Supplemental Table 3 Site ID Intron Poly(A) site Type NM/KG Inum Region Gene ID Gene Symbol Gene Annotation Hs.120277.1.10 chr3:170997234:170996860 170996950 b NM_153353 7 CDS 151827 LRRC34 leucine rich repeat containing 34 Hs.134470.1.27 chr17:53059664:53084458 53065543 b NM_138962 10 CDS 124540 MSI2 musashi homolog 2 (Drosophila) Hs.162889.1.18 chr14:80367239:80329208 80366262 b NM_152446 12 CDS 145508 C14orf145 chromosome 14 open reading frame 145 Hs.187898.1.27 chr22:28403623:28415294 28404458 b NM_181832 16 3UTR 4771 NF2 neurofibromin 2 (bilateral acoustic neuroma) Hs.228320.1.6 chr10:115527009:115530350 115527470 b BC036365 5 CDS 79949 C10orf81 chromosome 10 open reading frame 81 Hs.266308.1.2 chr11:117279579:117278191 117278967 b NM_032046 12 CDS 84000 TMPRSS13 transmembrane protease, serine 13 Hs.266308.1.4 chr11:117284536:117281662 117283722 b NM_032046 9 CDS 84000 TMPRSS13 transmembrane protease, serine 13 Hs.2689.1.4 chr10:53492398:53563605 53492622 b NM_006258 7 CDS 5592 PRKG1 protein kinase, cGMP-dependent, type I Hs.280781.1.6 chr18:64715646:64829150 64715837 b NM_024781 4 CDS 79839 C18orf14 chromosome 18 open reading frame 14 Hs.305985.2.25 chr12:8983686:8984438 8983942 b BX640639 17 3UTR NA NA NA Hs.312098.1.36 chr1:151843991:151844258 151844232 b NM_003815 15 CDS 8751 ADAM15 a disintegrin and metalloproteinase domain 15 (metargidin) Hs.314338.1.11 chr21:39490293:39481214 39487623 b NM_018963 41 CDS 54014 BRWD1 bromodomain and WD repeat domain containing 1 Hs.33368.1.3 chr15:92685158:92689361 92688314 b NM_018349 6 CDS 55784 MCTP2 multiple C2-domains with two transmembrane regions 2 Hs.346736.1.21 chr2:99270738:99281614 99272414 b AK126402 10 3UTR 51263 MRPL30 mitochondrial ribosomal protein L30 Hs.445061.1.19 chr16:69322898:69290216 69322712 b NM_018052 14 CDS 55697 VAC14 Vac14 homolog (S. cerevisiae) Hs.465061.1.12 chr18:43625708:43622320 43625678 b NM_001003652 10 CDS 4087 SMAD2 SMAD, mothers against DPP homolog 2 (Drosophila) Hs.480068.1.11 chr4:82734983:82726618 82729226 b NM_152545 4 CDS 153020 RASGEF1B RasGEF domain family, member 1B Hs.481361.1.17 chr4:187463566:187468216 187463958 b NM_001006655 13 CDS 25854 DKFZP564J102 DKFZP564J102 protein Hs.496684.1.15 chrX:119357466:119347200 119354582 b NM_002294 8 CDS 3920 LAMP2 lysosomal-associated membrane protein 2 Hs.501012.1.14 chr10:111868485:111868958 111868688 b NM_001121 6 CDS 120 ADD3 adducin 3 (gamma) CD44 antigen (homing function and Indian blood group Hs.502328.1.13 chr11:35168189:35192974 35168365 b NM_001001391 5 CDS 960 CD44 system) Hs.512461.1.17 chr9:129949373:129966747 129950152 b NM_020960 14 CDS 57720 GPR107 G protein-coupled receptor 107 Hs.512676.1.10 chr11:118393877:118393466 118393618 b NM_001028 2 CDS 6230 RPS25 ribosomal protein S25 Hs.523360.1.15 chr10:134390400:134413010 134390839 b NM_005539 9 CDS 3632 INPP5A inositol polyphosphate-5-phosphatase, 40kDa Hs.523360.1.24 chr10:134441277:134444342 134441371 b Z31695 12 CDS 3632 INPP5A inositol polyphosphate-5-phosphatase, 40kDa Hs.527874.1.36 chr12:70336931:70327861 70336390 b NM_144982 2 CDS 196441 MGC23401 hypothetical protein MGC23401 Hs.529303.1.16 chr2:218929080:218929619 218929420 b NM_005731 5 CDS 10109 ARPC2 actin related protein 2/3 complex, subunit 2, 34kDa Hs.531785.1.11 chr2:20745283:20740634 20743575 b NM_022460 6 CDS 64342 HS1BP3 HS1-binding protein 3 Hs.549079.1.1 chr7:71886910:72190310 71887445 b NM_003602 4 CDS 8468 FKBP6 FK506 binding protein 6, 36kDa Hs.6449.1.25 chr1:1296298:1290922 1294012 b AK021939 2 CDS 54973 CPSF3L cleavage and polyadenylation specific factor 3-like Hs.100299.1.13 chr17:30340796:30342094 30340956 c NM_002311 4 CDS 3980 LIG3 ligase III, DNA, ATP-dependent Hs.100299.1.14 chr17:30340796:30342094 30341012 c NM_002311 4 CDS 3980 LIG3 ligase III, DNA, ATP-dependent Hs.100299.1.15 chr17:30340796:30342094 30341167 c NM_002311 4 CDS 3980 LIG3 ligase III, DNA, ATP-dependent Hs.100743.1.7 chr2:159020745:158995915 159020613 c NM_138803 7 CDS 130940 LOC130940 hypothetical protein BC015395 Hs.100914.1.47 chr18:13104251:13106375 13104624 c NM_018069 36 3UTR 55125 Cep192 centrosomal protein 192 kDa Hs.101014.1.16 chr11:95194791:95200597 95195305 c D42054 7 CDS 9702 PIG8 translokin Hs.101014.1.18 chr11:95195389:95200597 95196027 c NM_014679 8 CDS 9702 PIG8 translokin Hs.101302.1.17 chr6:75879639:75875604 75879458 c NM_004370 51 CDS 1303 COL12A1 collagen, type XII, alpha 1 Hs.101439.1.10 chr9:121831027:121816813 121830743 c NM_194252 3 CDS 158135 TTLL11 tubulin tyrosine ligase-like family, member 11 Hs.101480.1.35 chr17:33018868:33011825 33018543 c NM_007247 6 CDS 11276 AP1GBP1 AP1 gamma subunit binding protein 1 solute carrier family 6 (neurotransmitter transporter, GABA), Hs.101791.1.3 chr3:10840078:10860898 10842183 c NM_014229 4 CDS 6538 SLC6A11 member 11 Hs.101840.1.13 chr1:177754471:177756017 177754813 c NM_001531 5 CDS 3140 MR1 major histocompatibility complex, class I-related Hs.102798.1.21 chr11:14589087:14497164 14588943 c NM_148976 2 CDS 5682 PSMA1 proteasome (prosome, macropain) subunit, alpha type, 1 Hs.102914.1.20 chrX:119448158:119445992 119448073 c NM_003588 20 CDS 8450 CUL4B cullin 4B Hs.102929.1.33 chr3:48693723:48692667 48693630 c NM_016453 5 CDS 51517 NCKIPSD NCK interacting protein with SH3 domain Hs.103183.1.25 chrX:146732683:146735799 146732780 c M67468 15 CDS 2332 FMR1 fragile X mental retardation 1 Hs.103527.1.4 chr1:153590039:153589439 153589922 c NM_003975 8 3UTR 9047 SH2D2A SH2 domain protein 2A Hs.104123.1.7 chrX:12587923:12597282 12588145 c NM_002765 4 CDS 5634 PRPS2 phosphoribosyl pyrophosphate synthetase 2 Hs.104672.1.15 chr3:101315586:101132565 101313731 c NM_182909 1 5UTR 11259 DOC1 downregulated in ovarian cancer 1 Hs.104806.1.4 chr20:3750941:3752517 3751143 c NM_018347 2 CDS 55317 C20orf29 chromosome 20 open reading frame 29 Hs.10499.1.26 chr16:57271261:57270300 57271015 c NM_018231 3 CDS 55238 FLJ10815 amino acid transporter Hs.105016.1.16 chr1:70470091:70454549 70469850 c NM_030816 9 CDS 81573 ANKRD13C ankyrin repeat domain 13C Hs.105134.1.12 chrX:131244225:131241836 131243943 c NM_018388 6 CDS 55796 MBNL3 muscleblind-like 3 (Drosophila) Hs.105153.1.3 chr3:20187219:20177723 20185982 c NM_001012410 8 CDS 151648 SGOL1 shugoshin-like 1 (S. pombe) Hs.105153.1.4 chr3:20187219:20177723 20186549 c NM_001012410 8 CDS 151648 SGOL1 shugoshin-like 1 (S. pombe) Hs.105153.1.8 chr3:20187219:20177723 20186990 c NM_001012410 8 CDS 151648 SGOL1 shugoshin-like 1 (S. pombe) Hs.105818.1.16 chr5:133730566:133730135 133730168 c BC041799 1 5UTR 51265 CDKL3 cyclin-dependent kinase-like 3 Hs.105818.1.7 chr5:133671727:133670293 133671469 c BC041799 9 CDS 51265 CDKL3 cyclin-dependent kinase-like 3 Hs.105818.1.8 chr5:133671727:133670293 133671591 c BC041799 9 CDS 51265 CDKL3 cyclin-dependent kinase-like 3 Hs.107101.1.8 chr1:2153313:2150808 2153168 c NM_182533 4 CDS 199990 C1orf86 chromosome 1 open reading frame 86 Hs.107149.1.11 chr1:181825732:181824709 181825629 c NM_030934 12 CDS 81627 C1orf25 chromosome 1 open reading frame 25 Hs.108530.1.16 chr6:76025215:76022732 76024690 c NM_018247 6 CDS 55754 TMEM30A transmembrane protein 30A Hs.10941.1.11 chr2:182807702:182819206 182807918 c BC017943 5 3UTR 151242 PPP1R1C protein phosphatase 1, regulatory (inhibitor) subunit 1C Hs.10941.1.12 chr2:182807702:182819206 182807989 c BC017943 5 3UTR 151242 PPP1R1C protein phosphatase 1, regulatory (inhibitor) subunit 1C Hs.109439.1.20 chr9:92231690:92228134 92231478 c NM_014057 5 CDS 4969 OGN osteoglycin (osteoinductive factor, mimecan) Hs.109520.1.15 chr13:51889192:51888230 51889050 c NM_016075 12 CDS 51028 VPS36 vacuolar protein sorting 36 (yeast) Hs.109590.1.7 chr4:77550101:77556400 77550268 c AK124936 5 CDS 8987 GENX-3414 genethonin 1 Hs.110445.1.7 chr7:65900273:65897637 65900196 c NM_016038 4 CDS 51119 SBDS Shwachman-Bodian-Diamond syndrome Hs.11067.1.24 chr17:70465830:70463647 70465662 c NM_030630 12 CDS 283987 C17orf28 chromosome 17 open reading frame 28 Hs.111286.1.4 chr15:86812260:86819344 86812490 c NM_176805 2 CDS 64963 MRPS11 mitochondrial ribosomal protein S11 Hs.111749.1.1 chr2:190474826:190482021 190475534 c NM_000534 1 5UTR 5378 PMS1 PMS1 postmeiotic segregation increased 1 (S. cerevisiae) Hs.111749.1.12 chr2:190495987:190508248 190497286 c NM_000534 4 CDS 5378 PMS1 PMS1 postmeiotic segregation increased 1 (S. cerevisiae) Hs.112160.1.17 chr15:62903029:62901863 62902506 c NM_025049 1 CDS 80119 C15orf20 chromosome 15 open reading frame 20 Hs.112377.1.4 chr11:124123495:124122774 124123216 c NM_014312 6 CDS 23584 VSIG2 V-set and immunoglobulin domain containing 2 Hs.112895.1.10 chr9:136134055:136131761 136133917 c NM_144653 3 CDS 138151 BTBD14A BTB (POZ) domain containing 14A Hs.112949.1.16 chr1:51473771:51472205 51473231 c AF007170 13 CDS 22996 C1orf34 chromosome 1 open reading frame 34 Hs.11314.1.10 chr20:34296263:34306913 34296691 c NM_015511 3 CDS 25980 C20orf4 chromosome 20 open reading frame 4 Hs.11314.1.6 chr20:34291962:34296032 34292188 c NM_015511 2 CDS 25980 C20orf4 chromosome 20 open reading frame 4 Hs.113150.1.29 chr14:35267318:35264111 35267297 c NM_014990 13 CDS 253959 GARNL1 GTPase activating Rap/RanGAP domain-like 1 Hs.113157.1.7 chr3:37645832:37670208 37646014 c NM_002207 16 CDS 3680 ITGA9 integrin, alpha 9 Hs.11355.1.18 chr12:97433819:97440475 97433959 c BC053675 4 CDS 7112 TMPO thymopoietin neurofibromin 1 (neurofibromatosis, von Recklinghausen Hs.113874.1.16 chr17:26573074:26574587 26573908 c NM_000267 15 CDS 4763 NF1 disease, Watson disease) neurofibromin 1 (neurofibromatosis, von Recklinghausen Hs.113874.1.59 chr17:26709767:26710112