SI Appendix Table S6.1 List of RBR-regulated transcription factors, and stress and stimulus-responsive transcripts in the egg cell, subtracted from the ovule transcriptomes (A) Transcription Factors

Arabidopsis Gene Model Description TF Family Name Locus ID I. Enriched in rbr-3 AT1G08970 nuclear factor Y%2C subunit C9 CCAAT-HAP5 AT1G14410 ssDNA-binding transcriptional regulator Whirly AT1G14510 alfin-like 7 Alfin AT1G22070 transcription factor TGA3 bZIP AT1G32700 PLATZ transcription factor family PLATZ AT1G34370 C2H2 and C2HC zinc fingers superfamily protein C2H2 AT1G42990 basic region/leucine zipper motif 60 bZIP AT1G63490 transcription factor jumonji (jmjC) domain-containing protein JUMONJI AT2G02160 CCCH-type family protein C3H AT2G17410 ARID/BRIGHT DNA-binding domain-containing protein ARID AT2G24430 NAC domain containing protein 38 NAC AT2G27050 ETHYLENE-INSENSITIVE3-like 1 EIL AT2G34720 nuclear factor Y%2C subunit A4 CCAAT-HAP2 AT2G35430 Zinc finger C-x8-C-x5-C-x3-H type family protein C3H AT2G36010 E2F transcription factor 3 E2F-DP AT2G39830 DA1-related protein 2 LIM AT3G07670 Rubisco family protein PcG AT3G10500 NAC domain containing protein 53 NAC AT3G10760 Homeodomain-like superfamily protein GARP-G2-like AT3G12130 KH domain-containing protein / zinc finger (CCCH type) family protein C3H AT3G59580 Plant regulator RWP-RK family protein Nin-like AT4G17750 heat shock factor 1 HSF AT4G24470 GATA-type zinc finger protein with TIFY domain-containing protein ZIM AT4G30935 WRKY DNA-binding protein 32 WRKY AT4G31610 Transcriptional factor B3 family protein ABI3-VP1 AT5G02810 pseudo-response regulator 7 C2C2-CO-like AT5G06770 KH domain-containing protein / zinc finger (CCCH type) family protein C3H AT5G08520 Duplicated homeodomain-like superfamily protein MYB AT5G11050 myb domain protein 64 MYB AT5G27610 protein ALWAYS EARLY 1 MYB-related AT5G51910 TCP family transcription factor TCP AT5G59820 C2H2-type zinc finger family protein C2H2 AT1G21000 PLATZ transcription factor family protein PLATZ AT1G25470 AP2 domain-containing transcription factor family protein AP2-EREBP AT1G47270 tubby like protein 6 TLP AT1G49950 telomere repeat binding factor 1 MYB-related AT1G68920 basic helix-loop-helix (bHLH) DNA-binding superfamily protein bHLH AT1G74950 TIFY domain/Divergent CCT motif family protein ZIM AT2G24500 Zinc finger protein 622 C2H2 AT2G28510 Dof-type zinc finger DNA-binding family protein C2C2-Dof AT2G32700 LEUNIG-like protein LUG AT2G47680 zinc finger (CCCH type) helicase family protein C3H AT3G06410 Zinc finger C-x8-C-x5-C-x3-H type family protein C3H AT3G10800 Basic-leucine zipper (bZIP) transcription factor family protein bZIP AT3G58680 multiprotein bridging factor 1B MBF1 AT4G17710 homeodomain GLABROUS 4 HB AT5G64060 NAC domain containing protein 103 NAC AT5G64220 Calmodulin-binding transcription activator protein with CG-1 and Ankyrin domain CAMTA AT2G35550 basic pentacysteine 7 BBR-BPC AT2G36480 pre-mRNA cleavage complex 2 Pcf11-like protein C2H2 AT3G24010 RING/FYVE/PHD zinc finger superfamily protein PHD AT3G25730 ethylene response DNA binding factor 3 AP2-EREBP AT3G62240 RING/U-box superfamily protein C2H2 AT5G05610 alfin-like 1 Alfin AT5G46910 Transcription factor jumonji (jmj) family protein / zinc finger (C5HC2 type) family protein JUMONJI AT5G52660 Homeodomain-like superfamily protein MYB-related AT5G59340 WUSCHEL related homeobox 2 HB AT2G40950 Basic-leucine zipper (bZIP) transcription factor family protein bZIP AT5G47390 myb-like transcription factor family protein MYB-related AT1G72050 transcription factor IIIA C2H2 AT3G53680 Acyl-CoA N-acyltransferase with RING/FYVE/PHD-type zinc finger domain-containing protein PHD AT1G34190 NAC domain containing protein 17 NAC AT5G38840 SMAD/FHA domain-containing protein FHA AT5G58080 response regulator 18 GARP-G2-like AT1G77950 AGAMOUS-like 67 MADS AT5G18680 tubby like protein 11 TLP

II. depleted in rbr-3 AT1G12860 basic helix-loop-helix (bHLH) DNA-binding superfamily protein bHLH AT1G50620 RING/FYVE/PHD zinc finger superfamily protein PHD AT1G51140 basic helix-loop-helix (bHLH) DNA-binding superfamily protein bHLH AT1G58220 Homeodomain-like superfamily protein MYB-related AT2G21530 SMAD/FHA domain-containing protein FHA AT2G28810 Dof-type zinc finger DNA-binding family protein C2C2-Dof AT2G32930 zinc finger nuclease 2 C3H AT2G36930 zinc finger (C2H2 type) family protein C2H2 AT2G37060 nuclear factor Y%2C subunit B8 CCAAT-HAP3 AT2G47890 B-box type zinc finger protein with CCT domain-containing protein C2C2-CO-like AT3G16500 phytochrome-associated protein 1 AUX-IAA AT3G17860 jasmonate-zim-domain protein 3 ZIM AT3G53340 nuclear factor Y%2C subunit B10 CCAAT-HAP3 AT4G14560 indole-3-acetic acid inducible AUX-IAA AT4G17230 SCARECROW-like 13 GRAS AT4G25210 DNA-binding storekeeper protein-related transcriptional regulator GeBP AT4G26640 WRKY family transcription factor family protein WRKY AT4G27910 SET domain protein 16 PHD AT4G36920 Integrase-type DNA-binding superfamily protein AP2-EREBP AT5G09790 TRITHORAX-RELATED PROTEIN 5 PHD AT5G12440 CCCH-type zinc fingerfamily protein with RNA-binding domain-containing protein C3H AT5G14960 DP-E2F-like 2 E2F-DP AT5G18550 Zinc finger C-x8-C-x5-C-x3-H type family protein C3H AT5G25475 AP2/B3-like transcriptional factor family protein ABI3-VP1 AT5G42520 basic pentacysteine 6 BBR-BPC AT5G45300 beta-amylase 2 BES1 AT5G45980 WUSCHEL related homeobox 8 HB AT5G60410 DNA-binding protein with MIZ/SP-RING zinc finger%2C PHD-finger and SAP domain-containing protein PHD AT3G23050 indole-3-acetic acid 7 AUX-IAA AT3G61150 homeodomain GLABROUS 1 HB AT4G38000 DNA binding with one finger 4.7 C2C2-Dof AT5G61190 putative endonuclease or glycosyl hydrolase with C2H2-type zinc finger domain-containing protein C2H2 AT1G76510 ARID/BRIGHT DNA-binding domain-containing protein ARID AT4G02560 Homeodomain-like superfamily protein HB AT4G15180 SET domain protein 2 PcG AT4G32880 homeobox-leucine zipper protein ATHB-8 HB AT1G54060 6B-interacting protein 1-like 1 Trihelix AT4G31060 Integrase-type DNA-binding superfamily protein AP2-EREBP AT1G15580 indole-3-acetic acid inducible 5 AUX-IAA

#H3K27M3 target was determined based on normalized read count value present in PlantDHS database for respective gene IDs.

# RBR/E2F binding site was predicted running FIMO algorithm using published E2F binding motifs as templates H3K27M3 RBR/E2F stress responsive TF description target binding site Yes/No Yes/No P-value Yes/No Yes Yes 2.55E-05 No CCAAT-box binding transcription factor Hap5a, putative chr1:2882546-2884285 FORWARD Aliases: F7G19.16, F7G19_16, HAP5C, HEME ACTIVATED PROTEIN 5C Yes Yes 9.65E-08 Yes DNA-binding protein-related, similar to DNA-binding protein p24 GI:9651810 from (Solanum tuberosum) chr1:4929118-4930888 REVERSE Aliases: F14L17.18, F14L17_18 Yes Yes 7.48E-05 No PHD finger family protein, contains Pfam domain, PF00628: PHD-finger chr1:4961882-4964420 REVERSE Aliases: F14L17.29, F14L17_29 Yes Yes 5.02E-05 Yes bZIP family transcription factor (TGA3), identical to transcription factor GI:304113 from (Arabidopsis thaliana) chr1:7789497-7792103 FORWARD Aliases: F2E2.14, F2E2_14, TRANSCRIPTION FACTOR TGA3 Yes Yes 7.51E-05 No zinc-binding family protein, similar to zinc-binding protein (Pisum sativum) GI:16117799; contains Pfam profile PF04640 : Protein of unknown function, DUF597 chr1:11827447-11829739 FORWARD Aliases: F6N18.8, F6N18_8 Yes Yes 2.99E-05 No similar to zinc finger (C2H2 type) family protein [Arabidopsis thaliana] (TAIR:At5g22890.1); similar to putative zinc finger protein [Oryza sativa (japonica cultivar-group)] (GB:XP_470361.1); contains InterPro domain Zn-finger, C2H2 type (InterPro:IPR007087) chr1:12550455-12552677 FORWARD Aliases: F7P12.7, F7P12_7 Yes No #N/A Yes 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. chr1:16138292-16139903 REVERSE Aliases: ATBZIP60, F13A11.5, F13A11_5 Yes Yes 9.48E-05 No transcription factor jumonji (jmjC) domain-containing protein, similar to PLU-1 protein (GI:4902724) (Homo sapiens) and PLU1 (GI:22726257) (Mus musculus); similar to Retinoblastoma-binding protein 2 (RBBP-2) (SP:P29375) {Homo sapiens}; contains Pfam PF02373: jmjC domain chr1:23548321-23555695 REVERSE Aliases: F2K11.14, F2K11_14 Yes No #N/A No zinc finger (CCCH-type) family protein, contains Pfam domain, PF00642: Zinc finger C-x8-C-x5-C-x3-H type (and similar) chr2:553109-556082 REVERSE Aliases: F5O4.7, F5O4_7 Yes Yes 9.2E-06 No ARID/BRIGHT DNA-binding domain-containing protein, contains Pfam profile PF01388: ARID/BRIGHT DNA binding domain chr2:7566080-7570834 FORWARD Aliases: AT2G17400, F5J6.17, F5J6_17 Yes Yes 6.07E-06 No no apical meristem (NAM) family protein, contains Pfam PF02365: No apical meristem (NAM) domain; chr2:10390597-10393560 REVERSE Aliases: ANAC038, ANAC039, T28I24.16, T28I24_16 Yes Yes 5.18E-05 Yes ethylene-insensitive3-like1 (EIL1), identical to ethylene-insensitive3-like1 GI:2224927 from (Arabidopsis thaliana) chr2:11552873-11555371 FORWARD Aliases: ETHYLENE INSENSITIVE3 LIKE 1, T20P8.10, T20P8_10 Yes Yes 4.02E-05 No CCAAT-binding transcription factor (CBF-B/NF-YA) family protein, contains Pfam profile: PF02045 CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B chr2:14656846-14658692 REVERSE Aliases: T29F13.7, T29F13_7 Yes Yes 1.58E-05 No zinc finger (CCCH-type) family protein, contains Pfam domain, PF00642: Zinc finger C-x8-C-x5-C-x3-H type (and similar) chr2:14907957-14909464 REVERSE Aliases: T32F12.19, T32F12_19 Yes Yes 2.91E-05 No E2F transcription factor-3 (E2F3), identical to E2F transcription factor-3 E2F3 (Arabidopsis thaliana) gi:10443853:gb:AAG17610 chr2:15126621-15130683 FORWARD Aliases: ATE2FA, E2F TRANSCRIPTION FACTOR 3, E2F TRANSCRIPTION FACTOR 3 E2F3, F11F19.8, F11F19_8 Yes Yes 1.38E-10 No LIM domain-containing protein, contains Pfam profile PF00412: LIM domain chr2:16626855-16630838 REVERSE Aliases: T5I7.13, T5I7_13 Yes Yes 2.06E-05 No SET domain-containing protein, similar to ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit N-methyltransferase I (Spinacia oleracea) GI:3403236; contains Pfam profile PF00856: SET domain chr3:2451614-2454866 FORWARD Aliases: MLP3.12 Yes Yes 0.000028 No no apical meristem (NAM) family protein, similar to to NAC2 (GI:645671) (Arabidopsis thaliana); contains Pfam PF02365: No apical meristem (NAM) protein chr3:3271617-3274035 FORWARD Aliases: ANAC053, F13M14.22 Yes Yes 6.31E-06 No myb family transcription factor, contains Pfam profile: PF00249 myb-like DNA-binding domain chr3:3369585-3371232 FORWARD Aliases: T7M13.16 Yes Yes 4.06E-05 No KH domain-containing protein / zinc finger (CCCH type) family protein chr3:3864158-3866596 REVERSE Aliases: T21B14.5 Yes Yes 5.64E-05 No similar to RWP-RK domain-containing protein [Arabidopsis thaliana] (TAIR:At2g43500.1); similar to OSJNBa0067K08.5 [Oryza sativa (japonica cultivar-group)] (GB:XP_473028.1); contains InterPro domain Plant regulator RWP-RK (InterPro:IPR003035); contains InterPro domain Octicosapeptide/Phox/Bem1p (InterPro:IPR000270) chr3:22020190-22023743 FORWARD Aliases: T16L24.130 Yes Yes 6.08E-07 Yes heat shock factor protein 1 (HSF1) / heat shock transcription factor 1 (HSTF1), identical to heat shock transcription factor 1 (HSF1) SP:P41151 from (Arabidopsis thaliana) ;contains Pfam profile: PF00447 HSF-type DNA-binding domain chr4:9869831-9871616 REVERSE Aliases: ARABIDOPSIS HEAT SHOCK FACTOR 1, ATHSF1, ATHSFA1A, DL4910C, FCAALL.107, HEAT SHOCK FACTOR, HSFA1A Yes Yes 7.4E-06 No zinc finger (GATA type) protein ZIM (ZIM), identical to zinc-finger protein expressed in Inflorescence Meristem, ZIM gi:8918533 from (Arabidopsis thaliana) chr4:12645600-12647950 FORWARD Aliases: T22A6.300, T22A6_300 Yes Yes 2.45E-05 No WRKY family transcription factor, contains Pfam profile: PF03106 WRKY DNA -binding domain chr4:15051820-15054031 REVERSE Aliases: None Yes Yes 2.61E-06 No transcriptional factor B3 family protein / reproductive meristem protein 1 (REM1), similar to reproductive meristem gene 1 from (Brassica oleracea var. botrytis) GI:3170424; contains Pfam profile PF02362: B3 DNA binding domain; identical to cDNA reproductive meristem protein 1 (REM1) GI:13604226 chr4:15317505-15320026 FORWARD Aliases: F28M20.200, F28M20_200, REPRODUCTIVE MERISTEM 1 Yes Yes 2.72E-06 No pseudo-response regulator 7 (APRR7), identical to pseudo-response regulator 7 GI:10281004 from (Arabidopsis thaliana) chr5:637895-641975 REVERSE Aliases: F9G14.120, F9G14_120, PRR7, PSEUDO RESPONSE REGULATOR 7 Yes Yes 4.8E-06 No KH domain-containing protein / zinc finger (CCCH type) family protein, contains Pfam domains PF00013: KH domain and PF00642: Zinc finger C-x8-C-x5-C-x3-H type (and similar) chr5:2090704-2092951 REVERSE Aliases: MPH15.13, MPH15_13 Yes Yes 4.05E-05 No myb family transcription factor, contains Pfam profile: PF00249 myb-like DNA-binding domain chr5:2755176-2758335 REVERSE Aliases: F8L15.2 Yes Yes 6.99E-06 No myb family transcription factor, contains Pfam profile: PF00249 myb-like DNA binding domain; identical to cDNA putative transcription factor MYB64 (MYB64) GI:15375309 chr5:3502093-3503835 FORWARD Aliases: T5K6.40, T5K6_40 Yes Yes 3.47E-05 No similar to myb family transcription factor [Arabidopsis thaliana] (TAIR:At3g05380.1); similar to P0671B11.29 [Oryza sativa (japonica cultivar-group)] (GB:NP_914584.1); contains InterPro domain Myb DNA-binding domain (InterPro:IPR001005) chr5:9764138-9769906 FORWARD Aliases: F15A18.70, F15A18_70 Yes Yes 1.42E-06 No TCP family transcription factor, putative, similar to PCF2 ((GI:2580440) Oryza sativa) chr5:21111811-21113058 REVERSE Aliases: MJM18.6, MJM18_6 Yes Yes 3.58E-06 Yes zinc finger (C2H2 type) family protein (ZAT12), identical to zinc finger protein ZAT12 (Arabidopsis thaliana) gi:1418325:emb:CAA67232 chr5:24120198-24121013 FORWARD Aliases: MMN10.11, MMN10_11, RESPONSIVE TO HIGH LIGHT 41, ZAT12 Yes No #N/A No zinc-binding family protein, similar to zinc-binding protein (Pisum sativum) GI:16117799; contains Pfam profile PF04640 : Protein of unknown function, DUF597 chr1:7337740-7339441 FORWARD Aliases: F9H16.1, F9H16_1 Yes Yes 0.000026 No 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. chr1:8944596-8946601 REVERSE Aliases: F2J7.8, F2J7_8 Yes Yes 0.000033 No 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) chr1:17328996-17331168 FORWARD Aliases: F8G22.1, F8G22_1 Yes Yes 1.38E-05 Yes DNA-binding protein, putative, contains similarity to DNA-binding protein PcMYB1 (Petroselinum crispum) gi:2224899:gb:AAB61699 chr1:18497832-18500855 REVERSE Aliases: F2J10.16, F2J10_16 Yes Yes 0.000072 No similar to basic helix-loop-helix (bHLH) family protein [Arabidopsis thaliana] (TAIR:At1g26260.1); similar to basic helix-loop-helix (bHLH) family protein [Arabidopsis thaliana] (TAIR:At1g26260.2); similar to hypothetical protein [Oryza sativa (japonica cultivar-group)] (GB:NP_910691.1); similar to putative TA1 protein [Oryza sativa (japonica cultivar-group)] (GB:BAD68029.1); contains InterPro domain Basic helix-loop-helix dimerization domain bHLH (InterPro:IPR001092) chr1:25918670-25921540 FORWARD Aliases: T6L1.10, T6L1_10 Yes Yes 1.17E-05 Yes expressed protein chr1:28152236-28154055 REVERSE Aliases: F25A4.8, F25A4_8 Yes Yes 1.56E-05 No zinc finger (C2H2 type) family protein, contains Pfam profile: PF00096 zinc finger, C2H2 type chr2:10408115-10409948 REVERSE Aliases: C2H2 ZINC FINGER PROTEIN FZF, T28I24.23, T28I24_23 Yes Yes 1.29E-05 No Dof-type zinc finger domain-containing protein, similar to elicitor-responsive Dof protein ERDP GI:6092016 from (Pisum sativum) chr2:12206175-12207842 REVERSE Aliases: T17D12.7, T17D12_7 Yes Yes 6.99E-05 No similar to WD-40 repeat family protein (LEUNIG) [Arabidopsis thaliana] (TAIR:At4g32551.1); similar to putative LEUNIG [Oryza sativa (japonica cultivar-group)] (GB:XP_468366.1); similar to OSJNBb0065L13.11 [Oryza sativa (japonica cultivar-group)] (GB:XP_473135.1); contains InterPro domain Lissencephaly type-1-like homology motif (InterPro:IPR006594); contains InterPro domain G-protein beta WD-40 repeat (InterPro:IPR001680) chr2:13873894-13879217 FORWARD Aliases: F24L7.16, F24L7_16 Yes Yes 0.00006 No zinc finger (CCCH type) helicase family protein, similar to SP:Q28141 ATP-dependent RNA helicase A (Nuclear DNA helicase II) (DEAD-box protein 9) {Bos taurus}; contains Pfam profiles PF00271: Helicase conserved C-terminal domain, PF00642: Zinc finger C-x8-C-x5-C-x3-H type (and similar) chr2:19552898-19557975 REVERSE Aliases: F17A22.7 Yes Yes 6.07E-06 No similar to zinc finger (CCCH-type) family protein [Arabidopsis thaliana] (TAIR:At5g18550.1); similar to putative floral homeotic protein HUA1 [Oryza sativa (japonica cultivar-group)] (GB:BAD81402.1); contains InterPro domain Zn-finger, C-x8-C-x5-C-x3-H type (InterPro:IPR000571) chr3:1947310-1949775 REVERSE Aliases: F24P17.12, F24P17_12 Yes Yes 4.87E-05 Yes 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) chr3:3379259-3381618 FORWARD Aliases: T7M13.12 Yes Yes 4.14E-05 No ethylene-responsive transcriptional coactivator, putative, similar to ethylene-responsive transcriptional coactivator (Lycopersicon esculentum) gi:5669634:gb:AAD46402 chr3:21718253-21719881 FORWARD Aliases: T20N10.30, T20N10_30 Yes Yes 7.39E-05 No homeobox-leucine zipper family protein / lipid-binding START domain-containing protein, similar to HD-Zip homeo domain OCL4 protein (GI:8920425) (Zea mays); contains Pfam PF00046: Homeobox domain and Pfam PF01852: START domain chr4:9856309-9859301 REVERSE Aliases: DL4890C, FCAALL.102 Yes Yes 2.21E-05 No no apical meristem (NAM) family protein, similar to NAC1 (GI:7716952) {Medicago truncatula}; contains Pfam PF02365: No apical meristem (NAM) protein chr5:25651044-25652378 REVERSE Aliases: ANAC103, MHJ24.4, MHJ24_4 Yes Yes 2.72E-06 No similar to ethylene-responsive calmodulin-binding protein, putative (SR1) [Arabidopsis thaliana] (TAIR:At2g22300.1); similar to calmodulin-binding protein [Arabidopsis thaliana] (TAIR:At5g09410.1); similar to putative calmodulin-binding transcription factor [Oryza sativa (japonica cultivar-group)] (GB:AAR06369.1); similar to anther ethylene-upregulated protein ER1 [Nicotiana tabacum] (GB:AAG39222.1); similar to putative calmodulin binding protein similar to ER66 [Oryza sativa (japonica cultivar-group)] (GB:AAP53419.1); contains InterPro domain IQ calmodulin-binding region (InterPro:IPR000048); contains InterPro domain CG-1 domain (InterPro:IPR005559); contains InterPro domain Ankyrin (InterPro:IPR002110) chr5:25703434-25709476 FORWARD Aliases: MSJ1.6, MSJ1_6 Yes Yes 3.06E-05 No similar to expressed protein [Arabidopsis thaliana] (TAIR:At1g14685.3); similar to expressed protein [Arabidopsis thaliana] (TAIR:At1g14685.1); similar to expressed protein [Arabidopsis thaliana] (TAIR:At1g14685.2); similar to GAGA-binding protein [Glycine max] (GB:AAM27201.1) chr2:14936453-14937741 FORWARD Aliases: T32F12.7, T32F12_7 Yes No #N/A No zinc finger (C2H2-type) family protein, weak similarity to S-locus protein 4 (GI:6069478) (Brassica rapa); weak similarity to Pre-mRNA cleavage complex II protein Pcf11 (Fragment) (Swiss-Prot:O94913) (Homo sapiens); contains Prosite PS00028: Zinc finger, C2H2 type, domain chr2:15309883-15313353 REVERSE Aliases: F1O11.23 Yes No #N/A No PHD finger family protein, contains Pfam profile: PF00628 PHD-finger chr3:8675965-8678227 REVERSE Aliases: F14O13.20 Yes Yes 1.61E-05 No AP2 domain-containing transcription factor, putative, contains Pfam profile: PF00847 AP2 domain; similar to RAV1 (DNA-binding protein) GB:BAA34250 (Arabidopsis thaliana) (Nucleic Acids Res. 27 (2), 470-478 (1999)) chr3:9397657-9398896 FORWARD Aliases: K13N2.14 Yes Yes 1.01E-05 No zinc finger (C2H2 type) family protein, contains Pfam PF00096: Zinc finger, C2H2 type chr3:23044417-23047740 REVERSE Aliases: T17J13.200 Yes Yes 0.000011 No PHD finger family protein, contains Pfam domain, PF00628: PHD-finger chr5:1676941-1679105 REVERSE Aliases: MOP10.15, MOP10_15 Yes Yes 8.05E-05 No transcription factor jumonji (jmj) family protein, contains Pfam domains PF02375: jmjN domain and PF02373: jmjC domain chr5:19065007-19068107 FORWARD Aliases: MQD22.4, MQD22_4 Yes Yes 4.71E-06 Yes myb family transcription factor, contains PFAM profile: PF00249 myb-like DNA-binding domain chr5:21376285-21379384 REVERSE Aliases: F6N7.15, F6N7_15 Yes Yes 2.69E-05 No similar to homeobox-leucine zipper transcription factor family protein [Arabidopsis thaliana] (TAIR:At3g18010.1); similar to putative homeodomain transcripition factor [Oryza sativa (indica cultivar-group)] (GB:CAC09359.1); similar to narrow sheath 2 [Zea mays] (GB:AAR31212.1); contains InterPro domain Homeobox (InterPro:IPR001356) chr5:23950630-23951916 REVERSE Aliases: MNC17.25, MNC17_25 Yes Yes 8.47E-05 Yes bZIP transcription factor family protein, similar to AtbZIP transcription factor GI:17065880 from (Arabidopsis thaliana); contains Pfam profile: bZIP transcription factor PF00170 chr2:17094698-17097502 REVERSE Aliases: T20B5.15, T20B5_15 Yes Yes 1.04E-05 Yes myb family transcription factor, contains Pfam profile: PF00249 myb-like DNA-binding domain chr5:19244017-19246085 FORWARD Aliases: MQL5.25, MQL5_25 Yes Yes 2.43E-05 No zinc finger (C2H2 type) family protein, contains multiple zinc finger domains: PF00096: Zinc finger, C2H2 type chr1:27118744-27121117 FORWARD Aliases: F28P5.6, F28P5_6 Yes Yes 2.14E-07 No PHD finger transcription factor, putative, predicted , Arabidopsis thaliana chr3:19903841-19908390 REVERSE Aliases: F4P12.380 Yes Yes 4.03E-05 No no apical meristem (NAM) family protein, contains Pfam PF02365: No apical meristem (NAM) protein; similar to NAM protein GI:6066595 (Petunia hybrida); nam-like protein 9 (GI:21105746) (Petunia x hybrida); NAC1 GI:7716952 (Medicago truncatula) chr1:12451431-12454120 FORWARD Aliases: ANAC017, F12G12.30 Yes Yes 2.28E-05 No forkhead-associated domain-containing protein / FHA domain-containing protein, related to adaptor protein kanadaptin (Homo sapiens) gi:13562130:gb:AAK29177 chr5:15568526-15572300 FORWARD Aliases: K15E6.5, K15E6_5 Yes Yes 0.000038 No two-component responsive regulator family protein / response regulator family protein, contains Pfam profile: PF00072 response regulator receiver domain chr5:23519011-23521227 REVERSE Aliases: ARABIDOPSIS RESPONSE REGULATOR 18, K21L19.7, K21L19_7 Yes Yes 3.71E-05 No similar to MADS-box family protein [Arabidopsis thaliana] (TAIR:At1g22130.1); similar to putative MADS-box protein [Oryza sativa (japonica cultivar-group)] (GB:XP_483124.1); contains InterPro domain Transcription factor, MADS-box (InterPro:IPR002100) chr1:29311851-29314757 FORWARD Aliases: F28K19.16, F28K19_16 Yes Yes 4.14E-05 No F-box family protein / tubby family protein, similar to phosphodiesterase (GI:467578) (Mus musculus); similar to Chain A, C-Terminal Domain Of Mouse Brain Tubby Protein (GI:6730158) (Mus musculus); contains Pfam PF00646: F-box domain and Pfam PF01167: Tub family chr5:6228167-6230539 REVERSE Aliases: T1A4.60, T1A4_60

Yes Yes 3.66E-05 Yes basic helix-loop-helix (bHLH) family protein / F-box family protein, contains Pfam profiles: PF00646 F-box domain, PF00010 helix-loop-helix DNA-binding domain chr1:4382221-4386390 FORWARD Aliases: F13K23.12, F13K23_12 Yes Yes 1.18E-05 No PHD finger family protein, contains Pfam domain, PF00628: PHD-finger chr1:18752205-18755006 FORWARD Aliases: F17J6.14, F17J6_14 Yes Yes 2.16E-05 No basic helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain chr1:18947125-18949421 REVERSE Aliases: F23H24.3, F23H24_3 Yes Yes 3.96E-05 No myb family transcription factor, contains Pfam profile: PF00249: Myb-like DNA-binding domain chr1:21561908-21566630 REVERSE Aliases: F16M22.4, F16M22_4 Yes No #N/A No forkhead-associated domain-containing protein / FHA domain-containing protein chr2:9226404-9227666 FORWARD Aliases: F3K23.29, F3K23_29 Yes No #N/A No Dof-type zinc finger domain-containing protein, similar to zinc finger protein OBP2 GI:5059394 from (Arabidopsis thaliana) chr2:12370707-12372454 FORWARD Aliases: F8N16.10, F8N16_10 Yes Yes 7.29E-05 No zinc finger (CCCH-type) family protein, contains Pfam domain, PF00642: Zinc finger C-x8-C-x5-C-x3-H type (and similar) chr2:13973067-13975496 REVERSE Aliases: T21L14.13, T21L14_13, ZINC FINGER PROTEIN 2 Yes Yes 8.42E-05 No zinc finger (C2H2 type) family protein, contains Prosite PS00028: Zinc finger, C2H2 type, domain; weak similarity to Zinc finger protein T86 (Swiss-Prot:O00488) (Homo sapiens) chr2:15516981-15518584 REVERSE Aliases: T1J8.11, T1J8_11 Yes Yes 4.05E-05 No similar to CCAAT-box binding transcription factor, putative [Arabidopsis thaliana] (TAIR:At3g53340.1); similar to CAAT-box DNA binding protein subunit B (NF-YB) [Zea mays] (GB:CAA42234.1); contains InterPro domain Transcription factor CBF/NF-Y/archaeal (InterPro:IPR003958); contains InterPro domain Histone-like transcription factor/archaeal histone/topoisomerase (InterPro:IPR003957); contains InterPro domain Histone-fold/TFIID-TAF/NF-Y (InterPro:IPR007124); contains InterPro domain Histone-like transcription factor CBF/NF-Y/archaeal histone, subunit A (InterPro:IPR003956) chr2:15583103-15584956 FORWARD Aliases: T2N18.18, T2N18_18 Yes Yes 1.69E-06 No zinc finger (B-box type) family protein chr2:19615066-19616702 FORWARD Aliases: F17A22.28 Yes Yes 4.93E-05 No auxin-responsive AUX/IAA family protein, similar to SP:O24408:AXII_ARATH Auxin-responsive protein IAA18 (Indoleacetic acid-induced protein 18) {Arabidopsis thaliana}; contains Pfam profile: PF02309: AUX/IAA family chr3:5612506-5614416 REVERSE Aliases: IAA26, MDC8.13, PAP1, PHYTOCHROME ASSOCIATED PROTEIN 1 Yes Yes 1.45E-06 No expressed protein chr3:6121059-6123017 FORWARD Aliases: MEB5.8 Yes Yes 6.17E-05 No CCAAT-box binding transcription factor, putative, 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 chr3:19785360-19786969 REVERSE Aliases: F4P12.40 Yes Yes 3.84E-06 No auxin-responsive protein / indoleacetic acid-induced protein 1 (IAA1), identical to SP:P49677 Auxin-responsive protein IAA1 (Indoleacetic acid-induced protein 1) {Arabidopsis thaliana} chr4:8361061-8361982 FORWARD Aliases: AUX/IAA PROTEIN 1, AUXIN REGULATED 1, DL3320W, FCAALL.409, INDOLE 3 ACETIC ACID INDUCIBLE, INDOLEACETIC ACID 1 Yes Yes 0.000032 No scarecrow-like transcription factor 13 (SCL13) chr4:9660996-9663782 REVERSE Aliases: DL4650C, FCAALL.225 Yes Yes 8.03E-05 No expressed protein, weak similarity to storekeeper protein (Solanum tuberosum) GI:14268476; contains Pfam profile PF04504: Protein of unknown function, DUF573 chr4:12918338-12919752 FORWARD Aliases: F24A6.50, F24A6_50 Yes Yes 5.19E-06 No WRKY family transcription factor, contains Pfam profile: PF03106 WRKY DNA -binding domain chr4:13437077-13440804 REVERSE Aliases: ATWRKY20, T15N24.90, T15N24_90, WRKY20 Yes Yes 9.59E-06 No PHD finger protein-related / SET domain-containing protein (TX4), nearly identical over 285 amino acids to trithorax 4 (Arabidopsis thaliana) GI:16118405; contains Pfam profiles PF00856: SET domain, PF00855: PWWP domain; identical to cDNA trithorax 4 (TX4) partial cds GI:16118404 chr4:13894700-13900472 FORWARD Aliases: T13J8.20, T13J8_20 Yes Yes 4.27E-05 No floral homeotic protein APETALA2 (AP2), Identical to (SP:P47927) Floral homeotic protein APETALA2. (Mouse-ear cress) {Arabidopsis thaliana} chr4:17400844-17403329 FORWARD Aliases: AP22.49, AP22_49, APETALA 2, APETALA2, FL1, FLO2, FLORAL HOMEOTIC PROTEIN APETALA 2, FLOWER1 Yes Yes 5.77E-05 No PHD finger family protein / SET domain-containing protein, contains Pfam domain, PF00628: PHD-finger and PF00856: SET domain chr5:3038979-3041045 REVERSE Aliases: F17I14.20, F17I14_20 Yes Yes 0.000041 No zinc finger (CCCH-type) family protein, contains Pfam domain, PF00642: Zinc finger C-x8-C-x5-C-x3-H type (and similar) chr5:4035295-4038798 REVERSE Aliases: None Yes Yes 1.62E-05 No transcription factor, putative / E2F-like repressor E2L1 (E2L1), identical to E2F-like repressor E2L1 GI:20502504 from (Arabidopsis thaliana) chr5:4843951-4846397 FORWARD Aliases: DEL2, DP E2F LIKE 2, E2FD, E2L1, F2G14.80, F2G14_80 Yes Yes 1.02E-05 No similar to zinc finger (CCCH-type) family protein [Arabidopsis thaliana] (TAIR:At3g06410.1); similar to putative floral homeotic protein HUA1 [Oryza sativa (japonica cultivar-group)] (GB:BAD81393.1); contains InterPro domain Zn-finger, C-x8-C-x5-C-x3-H type (InterPro:IPR000571) chr5:6160180-6163132 FORWARD Aliases: T28N17.30, T28N17_30 Yes No #N/A No expressed protein chr5:8867843-8869824 REVERSE Aliases: None Yes Yes 3.88E-05 No expressed protein chr5:17017511-17019835 FORWARD Aliases: MDH9.22, MDH9_22 Yes Yes 1.85E-05 No similar to glycosyl hydrolase family 14 protein [Arabidopsis thaliana] (TAIR:At2g45880.1); similar to beta-amylase [Castanea crenata] (GB:AAK30294.1); contains InterPro domain Glycoside hydrolase, family 14 (InterPro:IPR001554); contains InterPro domain Plant protein of unknown function DUF822 (InterPro:IPR008540) chr5:18370835-18374102 FORWARD Aliases: K9E15.8, K9E15_8 Yes Yes 1.01E-05 No expressed protein, similar to expressed protein [Arabidopsis thaliana] (TAIR:At2g33880.1); similar to hypothetical protein [Oryza sativa (japonica cultivar-group)] (GB:AAT77402.1); contains InterPro domain Homeobox (InterPro:IPR001356) chr5:18666136-18668063 FORWARD Aliases: MCL19.2, MCL19_2 Yes Yes 1.45E-05 Yes similar to putative zinc finger protein [Oryza sativa (japonica cultivar-group)] (GB:AAT77838.1); similar to putative protein inhibitor [Oryza sativa (japonica cultivar-group)] (GB:XP_469578.1); contains InterPro domain DNA-binding SAP (InterPro:IPR003034); contains InterPro domain Zn-finger-like, PHD finger (InterPro:IPR001965); contains InterPro domain Zn-finger, MIZ type (InterPro:IPR004181) chr5:24312116-24318351 FORWARD Aliases: AT5G60420, ATSIZ1, MUF9.5, MUF9_5 Yes Yes 7.34E-07 Yes auxin-responsive protein / indoleacetic acid-induced protein 7 (IAA7), identical to SP:Q38825:AXI7_ARATH Auxin-responsive protein IAA7 (Indoleacetic acid-induced protein 7) chr3:8194718-8196521 FORWARD Aliases: AUXIN RESISTANT 2, AXR2, MXC7.8 Yes Yes 1.32E-05 No homeobox-leucine zipper family protein / homeodomain GLABRA2 like protein 1 (HD-GL2-1), similar to Anthocyaninless2 (ANL2) (GP:5702094) Arabidopsis thaliana, EMBL:AF077335 chr3:22641585-22645950 FORWARD Aliases: T20K12.50 Yes Yes 1.22E-05 No Dof-type zinc finger domain-containing protein, Zn finger protein BBF2aO -Nicotiana tabacum,PID:e246547 chr4:17858354-17859316 FORWARD Aliases: F20D10.120, F20D10_120 Yes Yes 2.85E-07 No zinc finger protein-related, contains Pfam profile PF04396: Protein of unknown function DUF537, weak hit to PF00096: Zinc finger C2H2 type chr5:24632706-24637279 FORWARD Aliases: MAF19.19, MAF19_19 Yes No #N/A No ARID/BRIGHT DNA-binding domain-containing protein, contains Pfam profile PF01388: ARID/BRIGHT DNA binding domain chr1:28713614-28717846 REVERSE Aliases: F14G6.11, F14G6_11 Yes Yes 0.000034 No homeobox protein LUMINIDEPENDENS (LD), identical to Homeobox protein LUMINIDEPENDENS (Swiss-Prot:Q38796) (Arabidopsis thaliana) chr4:1123492-1128397 REVERSE Aliases: LUMINIDEPENDENS, T10P11.15, T10P11_15 Yes Yes 2.29E-05 No SET domain-containing protein, contains Pfam profile PF00856: SET domain chr4:8651999-8662587 FORWARD Aliases: DL3635W, FCAALL.214 Yes Yes 6.94E-07 No homeobox-leucine zipper transcription factor (HB-8), identical to HD-zip transcription factor (athb-8) (GI:7270235) (Arabidopsis thaliana) chr4:15863474-15868629 REVERSE Aliases: ATHB8, HOMEOBOX GENE 8, T16I18.90, T16I18_90 Yes Yes 2.96E-07 No expressed protein, similar to 6b-interacting protein 1 (NtSIP1) (Nicotiana tabacum) GI:18149189 chr1:20184347-20185992 FORWARD Aliases: F15I1.14, F15I1_14 Yes No #N/A No 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. chr4:15116856-15117662 FORWARD Aliases: F6I18.30, F6I18_30 Yes Yes 4.41E-05 No auxin-responsive protein / indoleacetic acid-induced protein 5 (IAA5) / auxin-induced protein (AUX2-27), identical to SP:P33078 Auxin-responsive protein IAA5 (Indoleacetic acid-induced protein 5) (Auxin-induced protein AUX2-27) {Arabidopsis thaliana} chr1:5365660-5366455 REVERSE Aliases: ATAUX2 27, AUX2 27, T16N11.9, T16N11_9