#id region start end strand GENCODE_exons GENCODE_flag start end strant overlappingSize #2 GIS pseudogenes RPL36_GISPgene_13 ENr333 290618 290998 - "RP3-477O4.12-005-exon4"; VEGA_Known 289057 291641 + 380 LAMR1_GISPgene_26 ENr223 266820 267795 + "RP11-398K22.12-001-exon3"; VEGA_Novel_transcript_val 267025 267832 + 770 #17 HAVAVA pseudogenes AC002543.2 ENm001 702988 705910 - "AC002543.1-007-exon2"; VEGA_Known 703246 703824 + 578 RP11-143H17.1 ENm006 1293946 1313338 + "GS1-273L24.4-006-exon1"; VEGA_Known 1304495 1304610 - 115 AC010492.4 ENm007 418181 419409 - "AC012314.14-002-exon5"; VEGA_Known 419179 421090 + 230 AC008984.5 ENm007 476942 477651 - "AC010518.2-003-exon2"; VEGA_Known 477420 477455 - 35 AC008984.4 ENm007 499704 500712 - "AC008984.2-001-exon5"; VEGA_Novel_transcript_val 499920 500086 - 166 AC008984.6 ENm007 507772 510934 - "AC008984.2-001-exon4"; VEGA_Novel_transcript_val 509600 509755 - 155 AC009892.8 ENm007 827621 828530 + "AC009892.7-001-exon2"; VEGA_Novel_transcript 827711 829277 + 819 AC006293.1 ENm007 888614 892962 + "AC006293.3-001-exon1"; VEGA_Novel_transcript 890219 890419 + 200 Z84721.2 ENm008 153121 155155 + "Z84721.3-002-exon1"; VEGA_Known 154481 154685 + 204 AC114812.6 ENr131 160010 160738 - "AC114812.3-001-exon1"; VEGA_Novel_transcript_val 159572 160837 - 728 AC114812.5 ENr131 171364 172091 - "AC114812.4-002-exon2"; VEGA_Novel_transcript_val 171127 171613 - 249 AC005538.2 ENr131 282959 285052 - "AC005538.3-001-exon2"; VEGA_Novel_transcript 282259 284172 - 1213 RP11-398K22.9 ENr223 268454 269769 + "RP11-257K9.4-005-exon2"; VEGA_Known 268490 268532 - 42 AC011330.5 ENr233 223056 243741 - "AC011330.3-010-exon2"; VEGA_Known 223820 223945 - 125 AC018512.3 ENr233 286583 304567 - "AC018512.2-002-exon4"; VEGA_Novel_transcript_val 295336 296410 - 1074 RP3-477O4.5 ENr333 267398 269487 - "RP3-477O4.8-001-exon2"; VEGA_Putative 267166 267457 - 59 RP3-477O4.4 ENr333 290661 290978 - "RP3-477O4.12-005-exon4"; VEGA_Known 289057 291641 + 317 #24 UCSC retrogenes AK090399 ENm007 446526 450643 - "AC010518.1-001-exon14"; VEGA_Known 445903 446911 - 385 AK091160 ENm001 702995 705915 - "AC002543.1-007-exon2"; VEGA_Known 703246 703824 + 578 CR457029 ENr223 268456 269767 + "RP11-257K9.4-005-exon2"; VEGA_Known 268490 268532 - 42 AF230412 ENm009 954684 956029 - "AC109341.3-001-exon6"; VEGA_Known 954984 955084 + 100 AK090399_dup2 ENm007 842664 847930 + "AC011515.1-001-exon3"; VEGA_Known 842499 842747 + 83 AF009634 ENm007 889560 890444 + "AC006293.3-001-exon1"; VEGA_Novel_transcript 890219 890419 + 200 AL080197 ENm004 750634 751258 - "RP1-127L4.6-001-exon1"; VEGA_Known 751018 751322 - 240 AK125808 ENm004 976208 979365 - "RP1-149A16.3-001-exon3"; VEGA_Novel_transcript 975290 976377 + 169 BC032342 ENm007 499611 500537 - "AC008984.2-001-exon5"; VEGA_Novel_transcript_val 499920 500086 - 166 BC070204 ENm011 70341 374955 + "AC051649.1-010-exon1"; VEGA_Known 106358 106528 + 170 BC065839 ENm005 200521 202010 - "AP000274.6-001-exon1"; VEGA_Novel_transcript 200521 201826 - 1305 BC062714 ENr223 266798 267822 + "RP11-398K22.12-001-exon3"; VEGA_Novel_transcript_val 267025 267832 + 797 AL050273 ENr333 290620 291011 - "RP3-477O4.12-005-exon4"; VEGA_Known 289057 291641 + 391 AF135565_dup2 ENm007 999395 999696 + "AC011501.6-001-exon4"; VEGA_Known 999396 999695 + 299 CR605093 ENr131 282306 285071 - "AC005538.3-001-exon2"; VEGA_Novel_transcript 282259 284172 - 1866 AF135565 ENm007 907304 907605 + "AC006293.2-001-exon4"; VEGA_Known 907305 907604 + 299 CR612433 ENr131 170876 172094 - "AC114812.4-002-exon2"; VEGA_Novel_transcript_val 171127 171613 - 486 CR614088 ENr223 494301 496522 - "RP11-505P4.2-001-exon7"; VEGA_Known 492242 494426 - 125 AF135563 ENm007 921653 921954 + "AC011501.1-001-exon3"; VEGA_Known 921654 921953 + 299 AF135565_dup1 ENm007 953012 953313 + "AC011501.3-001-exon3"; VEGA_Known 953013 953312 + 299 AJ010233 ENm004 782798 783724 + "RP1-90G24.3-001-exon5"; VEGA_Known 782472 783386 - 588 BC009343 ENm006 624177 628541 + "XX-FW81657B9.3-001-exon19"; VEGA_Known 624135 624374 + 197 CR533498 ENr131 159992 160736 - "AC114812.3-001-exon1"; VEGA_Novel_transcript_val 159572 160837 - 744 AF208683 ENm007 984475 985928 + "AC011501.5-001-exon3"; VEGA_Known 984476 984760 + 284 #17 Yale pseudogenes ENCODE_YalePgene_50 ENr233 288168 304567 - "AC018512.2-002-exon4"; VEGA_Novel_transcript_val 295336 296410 - 1074 ENCODE_YalePgene_148 ENm007 888908 893205 + "AC006293.3-001-exon1"; VEGA_Novel_transcript 890219 890419 + 200 ENCODE_YalePgene_21 ENr131 160012 160300 - "AC114812.3-001-exon1"; VEGA_Novel_transcript_val 159572 160837 - 288 ENCODE_YalePgene_22 ENr131 171366 172092 - "AC114812.4-002-exon2"; VEGA_Novel_transcript_val 171127 171613 - 247 ENCODE_YalePgene_23 ENr131 282960 285053 - "AC005538.3-001-exon2"; VEGA_Novel_transcript 282259 284172 - 1212 ENCODE_YalePgene_40 ENr223 266895 267786 + "RP11-398K22.12-001-exon3"; VEGA_Novel_transcript_val 267025 267832 + 761 ENCODE_YalePgene_41 ENr223 268454 269774 + "RP11-257K9.4-005-exon2"; VEGA_Known 268490 268532 - 42 ENCODE_YalePgene_53 ENr312 430556 430973 - "AP003039.2-001-exon1"; VEGA_Artifact 429782 433263 - 417 ENCODE_YalePgene_71 ENr333 290659 290959 - "RP3-477O4.12-005-exon4"; VEGA_Known 289057 291641 + 300 ENCODE_YalePgene_77 ENm001 702957 704906 - "AC002543.1-007-exon2"; VEGA_Known 703246 703824 + 578 ENCODE_YalePgene_132 ENm007 477364 477700 - "AC010518.2-003-exon2"; VEGA_Known 477420 477455 - 35 ENCODE_YalePgene_133 ENm007 499701 500718 - "AC008984.2-001-exon5"; VEGA_Novel_transcript_val 499920 500086 - 166 ENCODE_YalePgene_135 ENm007 509595 509898 - "AC008984.2-001-exon4"; VEGA_Novel_transcript_val 509600 509755 - 155 ENCODE_YalePgene_139 ENm007 713178 713457 + "AC009892.1-002-exon3"; VEGA_Known 713179 713457 + 278 ENCODE_YalePgene_142 ENm007 827612 828542 + "AC009892.7-001-exon2"; VEGA_Novel_transcript 827711 829277 + 831 ENCODE_YalePgene_11 ENr122 116108 116298 + "AC069356.3-001-exon1"; VEGA_Known 116108 116275 + 167 ENCODE_YalePgene_152 ENm008 1859 2739 + "Z84812.1-002-exon2"; VEGA_Novel_transcript 2294 2402 + 108