326) mRNA, Homo sapiens, gb:U06631 2870 At4g35150 D2 O-methyltransferase family 2 protein, similar to caffeic acid O-methyltransferase, Pinus taeda, gb:U39301 2871 At4g35160 Dm O-methyltransferase family 2 protein, similar to caffeic acid O-methyltransferase, Pinus taeda, gb:U39301 2872 At4g35250 D1 vestitone reductase-related, low similarity to vestitone reductase (Medicago sativa subsp. sativa) GI:973249 2873 At4g35300 D1, Dm transporter-related, low similarity to hexose transporter (Solanum tuberosum) GI:8347246; contains Pfam profile PF00083: major facilitator superfamily protein 2874 At4g35390 D2 DNA-binding protein-related, contains Pfam domain PF03479: Domain of unknown function (DUF296), found in AT-hook motifs Pfam:PF02178 2875 At4g35540 D2, Dm expressed protein, transcription factor IIIB chain BRF1, Saccharomycescerevisiae, PIR2:A44072

2876 At4g35590 D2 RWP-RK domain-containing protein, low similarity to minus dominance protein (Chlamydomonas reinhardtii) GI:1928929; contains Pfam profile: PF02042 RWP-RK domain 2877 At4g35740 Dm RecQl3__DNA helicase (RECQl3), identical to DNA Helicase (Arabidopsis thaliana) GI:11121447; contains Pfam profiles PF00270: DEAD/DEAH box helicase, PF00271: Helicase conserved C-terminal domain 2878 At4g35750 D1, D2, Dm Rho-GTPase-activating protein-related, contains weak similarity to Rho-GTPase-activating protein 1 (GTPase-activating protein rhoOGAP) (Rho-related small GTPase protein activator) (CDC42 GTPase-activating protein) (p50-rhoGAP) (Swiss-Prot:Q07960) (Homo sapiens) 2879 At4g35770 D1, D2, Dm SEN1_SENESCENCE ASSOCIATED GENE 1_SEN1_ATSEN1_DIN1__senescence-associated protein (SEN1), identical to senescence-associated protein GI:1046270 from (Arabidopsis thaliana) 2880 At4g35790 D1, D2, Dm ATPLDDELTA_PLDDELTA__phospholipase D delta / PLD delta (PLDDELTA), identical to phospholipase D delta SP: Q9C5Y0 from (Arabidopsis thaliana); supporting cDNA gi:11761141:dbj:AB031047.1:

2881 At4g35890 D2, Dm La domain-containing protein, contains Pfam PF05383: La domain 2882 At4g35940 D1, Dm expressed protein 2883 At4g36020 D1 cold-shock DNA-binding family protein, contains Pfam domains, PF00313: `Cold-shock` DNA- binding domain and PF00098: Zinc knuckle 2884 At4g36030 Dm armadillo/beta-catenin repeat family protein, contains Pfam profile: PF00514 armadillo/beta- catenin-like repeat 2885 At4g36040 D1, D2, Dm DNAJ heat shock N-terminal domain-containing protein (J11), identical to dnaJ heat shock protein J11 (Arabidopsis thaliana) GI:9843641; contains Pfam profile PF00226 DnaJ domain 2886 At4g36130 D1, D2, Dm 60S ribosomal protein L8 (RPL8C), ribosomal protein L8, cytosolic, tomato, PIR1:R5TOL8 2887 At4g36210 D1, D2, Dm expressed protein, contains Pfam PF05277: Protein of unknown function (DUF726) 2888 At4g36390 D1, D2, Dm radical SAM domain-containing protein / TRAM domain-containing protein, similar to CDK5 activator-binding protein (Rattus norvegicus) GI:7330738; contains Pfam profiles PF00919: UPF0004 family protein, PF01938: TRAM domain, PF04055: radical SAM domain protein 2889 At4g36420 Dm ribosomal protein L12 family protein 2890 At4g36530 D1, D2, Dm hydrolase, alpha/beta fold family protein, low similarity to hydrolase (Sphingomonas sp.) GI:3426124; contains Pfam profile PF00561: hydrolase, alpha/beta fold family 2891 At4g36540 D1, Dm basic helix-loop-helix (bHLH) family protein, contains Pfam domain, PF00010: Helix-loop-helix DNA-binding domain 2892 At4g36610 Dm hydrolase, alpha/beta fold family protein, low similarity to 2-hydroxy-6-oxo-7-methylocta-2,4- dienoate hydrolase (Pseudomonas fluorescens) GI:1871461; contains Pfam profile PF00561: hydrolase, alpha/beta fold family 2893 At4g36710 D2 scarecrow transcription factor family protein 2894 At4g36760 D1, Dm ATAPP1_APP1__aminopeptidase P, similar to Xaa-Pro aminopeptidase 2 (Lycopersicon esculentum) GI:15384991; contains Pfam profile PF00557: metallopeptidase family M24 2895 At4g36780 D2 brassinosteroid signalling positive regulator-related, contains similarity to BZR1 protein (Arabidopsis thaliana) gi:20270971:gb:AAM18490 2896 At4g36860 D2 LIM domain-containing protein, low similarity to LIM-domain protein (Branchiostoma floridae) GI:3360516, DRAL/Slim3/FHL2 (Homo sapiens) GI:7209525; contains Pfam profile PF00412: LIM domain 2897 At4g36900 D1, D2, Dm RAP2.10__encodes a member of the DREB subfamily A-5 of ERF/AP2 transcription factor family (RAP2.10). The protein contains one AP2 domain. There are 16 members in this subfamily including RAP2.9 and RAP2.1. 2898 At4g36980 D1, D2, Dm expressed protein 2899 At4g37000 D1 ACD2__accelerated cell death 2 (ACD2), identical to accelerated cell death 2 (ACD2) GI:12484129 from (Arabidopsis thaliana) 2900 At4g37040 D1, D2, Dm MAP1D__metallopeptidase M24 family protein, similar to SP:O33343 Methionine aminopeptidase (EC 3.4.11.18) (Peptidase M) {Mycobacterium tuberculosis}; contains Pfam profile PF00557: metallopeptidase family M24 2901 At4g37080 D1, Dm expressed protein, contains Pfam profile PF04784: Protein of unknown function, DUF547 2902 At4g37220 D2, Dm stress-responsive protein, putative, similar to cold acclimation WCOR413-like protein gamma form (Hordeum vulgare) gi:18449100:gb:AAL69988; similar to stress-regulated protein SAP1 (Xerophyta viscosa) gi:21360378:gb:AAM47505 2903 At4g37240 D2 expressed protein 2904 At4g37260 D2 MYB73__myb family transcription factor (MYB73), contains Pfam profile: PF00249 myb-like DNA- binding domain 2905 At4g37300 D2 expressed protein 2906 At4g37330 Dm CYP81D4__cytochrome P450 family protein 2907 At4g37470 D1, D2, Dm hydrolase, alpha/beta fold family protein, low similarity to SP:Q59093 3-oxoadipate enol- lactonase I (EC 3.1.1.24) (Enol-lactone hydrolase I) (Beta-ketoadipate enol-lactone hydrolase I) {Acinetobacter calcoaceticus}; contains Pfam profile PF00561: hydrolase, alpha/beta fold family 2908 At4g37510 D2 ribonuclease III family protein, contains Pfam profile PF00636 RNase3 domain 2909 At4g37540 D2 LOB domain protein 39 / lateral organ boundaries domain protein 39 (LBD39), identical to SP:Q9SZE8 LOB domain protein 39 {Arabidopsis thaliana} 2910 At4g37550 D2, Dm formamidase, putative / formamide amidohydrolase, putative, similar to SP:Q50228 Formamidase (EC 3.5.1.49) (Formamide amidohydrolase) {Methylophilus methylotrophus}; contains Pfam profile PF03069: Acetamidase/Formamidase family 2911 At4g37560 D1, D2, Dm formamidase, putative / formamide amidohydrolase, putative, similar to SP:Q50228 Formamidase (EC 3.5.1.49) (Formamide amidohydrolase) {Methylophilus methylotrophus}; contains Pfam profile PF03069: Acetamidase/Formamidase family 2912 At4g37760 D2 squalene monooxygenase, putative / squalene epoxidase, putative, similar to SP:O65404 (SE 1,1), SP:O65402 (SE 1,2), SP:O65403 (SE 2) 2913 At4g37790 D1 HAT22__homeobox-leucine zipper protein 22 (HAT22) / HD-ZIP protein 22, identical to homeobox- leucine zipper protein HAT22 (HD-ZIP protein 22) (SP:P46604) (Arabidopsis thaliana) 2914 At4g37910 D1, D2, Dm MTHSC70-1__heat shock protein 70, mitochondrial, putative / HSP70, mitochondrial, putative, strong similarity to SP:Q01899 Heat shock 70 kDa protein, mitochondrial precursor {Phaseolus vulgaris} 2915 At4g37920 D2, Dm similar to expressed protein [Arabidopsis thaliana] (TAIR:At1g36320.1); similar to P0552C05.25 [Oryza sativa (japonica cultivar-group)] (GB:NP_914200.1) 2916 At4g37930 D2 SHM1_SHMT1_STM__glycine hydroxymethyltransferase / serine hydroxymethyltransferase / serine/threonine aldolase (SHM1), identical to serine hydroxymethyl transferase (Arabidopsis thaliana) GI:6899945 2917 At4g37980 D1, D2, Dm ELI3-1__mannitol dehydrogenase, putative (ELI3-1), identical to GI:16267 2918 At4g38060 D1, D2, Dm expressed protein 2919 At4g38090 D2 expressed protein, contains Pfam PF01205: Uncharacterized protein family UPF0029 2920 At4g38210 D1 ATEXPA20_ATEXP20_ATHEXP ALPHA 1.23_EXP20__expansin, putative (EXP20), similar to alpha- expansin 3 GI:6942322 from (Triphysaria versicolor); alpha-expansin gene family, PMID:11641069

2921 At4g38460 D1, D2, Dm GGR__geranylgeranyl pyrophosphate synthase, putative / GGPP synthetase, putative / farnesyltranstransferase, putative, 65% similar to geranylgeranyl pyrophosphate synthase (GI:413730); 2922 At4g38470 D1, D2, Dm protein kinase family protein, similar to protein kinase (gi:170047) from Glycine max; contains Pfam protein kinase domain PF00069 2923 At4g38520 D2 protein phosphatase 2C family protein / PP2C family protein, similar to Ser/Thr protein phosphatase 2C (PP2C6) (GI:15020818) (Arabidopsis thaliana); similar to protein phosphatase 2C (GI:3608412) (Mesembryanthemum crystallinum); contains Pfam PF00481 : Protein phosphatase 2C domain; 2924 At4g38600 Dm KAK_UPL3__HECT-domain-containing protein / ubiquitin-transferase family protein, similar to SP:Q14669Thyroid receptor interacting protein 12 (TRIP12) {Homo sapiens}; contains Pfam profile PF00632: HECT-domain (ubiquitin-transferase) 2925 At4g38710 Dm glycine-rich protein, cylicin II - bovine, PIR2:I46014 2926 At4g38740 D1, D2, Dm ROC1__peptidyl-prolyl cis-trans isomerase / cyclophilin / rotamase / cyclosporin A-binding protein (ROC1), identical to SP:P34790 Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (Cyclosporin A-binding protein) {Arabidopsis thaliana} 2927 At4g38800 D1, D2, Dm phosphorylase family protein, contains weak similarity to Swiss-Prot:O51931 nucleosidase (Includes: 5`-methylthioadenosine nucleosidase (EC 3.2.2.16); S-adenosylhomocysteine nucleosidase (Buchnera aphidicola) 2928 At4g38840 Dm auxin-responsive protein, putative, auxin-inducible SAUR gene, Raphanus sativus,AB000708 2929 At4g38860 D1, D2, Dm auxin-responsive protein, putative, auxin-induced protein 10A, Glycine max., PIR2:JQ1099 2930 At4g38930 D1, D2, Dm ubiquitin fusion degradation UFD1 family protein, similar to SP:P70362 Ubiquitin fusion degradation protein 1 homolog (UB fusion protein 1) {Mus musculus}; contains Pfam profile PF03152: Ubiquitin fusion degradation protein UFD1 2931 At4g39080 Dm vacuolar proton ATPase, putative, similar to Swiss-Prot:Q93050 vacuolar proton translocating ATPase 116 kDa subunit A isoform 1 (Clathrin-coated vesicle/synaptic vesicle proton pump 116 kDa subunit, Vacuolar proton pump subunit 1, Vacuolar adenosine triphosphatase subunit Ac116) (Homo sapiens) 2932 At4g39090 D1, D2, Dm RD19_EMB3005_RD19A__cysteine proteinase RD19a (RD19A) / thiol protease, identical to cysteine proteinase RD19a, thiol protease SP:P43296, GI:435618 from (Arabidopsis thaliana) 2933 At4g39100 D2, Dm SHL1__PHD finger family protein / bromo-adjacent homology (BAH) domain-containing protein, contains Pfam domain, PF00628: PHD-finger and PF01426: BAH domain 2934 At4g39140 D2, Dm expressed protein 2935 At4g39150 D2, Dm DNAJ heat shock N-terminal domain-containing protein, similar to SP:P39101 CAJ1 protein, Saccharomyces cerevisiae, PIR2:S48085; contains Pfam profile PF00226 DnaJ domain 2936 At4g39200 Dm 40S ribosomal protein S25 (RPS25E), ribosomal protein S25, Lycopersicon esculentum, PIR2:S40089 2937 At4g39210 D1, D2, Dm APL3__glucose-1-phosphate adenylyltransferase large subunit 3 (APL3) / ADP-glucose pyrophosphorylase, identical to SP:P55231 2938 At4g39330 D2 mannitol dehydrogenase, putative, nearly identical to SP:P42734, probable mannitol dehydrogenase 2939 At4g39620 Dm EMB2453__pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat 2940 At4g39710 D1, D2, Dm immunophilin, putative / FKBP-type peptidyl-prolyl cis-trans isomerase, putative, similar to FK506 binding protein 1 (GP:21535744) (Arabidopsis thaliana) 2941 At4g39730 D1, D2, Dm lipid-associated family protein, contains PLAT/LH2 (Polycystin-1, Lipoxygenase, Alpha- Toxin/Lipoxygenase homology) domain Pfam:PF01477 2942 At4g39740 D2, Dm electron transport SCO1/SenC family protein, similar to SP:P23833 SCO1 protein, mitochondrial precursor {Saccharomyces cerevisiae}; contains Pfam profile PF02630: SCO1/SenC 2943 At4g39756 D1, Dm kelch repeat-containing F-box family protein, contains F-box domain Pfam:PF00646 and Kelch motif Pfam:PF01344 2944 At4g39800 D1, D2, Dm MI-1-P SYNTHASE__inositol-3-phosphate synthase isozyme 1 / myo-inositol-1-phosphate synthase 1 / MI-1-P synthase 1 / IPS 1, identical to SP:P42801 Inositol-3-phosphate synthase isozyme 1 (EC 5.5.1.4) (Myo-inositol-1- phosphate synthase 1) (MI-1-P synthase 1) (IPS 1) {Arabidopsis thaliana} 2945 At4g39940 D1, D2, Dm AKN2__adenylylsulfate kinase 2 (AKN2), identical to adenylylsulfate kinase 2, chloroplast precursor (APS kinase, Adenosine-5`phosphosulfate kinase, ATP adenosine-5`- phosphosulfate 3`- phosphotransferase) (Arabidopsis thaliana) SWISS-PROT:O49196 2946 At4g39960 D1, D2, Dm DNAJ heat shock family protein, similar to SP:Q9S5A3 Chaperone protein dnaJ {Listeria monocytogenes}; contains Pfam profiles PF00226 DnaJ domain, PF01556 DnaJ C terminal region, PF00684 DnaJ central domain (4 repeats) 2947 At4g40030 D1, D2, Dm histone H3.2, identical to Histone H3.2, minor Lolium temulentum SP:P11105, nearly identical to histone H3.2 Mus pahari GI:515005; contains Pfam profile PF00125 Core histone H2A/H2B/H3/H4

2948 At4g40040 D1, Dm histone H3.2, identical to Histone H3.2, minor Lolium temulentum SP:P11105, nearly identical to histone H3.2 Mus pahari GI:515005; contains Pfam profile PF00125 Core histone H2A/H2B/H3/H4

2949 At4g40090 D2 AGP3__arabinogalactan-protein (AGP3), InDels between the genome sequence and the cDNA prevent identical translations from being annotated; the basis for this is under investigation.

2950 At5g01020 Dm protein kinase family protein, contains protein kinase domain, Pfam:PF00069 2951 At5g01090 D2, Dm legume lectin family protein, contains Pfam domain, PF00139: Legume lectins beta domain 2952 At5g01240 D2 amino acid permease, putative, strong similarity to AUX1 GI:1531758 from (Arabidopsis thaliana); contains Pfam profile PF01490: Transmembrane amino acid transporter protein 2953 At5g01300 D1, D2, Dm phosphatidylethanolamine-binding family protein, similar to cold-regulated protein (Hordeum vulgare subsp. vulgare) GI:10799810; contains Pfam profile PF01161: Phosphatidylethanolamine- binding protein 2954 At5g01350 D2 expressed protein 2955 At5g01370 Dm expressed protein 2956 At5g01520 D1, D2, Dm zinc finger (C3HC4-type RING finger) family protein, similar to MTD2 (Medicago truncatula) GI:9294812; contains Pfam profile PF00097: Zinc finger, C3HC4 type (RING finger) 2957 At5g01600 D2 ATFER1__ferritin 1 (FER1), identical to ferritin (Arabidopsis thaliana) GI:1246401, GI:8163920

2958 At5g01620 D2 expressed protein, several hypothetical proteins - Arabidopsis thaliana 2959 At5g01750 D2 expressed protein, contains Pfam profile PF04525: Protein of unknown function (DUF567) 2960 At5g01800 Dm saposin B domain-containing protein, contains Pfam profiles: PF00026 eukaryotic aspartyl protease, PF03489 surfactant protein B, PF05184 saposin-like type B, region 1 2961 At5g01810 D2 CIPK15_ATPK10_PKS3__CBL-interacting protein kinase 15 (CIPK15), identical to CBL-interacting protein kinase 15 (Arabidopsis thaliana) gi:13249134:gb:AAK16692; identical to novel serine/threonine protein kinase (Arabidopsis thaliana) gi:1777312:dbj:BAA06311; contains Pfam profiles PF00069: Protein kinase domain and PF03822: NAF domain 2962 At5g01820 D1, D2, Dm ATSR1_CIPK14__CBL-interacting protein kinase 14 (CIPK14), identical to CBL-interacting protein kinase 14 (Arabidopsis thaliana) gi:13249127:gb:AAK16689; contains Pfam profiles PF00069: Protein kinase domain and PF03822: NAF domain; identical to cDNA CBL-interacting protein kinase 14 (CIPK14) GI:13249126 2963 At5g01880 D1, D2, Dm zinc finger (C3HC4-type RING finger) family protein, contains Pfam domain, PF00097: Zinc finger, C3HC4 type (RING finger) 2964 At5g01990 D2, Dm auxin efflux carrier family protein, contains auxin efflux carrier domain, Pfam:PF03547 2965 At5g02020 D1, D2, Dm expressed protein 2966 At5g02040 D2 prenylated rab acceptor (PRA1) family protein, contains Pfam PF03208: PRA1 family protein 2967 At5g02050 D2 mitochondrial glycoprotein family protein / MAM33 family protein, low similarity to SUAPRGA1 (Emericella nidulans) GI:6562379; contains Pfam profile PF02330: Mitochondrial glycoprotein 2968 At5g02160 D1, D2, Dm expressed protein 2969 At5g02230 D2 haloacid dehalogenase-like hydrolase family protein, contains InterPro accession IPR005834: Haloacid dehalogenase-like hydrolase 2970 At5g02240 D1, D2, Dm expressed protein 2971 At5g02280 D2 synbindin, putative, similar to Swiss-Prot:Q9ES56 synbindin (TRS23 homolog) (Mus musculus) 2972 At5g02380 D1, D2, Dm MT2B__metallothionein protein 2B (MT-2B), identical to SWISS-PROT:Q38805 metallothionein-like protein 2B (MT-2B) (Arabidopsis thaliana) 2973 At5g02450 D1, D2, Dm 60S ribosomal protein L36 (RPL36C), 60S ribosomal protein L36, Arabidopsis thaliana, EMBL:AC004684 2974 At5g02550 D1, D2, Dm expressed protein 2975 At5g02560 D2, Dm histone H2A, putative, similar to histone H2A from Pisum sativum SP:P25470, Zea mays SP:P40280, Petroselinum crispum SP:P19177; contains Pfam profile PF00125 Core histone H2A/H2B/H3/H4 2976 At5g02570 D1, Dm histone H2B, putative, similar to histone H2B-2 Lycopersicon esculentum GI:3021483, Gossypium hirsutum SP:O22582, Asparagus officinalis GI:563329; contains Pfam profile PF00125 Core histone H2A/H2B/H3/H4 2977 At5g02610 D1, D2, Dm 60S ribosomal protein L35 (RPL35D), ribosomal protein L35- cytosolic, Arabidopsis thaliana, PIR:T00549 2978 At5g02620 D2 ankyrin repeat family protein, contains ankyrin repeat domains, Pfam:PF00023 2979 At5g02760 D1, D2, Dm protein phosphatase 2C family protein / PP2C family protein, similar to Ser/Thr protein phosphatase 2C (PP2C6) (GI:15020818) (Arabidopsis thaliana); similar to protein phosphatase 2C (GI:3608412) (Mesembryanthemum crystallinum); contains Pfam PF00481 : Protein phosphatase 2C domain 2980 At5g02790 D1, D2, Dm In2-1 protein, putative, similar to In2-1, Zea mays, EMBL:X58573 2981 At5g02860 Dm pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat 2982 At5g02870 D1, D2, Dm 60S ribosomal protein L4/L1 (RPL4D), 60S roibosomal protein L4, Arabidopsis thaliana, EMBL:CAA79104 2983 At5g02890 D1, Dm transferase family protein, contains Pfam profile PF02458: Transferase family 2984 At5g03040 D2, Dm calmodulin-binding family protein, similar to SF16 protein (Helianthus annuus) GI:560150; contains Pfam profile PF00612: IQ calmodulin-binding motif 2985 At5g03120 D2, Dm expressed protein 2986 At5g03190 D1, Dm expressed protein 2987 At5g03210 D1, D2, Dm expressed protein 2988 At5g03230 D2, Dm expressed protein, contains Pfam profile PF04520: Protein of unknown function, DUF584 2989 At5g03240 D1, Dm UBQ3__polyubiquitin (UBQ3), identical to GI:928809 2990 At5g03290 Dm isocitrate dehydrogenase, putative / NAD+ isocitrate dehydrogenase, putative, strong similarity to isocitrate dehydrogenase (NAD+) (Nicotiana tabacum) GI:3021506 2991 At5g03300 D1, D2, Dm ADK2__adenosine kinase 2 (ADK2), contains Pfam profile: PF00294 pfkB family carbohydrate kinase; identical to cDNA adenosine kinase 2 (ADK2) GI:12017763 2992 At5g03350 Dm legume lectin family protein, contains Pfam domain, PF00139: Legume lectins beta domain 2993 At5g03455 D1, D2, Dm CDC25_ARATH;CDC25__rhodanese-like domain-containing protein, contains Rhodanese-like domain PF:00581 2994 At5g03460 D1, D2, Dm expressed protein 2995 At5g03520 D2 Ras-related GTP-binding protein, putative, similar to GTP-binding protein GI:871508 from (Pisum sativum) 2996 At5g03545 D2 expressed protein, No ATG start, annotated according to PMID:11123795 2997 At5g03560 D1, Dm expressed protein 2998 At5g03760 D1, Dm ATCSLA09_ATCSLA9_CSLA09_CSLA9_RAT4__glycosyl transferase family 2 protein, similar to beta-(1- 3)-glucosyl transferase GB:AAC62210 GI:3687658 from (Bradyrhizobium japonicum), cellulose synthase from Agrobacterium tumeficiens (gi:710492) and Agrobacterium radiobacter (gi:710493); contains Pfam glycosyl transferase, group 2 family protein domain PF00535 2999 At5g03850 D1, D2, Dm 40S ribosomal protein S28 (RPS28B), ribosomal protein S28, Arabidopsis thaliana, EMBL:ATRP28A

3000 At5g03880 D2 expressed protein 3001 At5g03910 D1 ATATH12__ABC transporter family protein, ABC-type transport protein sll1276, Synechocystis sp., PIR:S77239 3002 At5g03940 D1 FFC_54CP_CPSRP54_SRP54CP__signal recognition particle 54 kDa protein, chloroplast / 54 chloroplast protein / SRP54 (FFC), identical to Swiss-Prot:P37107 signal recognition particle 54 kDa protein, chloroplast precursor (SRP54) (54 chloroplast protein) (54CP) (FFC) (Arabidopsis thaliana) 3003 At5g04080 D2 expressed protein 3004 At5g04140 D2 GLU1_GLS1__glutamate synthase (GLU1) / ferredoxin-dependent glutamate synthase (Fd-GOGAT 1), identical to ferredoxin-dependent glutamate synthase precursor (Arabidopsis thaliana) GI:3869251 3005 At5g04410 D1, Dm ANAC078_NAC2__no apical meristem (NAM) family protein, contains Pfam PF02365: No apical meristem (NAM) protein; supporting cDNA gi:6456750:gb:AF201456.1:AF201456 3006 At5g04440 Dm expressed protein 3007 At5g04470 D2 expressed protein 3008 At5g04510 D2, Dm PDK1_ATPDK1__3-phosphoinositide-dependent protein kinase, putative, similar to 3- phosphoinositide-dependent protein kinase-1 (Oryza sativa) gi:5001830:gb:AAD37166 3009 At5g04550 D1, Dm expressed protein, contains Pfam domain PF05003: protein of unknown function (DUF668) 3010 At5g04590 D1, D2, Dm SIR__sulfite reductase / ferredoxin (SIR), identical to sulfite reductase (Arabidopsis thaliana) GI:804953, GI:2584721 3011 At5g04600 D2 RNA recognition motif (RRM)-containing protein, contains InterPro entry IPR000504: RNA-binding region RNP-1 (RNA recognition motif) (RRM) 3012 At5g04740 D2, Dm ACT domain-containing protein, contains Pfam profile PF01842: ACT domain 3013 At5g04750 D1, D2, Dm F1F0-ATPase inhibitor protein, putative, similar to F1F0-ATPase inhibitor protein (Oryza sativa (japonica cultivar-group)) gi:5106371:dbj:BAA81661 3014 At5g04770 D2 CAT6__amino acid permease family protein, similar to cationic amino acid transporter-1 (Rattus norvegicus) GI:1589917; contains Pfam profile PF00324: Amino acid permease 3015 At5g04790 D1, Dm expressed protein 3016 At5g04850 Dm SNF7 family protein, contains Pfam domain, PF03357: SNF7 family 3017 At5g04940 D2, Dm SUVH1__SET domain-containing protein (SUVH1), contains Pfam profiles PF00856: SET domain, PF05033: Pre-SET motif, PF02182: YDG/SRA domain; identical to cDNA SUVH1 (SUVH1) GI:13517742 3018 At5g04950 D1 nicotianamine synthase, putative, similar to nicotianamine synthase (Lycopersicon esculentum)(GI:4753801), nicotianamine synthase 2 (Hordeum vulgare)(GI:4894912) 3019 At5g04970 D2 pectinesterase, putative, contains similarity to pectinesterase from Vitis vinifera GI:15081598, Prunus persica SP:Q43062; contains Pfam profile PF01095 pectinesterase 3020 At5g05010 D2 clathrin adaptor complexes medium subunit-related, contains pfam profile: PF00928 adaptor complexes medium subunit family 3021 At5g05060 D1, D2, Dm expressed protein 3022 At5g05110 D1, D2, Dm cysteine protease inhibitor, putative / cystatin, putative, similar to cysteine proteinase inhibitor (Glycine max) GI:1944342; contains Pfam profile PF00031: Cystatin domain 3023 At5g05190 D2 expressed protein, similar to unknown protein (emb:CAB88044.1) 3024 At5g05200 D1, D2, Dm ABC1 family protein, contains Pfam domain, PF03109: ABC1 family 3025 At5g05580 D2 FAD8_SH1__omega-3 fatty acid desaturase, chloroplast, temperature-sensitive (FAD8), identical to SP:48622 Temperature-sensitive omega-3 fatty acid desaturase, chloroplast precursor (EC 1.14.19.-) {Arabidopsis thaliana}; contains Pfam profile PF00487: Fatty acid desaturase; identical to cDNA plastid fatty acid desaturase GI:1030694 3026 At5g05740 Dm peptidase M50 family protein / sterol-regulatory element binding protein (SREBP) site 2 protease family protein, contains Pfam PF02163: Sterol-regulatory element binding protein (SREBP) site 2 protease 3027 At5g05840 Dm expressed protein, contains Pfam profile PF04788: Protein of unknown function (DUF620); expression supported by MPSS 3028 At5g05960 D2, Dm protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 3029 At5g05990 Dm mitochondrial glycoprotein family protein / MAM33 family protein, low similarity to SUAPRGA1 (Emericella nidulans) GI:6562379; contains Pfam profile PF02330: Mitochondrial glycoprotein 3030 At5g06110 D2, Dm DNAJ heat shock N-terminal domain-containing protein / cell division protein-related, similar to GlsA (Volvox carteri f. nagariensis) GI:4633129; contains Pfam profiles PF00226 DnaJ domain, PF00249 Myb-like DNA-binding domain 3031 At5g06150 Dm CYCB1;2_CYC1BAT__cyclin 1b (CYC1b), identical to cyclin (Arabidopsis thaliana) GI:1360646 3032 At5g06290 D1, D2, Dm 2-cys peroxiredoxin, chloroplast, putative, very strong similarity to SP:Q96291 2-cys peroxiredoxin BAS1, chloroplast precursor {Arabidopsis thaliana}; contains Pfam profile: PF00578 AhpC/TSA (alkyl hydroperoxide reductase and thiol-specific antioxidant) family 3033 At5g06370 D1, Dm NC domain-containing protein, contains Pfam domain, PF04970: NC domain 3034 At5g06410 D2, Dm DNAJ heat shock N-terminal domain-containing protein, similar to SP:P36540 Chaperone protein hscB (HSC20) {Escherichia coli O157:H7}; contains Pfam profile PF00226 DnaJ domain 3035 At5g06490 D1, D2, Dm zinc finger (C3HC4-type RING finger) family protein, low similarity to RING-H2 finger protein ATL6 (Arabidopsis thaliana) GI:4928403; contains Pfam profile PF00097: Zinc finger, C3HC4 type (RING finger) 3036 At5g06530 D1, Dm similar to ABC transporter family protein [Arabidopsis thaliana] (TAIR:At3g52310.1); similar to putative ABC transporter AbcG1 [Oryza sativa (japonica cultivar-group)] (GB:XP_480256.1); contains InterPro domain AAA ATPase (InterPro:IPR003593); contains InterPro domain ABC transporter (InterPro:IPR003439); contains InterPro domain ATP/GTP-binding site motif A (P- loop) (InterPro:IPR001687) 3037 At5g06550 Dm similar to transcription factor jumonji (jmjC) domain-containing protein [Arabidopsis thaliana] (TAIR:At1g78280.1); similar to hypothetical protein [Neurospora crassa] (GB:XP_327705.1); contains InterPro domain Cyclin-like F-box (InterPro:IPR001810); contains InterPro domain Transcription factor jumonji, jmjC (InterPro:IPR003347) 3038 At5g06600 D1, D2, Dm UBP12__ubiquitin-specific protease 12 (UBP12), almost identical to ubiquitin-specific protease 12 GI:11993471 (Arabidopsis thaliana), one amino acid difference 3039 At5g06690 Dm thioredoxin family protein, low similiarity to SP:P34723 Thioredoxin {Penicillium chrysogenum}; contains Pfam profile: PF00085 Thioredoxin 3040 At5g06760 D1, D2, Dm late embryogenesis abundant group 1 domain-containing protein / LEA group 1 domain-containing protein, low similarity to SP:P46515 11 kDa late embryogenesis abundant protein (DS11) {Helianthus annuus}; contains Pfam profile PF03760: Late embryogenesis abundant (LEA) group 1

3041 At5g06839 D2 bZIP family transcription factor, contains Pfam profile: PF00170 bZIP transcription factor 3042 At5g07060 D2 zinc finger (CCCH-type) family protein, contains Pfam domain, PF00642: Zinc finger C-x8-C-x5- C-x3-H type (and similar) 3043 At5g07090 D1, D2, Dm 40S ribosomal protein S4 (RPS4B) 3044 At5g07110 D2 prenylated rab acceptor (PRA1) family protein, weak similarity to prenylated Rab acceptor 1 (PRA1) (Homo sapiens) GI:4877285; contains Pfam profile PF03208: Prenylated rab acceptor (PRA1) 3045 At5g07230 D2 protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, identical to tapetum-specific protein A9 (Precursor) SP: Q00762; contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 3046 At5g07250 Dm rhomboid family protein, contains PFAM domain PF01694, Rhomboid family 3047 At5g07440 D1, D2, Dm GDH2__glutamate dehydrogenase 2 (GDH2), identical to glutamate dehydrogenase 2 (GDH 2) (Arabidopsis thaliana) SWISS-PROT:Q38946 3048 At5g07460 D1 PMSR2__peptide methionine sulfoxide reductase, putative, similar to peptide methionine sulfoxide reductase (msr) (Arabidopsis thaliana) GI:4884033; contains Pfam profile PF01625: Peptide methionine sulfoxide reductase 3049 At5g07470 D1, D2, Dm PMSR3__peptide methionine sulfoxide reductase (MSR), nearly identical to peptide methionine sulfoxide reductase (msr) (Arabidopsis thaliana) GI:4884033 3050 At5g07580 D2, Dm encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 18 members in this subfamily including ATERF-1, ATERF-2, AND ATERF-5. 3051 At5g07720 D2 galactosyl transferase GMA12/MNN10 family protein, very low similarity to alpha-1,2- galactosyltransferase, Schizosaccharomyces pombe (SP:Q09174) 3052 At5g07950 Dm expressed protein, ferredoxin (2Fe-2S), Arabidopsis thaliana, PIR:B71412 3053 At5g08050 D1, D2, Dm expressed protein, predicted protein, Arabidopsis thaliana 3054 At5g08180 D2, Dm ribosomal protein L7Ae/L30e/S12e/Gadd45 family protein, Similar to NHP2/L7Ae family proteins, see SWISSPROT:P32495 and PMID:2063628. 3055 At5g08260 Dm SCPL35__serine carboxypeptidase S10 family protein, similar to Serine carboxypeptidase II chains A and B (SP:P08819) (EC 3.4.16.6) (Triticum aestivum (Wheat)); carboxypeptidase D - Triticum aestivum, PIR:A29639 3056 At5g08280 D1, Dm hydroxymethylbilane synthase / porphobilinogen deaminase, chloroplast / pre-uroporphyrinogen synthase, identical to SP:Q43316 3057 At5g08290 D2 YLS8__yellow-leaf-specific protein 8 (YLS8) / mitosis protein DIM1, putative, contains Pfam domain PF02966: Mitosis protein DIM1; identical to cDNA YLS8 mRNA for Dim1 homolog GI:13122293

3058 At5g08300 D2, Dm succinyl-CoA ligase (GDP-forming) alpha-chain, mitochondrial, putative / succinyl-CoA synthetase, alpha chain, putative / SCS-alpha, putative, identical to SP:P53586 Succinyl-CoA ligase (GDP-forming) alpha-chain, mitochondrial precursor (EC 6.2.1.4) (Succinyl-CoA synthetase, alpha chain) (SCS-alpha) {Arabidopsis thaliana}; strong similarity to SP:P13086 Succinyl-CoA ligase (GDP-forming) alpha-chain, mitochondrial precursor {Rattus norvegicus}; contains Pfam profiles PF00549: CoA-ligase, PF02629: CoA binding domain 3059 At5g08330 D1, D2, Dm TCP family transcription factor, putative, similar to PCF1 (GI:2580438) and PCF2 ((GI:2580440) Oryza sativa) ; auxin-induced basic helix-loop-helix transcription factor, Gossypium hirsutum, EMBL:AF165924 3060 At5g08380 Dm alpha-galactosidase, putative / melibiase, putative / alpha-D-galactoside galactohydrolase, putative, similar to alpha-galactosidase SP:Q42656 from (Coffea arabica); contains Pfam profile PF02065: Melibiase 3061 At5g08460 D2, Dm GDSL-motif lipase/hydrolase family protein, similar to family II lipase EXL3 (GI:15054386), EXL1 (GI:15054382), EXL2 (GI:15054384) (Arabidopsis thaliana); contains Pfam profile PF00657: Lipase/Acylhydrolase with GDSL-like motif 3062 At5g08520 D2 myb family transcription factor, contains Pfam profile: PF00249 myb-like DNA-binding domain 3063 At5g08560 D2 transducin family protein / WD-40 repeat family protein, contains 7 WD-40 repeats (PF00400); similar to will die slowly protein (WDS) (SP:Q9V3J8) (Drosophila melanogaster) 3064 At5g08590 D1, D2, Dm ASK2__serine/threonine protein kinase (ASK2), identical to serine/threonine-protein kinase ASK2, SWISS-PROT: P43292; contains protein kinase domain, Pfam:PF00069 3065 At5g08620 D2 DEAD box RNA helicase (RH25), identical to RNA helicase (Arabidopsis thaliana) GI:3776023; contains Pfam profiles PF00270: DEAD/DEAH box helicase, PF00271: Helicase conserved C-terminal domain 3066 At5g08650 D1, Dm GTP-binding protein LepA, putative 3067 At5g08690 Dm ATP synthase beta chain 2, mitochondrial, identical to SP:P83484 ATP synthase beta chain 2, mitochondrial precursor (EC 3.6.3.14) {Arabidopsis thaliana}; strong similarity to SP:P17614 ATP synthase beta chain, mitochondrial precursor (EC 3.6.3.14) {Nicotiana plumbaginifolia}; contains Pfam profiles PF00006: ATP synthase alpha/beta family nucleotide-binding domain, PF00306: ATP synthase ab C terminal, PF02874: ATP synthase alpha/beta family beta-barrel domain; supporting cDNA gi:26452187:dbj:AK118582.1: 3068 At5g08750 D2 zinc finger (C3HC4-type RING finger) family protein, contains Pfam profile: PF00097 zinc finger, C3HC4 type (RING finger) 3069 At5g09220 D2, Dm AAP2__amino acid permease 2 (AAP2), identical to amine acid permease AAP2 (Arabidopsis thaliana) GI:510236 3070 At5g09340 D1, D2, Dm ubiquitin, putative, similar to ubiquitin SP:P42740 from (Aglaothamnion neglectum) 3071 At5g09400 D2 KUP7__potassium transporter family protein, similar to K+ transporter HAK5 (Arabidopsis thaliana) GI:7108597; contains Pfam profile PF02705: K+ potassium transporter; KUP/HAK/KT Transporter family member, PMID:11500563; Note: possible sequencing error causes a frameshift in the 4th exon:15810448:gb:AY056263 3072 At5g09460 D2, Dm expressed protein 3073 At5g09500 D1, D2, Dm 40S ribosomal protein S15 (RPS15C), ribosomal protein S15 - Arabidopsis thaliana, EMBL:Z23161

3074 At5g09510 D1, D2, Dm 40S ribosomal protein S15 (RPS15D), ribosomal protein S15 - Arabidopsis thaliana, EMBL:Z23161

3075 At5g09590 D1 mtHSC70-2_HSC70-5__heat shock protein 70 / HSP70 (HSC70-5), identical to heat shock protein 70 (Arabidopsis thaliana) GI:6746590 3076 At5g09620 Dm octicosapeptide/Phox/Bem1p (PB1) domain-containing protein, predicted proteins, Arabidopsis thaliana and Drosophila melanogaster contains Pfam profile PF00564: PB1 domain 3077 At5g09650 D1, D2, Dm inorganic pyrophosphatase family protein, similar to SP:Q15181 Inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate {Homo sapiens}; contains Pfam profile PF00719: inorganic pyrophosphatase 3078 At5g09660 D2 PMDH2__encodes a microbody NAD-dependent malate dehydrogenase 3079 At5g09920 Dm RPB15.9_RPB15.9.9__RNA polymerase II 15.9 kDa subunit (RPB15.9), identical to 15.9 kDa subunit of RNA polymerase II GI:2760362 from (Arabidopsis thaliana) 3080 At5g09930 D1 ATGCN2__ABC transporter family protein 3081 At5g09990 D2 expressed protein 3082 At5g10070 Dm RNase L inhibitor protein-related, contains Pfam profiles PF04034: Domain of unknown function (DUF367), PF04068: Possible metal-binding domain in RNase L inhibitor, RLI 3083 At5g10200 Dm similar to tetratricopeptide repeat (TPR)-containing protein [Arabidopsis thaliana] (TAIR:At5g43120.1); similar to Hypothetical protein [Oryza sativa (japonica cultivar-group)] (GB:XP_470590.1) 3084 At5g10360 D2 EMB3010__40S ribosomal protein S6 (RPS6B) 3085 At5g10460 Dm haloacid dehalogenase-like hydrolase family protein, contains InterPro accession IPR005834: Haloacid dehalogenase-like hydrolase 3086 At5g10560 D2, Dm glycosyl hydrolase family 3 protein, beta-xylosidase, Aspergllus nidulans, EMBL:ANXLND 3087 At5g10650 Dm zinc finger (C3HC4-type RING finger) family protein, similar to Pfam domain, PF00097: Zinc finger, C3HC4 type (RING finger) 3088 At5g10750 D1, D2, Dm expressed protein 3089 At5g10830 D2 embryo-abundant protein-related, similar to embryo-abundant protein (Picea glauca) GI:1350531

3090 At5g10860 D1, D2, Dm CBS domain-containing protein, contains Pfam profile PF00571: CBS domain 3091 At5g10930 D1, D2, Dm CIPK5__CBL-interacting protein kinase 5 (CIPK5), identical to CBL-interacting protein kinase 5 GP:9280632:gb:AAF86504 (Arabidopsis thaliana) 3092 At5g11040 D2 expressed protein, weak similarity to hypercellular protein (Aspergillus nidulans) GI:9309269

3093 At5g11060 D1, D2, Dm KNAT4__homeobox protein knotted-1 like 4 (KNAT4), identical to homeobox protein knotted-1 like 4 ( KNAT4) SP:P48001 from (Arabidopsis thaliana) 3094 At5g11070 D2, Dm expressed protein 3095 At5g11110 Dm similar to sucrose-phosphate synthase, putative [Arabidopsis thaliana] (TAIR:At1g04920.1); similar to sucrose-phosphate synthase, putative [Arabidopsis thaliana] (TAIR:At5g20280.1); similar to sucrose-phosphate synthase, putative [Arabidopsis thaliana] (TAIR:At4g10120.1); similar to sucrose phosphate synthase [Lycopersicon esculentum] (GB:AAU29197.1); similar to sucrose-6-phosphate synthase [Nicotiana tabacum] (GB:AAF06792.1); similar to sucrose-phosphate synthase (EC 2.4.1.14) - spinach (GB:JQ2277); similar to sucrose-phosphate synthase [Solanum tuberosum] (GB:CAA51872.1); similar to sucrose phosphate synthase [Actinidia chinensis] (GB:AAL86360.1); contains InterPro domain Glycosyl transferase, group 1 (InterPro:IPR001296) 3096 At5g11150 D1 ATVAMP713_VAMP713__synaptobrevin / vesicle-associated membrane protein 713 (VAMP713), identified as AtVAMP713 by Sanderfoot, A.A., et al. in Plant Physiol. 124: 1558-69 (2000); similar to Vesicle-associated membrane protein 722 (AtVAMP722) Synaptobrevin-related protein 1 (SP:P47192) {Arabidopsis thaliana}; synaptobrevin-like protein Sybl1, Mus musculus, EMBL:MMU133536 3097 At5g11160 D1, Dm adenine phosphoribosyltransferase, putative, strong similarity to SP:Q42563 Adenine phosphoribosyltransferase 2 (EC 2.4.2.7) (APRT) {Arabidopsis thaliana}; contains Pfam profile PF00156: Phosphoribosyl transferase domain 3098 At5g11200 D2, Dm DEAD/DEAH box helicase, putative 3099 At5g11420 D1, D2, Dm expressed protein, contains Pfam profile PF04862: Protein of unknown function, DUF642 3100 At5g11450 D1, Dm oxygen-evolving complex-related, 23 kDa polypeptide of water-oxidizing complex of photosystem II, Nicotiana tabacum, EMBL:NT23WOP2B 3101 At5g11610 D1, Dm exostosin family protein, contains Pfam domain, PF03016: Exostosin family 3102 At5g11630 D2, Dm expressed protein 3103 At5g11650 Dm hydrolase, alpha/beta fold family protein, contains Pfam profile PF00561: hydrolase, alpha/beta fold family; low similarity to monoglyceride lipase from (Homo sapiens) GI:14594904, (Mus musculus) GI:2632162 3104 At5g11680 D1 expressed protein, predicted proteins, Arabidopsis thaliana 3105 At5g11740 D2, Dm AGP15__arabinogalactan-protein (AGP15), identical to gi:10880507:gb:AAG24283 3106 At5g11770 D1, D2, Dm NADH-ubiquinone oxidoreductase 20 kDa subunit, mitochondrial, identical to NADH-ubiquinone oxidoreductase 20 kDa subunit mitochondrial (precursor) SP:Q42577 from (Arabidopsis thaliana); contains Pfam profile: PF01058 NADH ubiquinone oxidoreductase, 20 Kd subunit 3107 At5g11810 Dm expressed protein 3108 At5g11840 D2, Dm expressed protein, predicted proteins in Synechococcus ,Cyanophora and other organisms 3109 At5g11910 D2 esterase/lipase/thioesterase family protein, low similarity to cinnamoyl ester hydrolase CinI (Butyrivibrio fibrisolvens) GI:1622732; contains Interpro entry IPR000379 3110 At5g12140 D1, D2, Dm ATCYS1__cysteine protease inhibitor, putative / cystatin, putative, similar to SP:P31726 Cystatin I precursor (CORN kernel cysteine proteinase inhibitor) {Zea mays}; contains Pfam profile PF00031: Cystatin domain 3111 At5g12200 D1, D2, Dm dihydropyrimidinase / DHPase / dihydropyrimidine amidohydrolase / hydantoinase (PYD2), identical to dihydropyrimidine amidohydrolase (PYD2) (Arabidopsis thaliana) GI:28194047; similar to SP:Q9EQF5 Dihydropyrimidinase (EC 3.5.2.2) (DHPase) (Hydantoinase) (DHP) {Mus musculus}; contains Pfam profile PF01979: Amidohydrolase family 3112 At5g12250 D2, Dm TUB6__tubulin beta-6 chain (TUB6), nearly identical to SP:P29514 Tubulin beta-6 chain {Arabidopsis thaliana} 3113 At5g12270 D2, Dm oxidoreductase, 2OG-Fe(II) oxygenase family protein, similarity to ripening protein E8, tomato, PIR:S01642; contains Pfam domain PF03171, 2OG-Fe(II) oxygenase superfamily 3114 At5g12320 Dm ankyrin repeat family protein, contains ankyrin repeats, Pfam:PF00023 3115 At5g12340 D1, D2, Dm expressed protein, ; expression supported by MPSS 3116 At5g12470 D1, D2, Dm expressed protein 3117 At5g12480 D2 CPK7__calmodulin-domain protein kinase isoform 7 (CPK7), identical to calmodulin-domain protein kinase CDPK isoform 7 (Arabidopsis thaliana) gi:1399277:gb:AAB03247 3118 At5g12840 D2, Dm EMB2220_HAP2A_ATHAP2A_HAP2__CCAAT-binding transcription factor (CBF-B/NF-YA) family protein, contains Pfam profile: PF02045 CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B 3119 At5g12860 D1, D2, Dm oxoglutarate/malate translocator, putative, similar to 2-oxoglutarate/malate translocator precursor, spinach, SWISSPROT:Q41364 3120 At5g12970 Dm C2 domain-containing protein, contains INTERPRO:IPR000008 C2 domain 3121 At5g13010 Dm EMB3011__RNA helicase, putative, similar to DEAH-box RNA helicase (Chlamydomonas reinhardtii) GI:12044832; contains Pfam profiles PF04408: Helicase associated domain (HA2), PF00271: Helicase conserved C-terminal domain 3122 At5g13030 Dm expressed protein, contains Pfam profile PF02696: Uncharacterized ACR, YdiU/UPF0061 family 3123 At5g13120 D1, Dm peptidyl-prolyl cis-trans isomerase cyclophilin-type family protein, contains Pfam domain, PF00160: peptidyl-prolyl cis-trans isomerase, cyclophilin-type 3124 At5g13140 D1 expressed protein 3125 At5g13170 Dm nodulin MtN3 family protein, similar to MtN3 GI:1619602 (root nodule development) from (Medicago truncatula); identical to cDNA senescence-associated protein (SAG29) mRNA, partial cds GI:4426938 3126 At5g13280 Dm AK-LYS1_AK__aspartate kinase, identical to aspartate kinase (Arabidopsis thaliana) GI:4376158

3127 At5g13410 D2, Dm immunophilin / FKBP-type peptidyl-prolyl cis-trans isomerase family protein, SP:Q9LYR5; similar to FK506-binding protein (Peptidyl-prolyl cis-trans isomerase) (PPiase) (Rotamase) (SP:P25138) ({Neisseria meningitidis); peptidyl-prolyl cis-trans isomerase, Spodoptera frugiperda, EMBL:SF15038; contains Pfam PF00254: peptidyl-prolyl cis-trans isomerase, FKBP- type 3128 At5g13440 D1, Dm ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial, putative / Rieske iron- sulfur protein, putative, similar to ubiquinol--cytochrome-c reductase from Solanum tuberosum (SP:P37841), Nicotiana tabacum (SP:P51132) (SP:P51133) 3129 At5g13470 D2, Dm expressed protein 3130 At5g13510 D1, D2, Dm ribosomal protein L10 family protein, ribosomal protein L10- Nicotiana tabacum, EMBL:AB010879 3131 At5g13570 Dm MutT/nudix family protein, similar to mRNA-decapping enzyme (Homo sapiens) GI:23268269; contains Pfam profile PF00293: NUDIX domain 3132 At5g13630 D1, D2, Dm GUN5_CCH_CCH1_CHLH__magnesium-chelatase subunit chlH, chloroplast, putative / Mg- protoporphyrin IX chelatase, putative (CHLH), nearly identical to magnesium chelatase subunit GI:1154627 from (Arabidopsis thaliana); contains Pfam profile: PF02514 CobN/magnesium chelatase family protein 3133 At5g13710 D1, D2, Dm SMT1_CPH__sterol 24-C-methyltransferase, putative, similar to SP:P25087 Sterol 24-C- methyltransferase, Delta(24)-sterol C- methyltransferase, Saccharomyces cerevisiae 3134 At5g13750 D2 transporter-related 3135 At5g13770 D1 pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat 3136 At5g13930 D1, Dm CHS_ATCHS_TT4__chalcone synthase / naringenin-chalcone synthase, identical to SP:P13114 3137 At5g14030 Dm translocon-associated protein beta (TRAPB) family protein, low similarity to SP:P23438 Translocon-associated protein, beta subunit precursor (TRAP-beta) (Signal sequence receptor beta subunit) {Canis familiaris}; contains Pfam profile PF05753: Translocon-associated protein beta (TRAPB) 3138 At5g14040 D1, D2, Dm mitochondrial phosphate transporter, identical to mitochondrial phosphate transporter GI:3318617 from (Arabidopsis thaliana) 3139 At5g14050 D2 transducin family protein / WD-40 repeat family protein, contains 4 WD-40 repeats (PF00400); similar to unknown protein (ref:NP_057085.1) 3140 At5g14110 D1, D2, Dm expressed protein 3141 At5g14120 D1, D2, Dm nodulin family protein, similar to nodulin-like protein (Arabidopsis thaliana) GI:3329368, nodule-specific protein Nlj70 (Lotus japonicus) GI:3329366 3142 At5g14170 Dm SWIB complex BAF60b domain-containing protein, similar to brahma associated protein 60 kDa (Drosophila melanogaster) GI:3378134, SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin D1 (Homo sapiens) GI:4566530; contains Pfam profile PF02201: BAF60b domain of the SWIB complex 3143 At5g14320 D1, Dm 30S ribosomal protein S13, chloroplast (CS13), ribosomal protein S13 precursor, chloroplast Arabidopsis thaliana, PIR:S59594; identical to cDNA ribosomal protein S13 GI:1515106 3144 At5g14520 D2 pescadillo-related, similar to pescadillo (Zebrafish, Danio rerio) SWISS-PROT:P79741 3145 At5g14570 D1, Dm ATNRT2.7__transporter, putative, similar to trans-membrane nitrate transporter protein AtNRT2:1 (Arabidopsis thaliana) GI:3747058, high-affinity nitrate transporter ACH1 (Arabidopsis thaliana) GI:3608362; contains Pfam profile PF00083: Sugar (and other) transporter 3146 At5g14590 D1, Dm isocitrate dehydrogenase, putative / NADP+ isocitrate dehydrogenase, putative, strong similarity to isocitrate dehydrogenase (NADP+) (Nicotiana tabacum) GI:3021512; contains Pfam domain PF00180: dehydrogenase, isocitrate/isopropylmalate family 3147 At5g14640 D1, D2, Dm protein kinase family protein, similar to glycogen synthase kinase-3 homolog MsK-3 SP:P51139 from (Medicago sativa); contains Pfam profile PF00069: Protein kinase domain 3148 At5g14690 D2 expressed protein, predicted protein, Arabidopsis thaliana 3149 At5g14740 D1, Dm CA2_CA18__carbonic anhydrase 2 / carbonate dehydratase 2 (CA2) (CA18), nearly identical to SP:P42737 Carbonic anhydrase 2 (EC 4.2.1.1) (Carbonate dehydratase 2) {Arabidopsis thaliana} 3150 At5g14780 D2, Dm FDH__formate dehydrogenase (FDH), identical to GI:7677266 3151 At5g14880 D2 potassium transporter, putative, similar to potassium transporter HAK2p (Mesembryanthemum crystallinum) gi:14091471:gb:AAK53759; KUP/HAK/KT Transporter family member, PMID:11500563; contains Pfam profile PF02705: K+ potassium transporter 3152 At5g14910 D2 heavy-metal-associated domain-containing protein, Pfam profile PF00403: Heavy-metal-associated domain 3153 At5g14920 D2, Dm gibberellin-regulated family protein, similar to SP:P46689 Gibberellin-regulated protein 1 precursor {Arabidopsis thaliana}; contains Pfam profile PF02704: Gibberellin regulated protein

3154 At5g15020 Dm paired amphipathic helix repeat-containing protein, similar to transcription co-repressor Sin3 (Xenopus laevis) GI:4960210; contains Pfam profile PF02671: Paired amphipathic helix repeat

3155 At5g15160 D2, Dm bHLH family protein 3156 At5g15190 D1, D2, Dm expressed protein 3157 At5g15200 D1 40S ribosomal protein S9 (RPS9B), 40S ribosomal protein S9, Chlamydomonas sp., EMBL:AU066528 3158 At5g15210 Dm zinc finger homeobox family protein / ZF-HD homeobox family protein, various predicted proteins, Arabidopsis thaliana 3159 At5g15230 D2 GASA4__gibberellin-regulated protein 4 (GASA4) / gibberellin-responsive protein 4, identical to SP:P46690 Gibberellin-regulated protein 4 precursor {Arabidopsis thaliana} 3160 At5g15320 Dm expressed protein, predicted protein, Arabidopsis thaliana 3161 At5g15350 D1, D2, Dm plastocyanin-like domain-containing protein, contains plastocyanin-like domain Pfam:PF02298 3162 At5g15460 D2 expressed protein 3163 At5g15500 D1, D2, Dm ankyrin repeat family protein, contains Pfam domain, PF00023: Ankyrin repeat 3164 At5g15520 D1, Dm 40S ribosomal protein S19 (RPS19B), 40S RIBOSOMAL PROTEIN S19 - Oryza sativa, SWISSPROT:RS19_ORYSA 3165 At5g15580 D1, D2, Dm expressed protein, unknown protein F14P3.18 - Arabidopsis thaliana, EMBL:AC009755 3166 At5g15600 D1, D2, Dm expressed protein 3167 At5g15650 D2 RGP2__reversibly glycosylated polypeptide-2 (RGP2), identical to reversibly glycosylated polypeptide-2 (Arabidopsis thaliana) GI:2317731 3168 At5g15670 D1, D2, Dm F-box family protein, contains F-box domain Pfam:PF00646 3169 At5g15740 Dm expressed protein, contains Pfam PF03138: Plant protein family. The function of this family of plant proteins is unknown; 3170 At5g15750 D2 RNA-binding S4 domain-containing protein, 40S RIBOSOMAL PROTEINs - different species 3171 At5g15860 Dm expressed protein 3172 At5g15950 D2 adenosylmethionine decarboxylase family protein, contains Pfam profile: PF01536 adenosylmethionine decarboxylase 3173 At5g15960 D1, D2, Dm KIN1__stress-responsive protein (KIN1) / stress-induced protein (KIN1), identical to SP:P18612 Stress-induced KIN1 protein {Arabidopsis thaliana} 3174 At5g15970 D1, D2, Dm KIN2_COR6.6__stress-responsive protein (KIN2) / stress-induced protein (KIN2) / cold- responsive protein (COR6.6) / cold-regulated protein (COR6.6), identical to SP:P31169 Stress- induced KIN2 protein (Cold-induced COR6.6 protein) {Arabidopsis thaliana} 3175 At5g16000 D1 leucine-rich repeat family protein / protein kinase family protein, contains Pfam domains PF00560: Leucine Rich Repeat and PF00069: Protein kinase domain 3176 At5g16010 D1, D2, Dm 3-oxo-5-alpha-steroid 4-dehydrogenase family protein / steroid 5-alpha-reductase family protein, similar to steroid 5alpha-reductase - Rattus norvegicus, PIR:A34239 (SP:24008); contains Pfam 3-oxo-5-alpha-steroid 4-dehydrogenase domain PF02544 3177 At5g16030 Dm expressed protein 3178 At5g16050 D1, D2, Dm GRF5_GF14 UPSILON__14-3-3 protein GF14 upsilon (GRF5), identical to 14-3-3 protein GF14 upsilon GI:2232148 from (Arabidopsis thaliana) 3179 At5g16070 D2 chaperonin, putative, similar to SWISS-PROT:P80317 T-complex protein 1, zeta subunit (TCP-1- zeta) (Mus musculus); contains Pfam:PF00118 domain, TCP-1/cpn60 chaperonin family 3180 At5g16110 D1, Dm expressed protein, hypothetical protein T26J14.6 - Arabidopsis thaliana, EMBL:AC011915 3181 At5g16120 D1, D2, Dm hydrolase, alpha/beta fold family protein, similar to monoglyceride lipase from (Homo sapiens) GI:14594904, (Mus musculus) GI:2632162; contains Pfam profile PF00561: hydrolase, alpha/beta fold family 3182 At5g16130 D1, D2, Dm 40S ribosomal protein S7 (RPS7C), 40S ribosomal protein S7 homolog - Brassica oleracea, EMBL:AF144752 3183 At5g16260 Dm RNA recognition motif (RRM)-containing protein, similar to Tat-SF1 - Homo sapiens, GI:1667611; contains InterPro entry IPR000504: RNA-binding region RNP-1 (RNA recognition motif) (RRM)

3184 At5g16290 D2 acetolactate synthase small subunit, putative, similar to gi:5931761 from Nicotiana plumbaginifolia 3185 At5g16390 D1, D2, Dm CAC1_BCCP_BCCP1_CAC1A__biotin carboxyl carrier protein 1 (BCCP1), identical to biotin carboxyl carrier protein of acetyl-CoA carboxylase precursor (Arabidopsis thaliana) gi:9759121:dbj:BAB09606 3186 At5g16400 D2 TRXF2__thioredoxin, putative, similar to SP:P29450 Thioredoxin F-type, chloroplast precursor (TRX-F) {Pisum sativum}; contains Pfam profile: PF00085 Thioredoxin 3187 At5g16450 Dm dimethylmenaquinone methyltransferase family protein, similar to bacterial S- adenosylmethionine:2-demethylmenaquinone methyltransferases; contains Pfam profile PF03737: Dimethylmenaquinone methyltransferase 3188 At5g16550 D1 expressed protein 3189 At5g16650 D1, Dm DNAJ heat shock N-terminal domain-containing protein, similar to SP:P30725 Chaperone protein dnaJ Clostridium acetobutylicum; contains Pfam profile PF00226: DnaJ domain 3190 At5g16715 D2, Dm EMB2247__tRNA synthetase class I (I, L, M and V) family protein, similar to SP:P11931 Valyl- tRNA synthetase (EC 6.1.1.9) (Valine--tRNA ligase) (VALRS) {Bacillus stearothermophilus}; contains Pfam profile PF00133: tRNA synthetases class I (I, L, M and V) 3191 At5g16760 D2, Dm Encodes a inositol 1,3,4-trisphosphate 5/6-kinase. 3192 At5g16780 D1, Dm SART-1 family protein, contains Pfam domain, PF03343: SART-1 family 3193 At5g16830 D1, Dm SYP21_ATPEP12_ATSYP21_PEP12__syntaxin 21 (SYP21) / PEP12 homolog, identical to Syntaxin homolog (PEP12 homolog) (SP:Q39233) and syntaxin of plants 21 (GP:899122) {Arabidopsis thaliana}; contains Pfam profiles PF05739:SNARE domain and PF00804: Syntaxin 3194 At5g16930 D1, D2, Dm AAA-type ATPase family protein, contains Pfam domain, PF00004: ATPase, AAA family 3195 At5g17030 Dm UDP-glucoronosyl/UDP-glucosyl transferase family protein, similar to UDP glucose:flavonoid 3- o-glucosyltransferase from Vitis vinifera, EMBL:AF000372 3196 At5g17170 D1, Dm rubredoxin family protein, contains Pfam profile PF00301: Rubredoxin 3197 At5g17190 Dm expressed protein, similar to unknown protein (gb:AAF26109.1) 3198 At5g17220 D1, D2, Dm ATGSTF12_GST26_TT19__glutathione S-transferase, putative 3199 At5g17310 D1, Dm UTP--glucose-1-phosphate uridylyltransferase, putative / UDP-glucose pyrophosphorylase, putative / UGPase, putative, strong similarity to SP:P19595 UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (UDP-glucose pyrophosphorylase) (UDPGP) (UGPase) {Solanum tuberosum}; contains Pfam profile PF01704: UTP--glucose-1-phosphate uridylyltransferase 3200 At5g17400 D2 ADP, ATP carrier protein, mitochondrial, putative / ADP/ATP translocase, putative / adenine nucleotide translocator, putative, similar to SWISS-PROT:Q09188 ADP,ATP carrier protein (ADP/ATP translocase) (Schizosaccharomyces pombe); contains Pfam profile: PF00153 mitochondrial carrier protein 3201 At5g17420 D2, Dm IRX3_ATCESA7_CESA7__cellulose synthase, catalytic subunit (IRX3), identical to gi:5230423 3202 At5g17440 D1 LUC7 N_terminus domain-containing protein, contains Pfam domain PF03194: Protein of unknown function, DUF259 3203 At5g17460 D1, D2, Dm expressed protein 3204 At5g17490 D2 RGL3__gibberellin response modulator, putative / gibberellin-responsive modulator, putative, putative member of the VHIID domain transcription factor family RGAL - Arabidopsis thaliana, EMBL:AJ224957 3205 At5g17520 D1, D2, Dm RCP1_MEX1__root cap 1 (RCP1), identical to GI:6137138 3206 At5g17580 D2 phototropic-responsive NPH3 family protein, contains NPH3 family domain, Pfam:PF03000 3207 At5g17630 D2, Dm glucose-6-phosphate/phosphate translocator, putative, similar to glucose-6- phosphate/phosphate-translocator precursor (Solanum tuberosum) gi:2997593:gb:AAC08526 3208 At5g17670 D1, D2, Dm expressed protein 3209 At5g17680 Dm disease resistance protein (TIR-NBS-LRR class), putative, domain signature TIR-NBS-LRR exists, suggestive of a disease resistance protein. 3210 At5g17710 D1, D2, Dm EMB1241__co-chaperone grpE family protein, similar to co-chaperone CGE1 precursor isoform a (Chlamydomonas reinhardtii) GI:15384277; contains Pfam profile PF01025: co-chaperone GrpE 3211 At5g17770 D2 ATCBR__NADH-cytochrome b5 reductase, identical to NADH-cytochrome b5 reductase (Arabidopsis thaliana) GI:4240116 3212 At5g17790 Dm VAR3__zinc finger (Ran-binding) family protein, contains Pfam domain, PF00641: Zn-finger in Ran binding protein and others 3213 At5g17870 D1, Dm plastid-specific ribosomal protein-related, contains similarity to plastid-specific ribosomal protein 6 precursor GI:7578927 from (Spinacia oleracea) 3214 At5g17900 Dm expressed protein 3215 At5g17920 D1, D2, Dm ATMETS_ATMS1_ATCIMS__The protein underdoes thiolation following treatment with the oxidant tert-butylhydroperoxide. 3216 At5g17950 D2 hypothetical protein 3217 At5g18010 D1 auxin-responsive protein, putative, similar to auxin-inducible SAUR (Small Auxin Up RNAs) (GI:3043536) (Raphanus sativus) 3218 At5g18050 D1, Dm auxin-responsive protein, putative, similar to auxin-inducible SAUR (Small Auxin Up RNAs) (GI:3043536) (Raphanus sativus) 3219 At5g18060 Dm auxin-responsive protein, putative, similar to auxin-inducible SAUR (Small Auxin Up RNAs) GI:3043536 from radish (Raphanus sativus) 3220 At5g18065 D2, Dm expressed protein 3221 At5g18080 D1 auxin-responsive protein, putative, similar to GP:3043536 SAUR {Raphanus sativus} 3222 At5g18100 D2 CSD3__superoxide dismutase (Cu-Zn) / copper/zinc superoxide dismutase (CSD3), identical to copper/zinc superoxide dismutase GI:3273755 3223 At5g18130 D2, Dm expressed protein, similar to unknown protein (gb:AAF00631.1) 3224 At5g18670 D2 BMY3__beta-amylase, putative (BMY3) / 1,4-alpha-D-glucan maltohydrolase, putative, almost identical to beta-amylase BMY3 GI:15149457 from (Arabidopsis thaliana); identical to cDNA putative beta-amylase BMY3 (BMY3) GI:15149456 3225 At5g19000 D1 ATBPM1__similar to speckle-type POZ protein-related [Arabidopsis thaliana] (TAIR:At3g06190.1); similar to putative speckle-type POZ protein [Oryza sativa (japonica cultivar-group)] (GB:XP_476350.1); contains InterPro domain BTB/POZ domain (InterPro:IPR000210); contains InterPro domain Meprin/TRAF-like MATH (InterPro:IPR002083) 3226 At5g19120 D1, D2, Dm expressed protein, low similarity to extracellular dermal glycoprotein EDGP precursor (Daucus carota) GI:285741, SP:P13917 Basic 7S globulin precursor {Glycine max} 3227 At5g19140 D1 auxin/aluminum-responsive protein, putative, strong similarity to auxin down-regulated protein ARG10 (Vigna radiata) GI:2970051, wali7 (aluminum-induced protein) (Triticum aestivum) GI:451193 3228 At5g19150 Dm carbohydrate kinase family, contains Pfam profile PF01256: Carbohydrate kinase 3229 At5g19520 D1, D2, Dm mechanosensitive ion channel domain-containing protein / MS ion channel domain-containing protein, contains Pfam profile PF00924: Mechanosensitive ion channel 3230 At5g19780 D1, D2, Dm TUA5__tubulin alpha-3/alpha-5 chain (TUA5), nearly identical to SP:P20363 Tubulin alpha- 3/alpha-5 chain {Arabidopsis thaliana} 3231 At5g19820 D2 EMB2734__PBS lyase HEAT-like repeat-containing protein, contains Pfam profile: PF03130 PBS lyase HEAT-like repeat 3232 At5g19860 D1, D2, Dm expressed protein, contains Pfam profile PF04398: Protein of unknown function, DUF538 3233 At5g20150 D1, D2, Dm SPX (SYG1/Pho81/XPR1) domain-containing protein, similar to PHO1 protein (Arabidopsis thaliana) GI:20069032; contains Pfam profile PF03105: SPX domain 3234 At5g20160 D1, D2, Dm ribosomal protein L7Ae/L30e/S12e/Gadd45 family protein, Similar to NHP2/L7Ae family proteins, see SWISSPROT:P32495 and PMID:2063628. 3235 At5g20230 D1, D2, Dm ATBCB_BCB__plastocyanin-like domain-containing protein 3236 At5g20250 D1, D2, Dm DIN10__similar to alkaline alpha galactosidase, putative [Arabidopsis thaliana] (TAIR:At3g57520.2); similar to alkaline alpha galactosidase, putative [Arabidopsis thaliana] (TAIR:At3g57520.3); similar to alkaline alpha galactosidase, putative [Arabidopsis thaliana] (TAIR:At1g55740.1); similar to alkaline alpha galactosidase, putative [Arabidopsis thaliana] (TAIR:At3g57520.1); similar to putative alkaline alpha-galactosidase seed imbibition protein [Oryza sativa (japonica cultivar-group)] (GB:XP_483143.1); similar to Sip1 protein - barley (GB:S27762); similar to putative imbibition protein [Brassica oleracea] (GB:CAA55893.1); similar to putative raffinose synthase or seed imbibition protein [Oryza sativa (japonica cultivar-group)] (GB:AAT77910.1); similar to alkaline alpha galactosidase II [Cucumis melo] (GB:AAM75140.1); contains InterPro domain Raffinose synthase (InterPro:IPR008811) 3237 At5g20280 D1, D2, Dm sucrose-phosphate synthase, putative, similar to sucrose-phosphate synthase (EC 2.4.1.14) isoform 1 - Citrus unshiu, EMBL:AB005023 3238 At5g20290 D1, D2, Dm 40S ribosomal protein S8 (RPS8A), ribosomal protein S8 - Zea mays, PIR:T04088 3239 At5g20350 D1, Dm TIP1__similar to ankyrin repeat family protein [Arabidopsis thaliana] (TAIR:At2g14250.1); similar to putative ankyrin repeat-containing protein [Oryza sativa (japonica cultivar-group)] (GB:XP_464354.1); contains InterPro domain Zn-finger, DHHC type (InterPro:IPR001594); contains InterPro domain Ankyrin (InterPro:IPR002110) 3240 At5g20630 D1, D2, Dm GLP3_GLP3A_GLP3B__germin-like protein (GER3), identical to germin-like protein subfamily 3 member 3 (SP:P94072) 3241 At5g20720 D1, Dm CPN20_ATCPN21_CHCPN10_CPN10_CPN21__20 kDa chaperonin, chloroplast (CPN21) (CHCPN10) (CPN20), identical to chloroplast 20 kDa chaperonin, chloroplast precursor (Protein Cpn21), chloroplast protein Cpn10, chloroplast chaperonin 10 (Ch-CPN10), SP:O65282 from (Arabidopsis thaliana); identical to cDNA chaperonin 20 GI:14587372 3242 At5g20730 Dm NPH4_ARF7_BIP_IAA21_MSG1_TIR5__auxin-responsive factor (ARF7), identical to auxin response factor 7 GI:4104929 from (Arabidopsis thaliana) 3243 At5g20830 D1, Dm SUS1_ASUS1_ATSUS1__sucrose synthase / sucrose-UDP glucosyltransferase (SUS1), identical to SP:P49040 Sucrose synthase (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase) {Arabidopsis thaliana} 3244 At5g20890 Dm chaperonin, putative, similar to SWISS-PROT:P78371- T-complex protein 1, beta subunit (TCP-1- beta) (Homo sapiens); contains Pfam:PF00118 domain, TCP-1/cpn60 chaperonin family 3245 At5g20900 D2, Dm expressed protein 3246 At5g21020 D1, D2, Dm expressed protein 3247 At5g21090 D1 leucine-rich repeat protein, putative, similar to leucine rich repeat protein (LRP) GI:1619300 from (Lycopersicon esculentum); contains leucine rich-repeat (LRR) domains Pfam:PF00560, INTERPRO:IPR001611 3248 At5g21105 D2 L-ascorbate oxidase, putative, similar to L-ascorbate oxidase from {Nicotiana tabacum} SP:Q40588, {Cucurbita pepo var. melopepo} SP:P37064; contains Pfam profile PF00394: Multicopper oxidase; supported by cDNA gi_15215753_gb_AY050406.1_; A false intron was added between exons 4 and 5 to circumvent the single nucleotide insertion in this BAC which, otherwise, causes a frameshift. 3249 At5g21160 D2 La domain-containing protein / proline-rich family protein, contains proline-rich extensin domains, INTERPRO:IPR002965, PF05383: La domain 3250 At5g21170 D1, D2, Dm 5`-AMP-activated protein kinase beta-2 subunit, putative, similar to Swiss-Prot:Q9QZH4 5`-AMP- activated protein kinase, beta-2 subunit (AMPK beta-2 chain) (Rattus norvegicus) 3251 At5g21920 D1, Dm YGGT family protein, contains Pfam profile PF02325: YGGT family (unknown function); supported by full length cDNA GI:22531282 from (Arabidopsis thaliana) 3252 At5g21930 D1, Dm PAA2__ATPase E1-E2 type family protein / haloacid dehalogenase-like hydrolase family protein / heavy-metal-associated domain-containing protein, contains InterPro accession IPR001757: ATPase, E1-E2 type; contains Pfam profiles PF00403: Heavy-metal-associated domain, PF00702: haloacid dehalogenase-like hydrolase 3253 At5g22000 D1, D2, Dm CIC7E11_RHF2A__zinc finger (C3HC4-type RING finger) family protein, contains Pfam profile: PF00097 zinc finger, C3HC4 type (RING finger) 3254 At5g22120 D2, Dm expressed protein 3255 At5g22210 D2 expressed protein 3256 At5g22240 D1, D2, Dm ATOFP10_OFP10__ovate family protein, 60% similar to ovate protein (GI:23429649) (Lycopersicon esculentum); contains TIGRFAM TIGR01568 : uncharacterized plant-specific domain TIGR01568

3257 At5g22270 D1, D2, Dm expressed protein, similar to unknown protein (gb AAF02129.1) 3258 At5g22290 D1, D2, Dm ANAC089__no apical meristem (NAM) family protein, contains Pfam PF02365: No apical meristem (NAM) domain 3259 At5g22340 D1, Dm expressed protein 3260 At5g22350 D1, Dm expressed protein 3261 At5g22440 D1, D2, Dm 60S ribosomal protein L10A (RPL10aC) 3262 At5g22460 D1, D2, Dm esterase/lipase/thioesterase family protein, low similarity to 2-hydroxy-6-oxo-6-phenylhexa- 2,4-dienoate hydrolase (Rhodococcus sp. RHA1) GI:8978311, SP:Q02104 Lipase 1 precursor (EC 3.1.1.3) (Triacylglycerol lipase) {Psychrobacter immobilis}; contains Interpro entry IPR000379

3263 At5g22510 D1, D2, Dm beta-fructofuranosidase, putative / invertase, putative / saccharase, putative / beta- fructosidase, putative, similar to neutral invertase (Daucus carota) GI:4200165; contains Pfam profile PF04853: Plant neutral invertase 3264 At5g22580 D1, D2, Dm expressed protein 3265 At5g22630 Dm prephenate dehydratase family protein, contains Pfam profile PF00800: prephenate dehydratase 3266 At5g22640 D1, Dm EMB1211__MORN (Membrane Occupation and Recognition Nexus) repeat-containing protein, contains Pfam profile PF02493: MORN repeat 3267 At5g22650 D2 HD2B_ATHD2B_HD2_HDA4_HDT02_HDT2__expressed protein, non-consensus AT donor splice site at exon 3, AC acceptor splice site at exon 4; 3268 At5g22800 D1, Dm aminoacyl-tRNA synthetase family protein, contains Pfam profiles: PF01411 tRNA synthetases class II (A), PF02272 DHHA1 domain 3269 At5g22810 D2, Dm GDSL-motif lipase, putative, similar to EXL3 (GP:15054386) (Arabidopsis thaliana) 3270 At5g22880 D1, D2, Dm histone H2B, putative, strong similarity to histone H2B-3 Lycopersicon esculentum GI:3021485, H2B Gossypium hirsutum SP:O22582; contains Pfam profile PF00125 Core histone H2A/H2B/H3/H4 3271 At5g22920 D2, Dm zinc finger (C3HC4-type RING finger) family protein, contains Pfam profiles:PF05495 CHY zinc finger, PF00097 zinc finger, C3HC4 type (RING finger) 3272 At5g23010 D2, Dm MAM1_IMS3__2-isopropylmalate synthase 3 (IMS3), identical to 2-isopropylmalate synthase (IMS3) (Arabidopsis thaliana) GI:15983745; identical to cDNA 2-isopropylmalate synthase (IMS3) GI:15983744 3273 At5g23060 D1, D2, Dm expressed protein 3274 At5g23120 D1 HCF136__photosystem II stability/assembly factor, chloroplast (HCF136), identical to SP:O82660 Photosystem II stability/assembly factor HCF136, chloroplast precursor {Arabidopsis thaliana}

3275 At5g23190 D2 CYP86B1__cytochrome P450 family protein, contains Pfam profile: PF00067 cytochrome P450 3276 At5g23280 D2 TCP family transcription factor, putative, similar to PCF2 ((GI:2580440) Oryza sativa) 3277 At5g23310 D2, Dm FSD3__superoxide dismutase (Fe) / iron superoxide dismutase 3 (FSD3), identical to iron superoxide dismutase 3 (Arabidopsis thaliana) gi:3273757:gb:AAC24834 3278 At5g23360 D2 GRAM domain-containing protein / ABA-responsive protein-related, contains similarity to ABA- responsive protein in barley (GI:4103635) (Hordeum vulgare) (J. Exp. Bot. 50, 727-728 (1999); contains Pfam PF02893: GRAM domain) 3279 At5g23440 D1, Dm ferredoxin-thioredoxin reductase, putative, similar to ferredoxin-thioredoxin reductase, variable chain (FTR-V, Ferredoxin- thioredoxin reductase subunit A, FTR-A) (Zea mays) SWISS- PROT:P80680 3280 At5g23450 Dm ATLCBK1__diacylglycerol kinase family protein, contains INTERPRO domain, IPR001206, DAG-kinase catalytic domain 3281 At5g23575 D2 transmembrane protein, putative, similar to cleft lip and palate transmembrane protein 1 (Homo sapiens) GI:4039014; contains Pfam profile PF05602: Cleft lip and palate transmembrane protein 1 (CLPTM1) 3282 At5g23660 D1, Dm MTN3__nodulin MtN3 family protein, similar to MtN3 GI:1619602 (root nodule development) from (Medicago truncatula) 3283 At5g23740 D1, D2, Dm RPS11-BETA__40S ribosomal protein S11 (RPS11C) 3284 At5g23750 D1, D2, Dm remorin family protein, contains Pfam domain, PF03766: Remorin, N-terminal region; contains Pfam domain, PF03763: Remorin, C-terminal region 3285 At5g23760 D1, D2, Dm heavy-metal-associated domain-containing protein, Pfam profile PF00403: Heavy-metal-associated domain 3286 At5g23790 D2 galactinol synthase, putative, similar to galactinol synthase, isoform GolS-1 GI:5608497 from (Ajuga reptans); contains Pfam profile: PF01501 glycosyl transferase family 8 3287 At5g23820 D1, Dm MD-2-related lipid recognition domain-containing protein / ML domain-containing protein, contains Pfam profile PF02221: ML domain 3288 At5g23830 D1 MD-2-related lipid recognition domain-containing protein / ML domain-containing protein, contains Pfam profile PF02221: ML domain 3289 At5g23840 D1, Dm MD-2-related lipid recognition domain-containing protein / ML domain-containing protein, contains Pfam profile PF02221: ML domain 3290 At5g23860 D2, Dm TUB7_TUB8__tubulin beta-8 chain (TUB8) (TUBB8), identical to SP:P29516 Tubulin beta-8 chain {Arabidopsis thaliana}; supporting cDNA gi:15451225:gb:AY054693.1: 3291 At5g23970 D1, D2, Dm transferase family protein, similar to acetyl CoA: benzylalcohol acetyltransferase; BEAT (Clarkia breweri)(GI:3170250)(PMID:9628024), deacetylvindoline 4-O-acetyltransferase (Catharanthus roseus)(GI:4091808)(PMID:9681034) 3292 At5g24030 D2 C4-dicarboxylate transporter/malic acid transport family protein, weak similarity to SP:P25396 Tellurite resistance protein tehA. {Escherichia coli}; contains Pfam profile PF03595: C4- dicarboxylate transporter/malic acid transport protein 3293 At5g24210 D2 lipase class 3 family protein, contains Pfam profile PF01764: Lipase 3294 At5g24360 D2 protein kinase family protein / Ire1 homolog-1 (IRE1-1), identical to Ire1 homolog-1 (Arabidopsis thaliana) GI:15277137; cDNA Ire1 homolog-1 GI:15277136; 3295 At5g24380 D1, Dm YSL2_ATYSL2__similar to transporter, putative [Arabidopsis thaliana] (TAIR:At5g53550.1); similar to oligopeptide transporter OPT family protein [Arabidopsis thaliana] (TAIR:At5g41000.1); similar to oligopeptide transporter OPT family protein [Arabidopsis thaliana] (TAIR:At1g65730.1); similar to oligopeptide transporter OPT family protein [Arabidopsis thaliana] (TAIR:At3g17650.1); similar to transporter, putative [Arabidopsis thaliana] (TAIR:At4g24120.1); similar to OSJNBb0103I08.15 [Oryza sativa (japonica cultivar- group)] (GB:XP_473374.1); similar to putative iron-phytosiderophore transporter protein yellow stripe 1 [Oryza sativa (japonica cultivar-group)] (GB:XP_467066.1); similar to iron transport protein 1 [Oryza sativa] (GB:AAS49493.1); similar to hypothetical protein [Oryza sativa (japonica cultivar-group)] (GB:BAD90812.1); similar to iron-phytosiderophore transporter protein yellow stripe 1 [Zea mays] (GB:AAG17016.2); contains InterPro domain Oligopeptide transporter OPT superfamily (InterPro:IPR004813) 3296 At5g24470 Dm APRR5_PRR5__pseudo-response regulator 5 (APRR5), identical to pseudo-response regulator 5 GI:10281006 from (Arabidopsis thaliana) 3297 At5g24490 D1, Dm 30S ribosomal protein, putative, similar to SP:P19954 Plastid-specific 30S ribosomal protein 1, chloroplast precursor (CS-S5) (CS5) (S22) (Ribosomal protein 1) (PSRP-1) {Spinacia oleracea}; contains Pfam profile PF02482: Sigma 54 modulation protein / S30EA ribosomal protein 3298 At5g24510 D1 60s acidic ribosomal protein P1, putative 3299 At5g24570 D2 expressed protein 3300 At5g24590 D1, Dm ANAC091_TIP__turnip crinkle virus-interacting protein / TCV-interacting protein (TIP), contains Pfam PF02365: No apical meristem (NAM) domain; similar to NAC2 (GI:6456751) {Arabidopsis thaliana}; identical to cDNA TIP mRNA, GI:9408600 3301 At5g24610 D1, Dm expressed protein, similar to unknown protein (emb:CAB62459.1) 3302 At5g24660 D2 expressed protein 3303 At5g24770 D1, D2, Dm VSP2__vegetative storage protein 2 (VSP2), identical to SP:O82122 Vegetative storage protein 2 precursor {Arabidopsis thaliana}; contains Pfam profile PF03767: HAD superfamily (subfamily IIIB) phosphatase 3304 At5g24780 D2 VSP1_ATVSP__vegetative storage protein 1 (VSP1), identical to SP:O49195 Vegetative storage protein 1 precursor {Arabidopsis thaliana}; contains Pfam profile PF03767: HAD superfamily (subfamily IIIB) phosphatase 3305 At5g24860 D2, Dm FPF1_FPF__expressed protein 3306 At5g24870 Dm zinc finger (C3HC4-type RING finger) family protein, similar to Pfam domain, PF00097: Zinc finger, C3HC4 type (RING finger) 3307 At5g25100 D2 endomembrane protein 70, putative, TM4 family; 3308 At5g25120 D2, Dm CYP71B11__cytochrome P450 family protein, CYTOCHROME P450 71B1 - Thlaspi arvense, EMBL:L24438

3309 At5g25130 Dm CYP71B12__cytochrome P450 family protein, CYTOCHROME P450 71B1 - Thlaspi arvense, EMBL:L24438

3310 At5g25190 D1, D2, Dm encodes a member of the ERF (ethylene response factor) subfamily B-6 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 12 members in this subfamily including RAP2.11. 3311 At5g25220 D1, D2, Dm KNAT3__homeobox protein knotted-1 like 3 (KNAT3), identical to homeobox protein knotted-1 like 3 (KNAT3) SP:P48000 from (Arabidopsis thaliana) 3312 At5g25460 D1, D2, Dm expressed protein, contains Pfam profile PF04862: Protein of unknown function, DUF642 3313 At5g25510 Dm serine/threonine protein phosphatase 2A (PP2A) regulatory subunit B`, putative, similar to SWISS-PROT:Q28653 serine/threonine protein phosphatase 2A, 56 kDa regulatory subunit, delta isoform (PP2A, B subunit, B` delta isoform, PP2A, B subunit, B56 delta isoform, PP2A, B subunit, PR61 delta isoform, PP2A, B subunit, R5 delta isoform, PP2A, B subunit, B`-gamma) (Oryctolagus cuniculus); contains Pfam domain, PF01603: Protein phosphatase 2A regulatory B subunit (B56 family) 3314 At5g25610 D1, D2, Dm RD22__dehydration-responsive protein (RD22), identical to SP:Q08298 Dehydration-responsive protein RD22 precursor {Arabidopsis thaliana} 3315 At5g25780 D2, Dm EIF3B-2_ATEIF3B-2__eukaryotic translation initiation factor 3 subunit 9, putative / eIF-3 eta, putative / eIF3b, putative, nearly identical to SP:Q9C5Z1 Eukaryotic translation initiation factor 3 subunit 9 (eIF-3 eta) (eIF3 p110) (eIF3b) {Arabidopsis thaliana} 3316 At5g25890 D1, Dm IAA28_IAR2__auxin-responsive protein / indoleacetic acid-induced protein 28 (IAA28), identical to SP:Q9XFM0:AXIS_ARATH Auxin-responsive protein IAA28 (Indoleacetic acid-induced protein 28) {Arabidopsis thaliana} 3317 At5g26000 D2 TGG1__glycosyl hydrolase family 1 protein, contains Pfam PF00232 : Glycosyl hydrolase family 1 domain; TIGRFAM TIGR01233: 6-phospho-beta-galactosidase; identical to Myrosinase precursor (Sinigrinase) (SP:P37702) (Arabidopsis thaliana) 3318 At5g26340 D2, Dm MSS1__hexose transporter, putative, strong similarity to hexose transporter, Lycopersicon esculentum, GI:5734440; contains Pfam profile PF00083: major facilitator superfamily protein 3319 At5g26360 D2 chaperonin, putative, similar to SWISS-PROT:P50143- T-complex protein 1, gamma subunit (TCP-1- gamma) (Xenopus laevis); contains Pfam:PF00118 domain, TCP-1/cpn60 chaperonin family 3320 At5g26667 D2 uridylate kinase / uridine monophosphate kinase / UMP kinase (PYR6), identical to uridylate kinase / UMP/CMP kinase SP:O04905 from (Arabidopsis thaliana) 3321 At5g26740 D2 expressed protein, contains Pfam profile PF03619: Domain of unknown function 3322 At5g26742 D2, Dm EMB1138__DEAD box RNA helicase (RH3), nearly identical to RNA helicase (Arabidopsis thaliana) GI:3775987; contains Pfam profiles PF00270: DEAD/DEAH box helicase, PF00271: Helicase conserved C-terminal domain, PF00098: Zinc knuckle 3323 At5g26830 D2 threonyl-tRNA synthetase / threonine--tRNA ligase (THRRS), identical to SP:O04630 Threonyl- tRNA synthetase, mitochondrial precursor (EC 6.1.1.3) (Threonine--tRNA ligase) (ThrRS) {Arabidopsis thaliana} 3324 At5g26860 D2 LON_ARA_ARA__similar to Lon protease, putative [Arabidopsis thaliana] (TAIR:At3g05790.1); similar to Lon protease, putative [Arabidopsis thaliana] (TAIR:At3g05780.1); similar to LON2 [Zea mays] (GB:AAC50021.1); similar to Lon protease, putative [Phytophthora infestans] (GB:CAI72282.1); similar to putative Lon2 protease [Oryza sativa (indica cultivar-group)] (GB:AAO34661.1); similar to putative ATP-dependent proteinase LON2 [Oryza sativa (japonica cultivar-group)] (GB:BAD30597.1); similar to Lon protease-like protein [Homo sapiens] (GB:CAA53625.1); contains InterPro domain AAA ATPase (InterPro:IPR003593); contains InterPro domain Peptidase family S16 (InterPro:IPR001984); contains InterPro domain Lon protease S16, C-terminal proteolytic (InterPro:IPR008269); contains InterPro domain ATP-dependent protease La, LON (InterPro:IPR003111); contains InterPro domain ATP-dependent protease La (InterPro:IPR004815); contains InterPro domain Peptidase family S16, active site (InterPro:IPR008268); contains InterPro domain AAA ATPase, central region (InterPro:IPR003959)

3325 At5g26880 D2 tRNA/rRNA methyltransferase (SpoU) family protein, low similarity to tRNA (Gm18) methyltransferase (Thermus thermophilus) GI:11079208; contains Pfam profile PF00588: SpoU rRNA Methylase (RNA methyltransferase, TrmH) family 3326 At5g27120 D2, Dm SAR DNA-binding protein, putative, strong similarity to SAR DNA-binding protein-1 (Pisum sativum) GI:3132696; contains Pfam profile PF01798: Putative snoRNA binding domain; has similarity to MAR binding NOP58 protein 3327 At5g27150 D1 NHX1_ATNHX_ATNHX1_AT-NHX1__sodium proton exchanger / Na+/H+ antiporter (NHX1), identical to Na+/H+ exchanger (Arabidopsis thaliana) gi:6650177:gb:AAF21755 and sodium proton exchanger Nhx1 (Arabidopsis thaliana) gi:4324597:gb:AAD16946; Member of The Monovalent Cation:Proton Antiporter (CPA1) Family, PMID:11500563 3328 At5g27280 D2, Dm zinc finger (DNL type) family protein, contains Pfam profile PF05180: DNL zinc finger 3329 At5g27380 D2, Dm GSH2_GSHB__glutathione synthetase (GSH2), non-consensus AT donor splice site at exon 6, AC acceptor splice site at exon 7; identical to Swiss-Prot:P46416 glutathione synthetase, chloroplast precursor (Glutathione synthase) (GSH synthetase) (GSH-S) (Arabidopsis thaliana) 3330 At5g27600 Dm LACS7__AMP-binding protein, putative, similar to AMP-binding protein (MF39P) gi:1617274 from Brassica napus, long-chain-fatty-acid--CoA ligase - Brassica napus, EMBL:Z72152; contains Pfam AMP-binding enzyme domain PF00501 3331 At5g27670 D1, D2 histone H2A, putative, similar to histone H2A Lycopersicon esculentum SP:P25469, Pisum sativum SP:P25470, Petroselinum crispum SP:P19177; contains Pfam profile PF00125 Core histone H2A/H2B/H3/H4 3332 At5g27770 D2 60S ribosomal protein L22 (RPL22C), ribosomal protein L22 (cytosolic), Rattus norvegicus, PIR:S52084 3333 At5g28050 D1 cytidine/deoxycytidylate deaminase family protein, similar to SP:O34598 Guanine deaminase (EC 3.5.4.3) (Guanase) (Guanine aminase) (Guanine aminohydrolase) (GAH) (GDEase) {Bacillus subtilis}; contains Pfam profile PF00383: Cytidine and deoxycytidylate deaminase zinc-binding region 3334 At5g28060 D1 40S ribosomal protein S24 (RPS24B), 40S ribosomal protein S19, Cyanophora paradoxa, EMBL:CPA245654 3335 At5g28500 D1, Dm expressed protein, predicted proteins, Arabidopsis thaliana and Synechocystis sp. 3336 At5g28570 D2 hypothetical protein 3337 At5g28770 D1, D2, Dm BZO2H3__bZIP transcription factor family protein, similar to seed storage protein opaque- 2(bZIP family)GI:168428 from Zea mays; contains Pfam profile PF00170: bZIP transcription factor; identical to cDNA bZIP protein BZO2H3 GI:10954098 3338 At5g30510 D1, Dm 30S ribosomal protein S1, putative, similar to Swiss-Prot:P29344 30S ribosomal protein S1, chloroplast precursor (CS1) (Spinacia oleracea) 3339 At5g32440 D2 expressed protein 3340 At5g33320 D2 CUE1_ARAPPT_PPT__triose phosphate/phosphate translocator, putative, similar to SWISS- PROT:P52178 triose phosphate/phosphate translocator (Cauliflower) {Brassica oleracea} 3341 At5g35180 D1, Dm expressed protein 3342 At5g35220 D2 EGY1__peptidase M50 family protein / sterol-regulatory element binding protein (SREBP) site 2 protease family protein, contains PFam PF02163: sterol-regulatory element binding protein (SREBP) site 2 protease 3343 At5g35360 Dm CAC2__acetyl-CoA carboxylase, biotin carboxylase subunit (CAC2), identical to acetyl-CoA carboxylase, biotin carboxylase subunit (CAC2) (Arabidopsis thaliana) GI:1905876 3344 At5g35460 Dm expressed protein 3345 At5g35475 D2 hypothetical protein, very low similarity to transposase (Ipomoea purpurea) GI:4063770 3346 At5g35490 D1, Dm expressed protein (MRU1), contains Pfam domain, PF04827: Protein of unknown function (DUF635)

3347 At5g35540 D1, D2, Dm hypothetical protein 3348 At5g35550 Dm TT2_MYB123__myb family transcription factor (MYB123), contains PFAM profile: myb DNA-binding domain PF00249 3349 At5g35620 D1, Dm LSP1_EIF(ISO)4E_LSP__eukaryotic translation initiation factor 4E 2 / eIF-4E2 / mRNA cap- binding protein 2 (EIF4E2), identical to SP:O04663 Eukaryotic translation initiation factor 4E (eIF-4E) (eIF4E) (mRNA cap-binding protein) (eIF-(iso)4F 25 kDa subunit) (eIF-(ISO)4F P28 subunit) (eIF4Eiso protein) {Arabidopsis thaliana} 3350 At5g35630 D2, Dm GS2_ATGSL1_GLN2__glutamine synthetase (GS2), identical to glutamine synthetase, chloroplast precursor (glutamate-- ammonia ligase, GS2) (Arabidopsis thaliana) SWISS-PROT:Q43127 3351 At5g35970 D2 DNA-binding protein, putative, similar to SWISS-PROT:Q60560 DNA-binding protein SMUBP-2 (Immunoglobulin MU binding protein 2, SMUBP-2) (Mesocricetus auratus) 3352 At5g36200 D2, Dm F-box family protein, contains Pfam PF00646: F-box domain; contains TIGRFAM TIGR01640: F-box protein interaction domain; similar to unknown protein (pir::T00841) 3353 At5g36700 D1, Dm phosphoglycolate phosphatase, putative, similar to phosphoglycolate phosphatase precursor (Chlamydomonas reinhardtii) GI:15982558; contains InterPro accession IPR005834: Haloacid dehalogenase-like hydrolase 3354 At5g37020 Dm ARF8__auxin-responsive factor (ARF8), identical to auxin response factor 8 GI:4104931 from (Arabidopsis thaliana) 3355 At5g37300 Dm expressed protein 3356 At5g37540 D1 aspartyl protease family protein, weak similarity to CND41, chloroplast nucleoid DNA binding protein (Nicotiana tabacum) GI:2541876; contains Prosite PS00141: Eukaryotic and viral aspartyl proteases active site; contains 1 predicted transmembrane domain 3357 At5g37550 D2, Dm expressed protein 3358 At5g37600 D2, Dm ATGSR1__glutamine synthetase, putative, similar to glutamine synthetase, cytosolic isozyme (Glutamate-- ammonia ligase, GS1) (Lotus japonicus) SWISS-PROT:Q42899 3359 At5g37640 D1, D2, Dm UBQ9__polyubiquitin (UBQ9), identical to polyubiquitin (ubq9) gene sequence GI:304120 from (Arabidopsis thaliana) 3360 At5g37710 D2 lipase class 3 family protein / calmodulin-binding heat-shock protein, putative, similar to almodulin-binding heat-shock protein, common tobacco, PIR:T04107; contains Pfam profilesPF03893: Lipase 3 N-terminal region, PF01764: Lipase 3361 At5g37720 D1, Dm RNA and export factor-binding protein, putative, transcriptional coactivator ALY, Mus musculus, EMBL:MMU89876 3362 At5g38280 D2, Dm PR5K__serine/threonine protein kinase (PR5K), identical to receptor serine/threonine kinase PR5K gi:1235680:gb:AAC49208 3363 At5g38290 D1, Dm peptidyl-tRNA hydrolase family protein, contains Pfam profile PF01195: peptidyl-tRNA hydrolase

3364 At5g38480 D1, D2 GRF3_RCI1__14-3-3 protein GF14 psi (GRF3) (RCI1), identical to 14-3-3 protein GF14 psi GI:1168200, SP:P42644 3365 At5g38520 D2 hydrolase, alpha/beta fold family protein, low similarity to hydrolase (Terrabacter sp. DBF63) GI:14196240; contains Pfam profile PF00561: hydrolase, alpha/beta fold family 3366 At5g38540 D2 jacalin lectin family protein, similar to myrosinase-binding protein homolog (Arabidopsis thaliana) GI:2997767; contains Pfam profile PF01419 jacalin-like lectin domain 3367 At5g38630 D2, Dm ACYB-1__cytochrome B561 family protein, contains Pfam domain, PF03188: Cytochrome b561 3368 At5g38710 D2 proline oxidase, putative / osmotic stress-responsive proline dehydrogenase, putative, similar to proline oxidase, mitochondrial precursor (Osmotic stress- induced proline dehydrogenase) (Arabidopsis thaliana) SWISS-PROT:P92983 3369 At5g38870 D1 transposable element gene 3370 At5g38880 D2 expressed protein 3371 At5g38940 Dm germin-like protein, putative, similar to germin-like portein GLP9 (SP:Q9LEA7); contains PS00725 Germin family signature 3372 At5g38970 D2, Dm BR6OX_ATBR6OX_BR6OX1_CYP85A1__cytochrome P450, putative, similar to Cytochrome P450 85 (SP:Q43147) {Lycopersicon esculentum}; 3373 At5g38980 D1, D2, Dm expressed protein 3374 At5g39030 D1, Dm protein kinase family protein, contains protein kinase domain, Pfam:PF00069 3375 At5g39100 D2 GLP6__germin-like protein (GLP6), nearly identical to SP:P92997 Germin-like protein subfamily 1 member 13 precursor {Arabidopsis thaliana}; exon 2 interrupted by a stop codon, creating non-consensus donor and acceptor splice sites. 3376 At5g39110 D2 germin-like protein, putative, nearly identical to SP:Q9FID0 Germin-like protein subfamily 1 member 14 precursor (Arabidopsis thaliana) 3377 At5g39210 D1, Dm expressed protein 3378 At5g39320 D2 UDP-glucose 6-dehydrogenase, putative, very strong similarity to SP:Q96558 UDP-glucose 6- dehydrogenase (EC 1.1.1.22) (UDP-Glc dehydrogenase) (UDP-GlcDH) (UDPGDH) {Glycine max}; contains Pfam profiles PF03721: UDP-glucose/GDP-mannose dehydrogenase family NAD binding domain, PF00984: UDP-glucose/GDP-mannose dehydrogenase family central domain, PF03720: UDP- glucose/GDP-mannose dehydrogenase family UDP binding domain 3379 At5g39420 D2, Dm CDC2CAT__protein kinase family protein, contains Pfam domain, PF00069: Protein kinase domain 3380 At5g39450 D2, Dm F-box family protein, contains Pfam:PF00646 F-box domain ; similar to SKP1 interacting partner 2 (SKIP2) TIGR_Ath1:At5g67250 3381 At5g39500 D2 pattern formation protein, putative, similar to SP:Q42510 Pattern formation protein EMB30 {Arabidopsis thaliana}; contains Pfam profile PF01369: Sec7 domain 3382 At5g39530 D1, D2 expressed protein, hypothetical protein, Synechocystis sp., PIR:S77152 3383 At5g39550 D1 zinc finger (C3HC4-type RING finger) family protein, contains zinc finger, C3HC4 type (RING finger), signature, PROSITE:PS00518 3384 At5g39590 D1, D2, Dm expressed protein 3385 At5g39730 D1, D2, Dm avirulence-responsive protein-related / avirulence induced gene (AIG) protein-related, similar to SP:P54121 AIG2 protein {Arabidopsis thaliana} 3386 At5g39740 D1, D2, Dm 60S ribosomal protein L5 (RPL5B), ribosomal protein L5, rice 3387 At5g39760 D2 zinc finger homeobox protein-related / ZF-HD homeobox protein-related, predicted proteins, Arabidopsis thaliana 3388 At5g39830 D1, Dm DegP protease, putative, contains similarity to DegP protease precursor GI:2565436 from (Arabidopsis thaliana) 3389 At5g39860 D1 bHLH protein, putative DNA-binding protein - Arabidopsis thaliana, EMBL:AC011765 3390 At5g39950 D1, D2, Dm ATTRX2__thioredoxin H-type 2 (TRX-H-2) (Gif2), identical to SP:Q38879 Thioredoxin H-type 2 (TRX-H-2) {Arabidopsis thaliana}; identical to cDNA (Gif2) mRNA for thioredoxin GI:992963 3391 At5g40130 D1, Dm pseudogene, 60S ribosomal protein L5 (RPL5C) 3392 At5g40170 D1, Dm disease resistance family protein, contains leucine rich-repeat (LRR) domains Pfam:PF00560, INTERPRO:IPR001611; similar to Cf-4 (Lycopersicon hirsutum) gi:2808683:emb:CAA05268 3393 At5g40240 Dm nodulin MtN21 family protein, similar to MtN21 (Medicago truncatula) GI:2598575; contains Pfam profile PF00892: Integral membrane protein 3394 At5g40370 D1, D2, Dm glutaredoxin, putative, similar to glutaredoxin (Ricinus communis) SWISS-PROT:P55143 3395 At5g40450 D2, Dm expressed protein 3396 At5g40480 D1, D2, Dm EMB3012__expressed protein, ; expression supported by MPSS 3397 At5g40490 D2, Dm RNA recognition motif (RRM)-containing protein, ribonucleoprotein, Xenopus laevis, PIR:S40778; contains InterPro entry IPR000504: RNA-binding region RNP-1 (RNA recognition motif) (RRM) 3398 At5g40570 Dm surfeit locus protein 2 family protein / SURF2 family protein, contains Pfam profile PF05477: Surfeit locus protein 2 (SURF2) 3399 At5g40580 D2 PBB1_PBB2__20S proteasome beta subunit B (PBB2) (PRCFC), identical to 20S proteasome beta subunit PBB2 (Arabidopsis thaliana) GI:3421104, cDNA proteasome subunit prcfc GI:2511575 3400 At5g40760 D1, D2, Dm G6PD6__Encodes a cytosolic glucose-6-phosphate dehydrogenase that is insensitive to reduction by DTT and whose mRNA is expressed ubiquitously. 3401 At5g40770 D2 ATPHB3__prohibitin, identical to prohibitin (Arabidopsis thaliana) GI:1946331 3402 At5g40830 D2 ATRAD3__expressed protein 3403 At5g40890 D1, D2 ATCLC-A_CLCA_CLC-A__chloride channel protein (CLC-a), identical to GI:1742952 (gb:AAC05742.1)

3404 At5g40950 D1, D2, Dm 50S ribosomal protein L27, chloroplast, putative (RPL27), identical to SP:Q9FLN4 ribosomal protein L27, chloroplast precursor {Arabidopsis thaliana}; similar to SP:P30155 50S ribosomal protein L27, chloroplast precursor (CL27) {Nicotiana tabacum} 3405 At5g41010 D2 DNA-directed RNA polymerases I, II, and III 7 kDa subunit, putative, similar to SP:P53803 DNA- directed RNA polymerases I, II, and III 7.0 kDa polypeptide (EC 2.7.7.6) (ABC10-alpha) (RPB7.0) (RPB10alpha) {Homo sapiens}; contains Pfam profile PF03604: DNA directed RNA polymerase, 7 kDa subunit 3406 At5g41060 D2 zinc finger (DHHC type) family protein, contains Pfam profile PF01529: DHHC zinc finger domain

3407 At5g41400 D2 zinc finger (C3HC4-type RING finger) family protein, similar to RING-H2 finger protein RHA1a (Arabidopsis thaliana) GI:3790554; contains Pfam profile PF00097: Zinc finger, C3HC4 type (RING finger) 3408 At5g41520 D1, D2, Dm 40S ribosomal protein S10 (RPS10B), contains similarity to 40S ribosomal protein S10 3409 At5g41560 D2, Dm expressed protein 3410 At5g41700 D1, D2, Dm UBC8_ATUBC8__ubiquitin-conjugating enzyme 8 (UBC8), E2; identical to gi:297882, SP:P35131 3411 At5g41960 D1, Dm expressed protein 3412 At5g41970 D2 similar to expressed protein [Arabidopsis thaliana] (TAIR:At3g49320.1); similar to LOC496075 protein [Xenopus laevis] (GB:AAH87491.1); contains InterPro domain Metal-dependent protein hydrolase (InterPro:IPR003226) 3413 At5g42020 D2, Dm BIP__luminal binding protein 2 (BiP-2) (BP2), similar to SWISS-PROT: Q39043; GI:1303695; luminal binding protein (BiP) (Arabidopsis thaliana) 3414 At5g42030 D1, D2, Dm expressed protein, similar to unknown protein (emb:CAB66408.1) 3415 At5g42050 D1, D2, Dm expressed protein, similar to gda-1 (Pisum sativum) GI:2765418 3416 At5g42070 Dm expressed protein, similar to unknown protein (dbj:BAA92898.1) 3417 At5g42090 D2, Dm expressed protein 3418 At5g42100 D1, D2, Dm glycosyl hydrolase family 17 protein, similar to beta-1,3-glucanase precursor GI:4097948 from (Oryza sativa) 3419 At5g42170 D1 family II extracellular lipase, putative, similar to family II lipase EXL3 (Arabidopsis thaliana) GI:15054386; contains InterPro Entry IPR001087 Lipolytic enzyme, G-D-S-L family 3420 At5g42190 Dm ASK2_SKP1B__E3 ubiquitin ligase SCF complex subunit SKP1/ASK1 (At2) / UFO-binding protein (UIP2), E3 ubiquitin ligase; skp1b; identical to UIP2 GI:3719211 from (Arabidopsis thaliana); contains Pfam profiles PF01466: Skp1 family, dimerisation domain and PF03931:Skp1 family, tetramerisation domain; identical to cDNA UFO binding protein UIP2 mRNA, partial cds GI:3719210 3421 At5g42240 D1, Dm SCPL42__serine carboxypeptidase S10 family protein, similar to Serine carboxypeptidase II-3 precursor (SP:P52711) (CP-MII.3. (Hordeum vulgare) 3422 At5g42270 D1, D2, Dm VAR1_FTSH5__FtsH protease, putative, similar to FtsH protease GI:13183728 from (Medicago sativa) 3423 At5g42290 Dm transcription activator-related, contains weak similarity to beta-cell E-box transcription activator 1 gi:529197:gb:AAA65702 3424 At5g42650 D2 AOS_CYP74A__allene oxide synthase (AOS) / hydroperoxide dehydrase / cytochrome P450 74A (CYP74A), identical to Allene oxide synthase, chloroplast precursor (Hydroperoxide dehydrase) (Cytochrome P450 74A) (SP:Q96242) {Arabidopsis thaliana} 3425 At5g42800 D1, D2, Dm DFR_M318_TT3_M318__dihydroflavonol 4-reductase (dihydrokaempferol 4-reductase) (DFR), nearly identical to GI:166686 3426 At5g42980 D1, D2, Dm ATTRX3__thioredoxin H-type 3 (TRX-H-3) (GIF1), identical to SP:Q42403 Thioredoxin H-type 3 (TRX-H-3) {Arabidopsis thaliana}; identical to cDNA (GIF1) mRNA for thioredoxin GI:992961 3427 At5g43080 D2 CYCA3;1__cyclin, putative, similar to A-type cyclins from (Nicotiana tabacum) GI:1064931, (Catharanthus roseus) GI:2190259; contains Pfam profiles PF00134: Cyclin, N-terminal domain, PF02984: Cyclin, C-terminal domain 3428 At5g43150 D1, D2, Dm expressed protein 3429 At5g43260 D1, D2, Dm chaperone protein dnaJ-related, similar to Chaperone protein dnaJ (SP:Q9WZV3) (Thermotoga maritima) 3430 At5g43270 Dm SPL2__squamosa promoter-binding protein-like 2 (SPL2), identical to squamosa promoter binding protein-like 2 (Arabidopsis thaliana) GI:5931645; contains Pfam profile PF03110: SBP domain

3431 At5g43440 D2 2-oxoglutarate-dependent dioxygenase, putative, similar to 2A6 (GI:599622) and tomato ethylene synthesis regulatory protein E8 (SP:P10967) 3432 At5g43450 D1, D2, Dm 2-oxoglutarate-dependent dioxygenase, putative, similar to 2A6 (GI:599622) and tomato ethylene synthesis regulatory protein E8 (SP:P10967) 3433 At5g43460 D1 lesion inducing protein-related, similar to ORF, able to induce HR-like lesions (Nicotiana tabacum) 3434 At5g43500 D1, Dm ATARP9__expressed protein 3435 At5g43640 D1, D2, Dm 40S ribosomal protein S15 (RPS15E) 3436 At5g43700 D1, D2, Dm ATAUX2-11_IAA4__auxin-responsive protein / indoleacetic acid-induced protein 4 (IAA4) / auxin- induced protein (AUX2-11), identical to SP:P33077 Auxin-responsive protein IAA4 (Indoleacetic acid-induced protein 4) (Auxin-induced protein AUX2-11) {Arabidopsis thaliana} 3437 At5g43750 D1, Dm expressed protein 3438 At5g43840 D1, D2, Dm AT-HSFA6A_HSFA6A__heat shock transcription factor family protein, contains Pfam profile: PF00447 HSF-type DNA-binding domain 3439 At5g43850 D1, D2, Dm acireductone dioxygenase (ARD/ARD`) family protein, similar to iron-deficiency induced gene (Hordeum vulgare) GI:14522834, SIPL (Homo sapiens) GI:16551383; contains Pfam profile PF03079: ARD/ARD` family 3440 At5g43870 D1, D2, Dm expressed protein 3441 At5g43890 D2, Dm SUPER1_YUCCA5__flavin-containing monooxygenase family protein / FMO family protein, similar to flavin-containing monooxygenases YUCCA (gi:16555352), YUCCA2 (gi:16555354), and YUCCA3 (gi:16555356) from Arabidopsis thaliana; contains Pfam profile PF00743 3442 At5g43920 Dm transducin family protein / WD-40 repeat family protein, contains 7 WD-40 repeats (PF00400); similar to will die slowly protein (WDS) (SP:Q9V3J8) (Drosophila melanogaster) 3443 At5g43940 D1, D2, Dm alcohol dehydrogenase class III / glutathione-dependent formaldehyde dehydrogenase / GSH-FDH (ADHIII), identical to gi:1143388 3444 At5g43960 D2 nuclear transport factor 2 (NTF2) family protein / RNA recognition motif (RRM)-containing protein, contains Pfam profiles PF02136: Nuclear transport factor 2 (NTF2) domain, PF00076: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 3445 At5g44190 D2 GLK2_ATGLK2_GPRI2__myb family transcription factor (GLK2), contains Pfam profile: PF00249 myb- like DNA-binding domain 3446 At5g44300 Dm dormancy/auxin associated family protein, contains Pfam profile: PF05564 dormancy/auxin associated protein 3447 At5g44340 D1, D2, Dm TUB4__tubulin beta-4 chain (TUB4), nearly identical to SP:P24636 Tubulin beta-4 chain {Arabidopsis thaliana} 3448 At5g44420 D1, Dm LCR77_PDF1.2a_PDF1.2__plant defensin protein, putative (PDF1.2a), plant defensin protein family member, personal communication, Bart Thomma ([email protected]); similar to antifungal protein 1 preprotein (Raphanus sativus) gi:609322:gb:AAA69541 3449 At5g44550 D1, D2, Dm integral membrane family protein, similar to unknown protein (pir::T10581) This family of plant proteins contains a domain that may have a catalytic activity. It has a conserved arginine and aspartate that could form an active site. These proteins are predicted to contain 3 or 4 transmembrane helices; contains TIGRFAM TIGR01569 : plant integral membrane protein TIGR01569; contains Pfam PF04535 : Domain of unknown function (DUF588) 3450 At5g44580 D2 expressed protein 3451 At5g44590 D2, Dm hypothetical protein 3452 At5g44610 D1, D2, Dm DREPP plasma membrane polypeptide-related, contains Pfam profile: PF05558 DREPP plasma membrane polypeptide 3453 At5g44650 D1, D2, Dm expressed protein 3454 At5g44680 D1, D2, Dm methyladenine glycosylase family protein, similar to SP:P05100 DNA-3-methyladenine glycosylase I (EC 3.2.2.20) (3-methyladenine-DNA glycosylase I, constitutive) {Escherichia coli}; contains Pfam profile PF03352: Methyladenine glycosylase 3455 At5g44720 D2 molybdenum cofactor sulfurase family protein, weak similarity to molybdenum cofactor sulfurase (LOS5/ABA3) (Arabidopsis thaliana) GI:15407262; contains Pfam profiles PF03476: MOSC N- terminal beta barrel domain, PF03473: MOSC domain 3456 At5g44820 D1, D2, Dm expressed protein, similar to unknown protein (pir::T04881) 3457 At5g44840 D1 glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family protein, similar to polygalacturonase (Persea americana) GI:166951; contains PF00295: Glycosyl hydrolases family 28 (polygalacturonases) 3458 At5g45050 Dm TTR1_ATWRKY16_WRKY16__disease resistance protein-related, similar to NL27 (Solanum tuberosum) GI:3947735; contains Pfam profiles PF03106: WRKY DNA -binding domain, PF00931: NB-ARC domain, PF00560: Leucine Rich Repeat 3459 At5g45130 D1, D2, Dm RHA1__Ras-related protein (RHA1) / small GTP-binding protein, identical to Ras-related protein RHA1 SP:P31582 from (Arabidopsis thaliana) 3460 At5g45280 D1, D2, Dm pectinacetylesterase, putative, similar to pectinacetylesterase precursor GI:1431629 from (Vigna radiata) 3461 At5g45310 D1, D2, Dm expressed protein 3462 At5g45390 D1 CLPP4_NCLPP3_NCLPP4__ATP-dependent Clp protease proteolytic subunit (ClpP4), identical to nClpP4 GI:5360593 from (Arabidopsis thaliana) 3463 At5g45410 D2 expressed protein, similar to unknown protein (pir::T05524) 3464 At5g45510 Dm leucine-rich repeat family protein, contains leucine rich repeat (LRR) domains, Pfam:PF00560 3465 At5g45550 D2 mob1/phocein family protein, contains Pfam profile: PF03637 Mob1/phocein family 3466 At5g45630 D1 expressed protein, contains Pfam profile PF04520: Protein of unknown function, DUF584 3467 At5g45640 D2, Dm subtilase family protein, contains Pfam domain, PF00082: Subtilase family; contains Pfam domain, PF02225: protease associated (PA) domain 3468 At5g45680 D1, Dm FK506-binding protein 1 (FKBP13), identical to Probable FKBP-type peptidyl-prolyl cis-trans isomerase 3, chloroplast precursor (Ppiase) (Rotamase) (SP:Q9SCY2) / FK506 binding protein 1 (GI:21535744) (Arabidopsis thaliana); contains Pfam PF00254: peptidyl-prolyl cis-trans isomerase, FKBP-type 3469 At5g45750 D2 Ras-related GTP-binding protein, putative, similar to GTP-binding protein GI:303744 from (Pisum sativum) 3470 At5g45775 D1, D2, Dm 60S ribosomal protein L11 (RPL11D) 3471 At5g45820 Dm CIPK20_PKS18__CBL-interacting protein kinase 20 (CIPK20), identical to CBL-interacting protein kinase 20 (Arabidopsis thaliana) gi:14486384:gb:AAK61493 3472 At5g45890 D2, Dm SAG12__senescence-specific SAG12 protein (SAG12) / cysteine proteinase, putative, identical to senescence-specific protein SAG12 GI:1046373 from (Arabidopsis thaliana) 3473 At5g45920 D2, Dm similar to GDSL-motif lipase/hydrolase family protein [Arabidopsis thaliana] (TAIR:At5g62930.1); similar to OSJNBa0038J17.19 [Oryza sativa (japonica cultivar-group)] (GB:NP_913321.1); contains InterPro domain Lipolytic enzyme, G-D-S-L family (InterPro:IPR001087) 3474 At5g45930 D1, Dm CHLI2_CHL I2__magnesium-chelatase subunit chlI, chloroplast, putative / Mg-protoporphyrin IX chelatase, putative, similar to SP:P161127 from Arabidopsis thaliana, SP:P93162 from Glycine max, SP:O22436 from Nicotiana tabacum; non-consensus AA donor splice site at exon 1, TG acceptor splice site at exon 2 3475 At5g45940 D2 ATNUDT11__MutT/nudix family protein, contains Pfam profile PF00293: NUDIX domain 3476 At5g46120 D1 hypothetical protein 3477 At5g46180 D1, D2, Dm delta-OAT__ornithine aminotransferase, putative / ornithine--oxo-acid aminotransferase, putative, similar to SP:Q92413 Ornithine aminotransferase (EC 2.6.1.13) (Ornithine--oxo-acid aminotransferase) (Aspergillus nidulans) {Emericella nidulans}; contains Pfam profile PF00202: aminotransferase, class III 3478 At5g46250 D2 RNA recognition motif (RRM)-containing protein, contains similarity to RNA-binding protein; contains InterPro entry IPR000504: RNA-binding region RNP-1 (RNA recognition motif) (RRM) 3479 At5g46280 D1, Dm DNA replication licensing factor, putative, similar to SP:Q43704 DNA replication licensing factor MCM3 homolog (Replication origin activator) (ROA protein) {Zea mays}; contains Pfam profile PF00493: MCM2/3/5 family 3480 At5g46290 D1, D2, Dm KAS I__3-oxoacyl-(acyl-carrier-protein) synthase I, identical to Swiss-Prot:P52410 3-oxoacyl- (acyl-carrier-protein) synthase I, chloroplast precursor (EC 2.3.1.41) (Beta-ketoacyl-ACP synthase I) (KAS I) (Arabidopsis thaliana) 3481 At5g46420 D2 16S rRNA processing protein RimM family, contains weak similarity to Swiss-Prot:O74933 UDP-N- acetylglucosamine pyrophosphorylase (Candida albicans); contains Pfam profiles PF01782: 16S rRNA processing protein RimM, PF05239: PRC-barrel domain 3482 At5g46580 D2, Dm pentatricopeptide (PPR) repeat-containing protein, contains similarity to 67kD chloroplastic RNA-binding protein, P67.1 (Raphanus sativus) GI:9755886; contains Pfam profile PF01535: PPR repeat 3483 At5g46710 D2 zinc-binding family protein, similar zinc-binding protein (Pisum sativum) GI:16117799; contains Pfam profile PF04640 : Protein of unknown function, DUF597 3484 At5g46790 D1, D2, Dm expressed protein, similar to unknown protein (pir::T05073) 3485 At5g46800 D2, Dm BOU__mitochondrial carnitine/acyl carrier, putative / a bout de souffle (BOU) / CAC-like protein, identical to SP:Q93XM7 Mitochondrial carnitine/acylcarnitine carrier-like protein (A BOUT DE SOUFFLE) (Carnitine/acylcarnitine translocase-like protein) (CAC-like protein) {Arabidopsis thaliana}; contains Pfam profile: PF00153 mitochondrial carrier protein 3486 At5g47060 Dm senescence-associated protein-related, similar to senescence-associated protein SAG102 (GI:22331931) (Arabidopsis thaliana); 3487 At5g47110 D1 lil3 protein, putative, similar to Lil3 protein (Arabidopsis thaliana) gi:4741966:gb:AAD28780

3488 At5g47120 D2 ATBI-1__Bax inhibitor-1 putative / BI-1 putative, SP:Q9LD45: Bax inhibitor-1 (BI-1) (AtBI-1). (Mouse-ear cress) {Arabidopsis thaliana} 3489 At5g47190 D1, Dm ribosomal protein L19 family protein, similar to plastid ribosomal protein L19 precursor (Spinacia oleracea) gi:7582403:gb:AAF64312 3490 At5g47210 D1, D2, Dm nuclear RNA-binding protein, putative, similar to nuclear RNA binding protein GI:6492264 from (Arabidopsis thaliana) 3491 At5g47240 D2, Dm ATNUDT8__MutT/nudix family protein, similar to SP:P53370 Nucleoside diphosphate-linked moiety X motif 6 {Homo sapiens}; contains Pfam profile PF00293: NUDIX domain 3492 At5g47370 D1, D2, Dm HAT2__homeobox-leucine zipper protein 2 (HAT2) / HD-ZIP protein 2, identical to homeobox- leucine zipper protein HAT2 (HD-ZIP protein 2) (Arabidopsis thaliana) SP:P46601; contains Pfam profiles PF04618: HD-ZIP protein N terminus, PF02183: Homeobox associated leucine zipper, PF00046: Homeobox domain 3493 At5g47390 D2 myb family transcription factor, contains Pfam profile: PF00249 myb-like DNA-binding domain 3494 At5g47435 D2, Dm formyltetrahydrofolate deformylase, putative, similar to formyltetrahydrofolate deformylase (strain PCC 6803- Synechocystis sp.) SWISS-PROT:Q55135 3495 At5g47450 D2, Dm DELTA-TIP3_TIP2;3_AtTIP2;3__major intrinsic family protein / MIP family protein, contains Pfam profile: MIP PF00230 3496 At5g47550 D1, D2, Dm cysteine protease inhibitor, putative / cystatin, putative, similar to SP:P09229 Cysteine proteinase inhibitor-I (Oryzacystatin-I) {Oryza sativa}; contains Pfam profile PF00031: Cystatin domain 3497 At5g47560 D1, D2, Dm ATSDAT_ATTDT__Encodes a tonoplast malate/fumarate transporter. 3498 At5g47570 D2 expressed protein 3499 At5g47610 D1, D2, Dm zinc finger (C3HC4-type RING finger) family protein, contains Pfam profile: PF00097 zinc finger, C3HC4 type (RING finger) 3500 At5g47640 D1, D2, Dm CCAAT-box binding transcription factor subunit B (NF-YB) (HAP3 ) (AHAP3) family (Hap3b), similar to CAAT-box DNA binding protein subunit B (NF-YB) (SP:P25209) (GI:22380) (Zea mays); contains Pfam PF00808 : Histone-like transcription factor (CBF/NF-Y) and archaeal histone; identical to cDNA transcription factor Hap3b (Hap3b) mRNA, partial cds GI:9965734 3501 At5g47650 D1, D2, Dm ATNUDT2__MutT/nudix family protein, similar to Nucleoside diphosphate-linked moiety X motif 6 (Protein GFG) from {Xenopus laevis} SP:P13420, {Homo sapiens} SP:P53370; contains Pfam profile PF00293: NUDIX domain 3502 At5g47700 D1, D2, Dm 60S acidic ribosomal protein P1 (RPP1C) 3503 At5g47770 D1, Dm FPS1__farnesyl pyrophosphate synthetase 1, mitochondrial (FPS1) / FPP synthetase 1 / farnesyl diphosphate synthase 1, identical to SP:Q09152 Farnesyl pyrophosphate synthetase 1, mitochondrial precursor (FPP synthetase 1) (FPS 1) (Farnesyl diphosphate synthetase 1) (Includes: Dimethylallyltransferase (EC 2.5.1.1); Geranyltranstransferase (EC 2.5.1.10)) {Arabidopsis thaliana} 3504 At5g47780 D2 glycosyl transferase family 8 protein, contains Pfam profile: PF01501 glycosyl transferase family 8; strong similarity to unknown protein (emb:CAB71043.1) 3505 At5g47840 D1 adenylate kinase, chloroplast, putative / ATP-AMP transphosphorylase, putative, similar to SP:P43188 Adenylate kinase, chloroplast (EC 2.7.4.3) (ATP-AMP transphosphorylase) {Zea mays}; contains Pfam profile PF00406: Adenylate kinase 3506 At5g47860 Dm expressed protein 3507 At5g47870 D1, Dm expressed protein 3508 At5g47890 D2 NADH-ubiquinone oxidoreductase B8 subunit, putative, similar to SP:O43678 NADH-ubiquinone oxidoreductase B8 subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-B8) (CI-B8) {Homo sapiens}; contains Pfam profile PF05047: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain 3509 At5g47930 D1, D2, Dm 40S ribosomal protein S27 (RPS27D) 3510 At5g48150 D2 PAT1__phytochrome A signal transduction 1 (PAT1) 3511 At5g48170 D2, Dm F-box family protein, contains Pfam PF00646: F-box domain; similar to unknown protein (pir::T09884); 3512 At5g48220 D1, Dm indole-3-glycerol phosphate synthase, putative, similar to SP:P49572 3513 At5g48230 D2, Dm EMB1276__acetyl-CoA C-acyltransferase, putative / 3-ketoacyl-CoA thiolase, putative, strong similarity to Acetoacetyl-coenzyme A thiolase (E.C. 2.3.1.9) (Raphanus sativus) GI:1542941; contains InterPro accession IPR002155: Thiolase 3514 At5g48270 D1, D2, Dm expressed protein 3515 At5g48370 Dm thioesterase family protein, similar to SP:Q9R0X4 48 kDa acyl-CoA thioester hydrolase, mitochondrial precursor (EC 3.1.2.-) {Mus musculus}; contains Pfam profile PF03061: thioesterase family protein 3516 At5g48450 D2 SKS3__multi-copper oxidase type I family protein, contains Pfam profile: PF00394 Multicopper oxidase; also similar to l-ascorbate oxidase and pollen-specific protein 3517 At5g48470 D1, D2, Dm expressed protein 3518 At5g48490 D1, Dm protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 3519 At5g48540 D2 33 kDa secretory protein-related, contains Pfam PF01657: Domain of unknown function, duplicated in 33 KDa secretory proteins 3520 At5g48580 Dm FKBP15-2__FK506-binding protein 2-2 (FKBP15-2) / immunophilin / peptidyl-prolyl cis-trans isomerase / rotamase, identical to SP:Q38936: FK506-binding protein 2-2 precursor (EC 5.2.1.8); 3521 At5g48760 D1, D2, Dm 60S ribosomal protein L13A (RPL13aD) 3522 At5g48810 D1, D2, Dm ATB5-B_B5 #3__cytochrome b5, identical to cytochrome b5 (Arabidopsis thaliana) GI:4240122; strong similarity to Cytochrome B5 SP:P49098 from (Nicotiana tabacum) 3523 At5g48830 D2, Dm expressed protein 3524 At5g48930 D2, Dm transferase family protein, similar to anthranilate N-hydroxycinnamoyl/benzoyltransferase from Dianthus caryophyllus (GI:3288180, GI:2239091); contains Pfam profile PF02458 transferase family 3525 At5g48940 D2 leucine-rich repeat transmembrane protein kinase, putative 3526 At5g49020 Dm protein arginine N-methyltransferase family protein, similar to protein arginine methyltransferase (Mus musculus) GI:5257221 3527 At5g49030 D1, D2, Dm tRNA synthetase class I (I, L, M and V) family protein, similar to SP:P41972 Isoleucyl-tRNA synthetase (EC 6.1.1.5) (Isoleucine--tRNA ligase) (IleRS) {Staphylococcus aureus}; contains Pfam profile PF00133: tRNA synthetases class I (I, L, M and V) 3528 At5g49100 D1, Dm expressed protein 3529 At5g49120 Dm senescence-associated protein-related, similar to senescence-associated protein SAG102 (GI:22331931) (Arabidopsis thaliana); 3530 At5g49280 Dm hydroxyproline-rich glycoprotein family protein, contains proline-rich extensin domains, INTERPRO:IPR002965 3531 At5g49360 D2, Dm BXL1_ATBXL1__glycosyl hydrolase family 3 protein 3532 At5g49480 D1, Dm ATCP1_ACP1__sodium-inducible calcium-binding protein (ACP1) / sodium-responsive calcium- binding protein (ACP1), identical to NaCl-inducible Ca2+-binding protein GI:2352828 from (Arabidopsis thaliana) 3533 At5g49650 Dm xylulose kinase, putative, similar to D-xylulokinase (Pichia stipitis) gi:8100400:gb:AAF72328

3534 At5g49660 Dm leucine-rich repeat transmembrane protein kinase, putative, contains leucine rich repeat (LRR) domains, Pfam:PF00560; contains protein kinase domain, Pfam:PF00069 3535 At5g49720 D1 KOR1_DEC_KOR_OR16PEP_RSW2__endo-1,4-beta-glucanase KORRIGAN (KOR) / cellulase (OR16pep), identical to endo-1,4-beta-D-glucanase KORRIGAN (Arabidopsis thaliana) GI:3978258; similar to endo-1,4-beta-D-glucanase; cellulase GI:5689613 from (Brassica napus); identical to cDNA cellulase (OR16pep) GI:1022806 3536 At5g49730 D1, D2, Dm ATFRO6__ferric reductase-like transmembrane component family protein, similar to ferric- chelate reductase (FRO1) (Pisum sativum) GI:15341529; contains Pfam profile PF01794: Ferric reductase like transmembrane componenent 3537 At5g49800 Dm expressed protein 3538 At5g49990 D1, Dm xanthine/uracil permease family protein, similar to permease 1 (Zea mays) GI:7844006; contains Pfam profile: PF00860 Xanthine/uracil permeases family 3539 At5g50000 Dm protein kinase, putative, similar to protein kinase ATMRK1 (Arabidopsis thaliana) gi:2351097:dbj:BAA22079 3540 At5g50100 D1, D2, Dm expressed protein, contains Pfam domain PF04134: Protein of unknown function, DUF393 3541 At5g50130 D2, Dm short-chain dehydrogenase/reductase (SDR) family protein, contains INTERPRO family IPR002198 Short-chain dehydrogenase/reductase (SDR) superfamily 3542 At5g50160 D1, D2, Dm ATFRO8__ferric reductase-like transmembrane component family protein, contains Pfam profile PF01794: Ferric reductase like transmembrane component 3543 At5g50280 D2 EMB1006__pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat 3544 At5g50360 D2 expressed protein 3545 At5g50420 D2, Dm expressed protein, strong similarity to unknown protein (gb:AAD50008.1) 3546 At5g50580 Dm SAE1B_AT-SAE1-2__SUMO activating enzyme, putative, nearly identical to SUMO activating enzyme 1b (Arabidopsis thaliana) GI:22652852; nearly identical to At5g50680; contains Pfam profile PF00899: ThiF family 3547 At5g50720 D1, Dm ATHVA22E__ABA-responsive protein (HVA22e), identical to AtHVA22e (Arabidopsis thaliana) GI:11225589 3548 At5g50730 D1, D2, Dm expressed protein, ; expression supported by MPSS 3549 At5g50740 D1, D2, Dm copper chaperone (CCH)-related, low similarity to copper homeostasis factor (GI:3168840)(PMID: 9701579); similar to farnesylated protein ATFP3 (GI:4097547); contains Pfam profile PF00403: Heavy-metal-associated domain 3550 At5g50750 D2, Dm RGP4__reversibly glycosylated polypeptide, putative, strong similarity to reversibly glycosylated polypeptide-1 (AtRGP) (Arabidopsis thaliana) GI:2317729; contains Pfam profile PF03214: Reversibly glycosylated polypeptide 3551 At5g50920 D2, Dm ATHSP93-V_CLPC_HSP93-V_CLPC__Similar to ATP-dependent Clp protease ATP-binding subunit / ClpC, almost identical to ClpC GI:2921158 from (Arabidopsis thaliana); contains Pfam profile PF02861: Clp amino terminal domain; contains Pfam profile PF00004: ATPase, AAA family; contains Pfam profile PF02151: UvrB/uvrC motif. Involved in protein import into the chloroplast. May provide ATP source that drives the TIC translocation machinery, 3552 At5g50950 D2, Dm fumarate hydratase, putative / fumarase, putative, similar to SP:P55250 Fumarate hydratase, mitochondrial precursor (EC 4.2.1.2) (Fumarase) {Rhizopus oryzae}; contains Pfam profile PF00206: Lyase 3553 At5g50960 Dm nucleotide-binding family protein, similar to Nucleotide-binding protein 1 (NBP 1) (SP:Q9R060) (Mus musculus); contains Pfam PF00991 : ParA family ATPase 3554 At5g51010 D1, Dm rubredoxin family protein, similar to SP:P04170 Rubredoxin (Rd) {Desulfovibrio desulfuricans}; contains Pfam profile PF00301: Rubredoxin 3555 At5g51020 D2 expressed protein, similar to unknown protein (pir::S76207) 3556 At5g51040 Dm expressed protein 3557 At5g51070 D1, D2, Dm ERD1_CLPD__ATP-dependent Clp protease ATP-binding subunit (ClpD), (ERD1), SAG15/ERD1; identical to ERD1 protein GI:497629, SP:P42762 from (Arabidopsis thaliana); contains Pfam profile PF02861: Clp amino terminal domain 3558 At5g51105 D2 expressed protein 3559 At5g51120 Dm polyadenylate-binding protein, putative / PABP, putative, contains similarity to poly(A)- binding protein II (Mus musculus) GI:2351846; contains InterPro entry IPR000504: RNA-binding region RNP-1 (RNA recognition motif) (RRM) 3560 At5g51270 Dm protein kinase family protein, contains Pfam profile: PF00069 Eukaryotic protein kinase domain

3561 At5g51290 D1, Dm ceramide kinase-related, contains weak similarity to ceramide kinases (GI:21624342) (Mus musculus) 3562 At5g51520 D1, D2, Dm invertase/pectin methylesterase inhibitor family protein, low similarity to pectinesterase from Lycopersicon esculentum SP:Q43143, Arabidopsis thaliana SP:Q42534; contains Pfam profile PF04043: Plant invertase/pectin methylesterase inhibitor 3563 At5g51560 D2 leucine-rich repeat transmembrane protein kinase, putative 3564 At5g51690 Dm ACS12__1-aminocyclopropane-1-carboxylate synthase, putative / ACC synthase, putative, similar to ACC synthases from Solanum tuberosum (GI:520958), Triticum aestivum (GI:1173638) 3565 At5g51830 D1, Dm pfkB-type carbohydrate kinase family protein, contains Pfam profile: PF00294 pfkB family carbohydrate kinase 3566 At5g51890 D1, Dm similar to peroxidase 64 (PER64) (P64) (PRXR4) [Arabidopsis thaliana] (TAIR:At5g42180.1); similar to cationic peroxidase [Zinnia elegans] (GB:BAD93164.1); contains InterPro domain Haem peroxidase (InterPro:IPR002016); contains InterPro domain Plant peroxidase (InterPro:IPR000823) 3567 At5g51970 D2 sorbitol dehydrogenase, putative / L-iditol 2-dehydrogenase, putative, similar to NAD- dependent sorbitol dehydrogenase from Malus x domestica (gi:4519539) 3568 At5g51990 D2 CBF4__encodes a member of the DREB subfamily A-1 of ERF/AP2 transcription factor family (CBF4). The protein contains one AP2 domain. There are six members in this subfamily, including CBF1, CBF2, and CBF3. This gene is involved in response to drought stress and abscisic acid treatment, but not to low temperature. 3569 At5g52100 D1, D2, Dm dihydrodipicolinate reductase family protein, weak similarity to dihydrodipicolinate reductase (Corynebacterium glutamicum) GI:311768; contains Pfam profiles PF01113: Dihydrodipicolinate reductase N-terminus, PF05173: Dihydrodipicolinate reductase C-terminus 3570 At5g52190 D1, D2, Dm sugar isomerase (SIS) domain-containing protein, similar to 6-phospho-3-hexuloisomerase (Mycobacterium gastri) GI:6899860; contains Pfam profile PF01380: SIS domain 3571 At5g52240 D1, D2, Dm ATMP1_MSBP1_ATMP1__cytochrome b5 domain-containing protein, similar to SP:P70580 Membrane associated progesterone receptor component 1 {Rattus norvegicus}; contains Pfam profile PF00173: Heme/Steroid binding domain 3572 At5g52300 D1, D2, Dm RD29B_LTI65__low-temperature-responsive 65 kD protein (LTI65) / desiccation-responsive protein 29B (RD29B), nearly identical to SP:Q04980 Low-temperature-induced 65 kDa protein (Desiccation-responsive protein 29B) {Arabidopsis thaliana} 3573 At5g52310 D2, Dm LTI78_RD29A_COR78_LTI140_LTI78_RD29A__low-temperature-responsive protein 78 (LTI78) / desiccation-responsive protein 29A (RD29A) 3574 At5g52390 D1 photoassimilate-responsive protein, putative, similar to PIR:S62698 photoassimilate-responsive protein precursor (clone PAR-1a) - common tobacco 3575 At5g52420 D2 expressed protein 3576 At5g52450 Dm MATE efflux protein-related, strong similarity to unknown protein (pir::T02324); contains Pfam profile PF01554 Uncharacterized membrane protein family 3577 At5g52470 D2 FIB1_ATFBR1_ATFIB1_FBR1_SKIP7_U60.1F__fibrillarin 1 (FBR1) (FIB1) (SKIP7), identical to fibrillarin 1 GI:9965653 from (Arabidopsis thaliana); C-terminus identical to SKP1 interacting partner 7 GI:10716959 from (Arabidopsis thaliana); contains Pfam domain PF01269: Fibrillarin

3578 At5g52630 D2 pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat 3579 At5g52640 Dm HSP81-1_ATHS83_HSP81.1_HSP83__heat shock protein 81-1 (HSP81-1) / heat shock protein 83 (HSP83), nearly identical to SP:P27323 Heat shock protein 81-1 (HSP81-1) (Heat shock protein 83) {Arabidopsis thaliana}; contains Pfam profiles PF02518: ATPase, histidine kinase-, DNA gyrase B-, and HSP90-like domain protein, PF00183: Hsp90 protein 3580 At5g52660 Dm myb family transcription factor, contains PFAM profile: PF00249 myb-like DNA-binding domain 3581 At5g52750 Dm heavy-metal-associated domain-containing protein, Pfam profile PF00403: Heavy-metal-associated domain 3582 At5g52810 Dm ornithine cyclodeaminase/mu-crystallin family protein, contains Pfam PF02423: Ornithine cyclodeaminase/mu-crystallin family 3583 At5g53120 D1 SPDS3_SPMS__spermidine synthase, putative / putrescine aminopropyltransferase, putative, similar to SP:O82147 Spermidine synthase (EC 2.5.1.16) (Putrescine aminopropyltransferase) (SPDSY) {Coffea arabica}; contains Pfam profile PF01564: Spermine/spermidine synthase 3584 At5g53150 Dm similar to DNAJ heat shock N-terminal domain-containing protein [Arabidopsis thaliana] (TAIR:At2g25560.1); similar to OSJNBa0053B21.9 [Oryza sativa (japonica cultivar-group)] (GB:XP_472289.1); contains InterPro domain Heat shock protein DnaJ (InterPro:IPR003095); contains InterPro domain Heat shock protein DnaJ, N-terminal (InterPro:IPR001623) 3585 At5g53160 D1, D2, Dm expressed protein, similar to unknown protein (pir::T02893) 3586 At5g53190 Dm nodulin MtN3 family protein, similar to MtN3 GI:1619602 (root nodule development) from (Medicago truncatula) 3587 At5g53300 D1, D2, Dm UBC10__ubiquitin-conjugating enzyme 10 (UBC10), E2; identical to gi:297877, SP:P35133 3588 At5g53350 D2, Dm CLPX__ATP-dependent Clp protease ATP-binding subunit ClpX1 (CLPX), identical to CLP protease regulatory subunit CLPX GI:2674203 from (Arabidopsis thaliana) 3589 At5g53400 D2 nuclear movement family protein, contains Pfam profile: PF03593 nuclear movement protein 3590 At5g53440 Dm expressed protein 3591 At5g53450 D1, Dm ORG1__protein kinase family protein, contains protein kinase domain, Pfam:PF00069 3592 At5g53490 D1, D2, Dm thylakoid lumenal 17.4 kDa protein, chloroplast, identical to SP:P81760 Thylakoid lumenal 17.4 kDa protein, chloroplast precursor (P17.4) {Arabidopsis thaliana} 3593 At5g53570 D2, Dm RabGAP/TBC domain-containing protein, similar to GTPase activating protein (Yarrowia lipolytica) GI:2370595; contains Pfam profile PF00566: TBC domain 3594 At5g53640 Dm F-box family protein, contains F-box domain Pfam:PF00646 3595 At5g53650 D1, Dm expressed protein 3596 At5g53730 Dm harpin-induced family protein / HIN1 family protein / harpin-responsive family protein, similar to harpin-induced protein hin1 ( GI:1619321) (Nicotiana tabacum); 3597 At5g53800 Dm expressed protein 3598 At5g53860 D2, Dm EMB2737__expressed protein 3599 At5g53870 D1, D2, Dm plastocyanin-like domain-containing protein, contains similarity to SP:Q02917 Early nodulin 55-2 precursor {Glycine max}; PF02298: Plastocyanin-like domain 3600 At5g53950 D1, Dm ANAC098_CUC2__no apical meristem (NAM) family protein, identical to no apical meristem protein CUC2 (GI:1944132) (Arabidopsis thaliana); contains Pfam PF02365: No apical meristem (NAM) domain; 3601 At5g53970 D2 aminotransferase, putative, similar to nicotianamine aminotransferase from Hordeum vulgare (GI:6498122, GI:6469087); contains Pfam profile PF00155 aminotransferase, classes I and II 3602 At5g54145 Dm expressed protein 3603 At5g54160 D1, D2, Dm ATOMT1_OMT1__quercetin 3-O-methyltransferase 1 / flavonol 3-O-methyltransferase 1 / caffeic acid/5-hydroxyferulic acid O-methyltransferase (OMT1), identical to O-methyltransferase 1 (Arabidopsis thaliana)(GI:2781394), SP:Q9FK25 Quercetin 3-O-methyltransferase 1 (EC 2.1.1.76) (AtOMT1) (Flavonol 3- O-methyltransferase 1) (Caffeic acid/5-hydroxyferulic acid O- methyltransferase) {Arabidopsis thaliana} 3604 At5g54190 D2, Dm PORA__protochlorophyllide reductase A, chloroplast / PCR A / NADPH-protochlorophyllide oxidoreductase A (PORA), identical to SP:Q42536 protochlorophyllide reductase A, chloroplast precursor (EC 1.3.1.33) (PCR A) (NADPH-protochlorophyllide oxidoreductase A) (POR A) (Arabidopsis thaliana) 3605 At5g54230 D2, Dm MYB49__myb family transcription factor (MYB49), contains Pfam profile: PF00249 myb-like DNA- binding domain 3606 At5g54390 D2, Dm AHL_ATAHL__inositol monophosphatase family protein, similar to SP:Q42546 3`(2`),5`- bisphosphate nucleotidase (EC 3.1.3.7) {Arabidopsis thaliana}; contains Pfam profile PF00459: Inositol monophosphatase family; supporting cDNA gi:1354509:gb:U55205.1:ATU55205 3607 At5g54430 D1, Dm universal stress protein (USP) family protein, low similarity to early nodulin ENOD18 (Vicia faba) GI:11602747, ER6 protein (Lycopersicon esculentum) GI:5669654; contains Pfam profile PF00582: universal stress protein family 3608 At5g54500 Dm FQR1__quinone reductase, putative, similar to 1,4-benzoquinone reductase (Phanerochaete chrysosporium)(GI:4454993); contains flavodoxin domain PF00258 3609 At5g54580 D1, Dm RNA recognition motif (RRM)-containing protein, low similarity to RNA-binding protein RGP-3 (Nicotiana sylvestris) GI:1009363; contains InterPro entry IPR000504: RNA-binding region RNP-1 (RNA recognition motif) (RRM) 3610 At5g54600 D1, Dm 50S ribosomal protein L24, chloroplast (CL24), identical to SP:P92959 50S ribosomal protein L24, chloroplast precursor {Arabidopsis thaliana} 3611 At5g54630 Dm zinc finger protein-related, contains Prosite:PS00028 Zinc finger, C2H2 type, domain 3612 At5g54740 D2 protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, similar to 2S seed storage proteins from Arabidosis thaliana: SP:P15457, SP:P15459, SP:P15458, SP:P15460 contains Pfam profile PF00234 Protease inhibitor/seed storage/LTP family 3613 At5g54760 D1, D2, Dm eukaryotic translation initiation factor SUI1, putative, similar to SP:P32911 Protein translation factor SUI1 {Saccharomyces cerevisiae}; contains Pfam profile PF01253: Translation initiation factor SUI1 3614 At5g54770 Dm THI1_TZ__thiazole biosynthetic enzyme, chloroplast (ARA6) (THI1) (THI4), identical to SP:Q38814 Thiazole biosynthetic enzyme, chloroplast precursor (ARA6) {Arabidopsis thaliana} 3615 At5g54870 D2, Dm expressed protein, strong similarity to unknown protein (pir::T04825) 3616 At5g54940 D1, Dm eukaryotic translation initiation factor SUI1, putative, similar to SP:P32911 Protein translation factor SUI1 {Saccharomyces cerevisiae}; contains Pfam profile PF01253: Translation initiation factor SUI1 3617 At5g54960 D1 PDC2__pyruvate decarboxylase, putative, strong similarity to pyruvate decarboxylase 1 (Vitis vinifera) GI:10732644; contains InterPro entry IPR000399: Pyruvate decarboxylase 3618 At5g55050 D1, Dm GDSL-motif lipase/hydrolase family protein, similar to family II lipases EXL3 GI:15054386, EXL1 GI:15054382, EXL2 GI:15054384 from (Arabidopsis thaliana); contains Pfam profile PF00657: GDSL-like Lipase/Acylhydrolase 3619 At5g55070 Dm 2-oxoacid dehydrogenase family protein, similar to SP:Q01205 Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (EC 2.3.1.61) {Rattus norvegicus}; contains Pfam profiles PF00198: 2-oxo acid dehydrogenases acyltransferase (catalytic domain), PF00364: Biotin-requiring enzyme 3620 At5g55120 D1, D2, Dm expressed protein, strong similarity to unknown protein (pir::T04808) 3621 At5g55140 Dm ribosomal protein L30 family protein, contains similarity to 50S ribosomal protein L30 3622 At5g55180 Dm glycosyl hydrolase family 17 protein, similar to elicitor inducible chitinase Nt-SubE76 GI:11071974 from (Nicotiana tabacum) 3623 At5g55220 D1, D2, Dm trigger factor type chaperone family protein, contains Pfam profiles PF05697: Bacterial trigger factor protein (TF), PF05698: Bacterial trigger factor protein (TF) C-terminus, PF00254: peptidyl-prolyl cis-trans isomerase, FKBP-type 3624 At5g55230 D2 ATMAP65-1__Binds and bundles microtubules. Plays a role in stabilizing anti-parallel microtubules in the central spindle at anaphase to early cytokinesis but is not essential at the midline of the phragmoplast at later stages. The timing with which the MAP65-1 was targeted to the spindle appears to be regulated by a phosphorylation sensitive switch. Enhances microtubule polymerization, promotes nucleation and stabilizes microtubules against cold treatment and dilution. 3625 At5g55280 D1, D2, Dm FTSZ1-1_ATFTSZ1-1_CPFTSZ__cell division protein FtsZ, chloroplast, putative (FTSZ), identical to SP:Q42545 Cell division protein ftsZ homolog, chloroplast precursor {Arabidopsis thaliana}; similar to FtsZ1 (Tagetes erecta) GI:8896066; contains Pfam profiles PF00091: Tubulin/FtsZ family, GTPase domain, PF03953: Tubulin/FtsZ family, C-terminal domain 3626 At5g55510 D2, Dm similar to mitochondrial import inner membrane translocase subunit Tim17/Tim22/Tim23 family protein [Arabidopsis thaliana] (TAIR:At4g26670.1); similar to Unknown protein [Oryza sativa (japonica cultivar-group)] (GB:AAN59775.1); contains InterPro domain Mitochondrial import inner membrane translocase, subunit Tim17/22 (InterPro:IPR003397) 3627 At5g55530 Dm C2 domain-containing protein, low similarity to cold-regulated gene SRC2 (Glycine max) GI:2055230; contains Pfam profile PF00168: C2 domain 3628 At5g55620 D1, Dm expressed protein, similar to unknown protein (gb:AAF04428.1) 3629 At5g55730 D1, D2, Dm FLA1__fasciclin-like arabinogalactan-protein (FLA1), identical to gi:13377776::AAK20857:13377775:gb:AF333970 3630 At5g55875 Dm transposable element gene 3631 At5g55920 D2 nucleolar protein, putative, similar to SP:P46087 Proliferating-cell nucleolar antigen p120 (Proliferation-associated nucleolar protein p120) {Homo sapiens}, SP:P40991 Nucleolar protein NOP2 {Saccharomyces cerevisiae}; contains Pfam profile PF01189: NOL1/NOP2/sun family 3632 At5g56000 D1, D2, Dm heat shock protein 81-4 (HSP81-4), nearly identical to heat shock protein hsp81.4 (Arabidopsis thaliana) GI:1906828; contains Pfam profiles PF02518: ATPase, histidine kinase-, DNA gyrase B- , and HSP90-like domain protein, PF00183: Hsp90 protein 3633 At5g56010 D1, Dm HSP81-3__heat shock protein, putative, strong similarity to SP:P55737 Heat shock protein 81-2 (HSP81-2) {Arabidopsis thaliana}; contains Pfam profiles PF02518: ATPase, histidine kinase-, DNA gyrase B-, and HSP90-like domain protein, PF00183: Hsp90 protein 3634 At5g56030 D1, D2, Dm HSP81-2__heat shock protein 81-2 (HSP81-2), nearly identical to SP:P55737 Heat shock protein 81-2 (HSP81-2) {Arabidopsis thaliana} 3635 At5g56150 D2, Dm ubiquitin-conjugating enzyme, putative, strong similarity to ubiquitin-conjugating enzyme UBC2 (Mesembryanthemum crystallinum) GI:5762457, UBC4 (Pisum sativum) GI:456568; contains Pfam profile PF00179: Ubiquitin-conjugating enzyme 3636 At5g56160 Dm SEC14 cytosolic factor family protein / phosphoglyceride transfer family protein, similar to similar to phosphatidylinositol transfer-like protein IV (GI:14486707) (Lotus japonicus) and SEC14 cytosolic factor (SP:P45816) (Candida lipolytica) 3637 At5g56170 D2 expressed protein, contains similarity to GPI-anchored protein 3638 At5g56270 D2, Dm WRKY2_WRKY23__WRKY family transcription factor 3639 At5g56600 D2, Dm PRF3_PFN3__profilin 5 (PRO5) (PRF3), identical to SP:Q9FE63 Profilin 5 {Arabidopsis thaliana}

3640 At5g56670 D1, D2, Dm 40S ribosomal protein S30 (RPS30C) 3641 At5g56680 D2 EMB2755__asparaginyl-tRNA synthetase 1, cytoplasmic / asparagine-tRNA ligase 1 (SYNC1), identical to SP:Q9SW96 3642 At5g56710 D1, D2, Dm 60S ribosomal protein L31 (RPL31C) 3643 At5g56760 D2 AtSerat1;1_SAT-52__serine O-acetyltransferase (SAT-52), identical to GI:905391 3644 At5g56950 D2, Dm nucleosome assembly protein (NAP), putative, similar to nucleosome assembly protein 1 (Glycine max) GI:1161252; contains Pfam profile PF00956: Nucleosome assembly protein (NAP) 3645 At5g57020 D2 NMT1_ATNMT1__myristoyl-CoA:protein N-myristoyltransferase 1 (NMT1), identical to N- myristoyltransferase 1 (NMT1) (Arabidopsis thaliana) GI:7339834 3646 At5g57040 D1, D2, Dm lactoylglutathione lyase family protein / glyoxalase I family protein, contains Pfam PF00903: glyoxalase family protein 3647 At5g57050 D1, D2, Dm ABI2__protein phosphatase 2C ABI2 / PP2C ABI2 / abscisic acid-insensitive 2 (ABI2), identical to SP:O04719 Protein phosphatase 2C ABI2 (EC 3.1.3.16) (PP2C) (Abscisic acid- insensitive 2) {Arabidopsis thaliana} 3648 At5g57120 D2 expressed protein, weak similarity to SP:Q14978 Nucleolar phosphoprotein p130 {Homo sapiens} 3649 At5g57170 D1, Dm macrophage migration inhibitory factor family protein / MIF family protein, contains Pfam profile: PF01187 Macrophage migration inhibitory factor(MIF) 3650 At5g57180 D2 CIA2__expressed protein, ; supporting cDNA gi:13991645:gb:AF359387.1:AF359387 3651 At5g57280 D2 expressed protein 3652 At5g57290 D1, D2, Dm 60S acidic ribosomal protein P3 (RPP3B) 3653 At5g57320 D1, D2, Dm villin, putative, similar to villin 2 (VLN2) (Arabidopsis thaliana) GI:3415115, villin 3 (VLN3) (Arabidopsis thaliana) GI:3415117; contains Pfam profiles PF00626: Gelsolin repeat, PF02209: Villin headpiece domain 3654 At5g57350 D1, D2, Dm AHA3__ATPase 3, plasma membrane-type / proton pump 3, nearly identical to SP:P20431 ATPase 3, plasma membrane-type (EC 3.6.3.6) (Proton pump 3) {Arabidopsis thaliana}; contains InterPro accession IPR001757: ATPase, E1-E2 type 3655 At5g57480 D1, D2, Dm AAA-type ATPase family protein, contains Pfam profile: PF00004 ATPase family 3656 At5g57490 D1, D2, Dm porin, putative, similar to 36kDA porin II (Solanum tuberosum) GI:515360; contains Pfam profile PF01459: Eukaryotic porin 3657 At5g57760 D1, Dm expressed protein 3658 At5g57800 D2 WAX2_FLP1_YRE__CER1 protein, putative (WAX2), similar to maize glossy1 homolog GI:2213643 from (Oryza sativa); contains Pfam profile PF01598: Sterol desaturase 3659 At5g57900 D1, D2, Dm SKIP1__SKP1/ASK1 interacting partner 1 (SKIP1) / SCF (Skp1-cullin-F-box) ubiquitin ligase, identical to SKP1 interacting partner 1 GI:10716947 from (Arabidopsis thaliana), PMID:11387208

3660 At5g57910 Dm expressed protein, similar to unknown protein (emb:CAB79781.1) 3661 At5g57930 Dm APO2_EMB1629__expressed protein 3662 At5g57990 D2 UBP23__ubiquitin-specific protease 23, putative (UBP23), identical to GI:11993486 3663 At5g58070 D1, D2, Dm lipocalin, putative, similar to temperature stress-induced lipocalin (Triticum aestivum) GI:18650668 3664 At5g58090 D2, Dm glycosyl hydrolase family 17 protein, similar to 3-glucanase GI:18483232 from (Sorghum bicolor) 3665 At5g58110 D1, Dm expressed protein, predicted proteins, Homo sapiens and Drosophila melanogaster 3666 At5g58140 D1, D2, Dm PHOT2_NPL1__protein kinase family protein / non phototropic hypocotyl 1-like protein (NPL1), contains Pfam domains, PF00069: Protein kinase domain and PF00785: PAC motif; similar to SP:O48963 Nonphototropic hypocotyl protein 1 (Phototropin) (Mouse-ear cress) {Arabidopsis thaliana}; identical to cDNA non phototropic hypocotyl 1-like (NPL1) GI:5391441 3667 At5g58180 D1 ATYKT62_YKT62__SNARE protein-related, similar to SNARE protein Ykt6 (Homo sapiens) GI:2507637

3668 At5g58200 D1, D2, Dm expressed protein 3669 At5g58250 D1, D2, Dm expressed protein 3670 At5g58420 D1, D2, Dm 40S ribosomal protein S4 (RPS4D), ribosomal protein S4, Arabidopsis thaliana, PIR:T48480 3671 At5g58490 D1 cinnamoyl-CoA reductase family, similar to cinnamoyl-CoA reductase from Pinus taeda (GI:17978649), Eucalyptus gunnii (GI:2058311) 3672 At5g58500 D1, D2, Dm expressed protein, contains Pfam profile PF04852: Protein of unknown function (DUF640) 3673 At5g58670 D1, Dm ATPLC1_ATPLC_PLC1__phosphoinositide-specific phospholipase C (PLC1), identical to phosphoinositide specific phospholipase C (Arabidopsis thaliana) GI:902923 3674 At5g58770 D1, D2, Dm dehydrodolichyl diphosphate synthase, putative / DEDOL-PP synthase, putative, similar to GI:796076 3675 At5g58900 D2 myb family transcription factor, contains Pfam profile: PF00249 myb-like DNA-binding domain 3676 At5g58950 Dm protein kinase family protein, concontains protein kinase domain, Pfam:PF00069 3677 At5g59010 D2, Dm protein kinase-related, low similarity to serine/threonine/tyrosine-specific protein kinase APK1, Arabidopsis thaliana, SP:Q06548 PIR:S28615; contains Pfam profile: PF00069 Eukaryotic protein kinase domain 3678 At5g59080 D1, Dm expressed protein 3679 At5g59140 D2 SKP1 family protein, similar to elongin C, Drosophila melanogaster, GI:2780365 PIR:JC5794; contains Pfam profile PF01466: Skp1 family, dimerisation domain 3680 At5g59220 D1, D2, Dm protein phosphatase 2C, putative / PP2C, putative, ABA induced protein phosphatase 2C, Fagus sylvatica, EMBL:FSY277743 3681 At5g59240 D2, Dm 40S ribosomal protein S8 (RPS8B), 40S ribosomal protein S8, Prunus armeniaca, EMBL:AF071889 3682 At5g59310 D1, D2, Dm LTP4__lipid transfer protein 4 (LTP4), identical to lipid transfer protein 4 from Arabidopsis thaliana (gi:8571923); contains Pfam protease inhibitor/seed storage/LTP family domain PF00234

3683 At5g59320 D1, D2, Dm LTP3__lipid transfer protein 3 (LTP3), identical to lipid transfer protein 3 from Arabidopsis thaliana (gi:8571921); contains Pfam protease inhibitor/seed storage/LTP family domain PF00234 3684 At5g59490 Dm haloacid dehalogenase-like hydrolase family protein, low similarity to SP:P53078 SSM1 protein {Saccharomyces cerevisiae}; contains InterPro accession IPR005834: Haloacid dehalogenase-like hydrolase 3685 At5g59500 D1, Dm expressed protein 3686 At5g59613 D1 expressed protein 3687 At5g59690 D2 histone H4, identical to histone H4 from Lycopersicon esculentum GI:297150, Lolium temulentum SP:P02308, Acropora formosa GI:455652, Citrus jambhiri GI:16797797 3688 At5g59740 Dm UDP-galactose/UDP-glucose transporter-related, weak similarity to UDP-galactose/UDP-glucose transporter (Arabidopsis thaliana) GI:22651763 3689 At5g59780 D2 MYB59__myb family transcription factor (MYB59), contains PFAM profile: myb DNA binding domain PF00249 3690 At5g59820 D1, Dm RHL41_ZAT12__zinc finger (C2H2 type) family protein (ZAT12), identical to zinc finger protein ZAT12 (Arabidopsis thaliana) gi:1418325:emb:CAA67232 3691 At5g59850 D1, D2, Dm 40S ribosomal protein S15A (RPS15aF), cytoplasmic ribosomal protein S15a, Arabidopsis thaliana, EMBL:ATAF1412 3692 At5g59870 D1, Dm histone H2A, putative, similar to histone H2A Petroselinum crispum SP:P19177, Lycopersicon esculentum SP:P25469, Zea mays SP:P40280; contains Pfam profile PF00125 Core histone H2A/H2B/H3/H4 3693 At5g59880 D1, D2, Dm ADF3__actin-depolymerizing factor 3 (ADF3), identical to SP:Q9ZSK4 Actin-depolymerizing factor 3 (ADF 3) (AtADF3) {Arabidopsis thaliana} 3694 At5g59890 D2, Dm ADF4__actin-depolymerizing factor 4 (ADF4), identical to SP:Q9ZSK3 Actin-depolymerizing factor 4 (ADF-4) (AtADF4) {Arabidopsis thaliana} 3695 At5g59960 Dm expressed protein 3696 At5g59990 D2 expressed protein, ; expression supported by MPSS 3697 At5g60390 D2 elongation factor 1-alpha / EF-1-alpha, identical to SWISS-PROT:P13905 elongation factor 1- alpha (EF-1-alpha) (Arabidopsis thaliana) 3698 At5g60510 D2, Dm undecaprenyl pyrophosphate synthetase family protein / UPP synthetase family protein, contains putative undecaprenyl diphosphate synthase domain (PF01255); similar to S. cerevisiae dehydrodolichyl diphosphate synthetase (DEDOL-PP synthase)(Rer2)(SP:P35196), a cis- prenyltransferase 3699 At5g60530 D1, D2, Dm late embryogenesis abundant protein-related / LEA protein-related, similar to late embryogenesis abundant protein (Picea glauca) GI:1350543 3700 At5g60580 D1 zinc finger (C3HC4-type RING finger) family protein, contains Pfam profile PF00097: Zinc finger, C3HC4 type (RING finger) 3701 At5g60600 D1, D2, Dm CLB4_CSB3_ISPG__1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, putative / GcpE family protein, similar to GcpE (Plasmodium falciparum) GI:13094969; contains Pfam profile PF04551: GcpE protein; supporting cDNA gi:27462471:gb:AF434673.1 3702 At5g60670 D1, D2, Dm 60S ribosomal protein L12 (RPL12C), 60S RIBOSOMAL PROTEIN L12 (like), Arabidopsis thaliana, PIR:T45883 3703 At5g60680 D2, Dm expressed protein, contains Pfam profile PF04520: Protein of unknown function, DUF584 3704 At5g60690 Dm REV_IFL_IFL1__homeodomain-leucine zipper protein Revoluta (REV) / fascicular fiberless 1 (IFL1), identical to HD-zip transcription factor Revoluta (GI:9759333) {Arabidopsis thaliana}; contains Pfam profiles PF01852: START domain and PF00046: Homeobox domain 3705 At5g60710 D2 zinc finger (C3HC4-type RING finger) family protein, low similarity to SP:P97280 Inter-alpha- trypsin inhibitor heavy chain H3 precursor {Mesocricetus auratus}; contains Pfam profiles PF00097: Zinc finger, C3HC4 type (RING finger), PF00092: von Willebrand factor type A domain

3706 At5g60790 D2 ATGCN1__ABC transporter family protein, similar to ABC transporter homolog PnATH GI:7573600 from (Populus nigra) 3707 At5g60920 D2 COB__phytochelatin synthetase, putative / COBRA cell expansion protein COB, putative, similar to phytochelatin synthetase GI:29570314; similar to GB:AAK56072; identified in Roudier, et al, Plant Phys. (2002) 130:538-548 (PMID:12376623); identical to cDNA putative phytochelatin synthetase GI:3559804; contains Pfam profile PF04833: Phytochelatin synthetase-like conserved region 3708 At5g60930 D1, Dm chromosome-associated kinesin, putative, microtubule-associated motor KIF4 , Mus musculus, PIR:A54803 3709 At5g60950 Dm phytochelatin synthetase-related, contains Pfam profile PF04833: Phytochelatin synthetase-like conserved region 3710 At5g61010 D1 exocyst subunit EXO70 family protein, leucine zipper-containing protein, tomato, PIR:S21495; contains Pfam domain PF03081: Exo70 exocyst complex subunit; similar to rexo70 (GI:2827160) {Rattus norvegicus} 3711 At5g61020 D1, D2, Dm ECT3__YT521-B-like family protein, contains Pfam profile PF04146: YT521-B-like family 3712 At5g61030 D2 RNA-binding protein, putative, similar to RNA-binding protein from (Solanum tuberosum) GI:15822705, (Nicotiana tabacum) GI:15822703, (Nicotiana sylvestris) GI:624925; contains InterPro entry IPR000504: RNA-binding region RNP-1 (RNA recognition motif) (RRM) 3713 At5g61150 Dm VIP4__leo1-like family protein, weak similarity to SP:P38439 LEO1 protein {Saccharomyces cerevisiae}; contains Pfam profile PF04004: Leo1-like protein; supporting cDNA gi:21929714:gb:AF490422.1: 3714 At5g61170 D1, D2, Dm 40S ribosomal protein S19 (RPS19C), 40S ribsomal protein S19, Oryza sativa, SWISSPROT:RS19_ORYSA 3715 At5g61320 D2 CYP89A3__cytochrome P450, putative, Similar to Cytochrome P450 89A2 (SP:Q42602)(Arabidopsis thaliana); contains Pfam profile: PF00067 cytochrome P450 3716 At5g61440 D2, Dm thioredoxin family protein, low similarity to thioredoxin (Callithrix jacchus) GI:13560979; contains Pfam profile: PF00085 Thioredoxin 3717 At5g61450 D2, Dm 2-phosphoglycerate kinase-related, contains weak similarity to 2-phosphoglycerate kinase (GI:467751) (Methanothermus fervidus) 3718 At5g61510 D1, Dm NADP-dependent oxidoreductase, putative, similar to zeta-crystallin homolog TED2 from Zinnia elegans (gi:531096); contains Pfam zinc-binding dehydrogenase domain PF00107 3719 At5g61530 D2 small G protein family protein / RhoGAP family protein, contains Pfam domain, PF00620: RhoGAP domain 3720 At5g61590 D2, Dm encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 18 members in this subfamily including ATERF-1, ATERF-2, AND ATERF-5. 3721 At5g61600 D2 encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 18 members in this subfamily including ATERF-1, ATERF-2, AND ATERF-5. 3722 At5g61660 D1, D2, Dm glycine-rich protein 3723 At5g61670 D1 expressed protein 3724 At5g61790 D1, D2, Dm calnexin 1 (CNX1), identical to calnexin homolog 1, Arabidopsis thaliana, EMBL:AT08315 (SP:P29402) 3725 At5g61820 D1, D2, Dm expressed protein, MtN19, Medicago truncatula, EMBL:MTY15367 3726 At5g61840 D2, Dm exostosin family protein, contains Pfam profile: PF03016 3727 At5g61980 D1, Dm ARF GTPase-activating domain-containing protein, similar to GCN4-complementing protein (GCP1) GI:6465806 from (Arabidopsis thaliana) 3728 At5g62040 D1, Dm brother of FT and TFL1 protein (BFT), identical to SP:Q9FIT4 BROTHER of FT and TFL1 protein {Arabidopsis thaliana}; contains Pfam profile PF01161: Phosphatidylethanolamine-binding protein 3729 At5g62200 D1, Dm embryo-specific protein-related, contains weak similarity to embryo-specific protein 3 (GI:3335171) (Arabidopsis thaliana) 3730 At5g62270 D2 expressed protein 3731 At5g62280 D1, Dm expressed protein 3732 At5g62300 D1, D2, Dm 40S ribosomal protein S20 (RPS20C), ribosomal protein S20, Arabidopsis thaliana, PIR:T12992 3733 At5g62350 D2, Dm invertase/pectin methylesterase inhibitor family protein / DC 1.2 homolog (FL5-2I22), similar to SP:Q42534 Pectinesterase 2 precursor (EC 3.1.1.11) (Pectin methylesterase 2) (PE 2) {Arabidopsis thaliana}; contains Pfam profile PF04043: Plant invertase/pectin methylesterase inhibitor; FL5-2I22 mRNA for DC 1.2 homolog, partial cds GI:11127598 3734 At5g62360 D2, Dm invertase/pectin methylesterase inhibitor family protein, similar to pectinesterase from Arabidosis thaliana SP:Q42534, Lycopersicon esculentum SP:Q43143; contains Pfam profile PF04043: Plant invertase/pectin methylesterase inhibitor 3735 At5g62390 D2 calmodulin-binding family protein, contains IQ calmodulin-binding motif, Pfam:PF00612 3736 At5g62400 D2, Dm expressed protein 3737 At5g62530 D1, Dm ALDH12A1_ATP5CDH__delta-1-pyrroline-5-carboxylate dehydrogenase (P5CDH), identical to delta-1- pyrroline-5-carboxylate dehydrogenase precursor (Arabidopsis thaliana) gi:15383744:gb:AAK73756; identical to cDNA delta-1-pyrroline-5-carboxylate dehydrogenase precursor (P5CDH) nuclear gene for mitochondrial product GI:15383743; contains Pfam profile PF00171:aldehyde dehydrogenase (NAD) family protein 3738 At5g62620 D1 galactosyltransferase family protein, contains Pfam profile: PF01762 galactosyltransferase 3739 At5g62670 D1, D2, Dm AHA11__ATPase, plasma membrane-type, putative / proton pump, putative, strong similarity to P- type H(+)-transporting ATPase from Nicotiana plumbaginifolia (SP:Q08435, SP:Q08436), Lycopersicon esculentum (GI:5901757, SP:P22180), Solanum tuberosum (GI:435003); contains InterPro accession IPR001757: ATPase, E1-E2 type 3740 At5g62720 D1, Dm integral membrane HPP family protein, contains Pfam domain, PF04982: HPP family 3741 At5g62890 D2 similar to xanthine/uracil permease family protein [Arabidopsis thaliana] (TAIR:At1g10540.1); similar to xanthine/uracil permease family protein [Arabidopsis thaliana] (TAIR:At1g60030.1); similar to xanthine/uracil permease family protein [Arabidopsis thaliana] (TAIR:At1g49960.1); similar to xanthine/uracil permease family protein [Arabidopsis thaliana] (TAIR:At5g49990.1); similar to putative permease 1 [Lycopersicon esculentum] (GB:AAX95758.1); similar to putative permease [Oryza sativa (japonica cultivar-group)] (GB:XP_482444.1); similar to putative permease 1 [Oryza sativa (japonica cultivar-group)] (GB:XP_450798.1); similar to putative permease 1 [Oryza sativa (japonica cultivar-group)] (GB:XP_467723.1); similar to putative permease [Oryza sativa (japonica cultivar-group)] (GB:NP_910042.1); contains InterPro domain Xanthine/uracil/vitamin C permease family (InterPro:IPR006043)

3742 At5g62920 D2 ARR6__two-component responsive regulator / response regulator 6 (ARR6), identical to response regulator 6 (Arabidopsis thaliana) GI:3953601 3743 At5g63050 D2, Dm EMB2759__expressed protein 3744 At5g63070 D2 40S ribosomal protein S15, putative 3745 At5g63180 D1, D2, Dm pectate lyase family protein, similar to pectate lyase GP:14289169 from (Salix gilgiana) 3746 At5g63190 D2, Dm MA3 domain-containing protein, low similarity to programmed cell death 4 protein (Gallus gallus) GI:12958564; contains Pfam profile PF02847: MA3 domain 3747 At5g63220 Dm expressed protein, contains Pfam PF04190: Protein of unknown function (DUF410) 3748 At5g63370 D1, D2, Dm protein kinase family protein, contains protein kinase domain, Pfam:PF00069 3749 At5g63510 D1 bacterial transferase hexapeptide repeat-containing protein, contains similarity to acetyltransferase; contains Pfam profile PF00132: Bacterial transferase hexapeptide (four repeats) 3750 At5g63570 D1, D2, Dm GSA1__glutamate-1-semialdehyde 2,1-aminomutase 1 (GSA 1) / glutamate-1-semialdehyde aminotransferase 1 (GSA-AT 1), identical to GSA 1 (SP:P42799) 3751 At5g63610 D2, Dm CDKE;1_HEN3__protein kinase, putative, similar to cyclin-dependent kinase cdc2MsE (Medicago sativa) gi:1806144:emb:CAA65981; contains protein kinase domain, Pfam:PF00069 3752 At5g63650 D1, Dm serine/threonine protein kinase, putative, similar to serine/threonine-protein kinase ASK2(Arabidopsis thaliana), SWISS-PROT:P43292; contains protein kinase domain, Pfam:PF00069 3753 At5g63670 D2 transcription initiation protein-related, contains weak similarity to Transcription initiation protein SPT4 homolog 1 (Swiss-Prot:Q16550) (Mus musculus) 3754 At5g63770 D2 ATDGK2__a member of the diacylglycerol kinase gene family. Encodes a functional diacylglycerol kinase. Involved in root elongation and plant development. Gene expression is induced by wounding or cold. 3755 At5g63810 Dm BGAL10__beta-galactosidase, putative / lactase, putative, similar to beta-galactosidase GI:7939621 from (Lycopersicon esculentum); contains Pfam profile PF01301: Glycosyl hydrolases family 35 3756 At5g63860 D1, Dm UVR8__UVB-resistance protein (UVR8), identical to UVB-resistance protein UVR8 (GI:5478530, GB:AAD43920.1) (Arabidopsis thaliana); contains Pfam 00415: Regulator of chromosome condensation (RCC1) 3757 At5g64000 Dm SAL2_ATSAL2__3`(2`),5`-bisphosphate nucleotidase, putative / inositol polyphosphate 1- phosphatase, putative, similar to SP:Q42546 3`(2`),5`-bisphosphate nucleotidase (EC 3.1.3.7) {Arabidopsis thaliana}; contains Pfam profile PF00459: Inositol monophosphatase family 3758 At5g64040 D1 PSI-N__photosystem I reaction center subunit PSI-N, chloroplast, putative / PSI-N, putative (PSAN), SP:P49107; Plant Physiol. 109 (3), 1126 (1995); similar to SP:P31093 Photosystem I reaction centre subunit N, chloroplast precursor (PSI- N) {Hordeum vulgare} 3759 At5g64050 Dm ATERS_ERS__glutamate-tRNA ligase family protein / glutamyl-tRNA synthetase family protein, similar to SP:P22250 from Bacillus subtilis, SP:P22249 from Bacillus stearothermophilus; contains Pfam tRNA synthetases class I (E and Q), catalytic domain PF00749 3760 At5g64140 D1, D2, Dm RPS28__40S ribosomal protein S28 (RPS28C) 3761 At5g64170 D2, Dm dentin sialophosphoprotein-related, contains weak similarity to Swiss-Prot:Q9NZW4 dentin sialophosphoprotein precursor (Homo sapiens) 3762 At5g64180 D1, D2, Dm expressed protein 3763 At5g64230 Dm expressed protein 3764 At5g64290 D1, D2, Dm oxoglutarate/malate translocator, putative, similar to SWISS-PROT:Q41364 2-oxoglutarate/malate translocator, chloroplast precursor. (Spinach){Spinacia oleracea} 3765 At5g64300 D2 ATGCH__similar to riboflavin biosynthesis protein, putative [Arabidopsis thaliana] (TAIR:At2g22450.1); similar to GTP cyclohydrolase II / 3,4-dihydroxy-2-butanone-4-phosphate synthase [Lycopersicon esculentum] (GB:CAA05308.1); similar to putative riboflavin biosynthesis protein ribA [Oryza sativa (japonica cultivar-group)] (GB:XP_483002.1); contains InterPro domain GTP cyclohydrolase II (InterPro:IPR000926); contains InterPro domain 3,4- Dihydroxy-2-butanone 4-phosphate synthase (InterPro:IPR000422) 3766 At5g64310 D2 AGP1__arabinogalactan-protein (AGP1), identical to gi:3883120 gb:AAC77823 3767 At5g64350 D2 FKBP12_ATFKBP12__FK506-binding protein (FKBP12) / immunophilin, identical to immunophilin (GI:2104957) (Arabidopsis thaliana) 3768 At5g64400 D1, D2, Dm expressed protein, contains Pfam domain, PF04933: Protein of unknown function (DUF657) 3769 At5g64420 D2 DNA polymerase V family, contains Pfam domain PF04931: DNA polymerase V 3770 At5g64430 D1, Dm octicosapeptide/Phox/Bem1p (PB1) domain-containing protein, contains Pfam profile PF00564: PB1 domain 3771 At5g64570 D1 XYL4_ATBXL4__glycosyl hydrolase family 3 protein 3772 At5g64580 D1, Dm AAA-type ATPase family protein, similar to zinc dependent protease (Arabidopsis thaliana) GI:7650138; contains Pfam profile PF00004: ATPase AAA family 3773 At5g64770 D2, Dm expressed protein 3774 At5g64816 D2 expressed protein 3775 At5g64820 D2, Dm expressed protein 3776 At5g64840 D1, D2, Dm ATGCN5__ABC transporter family protein 3777 At5g64850 D2 expressed protein 3778 At5g64860 D2 DPE1__4-alpha-glucanotransferase, putative / disproportionating enzyme, putative, similar to 4-alpha-glucanotransferase SP:Q06801 from (Solanum tuberosum) 3779 At5g64880 D2, Dm expressed protein 3780 At5g64920 D2 CIP8__COP1-interacting protein (CIP8) / zinc finger (C3HC4-type RING finger) family protein, identical to COP1-interacting protein CIP8 (Arabidopsis thaliana) gi:5929906:gb:AAD56636; contains Pfam profile: PF00097 zinc finger, C3HC4 type 3781 At5g64950 Dm mitochondrial transcription termination factor-related / mTERF-related, contains Pfam profile PF02536: mTERF 3782 At5g65020 D2 ANNAT2__annexin 2 (ANN2), identical to annexin (AnnAt2) (Arabidopsis thaliana) GI:4959108 3783 At5g65110 D2, Dm ACX2_ATACX2__acyl-CoA oxidase (ACX2), identical to acyl-CoA oxidase (Arabidopsis thaliana) GI:3044212 3784 At5g65130 D2 encodes a member of the DREB subfamily A-6 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 8 members in this subfamily including RAP2.4. 3785 At5g65140 D1, Dm trehalose-6-phosphate phosphatase, putative, similar to trehalose-6-phosphate phosphatase (AtTPPB) (Arabidopsis thaliana) GI:2944180; contains Pfam profile PF02358: Trehalose- phosphatase 3786 At5g65180 D1, Dm expressed protein, contains Pfam domain, PF04818: Protein of unknown function, DUF618 3787 At5g65205 D2 short-chain dehydrogenase/reductase (SDR) family protein, contains INTERPRO family IPR002198 short chain dehydrogenase/reductase SDR family 3788 At5g65220 D1, Dm ribosomal protein L29 family protein, contains Pfam profile PF00831: ribosomal protein L29 3789 At5g65280 Dm lanthionine synthetase C-like family protein, contains Pfam domain, PF05147: Lanthionine synthetase C-like protein 3790 At5g65390 D2, Dm AGP7__arabinogalactan-protein (AGP7) 3791 At5g65430 D1, Dm GRF8_GF14 KAPPA__14-3-3 protein GF14 kappa (GRF8), identical to 14-3-3 protein GF14 kappa GI:5802794, SP:P48348 from (Arabidopsis thaliana) 3792 At5g65440 D2 expressed protein 3793 At5g65480 D1, D2, Dm expressed protein 3794 At5g65610 D1 expressed protein, ; expression supported by MPSS 3795 At5g65630 D2 DNA-binding bromodomain-containing protein, similar to 5.9 kb fsh membrane protein (Drosophila melanogaster) GI:157455; contains Pfam profile PF00439: Bromodomain 3796 At5g65660 D2 hydroxyproline-rich glycoprotein family protein 3797 At5g65700 D1, D2, Dm leucine-rich repeat transmembrane protein kinase, putative 3798 At5g65730 D1, D2, Dm xyloglucan:xyloglucosyl transferase, putative / xyloglucan endotransglycosylase, putative / endo-xyloglucan transferase, putative, similar to endo-xyloglucan transferase GI:2244732 from (Gossypium hirsutum) 3799 At5g65840 D1, D2, Dm expressed protein 3800 At5g65860 D1, D2, Dm ankyrin repeat family protein, contains ankyrin repeats, Pfam:PF00023 3801 At5g65910 Dm BSD domain-containing protein, contains Pfam profile PF03909: BSD domain 3802 At5g65940 D2 CHY1__3-hydroxyisobutyryl-coenzyme A hydrolase / CoA-thioester hydrolase (CHY1), identical to gi:8572760; contains Pfam profile PF00388 enoyl-CoA hydratase/isomerase family protein 3803 At5g65980 D2, Dm auxin efflux carrier family protein, contains auxin efflux carrier domain, Pfam:PF03547 3804 At5g65990 D1, D2, Dm amino acid transporter family protein, similar to proton/amino acid transporter 1 (Mus musculus) GI:21908024; contains Pfam profile PF01490: Transmembrane amino acid transporter protein 3805 At5g66040 D1, D2, Dm senescence-associated family protein, almost identical to ketoconazole resistant protein GI:928938 from (Arabidopsis thaliana) full-length cDNA: Ceres:101608. 3806 At5g66110 D1 similar to heavy-metal-associated domain-containing protein / copper chaperone (CCH)-related [Arabidopsis thaliana] (TAIR:At4g38580.1); similar to Putative atfp6-like protein [Oryza sativa (japonica cultivar-group)] (GB:XP_470243.1); contains InterPro domain Heavy metal binding (InterPro:IPR006191); contains InterPro domain Heavy metal transport/detoxification protein (InterPro:IPR006121) 3807 At5g66120 D1, Dm 3-dehydroquinate synthase, putative, similar to aroB (Neisseria gonorrhoeae)(GI:2661441); contains 3-dehydroquinate synthase domain PF01761 3808 At5g66200 D1, Dm armadillo/beta-catenin repeat family protein, contains Pfam profile: PF00514 armadillo/beta- catenin-like repeat 3809 At5g66230 D2 expressed protein 3810 At5g66250 Dm kinectin-related, contains weak similarity to kinectin (GI:3766232) (Vulpes vulpes) 3811 At5g66360 D1, Dm ribosomal RNA adenine dimethylase family protein, similar to SP:P41819 Dimethyladenosine transferase (EC 2.1.1.-) (S-adenosylmethionine-6-N`, N`-adenosyl(rRNA) dimethyltransferase) {Saccharomyces cerevisiae}; contains Pfam profile PF00398: ribosomal RNA adenine dimethylase family protein 3812 At5g66370 Dm expressed protein, similar to unknown protein (emb CAB62624.1) 3813 At5g66390 D2 peroxidase 72 (PER72) (P72) (PRXR8), identical to SP:Q9FJZ9 Peroxidase 72 precursor (EC 1.11.1.7) (Atperox P72) (PRXR8) (ATP6a) {Arabidopsis thaliana} 3814 At5g66400 D1, D2, Dm RAB18_ATDI8__dehydrin (RAB18), nearly identical to SP:P30185 Dehydrin Rab18 {Arabidopsis thaliana} 3815 At5g66460 D1, D2, Dm (1-4)-beta-mannan endohydrolase, putative, similar to (1-4)-beta-mannan endohydrolase (Coffea arabica) GI:10178872; contains Pfam profile PF00150: Cellulase (glycosyl hydrolase family 5)

3816 At5g66470 D1, Dm expressed protein 3817 At5g66490 D1, D2, Dm expressed protein 3818 At5g66510 D1, Dm bacterial transferase hexapeptide repeat-containing protein, contains Pfam profile PF00132: Bacterial transferase hexapeptide (four repeats) 3819 At5g66530 D1, Dm aldose 1-epimerase family protein, similar to apospory-associated protein C; APOC (Chlamydomonas reinhardtii) GI:6970044; contains Pfam profile PF01263: Aldose 1-epimerase 3820 At5g66650 D2 expressed protein, contains Pfam domain, PF04678: Protein of unknown function, DUF607 3821 At5g66750 D2, Dm DDM1_SOM1_SOM4__SNF2 domain-containing protein / helicase domain-containing protein, similar to proliferation-associated SNF2-like protein (Homo sapiens) GI:8980660; contains Pfam profiles PF00271: Helicase conserved C-terminal domain, PF00176: SNF2 family N-terminal domain 3822 At5g66960 D1, D2, Dm prolyl oligopeptidase family protein, similar to OpdB (Treponema denticola) GI:13786054; contains Pfam profiles PF00326: prolyl oligopeptidase family, PF02897: Prolyl oligopeptidase, N-terminal beta-propeller domain 3823 At5g66980 Dm transcriptional factor B3 family protein, contains Pfam profile PF02362: B3 DNA binding domain

3824 At5g67030 D1, D2, Dm ABA1_ATABA1_IBS3_LOS6_NPQ2_ZEP__zeaxanthin epoxidase (ZEP) (ABA1), identical to GI:9857296 AtABA1; controls Pfam profiles PF01360: Monooxygenase and PF00498: FHA domain; identical to cDNA AtABA1, GI:9857295 3825 At5g67220 Dm nitrogen regulation family protein, similar to unknown protein (gb:AAF51525.1) ; contains Pfam domain PF01207: Dihydrouridine synthase (Dus); similar to (SP:P45672) NIFR3-like protein (SP:P45672) (Azospirillum brasilense) 3826 At5g67240 Dm similar to exonuclease family protein [Arabidopsis thaliana] (TAIR:At3g50100.1); similar to hypothetical protein AN7566.2 [Aspergillus nidulans FGSC A4] (GB:EAA62146.1); contains InterPro domain Exonuclease (InterPro:IPR006055) 3827 At5g67250 D2 SKIP2_VFB4__SKP1 interacting partner 2 (SKIP2), identical to SKP1 interacting partner 2 GI:10716949 from (Arabidopsis thaliana) 3828 At5g67300 D2 myb family transcription factor, contains PFAM profile: myb DNA binding domain PF00249 3829 At5g67330 D1, D2, Dm ATNRAMP4_NRAMP4__NRAMP metal ion transporter 4 (NRAMP4), identical to metal transporter Nramp4 (Arabidopsis thaliana) gi:6468014:gb:AAF13279; member of the natural resistance-associated macrophage protein (NRAMP) metal transporter family, PMID:11500563 3830 At5g67360 D1, D2, Dm ARA12__cucumisin-like serine protease (ARA12), Asp48; almost identical to cucumisin-like serine protease (ARA12) GI:3176874 from (Arabidopsis thaliana) 3831 At5g67370 D1, D2, Dm expressed protein, similar to unknown protein (gb:AAC18972.1) 3832 At5g67380 D1, D2, Dm CKA1_ATCKA1__casein kinase II alpha chain 1, identical to casein kinase II, alpha chain 1 (CK II) (Arabidopsis thaliana) SWISS-PROT:Q08467; contains protein kinase domain, Pfam:PF00069

3833 At5g67480 D2 TAZ zinc finger family protein / BTB/POZ domain-containing protein, contains Pfam PF00651 : BTB/POZ domain; contains Pfam PF02135 : TAZ zinc finger; simiar to Chain A, Taz2 Domain Of The Transcriptional Adaptor Protein Cbp (GI:11514507) (Homo sapiens); similar to (SP:Q09472) E1A- associated protein p300 (SP:Q09472) (Homo sapiens); similar to histone acetyltransferase HAC4 (GI:21105785) (Arabidopsis thaliana)