Chr PhyloCSF start PhyloCSF end Strand Number of PhyloCSF regions PhyloCSF region ID Top rank CpG island overlap Notes Category List Novel? 1 26164164 26171664 -1 7 chr1:26164164-26164448-, chr1:26165819-26165923-, chr1:26166032-26166109-, chr1:26168413-26168502-, chr1:26171219-26171335-, chr1:26171483-26171515-, chr1:26171623-26171664- 118 yes protein-coding gene ENSG00000282872 protein-coding gene first 1000 PCCRs yes 1 41628751 41628840 -1 1 chr1:41628751-41628840- 419 no protein-coding gene ENSG00000284895 protein-coding gene first 1000 PCCRs yes 1 42789876 42798195 1 5 chr1:42789876-42789926+, chr1:42792818-42792862+, chr1:42793600-42793740+, chr1:42794424-42794606+, chr1:42798121-42798195+ 135 no protein-coding gene ENSG00000274386 protein-coding gene first 1000 PCCRs no 1 46533057 46533488 -1 1 chr1:46533057-46533488- 991 yes protein-coding gene ENSG00000282881 protein-coding gene first 1000 PCCRs no 1 150912315 150912443 1 1 chr1:150912315-150912443+ 937 no protein-coding gene ENSG00000283324 protein-coding gene first 1000 PCCRs yes 1 152948552 152948878 1 1 chr1:152948552-152948878+ 233 no protein-coding gene ENSG00000283227 protein-coding gene first 1000 PCCRs yes 1 171623932 171623982 1 1 chr1:171623932-171623982+ 2157 no protein coding gene ENSG00000283683 protein-coding gene previously unannotated PCCR yes 1 173635609 173636934 1 3 chr1:173635609-173635647+, chr1:173635798-173635848+, chr1:173636908-173636934+ 1550 no protein coding gene ENSG00000232113 protein-coding gene lncRNA PCCR no 1 178479544 178490348 -1 4 chr1:178479544-178479624-, chr1:178482309-178482341-, chr1:178488562-178488600-, chr1:178490136-178490348- 820 no protein-coding gene ENSG00000188585 protein-coding gene first 1000 PCCRs no 1 244730511 244730827 -1 4 chr1:244730511-244730552-, chr1:244730558-244730710-, chr1:244730662-244730709-, chr1:244730714-244730827- 1827 yes protein coding gene ENSG00000284188 protein-coding gene previously unannotated PCCR no 2 97701174 97702729 1 2 chr2:97701174-97701245+, chr2:97702688-97702729+ 818 no protein-coding gene ENSG00000228486 protein-coding gene first 1000 PCCRs no 2 126898979 126899581 1 2 chr2:126898979-126899080+, chr2:126899522-126899581+ 15 no protein-coding gene ENSG00000237524 protein-coding gene first 1000 PCCRs no 2 131035089 131040270 1 2 chr2:131035089-131035271+, chr2:131040244-131040270+ 62 yes protein-coding gene ENSG00000284479 protein-coding gene first 1000 PCCRs no 2 206644318 206644590 1 1 chr2:206644318-206644590+ 527 no protein-coding gene ENSG00000235118 protein-coding gene first 1000 PCCRs no 2 224716279 224716368 -1 1 chr2:224716279-224716368- 583 no protein-coding gene ENSG00000283428 protein-coding gene first 1000 PCCRs yes 2 227598893 227617809 1 7 chr2:227598893-227598934+, chr2:227599052-227599102+, chr2:227599130-227599243+, chr2:227608778-227609095+, chr2:227614620-227614718+, chr2:227614734-227614832+, chr2:227617456-227617809+ 853 no protein-coding genes ENSG00000284643, ENSG00000284622, ENSG00000284704, ENSG00000284631 protein-coding gene (shared cluster) first 1000 PCCRs yes, all 4 2 227724476 227728420 -1 3 chr2:227724476-227724592-, chr2:227724617-227724757-, chr2:227728331-227728420- 1636 no protein coding gene ENSG00000284725 protein-coding gene previously unannotated PCCR yes 2 227745894 227746196 1 2 chr2:227745894-227746025+, chr2:227746074-227746196+ 608 no protein-coding gene ENSG00000284635 protein-coding gene first 1000 PCCRs yes 2 241897179 241897295 -1 1 chr2:241897179-241897295- 22742 no protein coding gene ENSG00000216921 protein-coding gene lncRNA PCCR yes 3 46617165 46625248 1 2 chr3:46617165-46617326+, chr3:46625129-46625248+ 79 no protein-coding gene ENSG00000283473 protein-coding gene first 1000 PCCRs no 3 70196929 70206785 -1 2 chr3:70196929-70197186-, chr3:70206606-70206785- 692 no protein-coding gene ENSG00000242120 protein-coding gene first 1000 PCCRs yes 3 88466612 88467418 1 4 chr3:88466612-88466896+, chr3:88467116-88467157+, chr3:88467191-88467220+, chr3:88467380-88467418+ 585 no protein-coding gene ENSG00000283434 protein-coding gene first 1000 PCCRs no 3 109148279 109148317 1 1 chr3:109148279-109148317+ 2594 no protein coding gene ENSG00000241224 protein-coding gene lncRNA PCCR yes 3 150891061 150894305 -1 4 chr3:150891061-150891105-, chr3:150893338-150893424-, chr3:150894204-150894239-, chr3:150894276-150894305- 469 no protein-coding gene ENSG00000214237 protein-coding gene first 1000 PCCRs no 3 155290950 155291024 -1 1 chr3:155290950-155291024- 553 no protein-coding gene ENSG00000240045 protein-coding gene first 1000 PCCRs no 4 574887 576356 -1 8 chr4:574887-575498-, chr4:575505-575531-, chr4:575540-575593-, chr4:575541-576239-, chr4:575629-575664-, chr4:575824-576240-, chr4:575930-576238-, chr4:576252-576356- 703 yes protein-coding gene ENSG00000273238 protein-coding gene first 1000 PCCRs yes 4 6070061 6070162 -1 1 chr4:6070061-6070162- 426 no protein-coding gene ENSG00000284684 protein-coding gene first 1000 PCCRs yes 4 6673946 6674539 1 2 chr4:6673946-6673984+, chr4:6674405-6674539+ 949 yes protein-coding gene ENSG00000170846; found after examing lncRNAs for coding potential protein-coding gene re-ranking yes 4 55820027 55820143 1 1 chr4:55820027-55820143+ 126 no protein-coding gene ENSG00000250821 protein-coding gene first 1000 PCCRs yes 4 106358309 106367411 -1 3 chr4:106358309-106358437-, chr4:106367043-106367153-, chr4:106367184-106367411- 338 no protein-coding gene ENSG00000250298 protein-coding gene first 1000 PCCRs no 4 121764920 121765120 -1 1 chr4:121764920-121765120- 472 yes protein-coding gene ENSG00000164112 protein-coding gene first 1000 PCCRs yes 4 146217013 146230318 1 5 chr4:146217013-146217075+, chr4:146222356-146222442+, chr4:146222482-146222577+, chr4:146224449-146224520+, chr4:146230244-146230318+ 309 no protein-coding gene ENSG00000250673 protein-coding gene first 1000 PCCRs yes 4 149548480 149553233 -1 3 chr4:149548480-149548587-, chr4:149553138-149553173-, chr4:149553183-149553233- 169 no protein-coding gene ENSG00000234828 protein-coding gene first 1000 PCCRs no 4 164770444 164770545 1 1 chr4:164770444-164770545+ 285 no protein-coding gene ENSG00000248771 protein-coding gene first 1000 PCCRs yes 5 127941235 127941354 1 1 chr5:127941235-127941354+ 127 no protein-coding gene ENSG00000230561 protein-coding gene first 1000 PCCRs no 5 136192216 136192524 -1 1 chr5:136192216-136192524- 256 yes protein-coding gene ENSG00000271824 protein-coding gene first 1000 PCCRs yes 5 139472562 139472807 1 3 chr5:139472562-139472618+, chr5:139472640-139472750+, chr5:139472772-139472807+ 56 no protein-coding gene ENSG00000283288 protein-coding gene first 1000 PCCRs yes 5 148243009 148243425 1 3 chr5:148243009-148243110+, chr5:148243279-148243326+, chr5:148243390-148243425+ 1343 no protein coding gene ENSG00000248109 protein-coding gene previously unannotated PCCR no 5 170234995 170235066 1 1 chr5:170234995-170235066+ 1010 no protein coding gene ENSG00000234511 protein-coding gene lncRNA PCCR no 6 33329029 33329271 -1 1 chr6:33329029-33329271- 635 no protein-coding gene ENSG00000285064 protein-coding gene first 1000 PCCRs yes 6 34235179 34247507 -1 20 chr6:34235179-34235205-, chr6:34235466-34235546-, chr6:34235549-34235656-, chr6:34236757-34236873-, chr6:34236758-34236784-, chr6:34236943-34236984-, chr6:34237335-34237421-, chr6:34237340-34237462-, chr6:34237414-34237551-, chr6:34237470-34237505-, chr6:34237580-34237642-, chr6:34237650-34237679-, chr6:34237652-34237774-, chr6:34237947-34238009-, chr6:34238107-34238196-, chr6:34238127-34238228-, chr6:34238271-34238306-, chr6:34246806-34246871-, chr6:34247041-34247148-, chr6:34247466-34247507- 204 yes protein-coding gene ENSG00000186577 protein-coding gene first 1000 PCCRs yes 6 44217472 44223932 1 3 chr6:44217472-44217672+, chr6:44217694-44217723+, chr6:44223897-44223932+ 864 yes protein-coding gene ENSG00000262179 protein-coding gene first 1000 PCCRs no 6 99531419 99531785 1 3 chr6:99531419-99531478+, chr6:99531637-99531714+, chr6:99531717-99531785+ 1091 no protein coding gene ENSG00000228439 protein-coding gene lncRNA PCCR no 6 138378073 138382799 1 3 chr6:138378073-138378186+, chr6:138382515-138382721+, chr6:138382770-138382799+ 212 no protein-coding gene ENSG00000262543 protein-coding gene first 1000 PCCRs yes 7 290122 291410 1 2 chr7:290122-290274+, chr7:291354-291410+ 506 yes protein-coding gene ENSG00000248767 protein-coding gene first 1000 PCCRs yes 7 7673372 7673452 1 1 chr7:7673372-7673452+ 1087 no protein coding gene ENSG00000219545 protein-coding gene lncRNA PCCR no 7 45863094 45866101 -1 2 chr7:45863094-45863165-, chr7:45866060-45866101- 944 no protein-coding gene ENSG00000283247 protein-coding gene first 1000 PCCRs yes 7 90319404 90319679 -1 1 chr7:90319404-90319679- 428 no protein-coding gene ENSG00000283267 protein-coding gene first 1000 PCCRs yes 7 99604416 99610562 1 4 chr7:99604416-99604595+, chr7:99606747-99606806+, chr7:99607681-99607779+, chr7:99610515-99610562+ 1102 no protein coding gene ENSG00000244219 protein-coding gene lncRNA PCCR no 7 102539611 102539706 -1 1 chr7:102539611-102539706- 367 no protein-coding gene ENSG00000284981; found after looking at high-scoring intergenic PCCRs protein-coding gene re-ranking no 7 113117405 113117578 -1 1 chr7:113117405-113117578- 726 no protein-coding gene ENSG00000214194 protein-coding gene first 1000 PCCRs no 7 128866410 128869879 1 5 chr7:128866410-128866577+, chr7:128866596-128866829+, chr7:128868665-128868772+, chr7:128869294-128869329+, chr7:128869847-128869879+ 206 yes protein-coding gene ENSG00000272899 protein-coding gene first 1000 PCCRs no 7 143639739 143647639 -1 12 chr7:143639739-143639837-, chr7:143639865-143639924-, chr7:143642640-143642978-, chr7:143643888-143644079-, chr7:143644473-143644682-, chr7:143645951-143646040-, chr7:143646671-143646697-, chr7:143646725-143646958-, chr7:143647001-143647084-, chr7:143647112-143647147-, chr7:143647157-143647273-, chr7:143647286-143647639- 81 no protein-coding gene ENSG00000283528 protein-coding gene first 1000 PCCRs yes 7 150407660 150408220 1 1 chr7:150407660-150408220+ 488 yes protein-coding gene ENSG00000284691 protein-coding gene first 1000 PCCRs no 7 151207868 151210318 -1 2 chr7:151207868-151208110-, chr7:151210190-151210318- 60 no protein-coding gene ENSG00000285480 protein-coding gene first 1000 PCCRs yes 8 10496192 10498809 -1 6 chr8:10496192-10496221-, chr8:10496290-10496466-, chr8:10496650-10496718-, chr8:10497773-10497907-, chr8:10498609-10498689-, chr8:10498693-10498809- 31 no protein-coding gene ENSG00000253649 protein-coding gene first 1000 PCCRs yes 8 141514697 141518615 1 3 chr8:141514697-141514771+, chr8:141518215-141518568+, chr8:141518571-141518615+ 102 yes protein-coding gene ENSG00000226490 protein-coding gene first 1000 PCCRs yes 8 143788915 143790593 1 7 chr8:143788915-143789058+, chr8:143789199-143789240+, chr8:143789436-143789489+, chr8:143789761-143789868+, chr8:143789973-143790071+, chr8:143790141-143790269+, chr8:143790351-143790593+ 85 no protein-coding gene ENSG00000203499 protein-coding gene first 1000 PCCRs no 9 32552441 32552896 1 3 chr9:32552441-32552476+, chr9:32552614-32552643+, chr9:32552801-32552896+ 324 yes protein-coding gene ENSG00000235453 protein-coding gene first 1000 PCCRs yes 9 35910464 35910637 1 1 chr9:35910464-35910637+ 389 no protein-coding gene ENSG00000235387 protein-coding gene first 1000 PCCRs no 9 38694791 38703999 -1 2 chr9:38694791-38694868-, chr9:38703856-38703999- 214 no protein-coding gene ENSG00000283329 protein-coding gene first 1000 PCCRs yes 9 87956321 87956437 1 1 chr9:87956321-87956437+ 67 no protein-coding gene ENSG00000283205 protein-coding gene first 1000 PCCRs yes 9 114657748 114666675 -1 2 chr9:114657748-114657774-, chr9:114666637-114666675- 2004 no protein coding gene ENSG00000230054 protein-coding gene lncRNA PCCR no 9 120793125 120799627 1 4 chr9:120793125-120793175+, chr9:120793151-120793186+, chr9:120793156-120793215+, chr9:120799571-120799627+ 982 yes protein-coding gene ENSG00000214654; found after looking at high-scoring intergenic PCCRs protein-coding gene re-ranking yes 9 131546695 131558199 1 5 chr9:131546695-131546730+, chr9:131554556-131554615+, chr9:131554655-131555038+, chr9:131556070-131556219+, chr9:131558047-131558199+ 95 yes protein-coding gene ENSG00000283526 protein-coding gene first 1000 PCCRs no 9 134025449 134027002 1 2 chr9:134025449-134025478+, chr9:134026745-134027002+ 592 yes protein-coding gene ENSG00000235106 protein-coding gene first 1000 PCCRs no 9 135614297 135617015 1 4 chr9:135614297-135614353+, chr9:135615365-135615454+, chr9:135616591-135616659+, chr9:135616938-135617015+ 1311 no protein coding gene ENSG00000236543 protein-coding gene lncRNA PCCR no 9 137217946 137221875 1 3 chr9:137217946-137217984+, chr9:137218066-137218593+, chr9:137221819-137221875+ 549 yes protein-coding gene ENSG00000284976 protein-coding gene first 1000 PCCRs yes 10 14838293 14843891 1 5 chr10:14838293-14838331+, chr10:14842282-14842623+, chr10:14842801-14842830+, chr10:14843424-14843504+, chr10:14843595-14843891+ 43 yes protein-coding gene ENSG00000284024 protein-coding gene first 1000 PCCRs yes 10 47922111 47923091 1 2 chr10:47922111-47922701+, chr10:47922753-47923091+ 121 no protein-coding gene ENSG00000264717 protein-coding gene first 1000 PCCRs no 10 102450527 102451009 -1 3 chr10:102450527-102450556-, chr10:102450572-102450766-, chr10:102450917-102451009- 493 yes protein-coding gene ENSG00000120055 protein-coding gene first 1000 PCCRs yes 10 130110698 130110751 -1 1 chr10:130110698-130110751- 1601 yes protein coding gene ENSG00000237489 protein-coding gene lncRNA PCCR yes 11 18599926 18603819 1 3 chr11:18599926-18599991+, chr11:18603124-18603189+, chr11:18603775-18603819+ 1296 no protein coding gene ENSG00000247595 protein-coding gene lncRNA PCCR no 11 62832028 62832534 -1 2 chr11:62832028-62832078-, chr11:62832442-62832534- 402 yes protein-coding gene ENSG00000283268 protein-coding gene first 1000 PCCRs yes 11 69157426 69157993 1 2 chr11:69157426-69157476+, chr11:69157865-69157993+ 219 no protein-coding gene ENSG00000284713 protein-coding gene first 1000 PCCRs yes 11 94528083 94528205 1 1 chr11:94528083-94528205+ 158 no protein-coding gene ENSG00000257057 protein-coding gene first 1000 PCCRs no 11 118013793 118015810 -1 3 chr11:118013793-118013879-, chr11:118014707-118014742-, chr11:118015682-118015810- 391 no protein-coding gene ENSG00000255274 protein-coding gene first 1000 PCCRs yes 11 125947712 125955911 1 15 chr11:125947712-125947852+, chr11:125947868-125948005+, chr11:125948304-125948417+, chr11:125948481-125948516+, chr11:125948547-125948585+, chr11:125950013-125950294+, chr11:125950960-125951061+, chr11:125951104-125951136+, chr11:125951827-125951910+, chr11:125951923-125952048+, chr11:125953399-125953587+, chr11:125954086-125954280+, chr11:125954293-125954388+, chr11:125955059-125955172+, chr11:125955867-125955911+ 249 no protein-coding gene ENSG00000283703 protein-coding gene first 1000 PCCRs no 12 2849327 2855413 -1 7 chr12:2849327-2849434-, chr12:2849453-2849512-, chr12:2854907-2854993-, chr12:2855057-2855125-, chr12:2855144-2855269-, chr12:2855276-2855317-, chr12:2855381-2855413- 6 no protein-coding gene ENSG00000283297 protein-coding gene first 1000 PCCRs yes 12 48759259 48773560 1 4 chr12:48759259-48759342+, chr12:48764850-48764993+, chr12:48765605-48765658+, chr12:48773525-48773560+ 184 no protein-coding gene ENSG00000257987 protein-coding gene first 1000 PCCRs no 12 51807534 51814833 -1 5 chr12:51807534-51807563-, chr12:51810574-51810603-, chr12:51814156-51814308-, chr12:51814417-51814629-, chr12:51814681-51814833- 173 yes protein-coding gene ENSG00000284730 protein-coding gene first 1000 PCCRs yes 12 52079777 52080025 1 2 chr12:52079777-52079845+, chr12:52079876-52080025+ 562 yes protein-coding gene ENSG00000284791 protein-coding gene first 1000 PCCRs yes 12 122226015 122226567 -1 3 chr12:122226015-122226056-, chr12:122226412-122226567-, chr12:122226504-122226563- 279 yes protein-coding gene ENSG00000284934 protein-coding gene first 1000 PCCRs yes 13 51084157 51088078 -1 5 chr13:51084157-51084216-, chr13:51084244-51084291-, chr13:51085309-51085428-, chr13:51085432-51085560-, chr13:51087929-51088078- 136 no protein-coding gene ENSG00000226792 protein-coding gene first 1000 PCCRs yes 13 51838501 51838536 -1 1 chr13:51838501-51838536- 10679 no protein coding gene ENSG00000281106 protein-coding gene lncRNA PCCR yes 13 113973839 113973997 -1 1 chr13:113973839-113973997- 257 no protein-coding gene ENSG00000283199 protein-coding gene first 1000 PCCRs no 13 114196396 114200402 1 2 chr13:114196396-114196425+, chr13:114200313-114200402+ 673 yes protein-coding gene ENSG00000283361 protein-coding gene first 1000 PCCRs no 14 23090103 23104878 -1 21 chr14:23090103-23090132-, chr14:23094729-23094782-, chr14:23094814-23094840-, chr14:23094851-23094910-, chr14:23095039-23095161-, chr14:23095064-23095189-, chr14:23100597-23100680-, chr14:23100873-23100905-, chr14:23101289-23101393-, chr14:23101457-23101564-, chr14:23101714-23101767-, chr14:23101877-23101912-, chr14:23102096-23102257-, chr14:23102338-23102490-, chr14:23102639-23102710-, chr14:23102923-23103051-, chr14:23103672-23103818-, chr14:23104234-23104293-, chr14:23104384-23104464-, chr14:23104600-23104656-, chr14:23104810-23104878- 156 yes protein-coding gene ENSG00000283654 protein-coding gene first 1000 PCCRs yes 14 66486676 66492148 1 5 chr14:66486676-66486807+, chr14:66488158-66488196+, chr14:66488218-66488256+, chr14:66489002-66489043+, chr14:66492071-66492148+ 330 no protein-coding gene ENSG00000196553 protein-coding gene first 1000 PCCRs no 14 94008609 94008641 1 1 chr14:94008609-94008641+ 8715 no protein coding gene ENSG00000175699 protein-coding gene lncRNA PCCR no 14 95922793 95923212 1 2 chr14:95922793-95922963+, chr14:95923183-95923212+ 392 no protein-coding gene ENSG00000250366 protein-coding gene first 1000 PCCRs no 14 96086221 96086732 1 2 chr14:96086221-96086256+, chr14:96086508-96086732+ 787 no protein-coding gene ENSG00000227051 protein-coding gene first 1000 PCCRs no 14 103088100 103088216 1 1 chr14:103088100-103088216+ 307 no protein-coding gene ENSG00000283071 protein-coding gene first 1000 PCCRs no 15 80201773 80201949 -1 1 chr15:80201773-80201949- 617 no protein-coding gene ENSG00000259417 protein-coding gene first 1000 PCCRs no 16 1432591 1433358 1 4 chr16:1432591-1432644+, chr16:1432789-1432947+, chr16:1433005-1433046+, chr16:1433101-1433358+ 320 yes protein-coding gene ENSG00000284395 protein-coding gene first 1000 PCCRs no 16 8884359 8885277 1 3 chr16:8884359-8884388+, chr16:8884401-8884451+, chr16:8885212-8885277+ 1466 no protein coding gene ENSG00000283516 protein-coding gene previously unannotated PCCR no 16 30054796 30063839 1 3 chr16:30054796-30054939+, chr16:30055172-30055285+, chr16:30063729-30063839+ 226 no protein-coding gene ENSG00000285043 protein-coding gene first 1000 PCCRs yes 16 53044015 53044083 -1 1 chr16:53044015-53044083- 2335 no protein coding gene ENSG00000277639 protein-coding gene lncRNA PCCR no 16 68014273 68015770 -1 2 chr16:68014273-68014344-, chr16:68015720-68015770- 1080 no protein coding gene ENSG00000263201 protein-coding gene lncRNA PCCR no 16 71430668 71432325 -1 4 chr16:71430668-71430742-, chr16:71431505-71431561-, chr16:71431928-71431981-, chr16:71432299-71432325- 1 no protein-coding gene ENSG00000260734 protein-coding gene first 1000 PCCRs no 17 4801292 4807131 -1 3 chr17:4801292-4801372-, chr17:4802266-4802322-, chr17:4807054-4807131- 651 yes protein-coding gene ENSG00000262165 protein-coding gene first 1000 PCCRs yes 17 7420340 7438334 1 9 chr17:7420340-7420384+, chr17:7428927-7429052+, chr17:7430507-7430533+, chr17:7430834-7430890+, chr17:7430948-7430992+, chr17:7432430-7432477+, chr17:7432601-7432699+, chr17:7438225-7438260+, chr17:7438257-7438334+ 1096 yes protein-coding gene ENSG00000283439 protein-coding gene previously unannotated PCCR no 17 7909339 7916216 -1 8 chr17:7909339-7909383-, chr17:7909341-7909400-, chr17:7910387-7910425-, chr17:7910412-7910438-, chr17:7915534-7915578-, chr17:7915686-7915727-, chr17:7915737-7915769-, chr17:7915866-7916216- 436 yes protein-coding gene ENSG00000179859 protein-coding gene first 1000 PCCRs no 17 10803748 10803966 -1 2 chr17:10803748-10803903-, chr17:10803919-10803966- 593 no protein-coding gene ENSG00000263429 protein-coding gene first 1000 PCCRs no 17 28716900 28717708 -1 3 chr17:28716900-28716941-, chr17:28717298-28717618-, chr17:28717643-28717708- 248 yes protein-coding gene ENSG00000109113 protein-coding gene first 1000 PCCRs no 17 38925691 38925768 1 1 chr17:38925691-38925768+ 699 no protein-coding gene ENSG00000263874 protein-coding gene first 1000 PCCRs no 17 42039741 42043379 -1 6 chr17:42039741-42040328-, chr17:42040353-42040796-, chr17:42040821-42040880-, chr17:42040914-42041186-, chr17:42042831-42043046-, chr17:42043062-42043379- 246 yes protein-coding gene ENSG00000267221 protein-coding gene first 1000 PCCRs no 17 43228447 43228554 -1 1 chr17:43228447-43228554- 228 no protein-coding gene ENSG00000236383 protein-coding gene first 1000 PCCRs yes 17 50750924 50761416 -1 5 chr17:50750924-50750956-, chr17:50751194-50751235-, chr17:50751359-50751427-, chr17:50751360-50751404-, chr17:50761366-50761416- 1462 no protein-coding gene ENSG00000167117; found after examing lncRNAs for coding potential protein-coding gene re-ranking yes 17 55511098 55511337 -1 1 chr17:55511098-55511337- 855 no protein-coding gene ENSG00000261873 protein-coding gene first 1000 PCCRs no 17 76568812 76569633 -1 3 chr17:76568812-76568838-, chr17:76568896-76569063-, chr17:76569085-76569633- 14 no protein-coding gene ENSG00000284526 protein-coding gene first 1000 PCCRs yes 17 81181263 81182071 1 3 chr17:81181263-81181340+, chr17:81181609-81181668+, chr17:81181991-81182071+ 7315 no protein coding gene ENSG00000225180 protein-coding gene lncRNA PCCR no 19 3482828 3483376 -1 2 chr19:3482828-3483052-, chr19:3483197-3483376- 30 yes protein-coding gene ENSG00000284638 protein-coding gene first 1000 PCCRs yes 19 5560211 5567933 -1 2 chr19:5560211-5560255-, chr19:5567670-5567933- 2076 yes protein coding gene ENSG00000223573 protein-coding gene lncRNA PCCR no 19 7019464 7019637 -1 2 chr19:7019464-7019529-, chr19:7019578-7019637- 7145 no protein coding gene ENSG00000196589 protein-coding gene lncRNA PCCR yes 19 12688049 12688369 1 2 chr19:12688049-12688144+, chr19:12688253-12688369+ 306 no protein-coding gene ENSG00000283980 protein-coding gene first 1000 PCCRs no 19 17390521 17394161 -1 5 chr19:17390521-17390628-, chr19:17391198-17391353-, chr19:17391754-17391840-, chr19:17393823-17393969-, chr19:17393982-17394161- 112 yes protein-coding gene ENSG00000269720 protein-coding gene first 1000 PCCRs no 19 18236900 18263956 -1 6 chr19:18236900-18237043-, chr19:18247666-18247713-, chr19:18250363-18250440-, chr19:18258203-18258274-, chr19:18263249-18263290-, chr19:18263924-18263956- 653 no protein-coding gene ENSG00000284797; found after looking at high-scoring intergenic PCCRs protein-coding gene re-ranking yes 19 35586254 35586481 1 2 chr19:35586254-35586409+, chr19:35586431-35586481+ 1763 no protein coding gene ENSG00000283758 protein-coding gene previously unannotated PCCR yes 19 46427757 46428416 -1 3 chr19:46427757-46427831-, chr19:46427952-46428050-, chr19:46428117-46428416- 191 no protein-coding gene ENSG00000277531 protein-coding gene first 1000 PCCRs yes 19 49017965 49020515 -1 7 chr19:49017965-49018117-, chr19:49018130-49018174-, chr19:49018875-49019000-, chr19:49019641-49019682-, chr19:49019728-49019760-, chr19:49019906-49020052-, chr19:49020417-49020515- 34 yes protein-coding gene ENSG00000268655 protein-coding gene first 1000 PCCRs yes 19 50785936 50790413 -1 3 chr19:50785936-50786001-, chr19:50786078-50786107-, chr19:50790357-50790413- 2506 no protein coding gene ENSG00000261341 protein-coding gene lncRNA PCCR no 19 51689064 51704502 1 17 chr19:51689064-51689132+, chr19:51689195-51689422+, chr19:51689268-51689348+, chr19:51689296-51689391+, chr19:51689562-51689594+, chr19:51690041-51690097+, chr19:51690780-51690878+, chr19:51690916-51690978+, chr19:51691060-51691191+, chr19:51692638-51692691+, chr19:51692776-51692850+, chr19:51692831-51692908+, chr19:51694477-51694539+, chr19:51703020-51703094+, chr19:51703248-51703328+, chr19:51704033-51704185+, chr19:51704269-51704502+ 36 yes protein-coding gene ENSG00000182310 protein-coding gene first 1000 PCCRs no 19 52915203 52915304 -1 1 chr19:52915203-52915304- 12307 no protein coding gene ENSG00000213793 protein-coding gene lncRNA PCCR no 19 55463745 55464557 -1 2 chr19:55463745-55463966-, chr19:55464384-55464557- 337 no protein-coding gene ENSG00000283567 protein-coding gene first 1000 PCCRs yes 19 56302000 56304825 1 2 chr19:56302000-56302101+, chr19:56304790-56304825+ 609 no protein-coding gene ENSG00000267710 protein-coding gene first 1000 PCCRs yes 20 10413765 10413893 -1 1 chr20:10413765-10413893- 296 no protein-coding gene ENSG00000285508 protein-coding gene first 1000 PCCRs no 20 35277717 35277935 -1 2 chr20:35277717-35277797-, chr20:35277828-35277935- 1109 yes protein coding gene ENSG00000126005 protein-coding gene lncRNA PCCR no 20 64037999 64038750 1 3 chr20:64037999-64038073+, chr20:64038299-64038433+, chr20:64038643-64038750+ 199 yes protein-coding gene ENSG00000196421 protein-coding gene first 1000 PCCRs yes 21 7789350 7789511 -1 1 chr21:7789350-7789511- 526 no protein-coding gene ENSG00000278961 protein-coding gene first 1000 PCCRs no 22 21467445 21469818 1 7 chr22:21467445-21467642+, chr22:21467895-21467999+, chr22:21468152-21468214+, chr22:21468354-21468434+, chr22:21469127-21469186+, chr22:21469278-21469355+, chr22:21469741-21469818+ 1328 yes protein coding gene ENSG00000206140 protein-coding gene lncRNA PCCR no 22 39496763 39504446 1 2 chr22:39496763-39496789+, chr22:39504207-39504446+ 860 no protein-coding gene ENSG00000285025 protein-coding gene first 1000 PCCRs no X 111518858 111519127 1 1 chrX:111518858-111519127+ 452 no protein-coding gene ENSG00000260802 protein-coding gene first 1000 PCCRs no X 135119106 135119168 -1 1 chrX:135119106-135119168- 27432 no protein coding gene ENSG00000224107 protein-coding gene lncRNA PCCR no X 135253382 135253432 1 1 chrX:135253382-135253432+ 41242 no protein coding gene ENSG00000238210 protein-coding gene lncRNA PCCR no X 149548419 149549612 -1 4 chrX:149548419-149548478-, chrX:149548857-149548895-, chrX:149549427-149549552-, chrX:149549583-149549612- 44 no protein-coding gene ENSG00000283697 protein-coding gene first 1000 PCCRs no X 149929879 149931078 1 2 chrX:149929879-149930070+, chrX:149931016-149931078+ 1263 no protein coding gene ENSG00000283463 protein-coding gene lncRNA PCCR no 1 923849 924956 1 3 chr1:923849-923884+, chr1:924432-924956+, chr1:924860-924913+ 201 yes SAMD11 5' extension coding exon(s) first 1000 PCCRs yes 1 1034466 1042172 1 3 chr1:1034466-1034504+, chr1:1034541-1034705+, chr1:1042143-1042172+ 50 yes AGRN intronic alternative START coding exon(s) first 1000 PCCRs yes 1 1922577 1922723 -1 1 chr1:1922577-1922723- 567 no CFAP74 cassette exon coding exon(s) first 1000 PCCRs no 1 2789592 2800821 -1 4 chr1:2789592-2790239-, chr1:2800063-2800140-, chr1:2800273-2800458-, chr1:2800480-2800821- 54 yes TTC34 5' extension coding exon(s) first 1000 PCCRs yes 1 6447414 6456191 1 7 chr1:6447414-6447458+, chr1:6454434-6455003+, chr1:6455052-6455120+, chr1:6455193-6455411+, chr1:6455463-6455543+, chr1:6455559-6455882+, chr1:6456072-6456191+ 235 yes ESPN very large alternative final exon coding exon(s) first 1000 PCCRs no 1 6497370 6506158 -1 2 chr1:6497370-6497474-, chr1:6506030-6506158- 243 yes PLEKHG5 alternative first exon coding exon(s) first 1000 PCCRs yes 1 14180434 14180598 1 1 chr1:14180434-14180598+ 414 no KAZN 5' extension coding exon(s) first 1000 PCCRs no 1 21089132 21089212 -1 1 chr1:21089132-21089212- 661 no EIF4G3 5' coding exons coding exon(s) first 1000 PCCRs yes 1 26354279 26360113 -1 4 chr1:26354279-26354311-, chr1:26354636-26354683-, chr1:26359999-26360052-, chr1:26360081-26360113- 2019 yes CRYBG2 3 alternative first coding exons coding exon(s) previously unannotated PCCR yes 1 28593695 28593799 1 1 chr1:28593695-28593799+ 236 no RAB42 first coding exon coding exon(s) first 1000 PCCRs no 1 29069160 29070606 1 3 chr1:29069160-29069291+, chr1:29070358-29070390+, chr1:29070466-29070606+ 715 no EPB41 alternative final exon coding exon(s) first 1000 PCCRs no 1 43426391 43426525 1 1 chr1:43426391-43426525+ 115 no SZT2 cassette exon coding exon(s) first 1000 PCCRs no 1 54132971 54136809 -1 2 chr1:54132971-54133300-, chr1:54136630-54136809- 189 no CDCP2 alternative final coding exons coding exon(s) first 1000 PCCRs yes 1 62153386 62161057 1 2 chr1:62153386-62153469+, chr1:62160908-62161057+ 477 no PATJ cassette exon coding exon(s) first 1000 PCCRs no 1 92166967 92168865 1 3 chr1:92166967-92167083+, chr1:92167093-92167140+, chr1:92168806-92168865+ 134 no Readthrough' protein-coding transcript added between BTBD8 and KIAA1107 containing 3 new coding exons; actually shows that this is really one locus, with HGNC retaining the BTBD8 symbol coding exon(s) first 1000 PCCRs yes 1 92662719 92662868 -1 1 chr1:92662719-92662868- 671 no EVI5 cassette exon coding exon(s) first 1000 PCCRs no 1 110228004 110230556 1 4 chr1:110228004-110228042+, chr1:110228565-110228696+, chr1:110229471-110229497+, chr1:110230515-110230556+ 166 no KCNC4 alternative final exon coding exon(s) first 1000 PCCRs yes 1 114091905 114092085 -1 2 chr1:114091905-114091934-, chr1:114092005-114092085- 743 no SYT6 alternative final exon coding exon(s) first 1000 PCCRs no 1 151766752 151766868 1 1 chr1:151766752-151766868+ 63 no OAZ3 first coding exon. coding exon(s) first 1000 PCCRs no 1 169795103 169795213 1 1 chr1:169795103-169795213+ 273 no C1orf112 5' coding exon coding exon(s) first 1000 PCCRs no 1 180950339 180950530 1 1 chr1:180950339-180950530+ 342 no KIAA1614 3' coding exon coding exon(s) first 1000 PCCRs yes 1 181413147 181413581 1 1 chr1:181413147-181413581+ 478 yes CACNA1E extended to upstream ATG coding exon(s) first 1000 PCCRs no 1 181779441 181779545 1 1 chr1:181779441-181779545+ 886 no CACNA1E partner of a mutually exclusive exon pair coding exon(s) first 1000 PCCRs no 1 182390538 182400521 -1 4 chr1:182390538-182390573-, chr1:182390586-182390642-, chr1:182390691-182390783-, chr1:182400486-182400521- 892 yes GLUL first exon coding exon(s) first 1000 PCCRs yes 1 197442293 197442418 1 1 chr1:197442293-197442418+ 308 no CRB1 alternative final exon coding exon(s) first 1000 PCCRs yes 1 204243114 204256899 -1 4 chr1:204243114-204243266-, chr1:204251534-204251641-, chr1:204256798-204256899-, chr1:204256802-204256888- 352 no PLEKHA6 4 cassette exons coding exon(s) first 1000 PCCRs no 1 206518412 206518492 1 1 chr1:206518412-206518492+ 584 no RASSF5 alternative 5' eon coding exon(s) first 1000 PCCRs yes 1 210016022 210016150 1 1 chr1:210016022-210016150+ 151 no SYT14 first coding exon coding exon(s) first 1000 PCCRs no 1 225275914 225277481 1 2 chr1:225275914-225276060+, chr1:225277425-225277481+ 144 no DNAH14 two cassette exons coding exon(s) first 1000 PCCRs no 2 27136918 27137052 -1 1 chr2:27136918-27137052- 992 no PRR30 alternative first exon coding exon(s) first 1000 PCCRs yes 2 38880184 38880706 1 2 chr2:38880184-38880234+, chr2:38880599-38880706+ 778 no MORN2 upstream coding exons led to the usage of a [CTG] for initiation, supported by human and mouse RP and conservation. coding exon(s) first 1000 PCCRs yes 2 73071669 73081530 -1 10 chr2:73071669-73071779-, chr2:73071755-73071799-, chr2:73079818-73080018-, chr2:73080301-73080339-, chr2:73080499-73080537-, chr2:73080697-73080762-, chr2:73080814-73080906-, chr2:73081261-73081344-, chr2:73081396-73081452-, chr2:73081492-73081530- 418 yes RAB11FIP5 2kb cassette exon coding exon(s) first 1000 PCCRs yes 2 74218630 74221468 -1 3 chr2:74218630-74218662-, chr2:74218687-74218791-, chr2:74221436-74221468- 200 no SLC4A5 exon skip leading to frameshift and alternative C terminus coding exon(s) first 1000 PCCRs yes 2 74421730 74426760 -1 2 chr2:74421730-74421765-, chr2:74426653-74426760- 445 yes RTKN 3' extension coding exon(s) first 1000 PCCRs no 2 86219982 86227399 -1 2 chr2:86219982-86220122-, chr2:86227370-86227399- 108 no REEP1 two cassette exons coding exon(s) first 1000 PCCRs no 2 101450602 101452446 -1 2 chr2:101450602-101450673-, chr2:101452390-101452446- 924 no RFX8 two cassette exons previously on an NMD model coding exon(s) first 1000 PCCRs no 2 127485902 127486009 -1 1 chr2:127485902-127486009- 649 no IWS1 alternative final exon coding exon(s) first 1000 PCCRs no 2 132668677 132673137 -1 5 chr2:132668677-132668706-, chr2:132669111-132669137-, chr2:132669972-132670067-, chr2:132670257-132670304-, chr2:132673030-132673137- 349 yes NCKAP5 alternative final exon coding exon(s) first 1000 PCCRs no 2 196990683 196990934 -1 2 chr2:196990683-196990772-, chr2:196990851-196990934- 511 no ANKRD44 alternative final exon coding exon(s) first 1000 PCCRs no 2 202202478 202202543 1 1 chr2:202202478-202202543+ 954 no KIAA2012 extended to full length at 5' and 3' ends coding exon(s) first 1000 PCCRs no 2 218010106 218010282 -1 2 chr2:218010106-218010216-, chr2:218010247-218010282- 1546 yes TNS1 alternative first exon coding exon(s) previously unannotated PCCR yes 2 224982207 224982383 -1 1 chr2:224982207-224982383- 519 no DOCK10 alternative first exon coding exon(s) first 1000 PCCRs no 2 230990378 230991124 1 5 chr2:230990378-230990437+, chr2:230990690-230990731+, chr2:230990768-230990950+, chr2:230990990-230991034+, chr2:230991092-230991124+ 544 yes SPATA3 alternative first exon coding exon(s) first 1000 PCCRs yes 2 236237283 236241502 -1 3 chr2:236237283-236237312-, chr2:236238735-236238773-, chr2:236241404-236241502- 822 yes ASB18 intronic alternative ATG coding exon(s) first 1000 PCCRs yes 2 240560378 240572566 1 7 chr2:240560378-240560404+, chr2:240568230-240568334+, chr2:240568386-240568559+, chr2:240568438-240568539+, chr2:240568614-240569123+, chr2:240568631-240568813+, chr2:240572420-240572566+ 225 yes RNPEPL1 extended 5' coding exon(s) first 1000 PCCRs no 3 13022008 13022103 -1 1 chr3:13022008-13022103- 945 no IQSEC1 alternative first exon coding exon(s) first 1000 PCCRs no 3 13042289 13047521 -1 3 chr3:13042289-13042363-, chr3:13043070-13043105-, chr3:13047486-13047521- 998 no IQSEC1 alternative first exon coding exon(s) first 1000 PCCRs no 3 14555892 14555954 -1 1 chr3:14555892-14555954- 1330 no GRIP2 alternative first coding exon coding exon(s) previously unannotated PCCR yes 3 14810490 14819071 1 4 chr3:14810490-14810543+, chr3:14810650-14810739+, chr3:14810652-14810768+, chr3:14818955-14819071+ 211 yes FGD5 alternative 5' CDS coding exon(s) first 1000 PCCRs yes 3 22168836 22169018 -1 1 chr3:22168836-22169018- 523 no ZNF385D alternative first 2 exons coding exon(s) first 1000 PCCRs no 3 29182956 29183132 1 1 chr3:29182956-29183132+ 356 no RBMS3 3 5' coding exons coding exon(s) first 1000 PCCRs yes 3 36738660 36739085 -1 2 chr3:36738660-36738968-, chr3:36738975-36739085- 53 no DCLK3 5' extension coding exon(s) first 1000 PCCRs yes 3 88086257 88086400 1 1 chr3:88086257-88086400+ 190 no ZNF654 5' extension coding exon(s) first 1000 PCCRs no 3 111720724 111720879 1 1 chr3:111720724-111720879+ 405 no PLCXD2 final coding exon coding exon(s) first 1000 PCCRs yes 3 113958541 113958627 1 1 chr3:113958541-113958627+ 454 no ZDHHC23 3' coding exon coding exon(s) first 1000 PCCRs no 3 125014720 125014926 -1 3 chr3:125014720-125014746-, chr3:125014810-125014842-, chr3:125014846-125014926- 776 no HEG1 cassette exon coding exon(s) first 1000 PCCRs no 3 128916104 128916211 -1 1 chr3:128916104-128916211- 168 no KIAA1257 cassette exon coding exon(s) first 1000 PCCRs no 3 155704147 155704227 -1 1 chr3:155704147-155704227- 780 no PLCH1 alternative first exon coding exon(s) first 1000 PCCRs no 3 183400367 183400471 -1 1 chr3:183400367-183400471- 142 no MCF2L2 5' coding exons coding exon(s) first 1000 PCCRs yes 4 2625247 2631004 1 3 chr4:2625247-2625393+, chr4:2626408-2626581+, chr4:2630936-2631004+ 164 no FAM193A 5' extended by 4 new coding exons coding exon(s) first 1000 PCCRs yes 4 3500310 3505629 1 5 chr4:3500310-3500402+, chr4:3500691-3500813+, chr4:3505153-3505218+, chr4:3505440-3505520+, chr4:3505495-3505629+ 272 no DOK7 3 3' coding exons coding exon(s) first 1000 PCCRs no 4 6008014 6018431 -1 5 chr4:6008014-6008238-, chr4:6008293-6008562-, chr4:6011836-6011898-, chr4:6011932-6011970-, chr4:6018291-6018431- 155 yes C4orf50 5' exons coding exon(s) first 1000 PCCRs yes 4 17873404 17884833 -1 19 chr4:17873404-17873505-, chr4:17873731-17873838-, chr4:17874085-17874129-, chr4:17874160-17874561-, chr4:17874610-17874762-, chr4:17874904-17875014-, chr4:17875150-17875293-, chr4:17875513-17875581-, chr4:17875681-17875779-, chr4:17876035-17876130-, chr4:17876461-17876532-, chr4:17876584-17876685-, chr4:17877082-17877282-, chr4:17877352-17877402-, chr4:17877610-17877696-, chr4:17878042-17878083-, chr4:17883742-17883768-, chr4:17884568-17884726-, chr4:17884750-17884833- 150 no LCORL 4.8kb cassette exon coding exon(s) first 1000 PCCRs no 4 20983815 20983967 -1 1 chr4:20983815-20983967- 533 no KCNIP4 alternative first exon coding exon(s) first 1000 PCCRs no 4 36281786 36281965 1 2 chr4:36281786-36281851+, chr4:36281873-36281965+ 92 no DTHD1 5' coding exon coding exon(s) first 1000 PCCRs no 4 56272320 56272475 1 2 chr4:56272320-56272394+, chr4:56272449-56272475+ 514 no KIAA1211 alternative first exon coding exon(s) first 1000 PCCRs yes 4 56511191 56511313 1 1 chr4:56511191-56511313+ 160 no ARL9 5' extension coding exon(s) first 1000 PCCRs no 4 71236180 71236576 1 2 chr4:71236180-71236209+, chr4:71236472-71236576+ 312 no SLC4A4 5' exons coding exon(s) first 1000 PCCRs yes 4 76639563 76639640 1 2 chr4:76639563-76639595+, chr4:76639614-76639640+ 1347 no SHROOM3 alternative first exon coding exon(s) lncRNA PCCR no 4 81602851 81602922 -1 1 chr4:81602851-81602922- 546 no RASGEF1B 5' exons coding exon(s) first 1000 PCCRs yes 4 93806712 93806870 1 1 chr4:93806712-93806870+ 240 no GRID2 alternative 3' coding exon coding exon(s) first 1000 PCCRs no 4 151175562 151187459 -1 6 chr4:151175562-151175615-, chr4:151175643-151175675-, chr4:151176550-151176687-, chr4:151176814-151176954-, chr4:151179357-151179392-, chr4:151187418-151187459- 192 no SH3D19 5' coding exons coding exon(s) first 1000 PCCRs yes 4 157360983 157365960 1 9 chr4:157360983-157361015+, chr4:157361189-157361215+, chr4:157361351-157361404+, chr4:157361368-157361397+, chr4:157361519-157361545+, chr4:157363420-157363455+, chr4:157363519-157363572+, chr4:157365651-157365704+, chr4:157365916-157365960+ 611 no GRIA2 alternative final exon coding exon(s) first 1000 PCCRs yes 4 183797080 183798363 1 4 chr4:183797080-183797127+, chr4:183797108-183797137+, chr4:183797635-183798060+, chr4:183798313-183798363+ 336 yes STOX2 alternative first coding exon coding exon(s) first 1000 PCCRs no 5 113239 113412 1 1 chr5:113239-113412+ 18618 no PLEKHG4B 5' extended. This CDS was not subject to further analysis as it was reclassified as coding once this work was completed. coding exon(s) lncRNA PCCR no 5 472967 473380 -1 2 chr5:472967-473221-, chr5:473333-473380- 874 yes SLC9A3 alternative final exon coding exon(s) first 1000 PCCRs yes 5 14441234 14441371 1 1 chr5:14441234-14441371+ 576 no TRIO first coding exon coding exon(s) first 1000 PCCRs yes 5 35787955 35790367 1 11 chr5:35787955-35788467+, chr5:35788498-35788686+, chr5:35788723-35788824+, chr5:35788837-35788944+, chr5:35788951-35789031+, chr5:35789215-35789346+, chr5:35789624-35789689+, chr5:35789809-35789919+, chr5:35790029-35790163+, chr5:35790206-35790301+, chr5:35790329-35790367+ 24 no SPEF2 5 consecutive coding exons including an alternative termination codon coding exon(s) first 1000 PCCRs yes 5 59430293 59430418 -1 1 chr5:59430293-59430418- 48 no PDE4D first coding exon coding exon(s) first 1000 PCCRs no 5 81087178 81087420 1 2 chr5:81087178-81087219+, chr5:81087280-81087420+ 110 no RASGRF2 alternative final coding exon coding exon(s) first 1000 PCCRs yes 5 140228762 140228830 1 1 chr5:140228762-140228830+ 913 no CYSTM1 alternative final exon coding exon(s) first 1000 PCCRs yes 5 160684840 160685226 -1 2 chr5:160684840-160685103-, chr5:160685143-160685226- 495 no ATP10B alternative first exon coding exon(s) first 1000 PCCRs no 5 170681069 170681185 1 1 chr5:170681069-170681185+ 130 no KCNIP1 first exon coding exon(s) first 1000 PCCRs yes 5 172356695 172356775 -1 1 chr5:172356695-172356775- 708 no SH3PXD2B first coding exon coding exon(s) first 1000 PCCRs no 5 175707783 175707866 1 1 chr5:175707783-175707866+ 269 no HRH2 alternative final coding exon coding exon(s) first 1000 PCCRs no 5 179121557 179124939 -1 2 chr5:179121557-179121658-, chr5:179124775-179124939- 485 yes ADAMTS2 alternative final exon coding exon(s) first 1000 PCCRs yes 6 2743890 2749408 -1 3 chr6:2743890-2743925-, chr6:2743962-2744036-, chr6:2749346-2749408- 749 no MYLK4 alternative first exon coding exon(s) first 1000 PCCRs no 6 4084643 4084744 -1 1 chr6:4084643-4084744- 223 no FAM217A 5' exon coding exon(s) first 1000 PCCRs yes 6 17821790 17821903 -1 1 chr6:17821790-17821903- 97 no KIF13A cassette exon coding exon(s) first 1000 PCCRs yes 6 30934623 30937307 1 2 chr6:30934623-30934661+, chr6:30937209-30937307+ 773 no DPCR1 3 cassette exons coding exon(s) first 1000 PCCRs yes 6 36311797 36311838 1 1 chr6:36311797-36311838+ 2113 no PNPLA1 alternative final coding exon coding exon(s) previously unannotated PCCR no 6 56540841 56541572 -1 1 chr6:56540841-56541572- 365 no DST cassette exon coding exon(s) first 1000 PCCRs yes 6 106461785 106461877 1 1 chr6:106461785-106461877+ 625 no CRYBG1 first coding exon. coding exon(s) first 1000 PCCRs yes 6 129292806 129293015 1 1 chr6:129292806-129293015+ 934 no LAMA2 cassette exon coding exon(s) first 1000 PCCRs no 6 130882577 130883107 -1 2 chr6:130882577-130882834-, chr6:130882955-130883107- 690 no EPB41L2 alternative final exon coding exon(s) first 1000 PCCRs yes 6 148513599 148520385 1 2 chr6:148513599-148513625+, chr6:148519894-148520385+ 746 no SASH1 splice donor site shift coding exon(s) first 1000 PCCRs no 6 150686873 150686956 1 1 chr6:150686873-150686956+ 796 no PLEKHG1 alternative first exon coding exon(s) first 1000 PCCRs yes 6 158093885 158094013 1 1 chr6:158093885-158094013+ 247 no SYNJ2 alternative final coding exon coding exon(s) first 1000 PCCRs no 7 11111351 11111467 1 1 chr7:11111351-11111467+ 522 no PHF14 alternative final exon coding exon(s) first 1000 PCCRs no 7 92058169 92058411 1 1 chr7:92058169-92058411+ 851 no AKAP9 alternative first exon coding exon(s) first 1000 PCCRs no 7 134208697 134210967 1 8 chr7:134208697-134208810+, chr7:134208937-134208969+, chr7:134209426-134209467+, chr7:134209516-134209674+, chr7:134209687-134209749+, chr7:134209804-134209851+, chr7:134209885-134209944+, chr7:134210926-134210967+ 457 no LRGUK alternative large final exon coding exon(s) first 1000 PCCRs no 7 151432147 151432281 -1 1 chr7:151432147-151432281- 321 no CRYGN cassette exon coding exon(s) first 1000 PCCRs no 7 155545831 155545944 -1 1 chr7:155545831-155545944- 385 no CNPY1 first coding exon coding exon(s) first 1000 PCCRs yes 8 907912 907962 1 1 chr8:907912-907962+ 1656 no DLGAP2 alternative first exons coding exon(s) lncRNA PCCR yes 8 11808518 11808793 1 2 chr8:11808518-11808655+, chr8:11808755-11808793+ 327 yes FDFT1 alternative first coding exon coding exon(s) first 1000 PCCRs no 8 26514326 26514682 1 1 chr8:26514326-26514682+ 358 yes DPYSL2 first coding exon coding exon(s) first 1000 PCCRs no 8 30849192 30875103 -1 5 chr8:30849192-30849308-, chr8:30858750-30858791-, chr8:30859923-30860057-, chr8:30867307-30867501-, chr8:30874954-30875103- 41 no TEX15 5' extended coding exon(s) first 1000 PCCRs no 8 53229213 53229293 -1 1 chr8:53229213-53229293- 742 no OPRK1 known STOP-codon readthrough coding exon(s) first 1000 PCCRs no 8 54755618 54759074 1 2 chr8:54755618-54755773+, chr8:54758925-54759074+ 181 no RP1 massive extension 3'; 28 exons vs existing 3 exon model. However, the 3 exon CDS is actually longer. coding exon(s) first 1000 PCCRs yes 8 131938225 131938314 1 1 chr8:131938225-131938314+ 381 no EFR3A 5' exon coding exon(s) first 1000 PCCRs yes 8 143733703 143738234 -1 5 chr8:143733703-143733927-, chr8:143733704-143733922-, chr8:143733708-143733872-, chr8:143737617-143737913-, chr8:143738130-143738234- 361 yes FAM83H 5' coding extension. coding exon(s) first 1000 PCCRs yes 8 144060060 144063934 -1 4 chr8:144060060-144060086-, chr8:144060708-144060743-, chr8:144063704-144063736-, chr8:144063743-144063934- 630 yes OPLAH alternative first exon coding exon(s) first 1000 PCCRs no 8 144462230 144473371 1 6 chr8:144462230-144462280+, chr8:144462427-144462459+, chr8:144462656-144462694+, chr8:144466306-144466353+, chr8:144466519-144466545+, chr8:144473132-144473371+ 652 yes KIFC2 frame corrected in final exon coding exon(s) first 1000 PCCRs no 9 8437052 8438823 1 4 chr9:8437052-8437081+, chr9:8438688-8438780+, chr9:8438698-8438760+, chr9:8438794-8438823+ 1439 no PTPRD cassette exon coding exon(s) previously unannotated PCCR yes 9 18163865 18163978 1 1 chr9:18163865-18163978+ 345 no ADAMTSL1 5' coding exons coding exon(s) first 1000 PCCRs no 9 35300167 35307879 1 11 chr9:35300167-35300217+, chr9:35300773-35300859+, chr9:35300980-35301087+, chr9:35301337-35301429+, chr9:35301814-35301849+, chr9:35303926-35304027+, chr9:35305528-35305569+, chr9:35305942-35305995+, chr9:35306035-35306085+, chr9:35307307-35307345+, chr9:35307826-35307879+ 5 no UNC13B cassette exon coding exon(s) first 1000 PCCRs yes 9 35829249 35842438 1 10 chr9:35829249-35829284+, chr9:35829283-35829318+, chr9:35829371-35829445+, chr9:35829442-35829468+, chr9:35829874-35829960+, chr9:35834460-35834651+, chr9:35835012-35835221+, chr9:35841137-35841274+, chr9:35841527-35841790+, chr9:35842391-35842438+ 362 yes TMEM8B 5' extension by 5 exons coding exon(s) first 1000 PCCRs no 9 69145704 69151696 1 2 chr9:69145704-69145820+, chr9:69151652-69151696+ 234 no TJP2 alternative first coding exon and cassette coding exon(s) first 1000 PCCRs yes 9 114097703 114099171 -1 5 chr9:114097703-114097741-, chr9:114098112-114098192-, chr9:114098283-114098429-, chr9:114098923-114099015-, chr9:114099106-114099171- 245 yes KIF12 coding exons added to make inferred transcript model coding exon(s) first 1000 PCCRs no 9 136327474 136332153 1 3 chr9:136327474-136327575+, chr9:136327508-136327573+, chr9:136332004-136332153+ 111 yes GPSM1 5' coding exon coding exon(s) first 1000 PCCRs no 10 10798762 10798815 1 1 chr10:10798762-10798815+ 2186 no CELF2 two coding exons at 5' coding exon(s) previously unannotated PCCR yes 10 14008063 14008155 -1 1 chr10:14008063-14008155- 363 no FRMD4A first coding exon coding exon(s) first 1000 PCCRs no 10 23239726 23239818 -1 1 chr10:23239726-23239818- 372 no C10orf67 multiple exons added to 3' coding exon(s) first 1000 PCCRs no 10 24042285 24042500 1 2 chr10:24042285-24042380+, chr10:24042393-24042500+ 346 no KIAA1217 alternative first coding exon coding exon(s) first 1000 PCCRs no 10 24590340 24590480 -1 2 chr10:24590340-24590480-, chr10:24590383-24590418- 640 no ARHGAP21 alternative final coding exon that would suggest NMD, although the CDS is conserved in vertebrates coding exon(s) first 1000 PCCRs yes 10 24706509 24706607 -1 1 chr10:24706509-24706607- 154 no ARHGAP21 alternative first exon coding exon(s) first 1000 PCCRs yes 10 48156119 48156259 -1 2 chr10:48156119-48156151-, chr10:48156200-48156259- 2053 no FRMPD2 alternative final exon coding exon(s) lncRNA PCCR yes 10 68827999 68828274 1 1 chr10:68827999-68828274+ 900 yes STOX1 5' extension coding exon(s) first 1000 PCCRs yes 10 77140289 77140504 -1 1 chr10:77140289-77140504- 676 no KCNMA1 alternative first exon coding exon(s) first 1000 PCCRs yes 10 80634284 80644070 1 2 chr10:80634284-80634508+, chr10:80643993-80644070+ 711 no SH2D4B cassette exon coding exon(s) first 1000 PCCRs yes 10 84452243 84452275 1 1 chr10:84452243-84452275+ 209 no CCSER2 first coding exon coding exon(s) first 1000 PCCRs yes 10 96004150 96004227 1 1 chr10:96004150-96004227+ 591 no CC2D2B greatly extended to incorporate lncRNAs now seen to part of the same locus coding exon(s) first 1000 PCCRs yes 10 96980833 96981009 1 2 chr10:96980833-96980943+, chr10:96980971-96981009+ 163 no LCOR alternative final exon; overlaps single exon gene C10orf12 and thus allows for the two to be merged coding exon(s) first 1000 PCCRs yes 10 99929612 99930589 -1 2 chr10:99929612-99929698-, chr10:99930539-99930589- 658 no DNMBP alternative first exon coding exon(s) first 1000 PCCRs no 10 101834274 101834369 -1 1 chr10:101834274-101834369- 862 no KCNIP2 alt first coding exon coding exon(s) first 1000 PCCRs no 10 102395633 102421154 -1 9 chr10:102395633-102395692-, chr10:102403063-102403092-, chr10:102408898-102409158-, chr10:102409182-102409211-, chr10:102418734-102418811-, chr10:102419090-102419176-, chr10:102419106-102419138-, chr10:102419677-102419727-, chr10:102421125-102421154- 680 yes PSD alternative first exon coding exon(s) first 1000 PCCRs yes 10 116834939 116836390 -1 4 chr10:116834939-116835028-, chr10:116836194-116836265-, chr10:116836225-116836260-, chr10:116836328-116836390- 922 no HSPA12A alternative first exon coding exon(s) first 1000 PCCRs no 10 126670241 126670417 -1 1 chr10:126670241-126670417- 571 no C10orf90 two 5' exons coding exon(s) first 1000 PCCRs no 10 132808795 132810723 -1 3 chr10:132808795-132808845-, chr10:132810440-132810490-, chr10:132810586-132810723- 153 no CFAP46 multiple cassette exons coding exon(s) first 1000 PCCRs yes 11 16807082 16815297 -1 3 chr11:16807082-16807204-, chr11:16807153-16807245-, chr11:16815166-16815297- 122 no PLEKHA7 multiple coding exons coding exon(s) first 1000 PCCRs no 11 57311253 57311354 -1 1 chr11:57311253-57311354- 420 no TNKS1BP1 first exon coding exon(s) first 1000 PCCRs yes 11 57638680 57647203 -1 2 chr11:57638680-57638739-, chr11:57647108-57647203- 565 no YPEL4 extended to upstream initiation codon coding exon(s) first 1000 PCCRs yes 11 66718423 66728928 -1 6 chr11:66718423-66718632-, chr11:66718826-66718963-, chr11:66728061-66728150-, chr11:66728310-66728393-, chr11:66728335-66728487-, chr11:66728902-66728928- 806 yes SPTBN2 alternative first coding exon. coding exon(s) first 1000 PCCRs no 11 67524212 67524376 -1 1 chr11:67524212-67524376- 123 no CABP2 alternative first exon coding exon(s) first 1000 PCCRs yes 11 70365343 70365973 1 2 chr11:70365343-70365438+, chr11:70365938-70365973+ 421 no PPFIA1 2 cassette exons coding exon(s) first 1000 PCCRs no 11 70895416 70895568 -1 1 chr11:70895416-70895568- 895 no SHANK2 cassette exon coding exon(s) first 1000 PCCRs yes 11 73343137 73343277 1 2 chr11:73343137-73343223+, chr11:73343251-73343277+ 791 yes ARHGEF17 alternative first exon coding exon(s) first 1000 PCCRs yes 11 111255991 111256092 1 1 chr11:111255991-111256092+ 424 no C11orf53 5' extension by two exons coding exon(s) first 1000 PCCRs no 11 117354932 117356374 1 6 chr11:117354932-117354982+, chr11:117355178-117355243+, chr11:117355502-117355531+, chr11:117355685-117355738+, chr11:117356027-117356089+, chr11:117356189-117356374+ 476 no CEP164 cassette exon coding exon(s) first 1000 PCCRs no 11 123491841 123491942 1 1 chr11:123491841-123491942+ 548 no GRAMD1B first exon coding exon(s) first 1000 PCCRs no 12 3199732 3201193 1 4 chr12:3199732-3199782+, chr12:3200691-3200723+, chr12:3200875-3200934+, chr12:3200918-3201193+ 479 yes TSPAN9 alternative 5' exon coding exon(s) first 1000 PCCRs yes 12 25004369 25004488 1 1 chr12:25004369-25004488+ 55 no LRMP 17 alternative coding exons at 5' end coding exon(s) first 1000 PCCRs no 12 51196844 51206842 -1 6 chr12:51196844-51196930-, chr12:51197770-51198024-, chr12:51198560-51198673-, chr12:51199747-51199866-, chr12:51204264-51204368-, chr12:51206789-51206842- 265 no POU6F1 first coding exons coding exon(s) first 1000 PCCRs no 12 57604808 57624781 1 8 chr12:57604808-57604906+, chr12:57610133-57610180+, chr12:57611390-57611425+, chr12:57611601-57611684+, chr12:57619578-57619691+, chr12:57619773-57619886+, chr12:57624500-57624604+, chr12:57624734-57624781+ 137 yes SLC26A10 alternative final exon coding exon(s) first 1000 PCCRs yes 12 64533268 64541660 1 2 chr12:64533268-64533333+, chr12:64541580-64541660+ 364 no RASSF3 5' extension by 3 exons coding exon(s) first 1000 PCCRs yes 12 64780731 64781264 1 3 chr12:64780731-64780913+, chr12:64780932-64781123+, chr12:64781139-64781264+ 857 yes TBC1D30 5' extension. coding exon(s) first 1000 PCCRs yes 12 77572192 77572266 1 1 chr12:77572192-77572266+ 1831 no NAV3 alternative first exon coding exon(s) lncRNA PCCR no 12 78036864 78037385 1 1 chr12:78036864-78037385+ 772 no NAV3 alternative first exon coding exon(s) first 1000 PCCRs no 12 92729000 92737518 1 3 chr12:92729000-92729110+, chr12:92736485-92736532+, chr12:92737435-92737518+ 171 no PLEKHG7 extended CDS significantly at 5' end, previous truncated domain now intact. coding exon(s) first 1000 PCCRs yes 12 96682174 96682335 1 1 chr12:96682174-96682335+ 467 no CFAP54 cassette exon coding exon(s) first 1000 PCCRs no 12 100733773 100740104 1 2 chr12:100733773-100733856+, chr12:100739853-100740104+ 626 no ANO4 extended by 3 5' exons coding exon(s) first 1000 PCCRs no 12 120216252 120219548 -1 5 chr12:120216252-120216341-, chr12:120216543-120216581-, chr12:120216835-120217116-, chr12:120219198-120219236-, chr12:120219486-120219548- 378 no PXN 2 cassette exons coding exon(s) first 1000 PCCRs no 12 123475663 123475743 -1 1 chr12:123475663-123475743- 719 no RILPL1 cassette exon coding exon(s) first 1000 PCCRs no 12 123762213 123762579 1 3 chr12:123762213-123762248+, chr12:123762334-123762519+, chr12:123762553-123762579+ 39 yes DNAH10 5' extension coding exon(s) first 1000 PCCRs no 12 130424136 130424786 -1 4 chr12:130424136-130424198-, chr12:130424352-130424528-, chr12:130424538-130424564-, chr12:130424742-130424786- 705 yes RIMBP2 3 cassette exons coding exon(s) first 1000 PCCRs no 12 132509173 132510440 1 8 chr12:132509173-132509274+, chr12:132509232-132509426+, chr12:132509505-132509570+, chr12:132509583-132509744+, chr12:132509802-132509915+, chr12:132509946-132509972+, chr12:132510003-132510275+, chr12:132510285-132510440+ 116 no FBRSL1 alternative final coding exon coding exon(s) first 1000 PCCRs no 13 31945974 31946174 1 1 chr13:31945974-31946174+ 532 no FRY alternative first exon coding exon(s) first 1000 PCCRs yes 13 98395479 98396402 1 7 chr13:98395479-98395580+, chr13:98395599-98395670+, chr13:98395707-98395952+, chr13:98396019-98396120+, chr13:98396166-98396204+, chr13:98396274-98396342+, chr13:98396361-98396402+ 221 no FARP1 alternative final exon coding exon(s) first 1000 PCCRs yes 13 98845373 98854737 -1 2 chr13:98845373-98845399-, chr13:98854585-98854737- 443 no DOCK9 cassette exon coding exon(s) first 1000 PCCRs yes 13 99015471 99015611 -1 1 chr13:99015471-99015611- 518 no DOCK9 alternative first exon coding exon(s) first 1000 PCCRs no 13 113403390 113410417 -1 7 chr13:113403390-113403497-, chr13:113406717-113406821-, chr13:113406906-113406950-, chr13:113407341-113407817-, chr13:113407827-113408024-, chr13:113408094-113408186-, chr13:113410385-113410417- 120 no ADPRHL1 alternative final coding exon coding exon(s) first 1000 PCCRs yes 14 20430676 20435763 -1 6 chr14:20430676-20430720-, chr14:20435053-20435169-, chr14:20435218-20435277-, chr14:20435287-20435352-, chr14:20435395-20435628-, chr14:20435722-20435763- 215 no KLHL33 alternative first exon coding exon(s) first 1000 PCCRs no 14 35688390 35689833 -1 5 chr14:35688390-35688578-, chr14:35688496-35688660-, chr14:35688685-35689089-, chr14:35689183-35689245-, chr14:35689555-35689833- 619 no RALGAPA1 intronic CDS coding exon(s) first 1000 PCCRs no 14 61970131 61970220 1 1 chr14:61970131-61970220+ 2881 no SYT16 alternative first exon coding exon(s) lncRNA PCCR no 14 72553290 72562586 1 4 chr14:72553290-72553343+, chr14:72553297-72553365+, chr14:72562452-72562505+, chr14:72562512-72562586+ 923 no RGS6 cassette exon leading to alternative frame final coding exon coding exon(s) first 1000 PCCRs no 14 73718846 73719007 -1 1 chr14:73718846-73719007- 368 yes ELMSAN1 final coding exon coding exon(s) first 1000 PCCRs no 14 78243088 78243801 1 1 chr14:78243088-78243801+ 348 no NRXN3 cassette exon coding exon(s) first 1000 PCCRs no 14 105852145 105856215 -1 10 chr14:105852145-105852261-, chr14:105854358-105854576-, chr14:105854610-105854720-, chr14:105854939-105855043-, chr14:105855532-105855585-, chr14:105855670-105855723-, chr14:105855766-105855798-, chr14:105855994-105856053-, chr14:105856093-105856149-, chr14:105856177-105856215- 70 no IGHM alternative final coding exons coding exon(s) first 1000 PCCRs yes 15 43564090 43569338 -1 2 chr15:43564090-43564155-, chr15:43569177-43569338- 786 no PPIP5K1 cassette exon coding exon(s) first 1000 PCCRs no 15 43879527 43879676 -1 1 chr15:43879527-43879676- 475 no FRMD5 alternative 5' exon coding exon(s) first 1000 PCCRs yes 15 63600698 63601024 1 1 chr15:63600698-63601024+ 456 yes FBXL22 3' exon coding exon(s) first 1000 PCCRs no 15 74217332 74218720 1 3 chr15:74217332-74217571+, chr15:74218496-74218570+, chr15:74218613-74218720+ 1097 no CCDC33 additional 5' exons coding exon(s) lncRNA PCCR no 15 82699633 82699875 -1 1 chr15:82699633-82699875- 666 no AP3B2 alternative first exon coding exon(s) first 1000 PCCRs yes 15 86079973 86080035 1 1 chr15:86079973-86080035+ 951 no AGBL1 alternative 5' exons coding exon(s) first 1000 PCCRs no 15 90934338 90943589 1 4 chr15:90934338-90934544+, chr15:90934942-90935040+, chr15:90935124-90935150+, chr15:90943503-90943589+ 390 yes UNC45A 5' exons coding exon(s) first 1000 PCCRs yes 16 540187 540369 1 1 chr16:540187-540369+ 539 no CAPN15 5' exon coding exon(s) first 1000 PCCRs no 16 3031428 3031502 -1 1 chr16:3031428-3031502- 798 no CCDC64B cassette exon coding exon(s) first 1000 PCCRs yes 16 10866284 10866481 1 1 chr16:10866284-10866481+ 990 no CIITA first coding exon coding exon(s) first 1000 PCCRs yes 16 19307548 19309068 1 2 chr16:19307548-19307676+, chr16:19309003-19309068+ 128 no CLEC19A alternative final coding exons coding exon(s) first 1000 PCCRs no 16 57937087 57937278 -1 1 chr16:57937087-57937278- 834 no CNGB1 alternative first exon coding exon(s) first 1000 PCCRs no 16 85169288 85171795 1 7 chr16:85169288-85169494+, chr16:85169289-85169495+, chr16:85169503-85169844+, chr16:85169504-85170364+, chr16:85169884-85170015+, chr16:85170476-85170544+, chr16:85170596-85171795+ 315 yes GSE1 5' extension coding exon(s) first 1000 PCCRs no 16 87358409 87358492 -1 1 chr16:87358409-87358492- 596 no FBXO31 cassette exon coding exon(s) first 1000 PCCRs yes 17 1125369 1125464 -1 1 chr17:1125369-1125464- 509 yes ABR 5' extension coding exon(s) first 1000 PCCRs yes 17 2770330 2770446 1 1 chr17:2770330-2770446+ 254 no RAP1GAP2 cassette exon coding exon(s) first 1000 PCCRs no 17 8344931 8344999 1 1 chr17:8344931-8344999+ 38 no ODF4 cassette exon, actually causes NMD in human but codes all the way through in all other animals; a single nucleotide deletion (no SNP currently present in dbSNP) causes a frameshift. coding exon(s) first 1000 PCCRs yes 17 17138263 17138427 1 1 chr17:17138263-17138427+ 317 no MPRIP cassette exon coding exon(s) first 1000 PCCRs no 17 27456338 27456877 1 4 chr17:27456338-27456382+, chr17:27456450-27456476+, chr17:27456626-27456877+, chr17:27456733-27456768+ 537 yes KSR1 alternative first exons coding exon(s) first 1000 PCCRs no 17 27793611 27793694 -1 1 chr17:27793611-27793694- 621 yes NOS2 alternative first exon coding exon(s) first 1000 PCCRs yes 17 29079734 29081017 -1 1 chr17:29079734-29081017- 520 yes MYO18A alternative final exon coding exon(s) first 1000 PCCRs yes 17 29124548 29133836 -1 6 chr17:29124548-29124580-, chr17:29125899-29125943-, chr17:29128029-29128415-, chr17:29128422-29128505-, chr17:29131386-29131442-, chr17:29133798-29133836- 176 no MYO18A alternative first exon plus four cassette exons coding exon(s) first 1000 PCCRs yes 17 32222769 32224838 1 2 chr17:32222769-32222885+, chr17:32224812-32224838+ 952 no RHOT1 cassette exon. coding exon(s) first 1000 PCCRs yes 17 40818394 40818474 -1 1 chr17:40818394-40818474- 942 no KRT10 alternative reading frame in final exon, M/S supported coding exon(s) first 1000 PCCRs no 17 55962062 55965666 1 2 chr17:55962062-55962160+, chr17:55965631-55965666+ 543 no ANKFN1 cassette exon coding exon(s) first 1000 PCCRs yes 17 64497052 64506947 -1 9 chr17:64497052-64497096-, chr17:64500762-64500791-, chr17:64501286-64501372-, chr17:64501344-64501370-, chr17:64501803-64501862-, chr17:64505437-64505595-, chr17:64505457-64505594-, chr17:64505471-64505500-, chr17:64506921-64506947- 1219 yes DDX5 alternative first exon coding exon(s) lncRNA PCCR yes 17 65100869 65100895 1 1 chr17:65100869-65100895+ 45627 no RGS9 alternative first exon coding exon(s) lncRNA PCCR yes 17 67993147 67996207 -1 5 chr17:67993147-67993236-, chr17:67993425-67993478-, chr17:67993533-67993853-, chr17:67995759-67995818-, chr17:67996127-67996207- 816 yes C17orf58 alternative 5' extension coding exon(s) first 1000 PCCRs yes 17 75590633 75590987 1 2 chr17:75590633-75590689+, chr17:75590907-75590987+ 876 no MYO15B two cassette exons coding exon(s) first 1000 PCCRs no 17 76307579 76307992 -1 2 chr17:76307579-76307704-, chr17:76307843-76307992- 9 yes QRICH2 large 5' extension to first exon coding exon(s) first 1000 PCCRs no 17 78031515 78031838 1 1 chr17:78031515-78031838+ 162 no TNRC6C alternative first coding exons coding exon(s) first 1000 PCCRs no 18 5398651 5407505 -1 4 chr18:5398651-5398812-, chr18:5398876-5399016-, chr18:5399038-5399316-, chr18:5407461-5407505- 284 no EPB41L3 cassette exon coding exon(s) first 1000 PCCRs yes 18 10708277 10714957 -1 2 chr18:10708277-10708465-, chr18:10714931-10714957- 750 no PIEZO2 cassette exon coding exon(s) first 1000 PCCRs yes 18 26546760 26549891 -1 10 chr18:26546760-26546861-, chr18:26546761-26548572-, chr18:26547971-26548066-, chr18:26548427-26548666-, chr18:26548894-26549199-, chr18:26549130-26549339-, chr18:26549376-26549429-, chr18:26549762-26549848-, chr18:26549763-26549801-, chr18:26549862-26549891- 768 yes KCTD1 5' extension coding exon(s) first 1000 PCCRs no 18 58255504 58256765 1 3 chr18:58255504-58255539+, chr18:58255614-58256153+, chr18:58256169-58256765+ 513 yes NEDD4L alternative first coding exon. This CDS was not subjected to further analysis as it was reclassified as coding once this work was completed. coding exon(s) first 1000 PCCRs yes 18 76931069 76931224 1 2 chr18:76931069-76931110+, chr18:76931114-76931224+ 769 no ZNF236 cassette exon coding exon(s) first 1000 PCCRs yes 19 1821684 1821785 -1 1 chr19:1821684-1821785- 1000 no REXO1 intronic CDS coding exon(s) first 1000 PCCRs yes 19 3314755 3324737 1 4 chr19:3314755-3314859+, chr19:3320404-3320466+, chr19:3323526-3323591+, chr19:3324666-3324737+ 842 no NFIC alternative first exon coding exon(s) first 1000 PCCRs yes 19 7556974 7557081 1 1 chr19:7556974-7557081+ 976 yes PNPLA6 cassette exon coding exon(s) first 1000 PCCRs yes 19 13599752 13599862 -1 1 chr19:13599752-13599862- 751 no CACNA1A alternative first exon coding exon(s) first 1000 PCCRs yes 19 14562387 14563734 1 2 chr19:14562387-14562524+, chr19:14563705-14563734+ 570 no TECR intronic CDS coding exon(s) first 1000 PCCRs yes 19 15428334 15450039 -1 20 chr19:15428334-15428402-, chr19:15428510-15428545-, chr19:15432345-15432536-, chr19:15432436-15432534-, chr19:15432464-15432535-, chr19:15432545-15432733-, chr19:15432546-15432722-, chr19:15432547-15432762-, chr19:15438582-15439160-, chr19:15439209-15439271-, chr19:15439326-15440087-, chr19:15440094-15440267-, chr19:15440331-15440405-, chr19:15440508-15440711-, chr19:15442667-15442699-, chr19:15449238-15449318-, chr19:15449645-15449767-, chr19:15449682-15449795-, chr19:15449893-15450039-, chr19:15449916-15450026- 471 yes WIZ 2 cassette exons coding exon(s) first 1000 PCCRs no 19 32826242 32826736 1 3 chr19:32826242-32826355+, chr19:32826443-32826604+, chr19:32826680-32826736+ 264 no TDRD12 alternative final coding exons coding exon(s) first 1000 PCCRs no 19 35767600 35790402 1 7 chr19:35767600-35767674+, chr19:35775513-35775593+, chr19:35775533-35775658+, chr19:35775550-35775594+, chr19:35775667-35775765+, chr19:35784653-35784688+, chr19:35790358-35790402+ 970 yes PROSER3 retained intron CDS coding exon(s) first 1000 PCCRs no 19 35897702 35900539 -1 4 chr19:35897702-35897791-, chr19:35898722-35898823-, chr19:35900443-35900505-, chr19:35900513-35900539- 360 yes NFKBID 5' extension coding exon(s) first 1000 PCCRs yes 19 40321274 40321357 -1 1 chr19:40321274-40321357- 986 no C19orf47 alternative final exon coding exon(s) first 1000 PCCRs no 19 40458139 40467303 -1 7 chr19:40458139-40458171-, chr19:40458265-40458378-, chr19:40466979-40467008-, chr19:40467081-40467116-, chr19:40467118-40467162-, chr19:40467164-40467205-, chr19:40467274-40467303- 841 yes BLVRB retained intron CDS coding exon(s) first 1000 PCCRs yes 19 42116895 42117029 -1 1 chr19:42116895-42117029- 292 no POU2F2 alternative coding exons coding exon(s) first 1000 PCCRs no 19 45234195 45239048 -1 2 chr19:45234195-45234836-, chr19:45238527-45239048- 29 yes EXOC3L2 extended 5' by two coding exons coding exon(s) first 1000 PCCRs yes 19 47273356 47273457 1 1 chr19:47273356-47273457+ 1237 yes CCDC9 alternative final coding exon coding exon(s) previously unannotated PCCR yes 19 48469331 48498684 -1 19 chr19:48469331-48469462-, chr19:48469354-48469506-, chr19:48469377-48469409-, chr19:48469475-48469516-, chr19:48469536-48469562-, chr19:48469676-48469705-, chr19:48469701-48469757-, chr19:48477680-48477721-, chr19:48479256-48479282-, chr19:48485546-48485635-, chr19:48485639-48485755-, chr19:48491391-48491540-, chr19:48493758-48494021-, chr19:48493771-48493986-, chr19:48497464-48497889-, chr19:48497920-48498123-, chr19:48498271-48498297-, chr19:48498307-48498405-, chr19:48498658-48498684- 328 yes LMTK3 alternative final coding exon, based on a translation that runs for at least 5 shared exons in a different frame. This annotation appeared for the first time in GENCODEv29. coding exon(s) first 1000 PCCRs yes 19 49832416 49838821 1 2 chr19:49832416-49832445+, chr19:49838582-49838821+ 638 no MED25 alternative final exon had frame corrected coding exon(s) first 1000 PCCRs no 20 15892926 15893009 1 1 chr20:15892926-15893009+ 831 no MACROD2 cassette exon coding exon(s) first 1000 PCCRs yes 20 16367827 16368564 -1 3 chr20:16367827-16368075-, chr20:16368157-16368210-, chr20:16368532-16368564- 678 no KIF16B alternate final exon coding exon(s) first 1000 PCCRs no 20 36205843 36208375 1 10 chr20:36205843-36205878+, chr20:36205945-36206034+, chr20:36206050-36206106+, chr20:36206368-36206505+, chr20:36207052-36207099+, chr20:36207271-36207336+, chr20:36207415-36207483+, chr20:36207550-36207624+, chr20:36207730-36207768+, chr20:36208346-36208375+ 125 no EPB41L1 three consectutive cassette exons coding exon(s) first 1000 PCCRs yes 20 58852721 58856213 1 6 chr20:58852721-58852780+, chr20:58852782-58852817+, chr20:58853267-58853329+, chr20:58853357-58853452+, chr20:58854210-58854257+, chr20:58856145-58856213+ 410 yes GNAS cassette exon coding exon(s) first 1000 PCCRs yes 20 64098800 64098883 1 1 chr20:64098800-64098883+ 752 yes OPRL1 known STOP codon readthrough coding exon(s) first 1000 PCCRs no 21 31160436 31160531 -1 1 chr21:31160436-31160531- 46 no TIAM1 first coding exon. coding exon(s) first 1000 PCCRs yes 21 36938884 36938994 -1 1 chr21:36938884-36938994- 230 no HLCS alternative first coding exons coding exon(s) first 1000 PCCRs no 22 25111740 25112471 1 2 chr22:25111740-25111781+, chr22:25112169-25112471+ 278 no KIAA1671 5' coding exon coding exon(s) first 1000 PCCRs yes 22 41971511 41976889 1 7 chr22:41971511-41971723+, chr22:41971802-41971846+, chr22:41971976-41972017+, chr22:41972042-41972089+, chr22:41972171-41972224+, chr22:41976793-41976828+, chr22:41976809-41976889+ 643 yes SEPT3 alternative first exon coding exon(s) first 1000 PCCRs no 22 50546280 50548166 1 4 chr22:50546280-50546414+, chr22:50546751-50546795+, chr22:50546988-50547044+, chr22:50548128-50548166+ 159 yes KLHDC7B 5' extension coding exon(s) first 1000 PCCRs yes X 12717136 12721843 1 4 chrX:12717136-12717162+, chrX:12720749-12720784+, chrX:12720824-12721129+, chrX:12721220-12721843+ 286 no FRMPD4 3' extended final exon coding exon(s) first 1000 PCCRs no X 139691925 139692026 -1 1 chrX:139691925-139692026- 645 yes MCF2 extended to upstream ATG coding exon(s) first 1000 PCCRs no 1 1734683 1734835 -1 1 chr1:1734683-1734835- 51 no SLC35E2 (ENSG00000215790) has been converted from coding to pseudogenic; a coding exon is out of frame compared to its paralog SLC35E2B pseudogene first 1000 PCCRs yes 1 5554747 5554881 1 1 chr1:5554747-5554881+ 1149 no MT-CO3 pseudogene (ENSG00000283356) pseudogene previously unannotated PCCR yes 1 9951232 9960787 -1 4 chr1:9951232-9951291-, chr1:9952339-9952470-, chr1:9955834-9955902-, chr1:9960725-9960787- 384 no unitary pseudogene ENSG00000283611 pseudogene first 1000 PCCRs yes 1 21950738 21951365 -1 4 chr1:21950738-21950881-, chr1:21951083-21951142-, chr1:21951161-21951205-, chr1:21951297-21951365- 280 no unitary pseudogene ENSG00000283234 pseudogene first 1000 PCCRs yes 1 108495475 108495582 -1 1 chr1:108495475-108495582- 849 no solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 24 (SLC25A24) pseudogene (ENSG00000283354) pseudogene first 1000 PCCRs yes 1 120620337 120620731 -1 2 chr1:120620337-120620495-, chr1:120620702-120620731- 253 no phosphodiesterase 4D interacting protein (PDE4DIP) transcribed unprocessed pseudogene (ENSG00000275131) pseudogene first 1000 PCCRs yes 1 121029605 121037796 -1 3 chr1:121029605-121029724-, chr1:121031096-121031134-, chr1:121037563-121037796- 7747 no phosphodiesterase 4D interacting protein (PDE4DIP) unprocessed pseudogene (ENSG00000275585) pseudogene lncRNA PCCR no 1 157205006 157205041 -1 1 chr1:157205006-157205041- 1863 no uncharacterised pseudogene (ENSG00000284592) pseudogene previously unannotated PCCR yes 1 200920454 200929951 1 3 chr1:200920454-200920483+, chr1:200921730-200921864+, chr1:200929916-200929951+ 83 no unitary pseudogene ENSG00000233217 pseudogene first 1000 PCCRs no 1 202825246 202828148 1 4 chr1:202825246-202825431+, chr1:202826141-202826191+, chr1:202826222-202826284+, chr1:202828113-202828148+ 422 no unitary pseudogene ENSG00000184774 pseudogene first 1000 PCCRs no 1 237940783 237943644 -1 8 chr1:237940783-237941067-, chr1:237941554-237941745-, chr1:237941800-237942213-, chr1:237942235-237942345-, chr1:237942358-237942459-, chr1:237942707-237943099-, chr1:237943145-237943555-, chr1:237943564-237943644- 302 no mitochondrially encoded NADH dehydrogenase 2 (MT-ND2) pseudogene (ENSG00000283166) pseudogene first 1000 PCCRs yes 1 248692176 248697161 1 2 chr1:248692176-248692208+, chr1:248697030-248697161+ 5148 no unitary pseudogene ENSG00000229703 pseudogene lncRNA PCCR yes 2 61177533 61186081 1 5 chr2:61177533-61177625+, chr2:61178982-61179170+, chr2:61181334-61181408+, chr2:61183560-61183655+, chr2:61185980-61186081+ 1432 yes AHSA2 has 4 pseudo exons upstream of the ATG, so switched to pseudogene AHSA2P (ENSG00000173209) pseudogene lncRNA PCCR yes 2 68925700 68926822 1 2 chr2:68925700-68925762+, chr2:68926742-68926822+ 623 no Polymorphic pseudogene GKN3P (ENSG00000283586); rs10187256 accounts for the PTC and rs564515112 accounts for the non-canonical splice site pseudogene first 1000 PCCRs yes 2 88811636 88818414 -1 3 chr2:88811636-88811692-, chr2:88814284-88814436-, chr2:88818310-88818414- 22295 no mal, T-cell differentiation protein-like (MALL) unprocessed pseudogene (ENSG00000283270) pseudogene lncRNA PCCR yes 2 89533188 89547118 1 6 chr2:89533188-89533313+, chr2:89537789-89537857+, chr2:89537864-89538052+, chr2:89538060-89538500+, chr2:89538681-89538731+, chr2:89546933-89547118+ 59 no Otopetrin 1 (OTPO1) unprocessed pseudogene (ENSG00000283427) pseudogene first 1000 PCCRs yes 2 89622214 89637657 -1 8 chr2:89622214-89622309-, chr2:89622313-89622426-, chr2:89624300-89624341-, chr2:89625698-89625844-, chr2:89626141-89626332-, chr2:89631587-89631700-, chr2:89631890-89631964-, chr2:89637535-89637657- 1710 no lysine (K)-specific methyltransferase 2C (KMT2C) pseudogene (ENSG00000283132) pseudogene previously unannotated PCCR yes 2 89662603 89662983 1 2 chr2:89662603-89662632+, chr2:89662657-89662983+ 897 no immunoglobulin superfamily member 3 (IGSF3) pseudogene (ENSG00000283214) pseudogene first 1000 PCCRs yes 2 109963466 109974092 1 8 chr2:109963466-109963531+, chr2:109964689-109964808+, chr2:109968070-109968201+, chr2:109971397-109971519+, chr2:109971618-109971659+, chr2:109971662-109971727+, chr2:109971920-109972024+, chr2:109973991-109974092+ 1038 no two-pore calcium channel 3 (TPCN3) pseudogene (ENSG00000186148) pseudogene lncRNA PCCR yes 2 110022446 110035237 -1 19 chr2:110022446-110022661-, chr2:110023200-110023280-, chr2:110023300-110023395-, chr2:110024163-110024210-, chr2:110024215-110024283-, chr2:110025066-110025125-, chr2:110025183-110025224-, chr2:110025240-110025269-, chr2:110025458-110025508-, chr2:110025524-110025556-, chr2:110025618-110025665-, chr2:110025925-110026032-, chr2:110027378-110027566-, chr2:110027760-110027909-, chr2:110028558-110028743-, chr2:110030008-110030124-, chr2:110030907-110031002-, chr2:110033857-110033913-, chr2:110035076-110035237- 386 no uncharacterised pseudogene ENSG00000283283, one of two pseudogenic copies of a large 51 exon mouse coding gene pseudogene first 1000 PCCRs yes 2 110261435 110272049 1 8 chr2:110261435-110261494+, chr2:110262676-110262771+, chr2:110266031-110266156+, chr2:110269357-110269482+, chr2:110269566-110269628+, chr2:110269625-110269690+, chr2:110269880-110269981+, chr2:110271930-110272049+ 71 no ion transport protein domain-containing transcribed unprocessed pseudogene (ENSG00000261760) pseudogene first 1000 PCCRs no 2 110330068 110348951 1 22 chr2:110330068-110330139+, chr2:110333912-110333953+, chr2:110335605-110335634+, chr2:110336203-110336235+, chr2:110336260-110336310+, chr2:110337521-110337574+, chr2:110340438-110340512+, chr2:110341310-110341426+, chr2:110342709-110342864+, chr2:110343526-110343678+, chr2:110343869-110343994+, chr2:110345359-110345403+, chr2:110345726-110345779+, chr2:110345838-110345978+, chr2:110346116-110346142+, chr2:110346170-110346325+, chr2:110347105-110347179+, chr2:110347175-110347228+, chr2:110347996-110348103+, chr2:110348102-110348197+, chr2:110348757-110348789+, chr2:110348796-110348951+ 220 no uncharacterised pseudogene ENSG00000283167, one of two pseudogenic copies of a large 51 exon mouse coding gene pseudogene first 1000 PCCRs yes 2 110397399 110408025 -1 8 chr2:110397399-110397497-, chr2:110399464-110399571-, chr2:110399770-110399829-, chr2:110399832-110399888-, chr2:110399972-110400097-, chr2:110403296-110403421-, chr2:110406679-110406798-, chr2:110407957-110408025- 1806 no two-pore calcium channel 3 (TPCN3) pseudogene (ENSG00000184115) pseudogene lncRNA PCCR no 2 112440419 112440583 -1 2 chr2:112440419-112440472-, chr2:112440491-112440583- 803 no unitary pseudogene ENSG00000283698 pseudogene first 1000 PCCRs yes 2 131355599 131355781 1 1 chr2:131355599-131355781+ 13 no FAR2 pseudogene (ENSG00000284706); found after looking at high-scoring intergenic PCCRs pseudogene re-ranking yes 2 131419666 131419782 -1 1 chr2:131419666-131419782- 42 no SFRP4 pseudogene (ENSG00000284659); found after looking at high-scoring intergenic PCCRs pseudogene re-ranking yes 2 166414489 166414729 1 2 chr2:166414489-166414578+, chr2:166414577-166414729+ 1436 no mitochondrially encoded cytochrome c oxidase I (MT-CO1) pseudogene (ENSG00000283657) pseudogene previously unannotated PCCR yes 2 230138601 230138765 1 1 chr2:230138601-230138765+ 569 no Component of Sp100-rs (Csprs) pseudogene (ENSG00000283451) pseudogene first 1000 PCCRs yes 3 44421325 44421772 -1 2 chr3:44421325-44421354-, chr3:44421725-44421772- 2995 no unitary pseudogene ENSG00000225873 pseudogene lncRNA PCCR yes 3 46719752 46719997 -1 2 chr3:46719752-46719787-, chr3:46719827-46719997- 462 no unitary pseudogene ENSG00000261603 pseudogene first 1000 PCCRs yes 3 58180356 58180517 1 2 chr3:58180356-58180451+, chr3:58180482-58180517+ 64 no unitary pseudogene ENSG00000283511 pseudogene first 1000 PCCRs yes 3 100208048 100211682 1 4 chr3:100208048-100208074+, chr3:100208090-100208179+, chr3:100208198-100208245+, chr3:100211575-100211682+ 486 no TMEM30C converted to a transcribed unitary pseudogene TMEM30CP (ENSG00000235156) due to disablement of the longer isoform, lack of expression data for last 4 exons and PMID:17258408. pseudogene first 1000 PCCRs yes 3 120366477 120368084 1 7 chr3:120366477-120366563+, chr3:120366639-120366722+, chr3:120366732-120366758+, chr3:120366780-120366827+, chr3:120367884-120367967+, chr3:120367974-120368024+, chr3:120368031-120368084+ 11 no unitary pseudogene ENSG00000240661 pseudogene first 1000 PCCRs yes 3 141681521 141685950 1 3 chr3:141681521-141681628+, chr3:141685069-141685197+, chr3:141685870-141685950+ 32 no unitary pseudogene ENSG00000242104 pseudogene first 1000 PCCRs yes 3 151803778 151803906 1 2 chr3:151803778-151803810+, chr3:151803868-151803906+ 5501 no arylacetamide deacetylase (esterase) (AADAC) unprocessed pseudogene (ENSG00000250271) pseudogene lncRNA PCCR yes 3 167912863 167917494 1 4 chr3:167912863-167912901+, chr3:167915073-167915105+, chr3:167915124-167915201+, chr3:167917330-167917494+ 287 no unitary pseuodgene ENSG00000244227 pseudogene first 1000 PCCRs no 3 184499610 184500370 -1 7 chr3:184499610-184499639-, chr3:184499723-184499860-, chr3:184499882-184499986-, chr3:184500020-184500067-, chr3:184500089-184500151-, chr3:184500281-184500322-, chr3:184500338-184500370- 22 no transmembrane epididymal protein 1 (TEDDM1) pseudogene (ENSG00000283625) pseudogene first 1000 PCCRs yes 3 195708133 195711628 1 2 chr3:195708133-195708165+, chr3:195711593-195711628+ 5786 no unitary pseudogene ENSG00000283426 pseudogene lncRNA PCCR yes 4 6228024 6228137 1 1 chr4:6228024-6228137+ 1336 no High-mobility group family pseudogene (ENSG00000249896) pseudogene lncRNA PCCR yes 4 17557911 17557994 -1 1 chr4:17557911-17557994- 1417 no mitochondrially encoded cytochrome b (MT-CYB) pseudogene (ENSG00000283219) pseudogene previously unannotated PCCR yes 4 56410528 56419951 1 4 chr4:56410528-56410578+, chr4:56410675-56410806+, chr4:56419655-56419774+, chr4:56419829-56419951+ 1197 no Transcribed unprocessed pseudogene. Myb/SANT-like DNA-binding domain containing (ENSG00000283156) pseudogene previously unannotated PCCR yes 4 68049815 68050392 -1 3 chr4:68049815-68049997-, chr4:68050094-68050129-, chr4:68050306-68050392- 2071 no mitochondrial pseudogene region (ENSG00000283156) pseudogene previously unannotated PCCR yes 4 82285065 82295757 1 4 chr4:82285065-82285130+, chr4:82285263-82285295+, chr4:82290504-82290551+, chr4:82295689-82295757+ 819 yes unitary pseudogene ENSG00000284516 pseudogene first 1000 PCCRs yes 5 82304663 82304848 1 2 chr5:82304663-82304815+, chr5:82304822-82304848+ 881 no ATP6AP1L has been switched to pseudogene ENSG00000205464 from coding based on the discovery of pseudo exons pseudogene first 1000 PCCRs yes 5 140590883 140594367 -1 5 chr5:140590883-140590909-, chr5:140591081-140591131-, chr5:140591663-140591701-, chr5:140592018-140592047-, chr5:140594242-140594367- 66 no unitary pseudogene ENSG00000283602 pseudogene first 1000 PCCRs yes 5 148366071 148366142 1 1 chr5:148366071-148366142+ 807 no serine peptidase inhibitor, Kazal type 6 (SPINK6) pseudogene (ENSG00000283653) pseudogene first 1000 PCCRs yes 5 157689958 157690896 -1 4 chr5:157689958-157690125-, chr5:157690112-157690366-, chr5:157690412-157690597-, chr5:157690600-157690896- 1295 yes SRY-box 30 (SOX30) pseuodgene (ENSG00000253798) pseudogene lncRNA PCCR yes 5 176146963 176156969 -1 7 chr5:176146963-176147109-, chr5:176147727-176147867-, chr5:176148043-176148111-, chr5:176151947-176152000-, chr5:176153725-176153838-, chr5:176154919-176154963-, chr5:176156913-176156969- 8635 no centrosomal protein 192kDa (CEP192) pseudogene (ENSG00000283559) pseudogene lncRNA PCCR no 6 4115457 4115663 1 1 chr6:4115457-4115663+ 660 no C6orf201 pseudoexon, led to locus being reannotated as a unitary pseudogene ENSG00000185689 pseudogene first 1000 PCCRs yes 6 26196321 26196594 1 3 chr6:26196321-26196368+, chr6:26196374-26196508+, chr6:26196547-26196594+ 1475 no histone 1, H1, pseudogene 1 (ENSG00000216331) pseudogene previously unannotated PCCR yes 6 30056989 30058171 -1 5 chr6:30056989-30057018-, chr6:30057112-30057156-, chr6:30057241-30057297-, chr6:30057580-30057663-, chr6:30058118-30058171- 93 no unitary pseudogene ENSG00000204623 pseudogene first 1000 PCCRs yes 6 60281444 60283705 1 2 chr6:60281444-60281494+, chr6:60283565-60283705+ 143 no DNA primase subunit 2 (PRIM2) unprocessed pseudogene (ENSG00000283453) pseudogene first 1000 PCCRs yes 6 60400254 60400316 1 1 chr6:60400254-60400316+ 1065 no primase, DNA, polypeptide 2 (58kDa) (PRIM2) pseudogene (ENSG00000283453) pseudogene previously unannotated PCCR yes 6 109239409 109242294 1 2 chr6:109239409-109239516+, chr6:109242223-109242294+ 146 no unitary pseudogene CCDC162P (ENSG00000203799) pseudogene first 1000 PCCRs yes 7 2384592 2388658 1 2 chr7:2384592-2384675+, chr7:2388551-2388658+ 304 no unitary pseuodgene, KIF19 family member (ENSG00000230914) pseudogene first 1000 PCCRs yes 7 37796070 37796888 1 6 chr7:37796070-37796132+, chr7:37796163-37796255+, chr7:37796281-37796406+, chr7:37796513-37796542+, chr7:37796595-37796783+, chr7:37796802-37796888+ 35 no unitary pseudogene ENSG00000283444 pseudogene first 1000 PCCRs yes 7 57167069 57169403 1 6 chr7:57167069-57167101+, chr7:57167200-57167877+, chr7:57168773-57168826+, chr7:57168825-57168938+, chr7:57169000-57169044+, chr7:57169158-57169403+ 311 no MTCO3P10 mitochondrially encoded cytochrome c oxidase III pseudogene 10 (ENSG00000231537) pseudogene first 1000 PCCRs yes 7 57173053 57173256 -1 1 chr7:57173053-57173256- 974 no mitochondrially encoded NADH dehydrogenase 6 (MT-ND6) pseudogene (ENSG00000283311) pseudogene first 1000 PCCRs yes 7 57190149 57192692 1 7 chr7:57190149-57190199+, chr7:57190300-57190362+, chr7:57190494-57191138+, chr7:57192014-57192091+, chr7:57192090-57192224+, chr7:57192268-57192327+, chr7:57192420-57192692+ 73 no MTCO3P4 mitochondrially encoded cytochrome c oxidase III pseudogene 4 (ENSG00000228851) pseudogene first 1000 PCCRs yes 7 57196059 57196531 -1 2 chr7:57196059-57196118-, chr7:57196334-57196531- 1525 no mitochondrial pseudogene region (ENSG00000284572) pseudogene previously unannotated PCCR yes 7 73735456 73743100 1 4 chr7:73735456-73735500+, chr7:73735729-73735848+, chr7:73735924-73735983+, chr7:73743038-73743100+ 140 no unitary pseudogene ENSG00000225969 pseudogene first 1000 PCCRs yes 7 81560120 81607572 -1 10 chr7:81560120-81560206-, chr7:81560743-81560862-, chr7:81570270-81570329-, chr7:81570403-81570444-, chr7:81574077-81574166-, chr7:81581744-81581842-, chr7:81586891-81586944-, chr7:81590981-81591064-, chr7:81597741-81597815-, chr7:81607525-81607572- 904 no unitary pseudogene ENSG00000233491 pseudogene first 1000 PCCRs yes 7 135307168 135310600 -1 3 chr7:135307168-135307194-, chr7:135307197-135307313-, chr7:135310565-135310600- 183 no solute carrier family 23 (ascorbic acid transporter), member 1 (SLC23A1) pseudogene (ENSG00000276067) pseudogene first 1000 PCCRs yes 7 143620652 143624390 1 3 chr7:143620652-143620696+, chr7:143623776-143624021+, chr7:143624127-143624390+ 837 yes transient receptor potential cation channel, subfamily M, member 8 channel-associated factor (TRPM8) pseudogene existed on the wrong strand (ENSG00000283537) pseudogene first 1000 PCCRs yes 7 149294749 149295236 1 3 chr7:149294749-149294802+, chr7:149294805-149295095+, chr7:149295117-149295236+ 926 yes zinc finger family pseudogene (ENSG00000244560) pseudogene first 1000 PCCRs no 7 155074599 155074748 1 1 chr7:155074599-155074748+ 512 no mitochondrially encoded cytochrome c oxidase II (MT-CO2) pseudogene (ENSG00000283339) pseudogene first 1000 PCCRs yes 8 1726279 1726557 1 1 chr8:1726279-1726557+ 720 no mitochondrially encoded cytochrome c oxidase II (MT-CO2) pseudogene (ENSG00000283576) pseudogene first 1000 PCCRs yes 8 8714226 8719546 -1 5 chr8:8714226-8714285-, chr8:8714879-8714917-, chr8:8715416-8715499-, chr8:8715532-8715576-, chr8:8719469-8719546- 167 no unitary pseudogene ENSG00000284717 pseudogene first 1000 PCCRs yes 8 18849276 18849713 1 1 chr8:18849276-18849713+ 1164 no MT-CO2 pseudogene (ENSG00000283402) pseudogene previously unannotated PCCR yes 8 133515503 133516257 1 2 chr8:133515503-133515715+, chr8:133516186-133516257+ 255 no mitochondrially encoded NADH dehydrogenase 3 (MT-ND3) pseudogene (ENSG00000283176) pseudogene first 1000 PCCRs yes 8 142797632 142806142 -1 3 chr8:142797632-142797829-, chr8:142801084-142801176-, chr8:142806077-142806142- 399 no lymphocyte antigen 6 complex, locus K (LY6K) pseudogene (ENSG00000283686) pseudogene first 1000 PCCRs yes 8 144049161 144051191 1 9 chr8:144049161-144049202+, chr8:144049291-144049581+, chr8:144049636-144049896+, chr8:144050020-144050055+, chr8:144050302-144050370+, chr8:144050386-144050448+, chr8:144050794-144050856+, chr8:144051015-144051050+, chr8:144051114-144051191+ 902 yes unitary pseudogene (ENSG00000204791) pseudogene first 1000 PCCRs yes 9 27261849 27261935 -1 1 chr9:27261849-27261935- 12553 no REX1, RNA exonuclease 1 homolog (REXO1) unprocessed pseudogene (ENSG00000283945) pseudogene lncRNA PCCR yes 9 38456161 38469956 1 3 chr9:38456161-38456193+, chr9:38462104-38462229+, chr9:38469846-38469956+ 172 no STRA6-like (Stra6l) pseudogene (ENSG00000283162) pseudogene first 1000 PCCRs yes 9 40500639 40503286 1 2 chr9:40500639-40500782+, chr9:40503128-40503286+ 38203 no methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like (MTHFD1L) pseudogene (ENSG00000184906) pseudogene lncRNA PCCR yes 9 41039613 41053896 -1 6 chr9:41039613-41039765-, chr9:41040360-41040551-, chr9:41044507-41044626-, chr9:41047538-41047564-, chr9:41047568-41047696-, chr9:41053753-41053896- 205 no PGM5P2 unprocessed pseudogene (ENSG00000277778) pseudogene first 1000 PCCRs no 9 41074191 41074550 -1 1 chr9:41074191-41074550- 1649 yes FSHD region gene 1, member H unprocessed pseudogene (ENSG00000184906) pseudogene lncRNA PCCR no 9 61063756 61073097 -1 5 chr9:61063756-61063893-, chr9:61063918-61063992-, chr9:61066335-61066553-, chr9:61067571-61067744-, chr9:61072984-61073097- 57 no contactin associated protein-like 3B (CNTNAP3B) unprocessed pseudogene (ENSG00000283541) pseudogene first 1000 PCCRs yes 9 63121682 63124298 -1 2 chr9:63121682-63121846-, chr9:63124158-63124298- 39917 no methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like (MTHFD1L) pseudogene (ENSG00000182021) pseudogene lncRNA PCCR yes 9 66182325 66188394 1 6 chr9:66182325-66182456+, chr9:66182461-66182640+, chr9:66182647-66182721+, chr9:66183809-66183964+, chr9:66184640-66184759+, chr9:66188329-66188394+ 30 no MEP1A pseudogene (ENSG00000284706); found after looking at high-scoring intergenic PCCRs pseudogene re-ranking yes 9 82428199 82428285 1 1 chr9:82428199-82428285+ 10199 no serine palmitoyltransferase long chain base subunit 1 (SPTLC1) pseudogene (ENSG00000228430) pseudogene lncRNA PCCR yes 9 92141418 92141672 1 4 chr9:92141418-92141507+, chr9:92141425-92141532+, chr9:92141426-92141536+, chr9:92141592-92141672+ 42668 no leucine rich repeat containing G protein-coupled receptor 6 (LGR6) pseudogene (ENSG00000225511) pseudogene lncRNA PCCR yes 9 112997453 112997611 -1 1 chr9:112997453-112997611- 6200 no ZNF883, coding according to RefSeq though pseudogene seems more likely given its odd structure (ENSG00000228623) pseudogene lncRNA PCCR yes 9 120847295 120847354 1 1 chr9:120847295-120847354+ 1125 no unitary pseudogene ENSG00000226752 pseudogene lncRNA PCCR yes 10 19747190 19747432 -1 1 chr10:19747190-19747432- 69 no MTND1P37 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 pseudogene 37 (ENSG00000283456) pseudogene first 1000 PCCRs yes 10 26593998 26594236 1 2 chr10:26593998-26594057+, chr10:26594102-26594236+ 42217 no amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein (APBB1IP) pseudogene (ENSG00000233261) pseudogene lncRNA PCCR yes 10 26653130 26653357 1 2 chr10:26653130-26653189+, chr10:26653289-26653357+ 45866 no family with sequence similarity 238 member B (non-protein coding) FAM238B pseudogene (ENSG00000231976) pseudogene lncRNA PCCR yes 10 26664276 26667644 -1 2 chr10:26664276-26664392-, chr10:26667561-26667644- 1751 no unitary pseudogene ENSG00000227932 pseudogene lncRNA PCCR yes 10 27397748 27398290 -1 2 chr10:27397748-27397846-, chr10:27397862-27398290- 622 no PTCHD3 (ENSG00000182077) converted from coding to a polymorphic pseudogene based on a truncation of the CDS by rs250532 ENSG00000182077 pseudogene first 1000 PCCRs yes 10 30655672 30655722 1 1 chr10:30655672-30655722+ 50193 no SVIL pseudogene extended (ENSG00000234814) pseudogene lncRNA PCCR yes 10 38175849 38176196 1 2 chr10:38175849-38175908+, chr10:38175990-38176196+ 38120 no cyclin Y-like pseudogene (ENSG00000224761) pseudogene lncRNA PCCR no 10 38247919 38248044 1 1 chr10:38247919-38248044+ 2142 no phospholipase D family member 5 (PLD5) pseudogene (ENSG00000226113) pseudogene lncRNA PCCR yes 10 89786640 89787109 1 3 chr10:89786640-89786834+, chr10:89786837-89787004+, chr10:89787083-89787109+ 1123 no NADH dehydrogenase subunit 5 pseudogene (ENSG00000283402) pseudogene previously unannotated PCCR yes 10 100105748 100122651 -1 8 chr10:100105748-100105804-, chr10:100108360-100108389-, chr10:100108448-100108504-, chr10:100117267-100117368-, chr10:100117406-100117438-, chr10:100121044-100121079-, chr10:100122506-100122571-, chr10:100122574-100122651- 105 no unitary pseudogene ENSG00000283232 pseudogene first 1000 PCCRs yes 10 100135400 100140071 -1 3 chr10:100135400-100135462-, chr10:100135484-100135513-, chr10:100139997-100140071- 1114 no unitary pseudogene ENSG00000283232 pseudogene previously unannotated PCCR yes 10 121951540 121951927 1 4 chr10:121951540-121951599+, chr10:121951702-121951755+, chr10:121951751-121951777+, chr10:121951892-121951927+ 1171 no unitary pseudogene ENSG00000226864 pseudogene lncRNA PCCR yes 11 3500470 3500577 -1 1 chr11:3500470-3500577- 37061 no ectonucleotide pyrophosphatase/phosphodiesterase 7 (ENPP7) pseudogene (ENSG00000284605) pseudogene lncRNA PCCR yes 11 3614740 3614790 1 1 chr11:3614740-3614790+ 496 no TRPC2 transient receptor potential cation channel, subfamily C, member 2 pseudogene (ENSG00000182048) pseudogene first 1000 PCCRs yes 11 5402904 5403164 1 2 chr11:5402904-5403029+, chr11:5403045-5403164+ 4 no OR51J1 protein-coding gene switched to pseudogene (ENSG00000184321) pseudogene first 1000 PCCRs yes 11 47323975 47326737 1 5 chr11:47323975-47324124+, chr11:47326311-47326373+, chr11:47326319-47326354+, chr11:47326449-47326478+, chr11:47326705-47326737+ 725 no Mitochondrially encoded NADH dehydrogenase 5 (MT-ND5) unprocessed pseudogene (ENSG00000283338) pseudogene first 1000 PCCRs yes 11 57037567 57038422 1 8 chr11:57037567-57037593+, chr11:57037633-57037788+, chr11:57037804-57037848+, chr11:57037857-57038108+, chr11:57038115-57038153+, chr11:57038160-57038243+, chr11:57038246-57038311+, chr11:57038336-57038422+ 463 no OR5AK4P olfactory receptor family 5 subfamily AK member 4 pseudogene (ENSG00000283307) pseudogene first 1000 PCCRs no 11 60608382 60608408 1 1 chr11:60608382-60608408+ 733 no membrane-spanning 4-domains subfamily A member family unprocessed pseudogene (ENSG00000283601) pseudogene first 1000 PCCRs yes 11 67538911 67540581 1 5 chr11:67538911-67538949+, chr11:67539108-67539134+, chr11:67539169-67539219+, chr11:67539375-67539425+, chr11:67540459-67540581+ 590 no glutathione S-transferase pi 1 (GSTP1) unprocessed pseudogene (ENSG00000283257) pseudogene first 1000 PCCRs yes 11 111447053 111473375 1 37 chr11:111447053-111447100+, chr11:111448458-111448505+, chr11:111448581-111448643+, chr11:111449336-111449365+, chr11:111449437-111449472+, chr11:111449753-111449803+, chr11:111450349-111450399+, chr11:111450415-111450444+, chr11:111451043-111451141+, chr11:111451248-111451313+, chr11:111451338-111451409+, chr11:111452409-111452501+, chr11:111453424-111453489+, chr11:111454244-111454366+, chr11:111454984-111455016+, chr11:111455382-111455477+, chr11:111455806-111455871+, chr11:111456553-111456738+, chr11:111457066-111457335+, chr11:111457329-111457391+, chr11:111457847-111457927+, chr11:111457988-111458044+, chr11:111458117-111458194+, chr11:111459630-111459725+, chr11:111459756-111459782+, chr11:111460211-111460348+, chr11:111461911-111461937+, chr11:111462322-111462393+, chr11:111462672-111462710+, chr11:111463102-111463155+, chr11:111463318-111463368+, chr11:111463396-111463428+, chr11:111466815-111466889+, chr11:111469225-111469287+, chr11:111469784-111469840+, chr11:111469916-111469942+, chr11:111473319-111473375+ 394 no unitary pseudogene ENSG00000255093 pseudogene first 1000 PCCRs yes 12 2726421 2727050 -1 5 chr12:2726421-2726495-, chr12:2726523-2726633-, chr12:2726633-2726722-, chr12:2726741-2726992-, chr12:2726994-2727050- 216 no gap junction beta family pseudogene (ENSG00000283587) pseudogene first 1000 PCCRs yes 12 2767965 2775661 -1 3 chr12:2767965-2768021-, chr12:2770415-2770456-, chr12:2775566-2775661- 2025 no unitary pseudogene ENSG00000255669 pseudogene lncRNA PCCR yes 12 3298233 3307795 -1 7 chr12:3298233-3298262-, chr12:3303334-3303387-, chr12:3303776-3303862-, chr12:3303870-3303908-, chr12:3303911-3303937-, chr12:3306764-3306868-, chr12:3307745-3307795- 799 no tetraspanin 11 (TSPAN11) pseudogene (ENSG00000250770); single locus on multiple rows pseudogene first 1000 PCCRs yes 12 7620539 7626372 1 10 chr12:7620539-7620643+, chr12:7620726-7620755+, chr12:7620831-7620890+, chr12:7620925-7620951+, chr12:7621220-7621318+, chr12:7621364-7621432+, chr12:7621464-7621520+, chr12:7621548-7621604+, chr12:7626187-7626249+, chr12:7626289-7626372+ 1528 no mitochondrial protein pseudogene region (ENSG00000284591) pseudogene previously unannotated PCCR yes 12 22116633 22134940 -1 6 chr12:22116633-22116662-, chr12:22116662-22116733-, chr12:22126639-22126758-, chr12:22130471-22130527-, chr12:22134804-22134851-, chr12:22134869-22134940- 65 no unitary pseudogene ENSG00000283582 pseudogene first 1000 PCCRs yes 12 30306062 30306205 1 1 chr12:30306062-30306205+ 665 no maestro heat-like repeat-containing protein family member pseudogene (ENSG00000284682) pseudogene first 1000 PCCRs yes 12 31005780 31005848 -1 1 chr12:31005780-31005848- 16771 no tetraspanin family pseuodgene (ENSG00000226472) pseudogene lncRNA PCCR yes 12 31015442 31015824 1 3 chr12:31015442-31015582+, chr12:31015588-31015668+, chr12:31015711-31015824+ 7035 no mitochondrially encoded cytochrome c oxidase I (MT-CO1) processed pseudogene (ENSG00000256984) pseudogene lncRNA PCCR yes 12 52264108 52277736 1 7 chr12:52264108-52264227+, chr12:52266552-52266707+, chr12:52266960-52267085+, chr12:52267330-52267536+, chr12:52275866-52275919+, chr12:52277540-52277659+, chr12:52277662-52277736+ 722 no keratin family pseudogene (ENSG00000284883) pseudogene first 1000 PCCRs yes 12 95405372 95408124 -1 4 chr12:95405372-95405443-, chr12:95405471-95405503-, chr12:95407918-95407956-, chr12:95408086-95408124- 1638 no unitary pseudogene ENSG00000257943 pseudogene lncRNA PCCR yes 12 121053768 121059655 -1 7 chr12:121053768-121053842-, chr12:121053873-121053899-, chr12:121053950-121054006-, chr12:121054019-121054045-, chr12:121059440-121059478-, chr12:121059542-121059586-, chr12:121059614-121059655- 1742 no unitary pseudogene, orthlog of mouse 2'-5' oligoadenylate synthetase-like 2 (Oasl2) (ENSG00000283542) pseudogene previously unannotated PCCR yes 13 24611978 24613986 1 2 chr13:24611978-24612046+, chr13:24613945-24613986+ 1873 no pseudogene ENSG00000285228 pseudogene previously unannotated PCCR yes 13 86266842 86266928 -1 1 chr13:86266842-86266928- 481 no IQ motif containing K (IQCK) pseudogene (ENSG00000283371) pseudogene first 1000 PCCRs yes 13 88571657 88572214 1 4 chr13:88571657-88571722+, chr13:88571725-88571997+, chr13:88571997-88572035+, chr13:88572047-88572214+ 524 no mitochondrially encoded NADH dehydrogenase 5 (MT-ND5) pseudogene (ENSG00000283130) pseudogene first 1000 PCCRs yes 13 110989986 110990123 1 1 chr13:110989986-110990123+ 44980 no tubulin gamma complex associated protein 3 (TUBGCP3) pseudogene (ENSG00000225760) pseudogene lncRNA PCCR yes 14 34954880 34969313 -1 6 chr14:34954880-34954954-, chr14:34963938-34964000-, chr14:34963987-34964040-, chr14:34965561-34965683-, chr14:34969171-34969233-, chr14:34969251-34969313- 836 no unitary pseudogene ENSG00000258704 pseudogene first 1000 PCCRs yes 14 62127829 62128391 1 3 chr14:62127829-62127903+, chr14:62127863-62127889+, chr14:62128023-62128391+ 275 no unitary pseudogene ENSG00000186369 pseudogene first 1000 PCCRs yes 15 21609137 21614980 1 7 chr15:21609137-21609181+, chr15:21609269-21609349+, chr15:21609377-21609490+, chr15:21609543-21610010+, chr15:21614124-21614327+, chr15:21614340-21614888+, chr15:21614891-21614980+ 756 no two olfactory receptor pseudogenes in close proximity (ENSG00000285491 & ENSG00000285116) pseudogene (shared cluster) first 1000 PCCRs yes, both 15 30072627 30072923 -1 3 chr15:30072627-30072707-, chr15:30072759-30072791-, chr15:30072894-30072923- 1627 no tight junction protein 1 (zona occludens 1) (TJP1) pseudogene (ENSG00000229389) pseudogene lncRNA PCCR yes 15 41157178 41157345 -1 1 chr15:41157178-41157345- 138 no mitochondrially encoded NADH dehydrogenase 4 (MT-ND4) pseudogene (ENSG00000283133) pseudogene first 1000 PCCRs yes 15 75228852 75229646 -1 2 chr15:75228852-75228920-, chr15:75229590-75229646- 22059 no unitary pseuodgene ENSG00000260660 pseudogene lncRNA PCCR yes 15 81385501 81385784 1 2 chr15:81385501-81385569+, chr15:81385659-81385784+ 66 no STARD5 pseudogene (ENSG00000284709); found after looking at high-scoring intergenic PCCRs pseudogene re-ranking yes 15 82711282 82711838 -1 4 chr15:82711282-82711380-, chr15:82711677-82711727-, chr15:82711740-82711784-, chr15:82711806-82711838- 594 no unitary pseudogene ENSG00000228141 pseudogene first 1000 PCCRs no 15 98446010 98446129 -1 1 chr15:98446010-98446129- 438 no FAM169B (ENSG00000283597) changed from protein-coding to pseudogene based on pseudo exons pseudogene first 1000 PCCRs yes 15 101737259 101737336 -1 1 chr15:101737259-101737336- 41929 no ubiquitin-conjugating enzyme E2Q family member 2 (UBE2Q2) pseudogene (ENSG00000260660) pseudogene lncRNA PCCR yes 16 20711460 20732984 1 13 chr16:20711460-20711675+, chr16:20718348-20718494+, chr16:20719247-20719390+, chr16:20725362-20725445+, chr16:20727341-20727466+, chr16:20728163-20728216+, chr16:20728219-20728245+, chr16:20728394-20728465+, chr16:20729230-20729355+, chr16:20729458-20729553+, chr16:20731620-20731661+, chr16:20731714-20731740+, chr16:20732907-20732984+ 197 no ACSM3 acyl-CoA synthetase medium chain family member 3 (ENSG00000005187) pseudogene first 1000 PCCRs yes 16 20720997 20722053 -1 7 chr16:20720997-20721044-, chr16:20721047-20721181-, chr16:20721184-20721384-, chr16:20721387-20721656-, chr16:20721724-20721777-, chr16:20721780-20721905-, chr16:20721910-20722053- 1782 no mitochondrially encoded NADH dehydrogenase 5 (MT-ND5) pseudogene (ENSG00000283399) pseudogene previously unannotated PCCR yes 16 21338456 21339031 1 3 chr16:21338456-21338497+, chr16:21338933-21338971+, chr16:21339005-21339031+ 20 no ATP-binding cassette, sub-family A (ABC1), member 15 (Abca15) unprocessed pseudogene (ENSG00000189149) pseudogene first 1000 PCCRs yes 16 29113049 29116327 1 2 chr16:29113049-29113150+, chr16:29116124-29116327+ 706 no BTG3 associated nuclear protein (BANP) pseudogene (ENSG00000284649) pseudogene first 1000 PCCRs no 16 29864731 29864880 1 2 chr16:29864731-29864790+, chr16:29864836-29864880+ 1160 no unitary pseudogene ENSG00000214725 pseudogene lncRNA PCCR yes 16 49963347 49963418 -1 1 chr16:49963347-49963418- 1450 no unitary pseudogene ENSG00000283365 pseudogene previously unannotated PCCR yes 16 67210140 67211021 -1 3 chr16:67210140-67210226-, chr16:67210233-67210505-, chr16:67210566-67211021- 474 no LRRC29 (ENSG00000125122) changed to pseudogene from protein-coding after complete structure became apparent and disablements thus revealed pseudogene first 1000 PCCRs yes 17 22519261 22522960 -1 3 chr17:22519261-22519326-, chr17:22519346-22519480-, chr17:22522934-22522960- 918 no mitochondrially encoded NADH dehydrogenase 6 (MT-ND6) pseudogene (ENSG00000283879) pseudogene first 1000 PCCRs yes 17 33692259 33692461 1 2 chr17:33692259-33692357+, chr17:33692378-33692461+ 1449 no MT-ND2 pseudogene (ENSG00000283381) pseudogene previously unannotated PCCR yes 17 45517900 45519352 -1 4 chr17:45517900-45518139-, chr17:45519111-45519176-, chr17:45519176-45519232-, chr17:45519290-45519352- 86 no LRRC37A4P transcribed unprocessed pseudogene (ENSG00000282331) pseudogene first 1000 PCCRs no 17 66278104 66278199 1 1 chr17:66278104-66278199+ 1705 no mitochondrially encoded ATP synthase 6 (MT-ATP6) pseudogene (ENSG00000284242) pseudogene previously unannotated PCCR yes 17 68693973 68694062 -1 1 chr17:68693973-68694062- 839 no unitary pseudogene ENSG00000283376 pseudogene first 1000 PCCRs yes 18 14242348 14244664 1 2 chr18:14242348-14242431+, chr18:14244569-14244664+ 42572 no ankyrin repeat domain 20 family, member A5, pseudogene (ENSG00000186481) pseudogene lncRNA PCCR yes 18 54415278 54424623 1 10 chr18:54415278-54415334+, chr18:54415417-54415458+, chr18:54415951-54415986+, chr18:54416014-54416139+, chr18:54418828-54418854+, chr18:54418872-54419021+, chr18:54419940-54419978+, chr18:54421453-54421557+, chr18:54424499-54424558+, chr18:54424561-54424623+ 1020 no unitary pseudogene ENSG00000283613 pseudogene previously unannotated PCCR yes 19 6411742 6424885 1 8 chr19:6411742-6411786+, chr19:6411844-6411915+, chr19:6412270-6412332+, chr19:6414855-6414923+, chr19:6414920-6414964+, chr19:6424412-6424450+, chr19:6424801-6424848+, chr19:6424859-6424885+ 18 yes unitary pseudogene ENSG00000214347 pseudogene first 1000 PCCRs yes 19 10044071 10052967 1 4 chr19:10044071-10044181+, chr19:10050065-10050148+, chr19:10052770-10052808+, chr19:10052839-10052967+ 77 no C3P1 transcribed unprocessed pseudogene (ENSG00000167798) pseudogene first 1000 PCCRs no 19 12207347 12208769 1 2 chr19:12207347-12207427+, chr19:12208728-12208769+ 41986 no zinc finger protein pseudogene (ENSG00000234773) pseudogene lncRNA PCCR yes 19 35407926 35408066 1 2 chr19:35407926-35407973+, chr19:35408034-35408066+ 5047 no free fatty acid receptor 2 (FFAR2) unprocessed pseudogene (ENSG00000283479) pseudogene lncRNA PCCR yes 19 35784826 35796859 -1 12 chr19:35784826-35784855-, chr19:35789038-35789073-, chr19:35790321-35790509-, chr19:35790588-35790713-, chr19:35791034-35791195-, chr19:35791248-35791343-, chr19:35791768-35791848-, chr19:35791977-35792051-, chr19:35792377-35792436-, chr19:35792534-35792614-, chr19:35793084-35793188-, chr19:35796794-35796859- 260 yes protein tyrosine kinase family pseudogene (ENSG00000225872) pseudogene first 1000 PCCRs yes 19 37822686 37830193 1 4 chr19:37822686-37822721+, chr19:37823834-37823890+, chr19:37830020-37830049+, chr19:37830164-37830193+ 3865 no zinc finger protein pseudogene (ENSG00000267640) pseudogene lncRNA PCCR yes 19 37829091 37833481 -1 17 chr19:37829091-37829117-, chr19:37829169-37829255-, chr19:37829616-37829672-, chr19:37829881-37829973-, chr19:37830016-37830048-, chr19:37830103-37830333-, chr19:37830421-37830459-, chr19:37830592-37830642-, chr19:37830658-37830711-, chr19:37830805-37830840-, chr19:37830880-37831143-, chr19:37831171-37831245-, chr19:37831252-37831518-, chr19:37831567-37831674-, chr19:37831711-37831743-, chr19:37831750-37831812-, chr19:37833371-37833481- 132 no WD repeat domain 87 (WDR87) pseudogene (ENSG00000225868) pseudogene first 1000 PCCRs yes 19 50808166 50808759 -1 2 chr19:50808166-50808204-, chr19:50808655-50808759- 99 no unitary pseudogene ENSG00000284711 pseudogene first 1000 PCCRs yes 19 51843199 51843309 -1 1 chr19:51843199-51843309- 4546 no zinc finger protein pseudogene (ENSG00000269483) pseudogene lncRNA PCCR yes 19 51914745 51917661 -1 5 chr19:51914745-51914813-, chr19:51914940-51915029-, chr19:51915054-51915275-, chr19:51915465-51915632-, chr19:51917587-51917661- 195 no zinc finger protein pseudogene (ENSG00000283285) pseudogene first 1000 PCCRs yes 19 53204022 53212191 1 4 chr19:53204022-53204120+, chr19:53211811-53211855+, chr19:53211973-53212077+, chr19:53212144-53212191+ 7119 no zinc finger protein pseudogene (ENSG00000269001) pseudogene lncRNA PCCR yes 19 58578105 58581980 1 6 chr19:58578105-58578158+, chr19:58581421-58581672+, chr19:58581703-58581729+, chr19:58581769-58581825+, chr19:58581861-58581905+, chr19:58581942-58581980+ 664 yes CENPBD1P1 CENPB DNA-binding domains containing 1 pseudogene 1 (ENSG00000285138) pseudogene first 1000 PCCRs no 20 49318436 49340428 1 7 chr20:49318436-49318561+, chr20:49318489-49318521+, chr20:49318534-49318575+, chr20:49328530-49328637+, chr20:49328656-49328682+, chr20:49335620-49335685+, chr20:49340399-49340428+ 2047 yes somatomedin B and thrombospondin type 1 domain containing (SBSPON) transcribed_unprocessed_pseudogene (ENSG00000283529) pseudogene previously unannotated PCCR yes 22 16844398 16846040 1 4 chr22:16844398-16844508+, chr22:16844869-16845012+, chr22:16845049-16845078+, chr22:16845918-16846040+ 1086 no uncharacterised pseudogene (ENSG00000283535) pseudogene previously unannotated PCCR yes 22 17044888 17047449 1 3 chr22:17044888-17044998+, chr22:17046358-17046447+, chr22:17047306-17047449+ 11264 no cat eye syndrome chromosome region, candidate 7 unprocessed pseudogene (ENSG00000237438) pseudogene lncRNA PCCR yes 22 18985824 18997940 1 5 chr22:18985824-18986033+, chr22:18990698-18990922+, chr22:18991818-18991982+, chr22:18994363-18994509+, chr22:18997857-18997940+ 9432 no DiGeorge syndrome critical region gene 5 (non-protein coding) unprocessed pseudogene (ENSG00000237517) pseudogene lncRNA PCCR no 22 20702136 20704490 1 10 chr22:20702136-20702264+, chr22:20702263-20702322+, chr22:20702587-20702742+, chr22:20702852-20702914+, chr22:20703045-20703125+, chr22:20703471-20703536+, chr22:20703645-20703695+, chr22:20703816-20703872+, chr22:20704002-20704046+, chr22:20704305-20704490+ 2244 yes transmembrane protein 191A pseudogene (ENSG00000226287) pseudogene lncRNA PCCR no 22 21011391 21013083 -1 4 chr22:21011391-21011492-, chr22:21011526-21011588-, chr22:21012531-21012617-, chr22:21013042-21013083- 147 no TUBA3FP transcribed unprocessed pseudogene (ENSG00000161149) pseudogene first 1000 PCCRs no 22 21228804 21229136 -1 1 chr22:21228804-21229136- 316 no immunoglobulin superfamily member 3 (IGSF3) pseudogene (ENSG00000283145) pseudogene first 1000 PCCRs yes 22 21657814 21660946 1 3 chr22:21657814-21658014+, chr22:21658266-21658385+, chr22:21660896-21660946+ 82 yes unitary pseudogene (ENSG00000284630) pseudogene first 1000 PCCRs yes 22 25374157 25381577 -1 4 chr22:25374157-25374300-, chr22:25375820-25375852-, chr22:25375849-25376007-, chr22:25381371-25381577- 747 no LRP5L converted to pseudogene (ENSG00000100068) after 3 exons added. This is still a protein-locus in GENCODEv28; it will be updated as a pseudogene in v29 pseudogene first 1000 PCCRs yes X 64405660 64406073 1 1 chrX:64405660-64406073+ 335 no unitary pseudogene ENSG00000283349 pseudogene first 1000 PCCRs yes X 85153749 85153802 1 1 chrX:85153749-85153802+ 871 no meprin A subunit beta (MEP1B) unprocessed pseudogene (ENSG00000283446) pseudogene first 1000 PCCRs yes X 135397529 135397603 1 1 chrX:135397529-135397603+ 10697 no pseudogene similar to embryonic testis differentiation (M. musculus) (ENSG00000229015) pseudogene lncRNA PCCR yes X 153481540 153486067 1 8 chrX:153481540-153481635+, chrX:153481809-153481895+, chrX:153482727-153482765+, chrX:153483299-153483340+, chrX:153483416-153483442+, chrX:153485780-153485842+, chrX:153485894-153485962+, chrX:153485990-153486067+ 2093 no unitary pseudogene ENSG00000224963 pseudogene lncRNA PCCR yes 1 6066065 6066244 1 1 chr1:6066065-6066244+ 535 no KCNAB2 pseudo-exon pseudo-exon first 1000 PCCRs 1 42497121 42497198 1 1 chr1:42497121-42497198+ 748 no CCDC30 multiple pseudo-exons pseudo-exon first 1000 PCCRs 1 53274696 53274821 -1 3 chr1:53274696-53274821-, chr1:53274749-53274784-, chr1:53274751-53274783- 415 no LRP8 pseudo-exon. pseudo-exon first 1000 PCCRs 1 78939653 78939799 -1 1 chr1:78939653-78939799- 103 no ADGRL4 untranscribed pseudo-exon pseudo-exon first 1000 PCCRs 1 228313613 228315088 1 2 chr1:228313613-228313876+, chr1:228314813-228315088+ 341 no OBSCN has two pseudo-exons pseudo-exon first 1000 PCCRs 2 135024648 135040536 -1 4 chr2:135024648-135024740-, chr2:135027538-135027678-, chr2:135030309-135030470-, chr2:135040378-135040536- 124 no MAP3K19 has three upstream coding exons in other species, although in human the second has a non-variant premature termination codon, so the gene had been made to use a downstream ATG. It has been maintained as coding due to PMID:27144281 pseudo-exon first 1000 PCCRs 2 206670493 206670552 -1 1 chr2:206670493-206670552- 873 no DYTN pseudo-exons pseudo-exon first 1000 PCCRs 2 219269630 219279492 1 6 chr2:219269630-219269665+, chr2:219269765-219269854+, chr2:219271576-219271893+, chr2:219271893-219272093+, chr2:219279398-219279448+, chr2:219279457-219279492+ 274 yes TUBA4B pseudo-exon pseudo-exon first 1000 PCCRs 4 103142463 103142621 -1 2 chr4:103142463-103142516-, chr4:103142571-103142621- 550 no CENPE pseudo exon pseudo-exon first 1000 PCCRs 4 145760752 145763106 -1 4 chr4:145760752-145761126-, chr4:145761968-145762054-, chr4:145762943-145763062-, chr4:145763053-145763106- 266 no ZNF827 has pseudo repeats downstream of the STOP codon. pseudo-exon first 1000 PCCRs 5 75640608 75640694 1 1 chr5:75640608-75640694+ 713 no ANKDD1B pseudo-exon pseudo-exon first 1000 PCCRs 5 122373512 122374412 1 6 chr5:122373512-122373583+, chr5:122373588-122373812+, chr5:122373885-122373965+, chr5:122374053-122374133+, chr5:122374152-122374286+, chr5:122374317-122374412+ 96 no SNCAIP untranscribed pseudo-exon. Subsequent reanalysis following the completion of this study suggests it may in fact be an ancient vomeronasal receptor unitary pseuodgene. pseudo-exon first 1000 PCCRs 6 111259542 111259622 1 1 chr6:111259542-111259622+ 927 yes MFSD4B PhyloCSF signal found upstream of ATG. Clearly genuine, as coding continues upstream in non-mammals. pseudo-exon first 1000 PCCRs 6 167358152 167359401 -1 2 chr6:167358152-167358295-, chr6:167359306-167359401- 636 no TCP10 pseudo-exon pseudo-exon first 1000 PCCRs 6 167976938 168002143 1 9 chr6:167976938-167977060+, chr6:167986865-167986927+, chr6:167993700-167993750+, chr6:167996539-167996661+, chr6:167999232-167999294+, chr6:168001760-168001840+, chr6:168001870-168001959+, chr6:168002010-168002075+, chr6:168002105-168002143+ 446 yes KIF25 has 8 exons upstream that are coding as part of this locus in other mammals. At least two of these exons are clearly pseudogenic. This suggests the locus may be a pseudogene, although it has been maintained as coding due to published experimental support for its functionality. pseudo-exon first 1000 PCCRs 7 100882699 100896048 -1 10 chr7:100882699-100882761-, chr7:100882767-100882883-, chr7:100882793-100882909-, chr7:100882958-100883086-, chr7:100889272-100889445-, chr7:100889458-100889508-, chr7:100891059-100891088-, chr7:100895788-100895952-, chr7:100895964-100895999-, chr7:100896022-100896048- 564 yes UFSP1 is a retrogene that has apparently evolved to use a downstream ATG, so this is 5' pseudo-exon sequence pseudo-exon first 1000 PCCRs 7 150329868 150331248 1 4 chr7:150329868-150329918+, chr7:150330048-150330257+, chr7:150330294-150330350+, chr7:150331153-150331248+ 74 no ZBED6CL pseudogenic sequence upstream of ATG pseudo-exon first 1000 PCCRs 10 122624536 122624832 1 4 chr10:122624536-122624607+, chr10:122624611-122624673+, chr10:122624689-122624748+, chr10:122624752-122624832+ 670 no DMBT1 pseudo_exon pseudo-exon first 1000 PCCRs 11 5514607 5515011 -1 3 chr11:5514607-5514705-, chr11:5514712-5514744-, chr11:5514949-5515011- 13 no UBQLNL 3' UTR signal; this is CDS in the parent of this retrogene pseudo-exon first 1000 PCCRs 11 67666936 67667628 -1 2 chr11:67666936-67667019-, chr11:67667461-67667628- 52 no ALDH3B2 has a premature termination codon compared to other family members, and this signal follows downstream pseudo-exon first 1000 PCCRs 12 9491499 9566349 1 12 chr12:9491499-9491558+, chr12:9497707-9497760+, chr12:9503064-9503144+, chr12:9511699-9511773+, chr12:9512795-9512938+, chr12:9517687-9517809+, chr12:9518162-9518314+, chr12:9540386-9540421+, chr12:9552442-9552495+, chr12:9555055-9555123+, chr12:9562969-9563007+, chr12:9566305-9566349+ 921 no AC092821.1 pseudo exons pseudo-exon first 1000 PCCRs 14 73612572 73617174 1 6 chr14:73612572-73612604+, chr14:73612614-73613027+, chr14:73612685-73612723+, chr14:73612736-73612783+, chr14:73616995-73617123+, chr14:73617145-73617174+ 305 yes ACOT6 untranscribed pseudo-exon pseudo-exon first 1000 PCCRs 14 75077565 75077786 1 1 chr14:75077565-75077786+ 854 no ZC2HC1C has ZNF repeats downstream of the STOP codon pseudo-exon first 1000 PCCRs 15 25679379 25679462 -1 1 chr15:25679379-25679462- 25 no ATP10A has a fameshift in the final exon leading to an alternative STOP in primates; maintained as coding on the basis that this is a minor disruption to the CDS pseudo-exon first 1000 PCCRs 15 42374287 42374531 1 2 chr15:42374287-42374400+, chr15:42374406-42374531+ 174 no CAPN3 alternative first coding exon is pseudogenised compared to other paralogs and orthologs pseudo-exon first 1000 PCCRs 15 50500670 50500768 -1 1 chr15:50500670-50500768- 313 no USP8 has a human-specific premature termination codon in the final coding exon, removing 30aa compared to other mammals pseudo-exon first 1000 PCCRs 16 75646606 75646683 1 1 chr16:75646606-75646683+ 1852 no TERF2IP pseudo-exon pseudo-exon previously unannotated PCCR 17 41160014 41160169 -1 1 chr17:41160014-41160169- 23 no KRTAP4-4 has a premature termination codon compared to other family members, and this signal follows downstream pseudo-exon first 1000 PCCRs 19 1524154 1533821 1 8 chr19:1524154-1524252+, chr19:1525302-1525397+, chr19:1525592-1525714+, chr19:1526483-1526611+, chr19:1526706-1526774+, chr19:1526910-1526996+, chr19:1531846-1531878+, chr19:1533756-1533821+ 68 yes PLK5 pseudo exons pseudo-exon first 1000 PCCRs 19 16727565 16731241 1 2 chr19:16727565-16727672+, chr19:16731191-16731241+ 739 no NWD1 pseudo-exon pseudo-exon first 1000 PCCRs 20 63572386 63573033 -1 3 chr20:63572386-63572568-, chr20:63572620-63572688-, chr20:63572713-63573033- 75 no HELZ2 pseudo-exon pseudo-exon first 1000 PCCRs 22 41696892 41696996 1 1 chr22:41696892-41696996+ 161 no C22orf46 has a premature termination codon, and the signal follows downstream; maintained as coding as this is a minor truncation pseudo-exon first 1000 PCCRs X 49878962 49880307 1 5 chrX:49878962-49879033+, chrX:49879268-49879330+, chrX:49879412-49879462+, chrX:49879588-49879755+, chrX:49879843-49880307+ 724 yes USP27X pseudogenic sequence upstream of ATG pseudo-exon first 1000 PCCRs X 103707227 103707343 -1 1 chrX:103707227-103707343- 411 no GLRA4 has a premature termination codon in the final exon that is human specific pseudo-exon first 1000 PCCRs 1 146685740 146685886 1 1 chr1:146685740-146685886+ 45 no HYDIN2 pseudogene extended (ENSG00000276975) pseudogene extension first 1000 PCCRs 1 149721425 149729612 -1 3 chr1:149721425-149721538-, chr1:149722916-149722954-, chr1:149729379-149729612- 9995 no pseudogene of PDE4DIP extended (ENSG00000234232) pseudogene extension lncRNA PCCR 1 178037720 178037779 -1 1 chr1:178037720-178037779- 1508 yes quinone oxidoreductase-like protein pseudogene extended (ENSG00000242193) pseudogene extension lncRNA PCCR 2 131370351 131386316 -1 9 chr2:131370351-131370419-, chr2:131373653-131373799-, chr2:131379483-131379524-, chr2:131379592-131379681-, chr2:131379743-131379817-, chr2:131379847-131380083-, chr2:131381679-131381744-, chr2:131382613-131382642-, chr2:131386275-131386316- 988 no mitochondrial pseudogene region extended (e.g. ENSG00000284003) pseudogene extension first 1000 PCCRs 2 200750467 200750577 1 1 chr2:200750467-200750577+ 131 no AOX2P unitary pseudogene exon added (ENSG00000243478) pseudogene extension first 1000 PCCRs 5 177631373 177632741 -1 6 chr5:177631373-177631477-, chr5:177631532-177631672-, chr5:177632135-177632218-, chr5:177632324-177632509-, chr5:177632519-177632680-, chr5:177632676-177632741- 581 no SUMO interacting motifs containing 1 (SIMC1) pseudogene significantly rebuilt (ENSG00000246596) pseudogene extension first 1000 PCCRs 6 9673032 9673175 -1 1 chr6:9673032-9673175- 310 no OFCC1 extended pseudogene (ENSG00000181355) pseudogene extension first 1000 PCCRs 6 41108763 41109041 1 2 chr6:41108763-41108855+, chr6:41108964-41109041+ 573 no ADCY10P1 pseudogene improved over its internal section (ENSG00000161912) pseudogene extension first 1000 PCCRs 8 11362895 11365716 1 3 chr8:11362895-11362972+, chr8:11364806-11364988+, chr8:11365582-11365716+ 367 no TDH pseudogene extended by 2 exons (ENSG00000154316) pseudogene extension first 1000 PCCRs 8 39557357 39558448 1 3 chr8:39557357-39557395+, chr8:39557408-39557440+, chr8:39558419-39558448+ 4684 no ADAM family pseudogene extended ENSG00000254067 pseudogene extension lncRNA PCCR 8 142572180 142575904 -1 8 chr8:142572180-142572218-, chr8:142573733-142573786-, chr8:142573799-142573825-, chr8:142574537-142574590-, chr8:142574612-142574650-, chr8:142575392-142575457-, chr8:142575785-142575841-, chr8:142575875-142575904- 1386 no MROH4P 6 new exons at 5' end pseudogene extension previously unannotated PCCR 9 35471105 35471218 1 1 chr9:35471105-35471218+ 104 no ATP8B5P pseudogene extension (ENSG00000179766) pseudogene extension first 1000 PCCRs 9 122607894 122608010 1 2 chr9:122607894-122607920+, chr9:122607942-122608010+ 629 no OR1H1P pseudogene extended (ENSG00000228914) pseudogene extension first 1000 PCCRs 10 5158611 5158709 -1 1 chr10:5158611-5158709- 458 no AKR1C8P pseudogene extended (ENSG00000264006) pseudogene extension first 1000 PCCRs 10 46625814 46626008 -1 1 chr10:46625814-46626008- 542 no FAM35BP additional exon (ENSG00000165874) pseudogene extension first 1000 PCCRs 10 122749907 122802385 1 20 chr10:122749907-122749990+, chr10:122749993-122750163+, chr10:122750185-122750217+, chr10:122756717-122756959+, chr10:122764349-122764585+, chr10:122768086-122768316+, chr10:122768335-122768376+, chr10:122772109-122772243+, chr10:122774748-122774930+, chr10:122777743-122778015+, chr10:122778017-122778046+, chr10:122785959-122786165+, chr10:122788225-122788353+, chr10:122788357-122788515+, chr10:122792298-122792438+, chr10:122795270-122795464+, chr10:122798816-122798863+, chr10:122798876-122799046+, chr10:122799074-122799115+, chr10:122802335-122802385+ 28 no DMBT1P1 pseudogene was extended to cover additional homologies (ENSG00000176584) pseudogene extension first 1000 PCCRs 11 4418964 4419008 1 1 chr11:4418964-4419008+ 1156 no OR51R1P extended to stop codon pseudogene extension previously unannotated PCCR 11 55714823 55715679 1 2 chr11:55714823-55714993+, chr11:55715635-55715679+ 377 no OR5D2P pseudogene extended (ENSG00000254457) pseudogene extension first 1000 PCCRs 11 57018887 57018997 1 1 chr11:57018887-57018997+ 224 no OR5AK1P pseudogene extension (ENSG00000255083) pseudogene extension first 1000 PCCRs 11 76712306 76719866 -1 8 chr11:76712306-76712350-, chr11:76712387-76712416-, chr11:76712696-76712815-, chr11:76713051-76713113-, chr11:76714935-76714961-, chr11:76716336-76716365-, chr11:76719640-76719792-, chr11:76719816-76719866- 98 no GUCY2EP extended [ENSG00000204529] pseudogene extension first 1000 PCCRs 11 124054811 124054867 1 1 chr11:124054811-124054867+ 1162 no OR10D5P extended pseudogene extension previously unannotated PCCR 12 52353887 52353940 1 1 chr12:52353887-52353940+ 1467 no KRT89P pseudogene extension pseudogene extension previously unannotated PCCR 12 52411742 52413387 -1 3 chr12:52411742-52411813-, chr12:52411820-52411939-, chr12:52413358-52413387- 1734 no KRT90P 2 exons added pseudogene extension previously unannotated PCCR 12 52721165 52729639 -1 5 chr12:52721165-52721284-, chr12:52721351-52721479-, chr12:52721510-52721650-, chr12:52721655-52721750-, chr12:52729520-52729639- 810 no KRT125P (ENSG00000258036) and KRT126P (ENSG00000257402) extended, i.e. two distinct keratin pseudogenes within the same genomic window pseudogene extension first 1000 PCCRs 12 55834568 55834729 1 1 chr12:55834568-55834729+ 777 no TMEM198B was missing an internal portion (ENSG00000182796) pseudogene extension first 1000 PCCRs 12 132104171 132104377 1 1 chr12:132104171-132104377+ 600 no EP400NL pseudogene extended (ENSG00000185684) pseudogene extension first 1000 PCCRs 13 26094743 26094814 -1 1 chr13:26094743-26094814- 870 no ATPase, aminophospholipid transporter-like, class I, type 8A, member 2 (ATP8A2) pseudogene extended (ENSG00000233963) pseudogene extension first 1000 PCCRs 15 22044494 22044847 1 3 chr15:22044494-22044538+, chr15:22044626-22044706+, chr15:22044734-22044847+ 3813 no olfactory receptor, family 4, subfamily Q, member 3 (OR4Q3) pseudogene (ENSG00000285135) pseudogene extension lncRNA PCCR 15 62246165 62256086 -1 3 chr15:62246165-62246323-, chr15:62246492-62246656-, chr15:62256060-62256086- 1081 no golgin subfamily A pseudogene extended (ENSG00000166104) pseudogene extension lncRNA PCCR 16 3144015 3150751 1 11 chr16:3144015-3144065+, chr16:3144184-3144294+, chr16:3144507-3144533+, chr16:3144605-3144640+, chr16:3144754-3144789+, chr16:3144808-3144834+, chr16:3145710-3145745+, chr16:3145936-3146025+, chr16:3147312-3147338+, chr16:3150674-3150751+, chr16:3150679-3150747+ 334 yes CASP16P pseudogene extended (ENSG00000228146) pseudogene extension first 1000 PCCRs 17 19580044 19580344 1 2 chr17:19580044-19580118+, chr17:19580237-19580344+ 441 yes SLC47A1P1 pseudogene extended (ENSG00000228983) pseudogene extension first 1000 PCCRs 17 63862742 63862810 1 1 chr17:63862742-63862810+ 17 no TCAM1P 3' extension (ENSG00000240280) pseudogene extension first 1000 PCCRs 19 28722658 28722771 -1 1 chr19:28722658-28722771- 1997 no pseudogene of SHCBP1 extended (ENSG00000283269) pseudogene extension lncRNA PCCR 22 20602774 20602866 -1 1 chr22:20602774-20602866- 578 no SMPD4P1 pseudogene extended (ENSG00000223553) pseudogene extension first 1000 PCCRs X 130515787 130523549 -1 3 chrX:130515787-130515849-, chrX:130516599-130516679-, chrX:130523466-130523549- 894 no fibrous sheath interacting protein 2 (FSIP2) pseudogene extended (ENSG00000274775) pseudogene extension first 1000 PCCRs 1 15721341 15731942 1 3 chr1:15721341-15721394+, chr1:15727484-15727621+, chr1:15731898-15731942+ 198 no PLEKHM2 has a PhyloCSF signal that changes frame within coding exon 9. The signal in that frame ends after approximately 130bp, prior to a STOP codon, and resumes in the original frame later in the same exon. The event is supported by PhyloCSF in the chicken genome [ICGSC Gallus_gallus-4.0/galGal4 ~chr21:4,217,442-4,217,718). Under investigation as a potential programmed frameshift. under investigation first 1000 PCCRs 1 46718088 46718183 -1 1 chr1:46718088-46718183- 932 no EFCAB14 potential non-ATG start under investigation first 1000 PCCRs 1 205440910 205457273 -1 6 chr1:205440910-205441029-, chr1:205448289-205448330-, chr1:205456881-205456922-, chr1:205457046-205457075-, chr1:205457057-205457206-, chr1:205457238-205457273- 602 yes Finds a 33aa single exon CDS within a 5' exon of LEMD1 in GENCODE [chr1:205441026-205440925], although this exon is part of lncRNA BLACAT1 in RefSeq. Transcriptomics data make it clear that the locus should indeed be considered an independent gene from LEMD1, with an indication of potential brain / neuronal specificity (e.g. SRR486241). The CDS was initially considered hard to appraise because of its small size, although the reading frame is conserved across vertebrates with only 3mer indels in the genomic alignments. Following the analytical work presented here, it was decided to convert this gene (i.e. BLACAT1) to protein-coding, and ENSG00000281406 appeared in GENCODEv31. under investigation; now made coding first 1000 PCCRs 2 25743963 25744166 -1 2 chr2:25743963-25744037-, chr2:25744092-25744166- 657 no The PhyloCSF signal for ASXL2 changes frame in the final exon and is restored to the orginal frame after ~200bp. This sequence conformation is conserved in mammals, and while this could conceivably indicate a programmed frameshift, it could instead be explained by an unknown splice variant that causes this exon to be translated in a different frame. under investigation first 1000 PCCRs 3 49108464 49120972 -1 5 chr3:49108464-49108658-, chr3:49115888-49115917-, chr3:49119146-49119241-, chr3:49120805-49120861-, chr3:49120940-49120972- 782 yes USP19 potential non-ATG start under investigation first 1000 PCCRs 3 187739883 187745776 1 6 chr3:187739883-187739924+, chr3:187744855-187744923+, chr3:187744856-187744900+, chr3:187745311-187745421+, chr3:187745322-187745399+, chr3:187745723-187745776+ 875 yes Finds a putative 38aa CDS antisense to the 5' UTR of BCL6. However, it is difficult to interpret the accuracy of the PhyloCSF signal here as the region has deep conservation over a wider region, presumptively due to being the promoter of BCL6, and the 38aa CDS has very low complexity. There is also very little transcriptional support for the locus in human or mouse. under investigation first 1000 PCCRs 3 195908695 195909767 -1 7 chr3:195908695-195908724-, chr3:195908782-195908916-, chr3:195909040-195909219-, chr3:195909277-195909552-, chr3:195909572-195909622-, chr3:195909641-195909766-, chr3:195909684-195909767- 435 yes TNK2 contains a series of NPRs in its 5' UTR that highlight a reading frame and STOP codon that are conserved in placental mammals, although no ATG initiation codon has been identified. However, a [CTG] codon has been identified that corresponds well to the 5' end of the NPR region and a consistent initiation codon peak in ribosome profiling data, giving a prospective 153aa single exon CDS [chr3:195909582-195908695]. under investigation first 1000 PCCRs 8 32647141 32647662 1 3 chr8:32647141-32647170+, chr8:32647172-32647387+, chr8:32647627-32647662+ 825 no Finds a potential 62aa single exon CDS in a 5' UTR exon of NRG1 [chr8:32647202-32647390]. This CDS was initially considered potentially suspect as it overlaps with a highly conserved promoter region, and is fairly low complexity in terms of amino acid sequence. However, the CDS is conserved across to amphibians with an almost complete absence of non-3mer indels.Following the analytical stage of this work the decision was made to annotate a protein-coding gene, and ENSG00000286131 appeared in GENCODEv31. under investigation; now made coding first 1000 PCCRs 9 27455551 27455661 -1 1 chr9:27455551-27455661- 919 no MOB3B potential non-ATG start under investigation first 1000 PCCRs 11 64234553 64251600 1 13 chr11:64234553-64234789+, chr11:64234557-64234709+, chr11:64234684-64234749+, chr11:64241115-64241153+, chr11:64241149-64241190+, chr11:64241280-64241378+, chr11:64241673-64242074+, chr11:64242133-64242189+, chr11:64246774-64246932+, chr11:64246785-64246988+, chr11:64251466-64251507+, chr11:64251531-64251566+, chr11:64251571-64251600+ 482 yes FKBP2 contains a potential 265aa single exon CDS in its complex 5' UTR region, conserved in placental mammals [chr11:64241280-64242077]. The recent discovery of excellent cDNA support from in-house Oxford Nanopore experiments influenced the decision to annotate this as a protein-coding gene, and ENSG00000286264 appeared in GENCODEv31. under investigation; now made coding first 1000 PCCRs 14 23352215 23352971 -1 6 chr14:23352215-23352454-, chr14:23352321-23352395-, chr14:23352606-23352665-, chr14:23352646-23352732-, chr14:23352833-23352961-, chr14:23352900-23352971- 930 yes SLC22A17 potential non-ATG start under investigation first 1000 PCCRs 15 89330211 89335145 -1 8 chr15:89330211-89330273-, chr15:89333090-89333260-, chr15:89333459-89333491-, chr15:89333549-89333596-, chr15:89333627-89333713-, chr15:89333771-89333812-, chr15:89335071-89335145-, chr15:89335097-89335144- 867 yes POLG contains a series of NPRs in the first and second coding exon that are out of frame to the annotated CDS (the POLG CDS is conserved in vertebrates). These NPRs in combination find a prospective alternative CDS with a STOP codon conserved in therian mamamls - found precisely at the terminus of the most 3' NPR - although no ATG initiation codon has been identified. However, a potential non-ATG initiation codon [CTG] at chr15:89333809 corresponds well with the beginning of the NPR series, creating a predicted 261aa CDS that is conserved in therian mammals. We have identified additional support for the translation of this alternative CDS within the mass spectrometry datasets provided by Pandey et al, specifically peptides [AAAAQPJGHPDAJER] and [AAAAAAAAAAAAAAATAASAAASAJJGGR] in CD8 cells. However, at the present time there is no evidence to suggest how this alternative CDS may be transcribed and translated, and it is unclear how to construct a transcript model. under investigation first 1000 PCCRs 16 27067257 27067584 1 3 chr16:27067257-27067283+, chr16:27067423-27067473+, chr16:27067498-27067584+ 1766 no ENSG00000234186 has long been considered as an ambiguous gene. RefSeq recognise human C16orf82 and its mouse ortholog 4930571K23Rik as single exon protein-coding genes, although both are lncRNAs in GENCODE (where the transcript structure is certainly well supported). The human CDS is poorly conserved over its first half, although the putative STOP codon and sequence upstream produce a PhyloCSF signal that looks genuine, suggesting the potential for partial translation in mammalian genomes. However, there is no obvious ATG initiation codon to use. A [CTG] codon conserved in mammals seems to demarcate the conserved sequence, which would give a 154aa CDS in human [chr16:27066996-27067460]. under investigation lncRNA PCCR 16 28259225 28259497 1 3 chr16:28259225-28259263+, chr16:28259276-28259305+, chr16:28259366-28259497+ 499 no SBK1 potential non-ATG start under investigation first 1000 PCCRs 17 5500603 5500902 -1 2 chr17:5500603-5500728-, chr17:5500741-5500902- 89 yes A 119aa single exon CDS in the 3' UTR of NLRP1 [chr17:5500956-5500597] was initially thought to be an alternative coding exon. However, after revaluation it became clearer that the evidence linking the two loci together is weaker than that which separates them. Specifically, the 119aa CDS can be defined on a single-exon gene model that shows a brain-specific expression profile that differs from the general expression profile of NLRP1. Following the completion of the analytical work presented here, it was decided to annotate a protein-coding gene, and ENSG00000286190 appeared in GENCODEv31. under investigation; now made coding first 1000 PCCRs 17 18123241 18123396 1 1 chr17:18123241-18123396+ 374 no Intronic to MYO15A. Potentially a coding exon, although no evidence for transcription in human or mouse. under investigation first 1000 PCCRs 17 59353314 59353409 1 1 chr17:59353314-59353409+ 891 no YPEL2 potential non-ATG start under investigation first 1000 PCCRs 19 46412811 46413023 -1 1 chr19:46412811-46413023- 840 yes CCDC8 potential non-ATG start under investigation first 1000 PCCRs 20 32434565 32434819 1 2 chr20:32434565-32434819+, chr20:32434626-32434715+ 668 no The PhyloCSF signal for ASXL1 changes frame in the final exon and goes back to the original frame after ~250bp. This sequence conformation is conserved in mammals, and while this could conceivably indicate a programmed frameshift, it could instead be explained by an unknown splice variant that causes this exon to be translated in a different frame. under investigation first 1000 PCCRs 20 33667087 33667497 1 1 chr20:33667087-33667497+ 566 yes ACTL10 retrogene potential non-ATG start under investigation first 1000 PCCRs 21 46324103 46326488 1 2 chr21:46324103-46324132+, chr21:46326297-46326488+ 460 yes Identifies a prospective 68aa single exon CDS at chr21:46,326,288-46,326,491, which overlaps with a coding exon of PCNT in a different frame. Conservation of the 68aa CDS is apparent across vertebrates, as is conservation of the PCNT exonic translation. There is currently no evidence to support the transcription of the 68aa CDS in human or mouse. The candidate ORF includes the variant RCV000147149, which is linked in ClinVar to Microcephalic osteodysplastic primordial dwarfism type II, a condition that develops in-utero. If the transcript is only be expressed in utero, that might explain the lack of support from existing transcription databases. under investigation first 1000 PCCRs 22 19029521 19030212 1 2 chr22:19029521-19029805+, chr22:19029781-19030212+ 510 yes Two adjacent NPRs highlight ORFs in a previously unannotated region, although in distinct frames. However, indel variants rs10709444 and rs11356224 have no support for the genomic conformation in 1000 genomes data, and if these are 'corrected' the NPRs can be united into a prospective single exon 233aa CDS. These variants are now under investigation by the Genome Reference Consortium as possible errors in the genome assembly, and GENCODE cannot annotate this as a protein-coding gene until fixed genomic sequence becomes available. However, previously unidentified duplicants of this locus with coding potential have now been identfiied at [chr22:21,360,601-21,361,299 (-)] and [chr22:18,633,984-18,634,682 (+)], and these have been respectively annotated as protein-coding genes ENSG00000286102 and ENSG00000286175 in GENCODEv31. These three loci share homology with mouse protein-coding gene B830017H08Rik / ENSMUSG00000116652. under investigation; now made coding first 1000 PCCRs 22 30968818 30969787 -1 8 chr22:30968818-30968871-, chr22:30968825-30968902-, chr22:30969231-30969311-, chr22:30969257-30969283-, chr22:30969359-30969787-, chr22:30969384-30969494-, chr22:30969400-30969435-, chr22:30969549-30969593- 554 yes Identifies a putative CDS within exonic sequence of lncRNA TUG1. The STOP codon and reading frame are conserved in mammals, although no ATG initiation codon has been found. The 5' NPR terminus falls close to a [CTG] codon that is conserved in mammals, which would demarcate a single exon 153aa CDS [chr22:30969357-30969818]. This translation has now been experimentally confirmed by Lewandowski et al in a manuscript submitted to bioRxiv (https://www.biorxiv.org/content/10.1101/562066v1), and TUG1 will be annotated as a protein-coding gene in GENCODEv32. under investigation; now made coding first 1000 PCCRs 22 40552101 40552358 -1 1 chr22:40552101-40552358- 561 no MKL1 potential non-ATG start under investigation first 1000 PCCRs X 56563562 56563899 1 3 chrX:56563562-56563594+, chrX:56563624-56563650+, chrX:56563828-56563899+ 901 yes UBQLN2 potential non-ATG start under investigation first 1000 PCCRs X 119574523 119574809 1 2 chrX:119574523-119574666+, chrX:119574777-119574809+ 359 yes UBE2A potential non-ATG start under investigation first 1000 PCCRs 2 88857382 88861919 -1 5 chr2:88857382-88857516-, chr2:88857535-88857570-, chr2:88857601-88857675-, chr2:88861529-88861555-, chr2:88861884-88861919- 10 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 7 38240099 38249549 -1 6 chr7:38240099-38240134-, chr7:38249250-38249276-, chr7:38249292-38249333-, chr7:38249343-38249405-, chr7:38249448-38249492-, chr7:38249520-38249549- 880 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 7 142308759 142313661 1 6 chr7:142308759-142308797+, chr7:142308822-142308872+, chr7:142308999-142309043+, chr7:142313431-142313517+, chr7:142313539-142313571+, chr7:142313632-142313661+ 301 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 7 142381077 142408131 1 9 chr7:142381077-142381121+, chr7:142381149-142381178+, chr7:142389398-142389457+, chr7:142389635-142389667+, chr7:142392379-142392420+, chr7:142400193-142400237+, chr7:142400262-142400291+, chr7:142400316-142400369+, chr7:142408099-142408131+ 503 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 7 142715668 142721155 1 4 chr7:142715668-142715730+, chr7:142715746-142715778+, chr7:142720961-142721023+, chr7:142721129-142721155+ 741 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 7 142740698 142740844 1 1 chr7:142740698-142740844+ 403 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 7 142791723 142802211 1 13 chr7:142791723-142791800+, chr7:142791807-142791878+, chr7:142791918-142792013+, chr7:142792035-142792061+, chr7:142796384-142796410+, chr7:142796574-142796609+, chr7:142796853-142796894+, chr7:142797121-142797165+, chr7:142797457-142797498+, chr7:142801070-142801225+, chr7:142801265-142801360+, chr7:142801382-142801408+, chr7:142802107-142802211+ 263 yes overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 7 142812591 142812824 -1 2 chr7:142812591-142812674-, chr7:142812744-142812824- 558 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 14 21712704 21712793 1 1 chr14:21712704-21712793+ 997 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 14 21736694 21736969 1 3 chr14:21736694-21736726+, chr14:21736739-21736930+, chr14:21736943-21736969+ 291 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 14 21846938 21869364 1 6 chr14:21846938-21846982+, chr14:21852723-21852881+, chr14:21852906-21852983+, chr14:21861800-21861826+, chr14:21861937-21862005+, chr14:21869326-21869364+ 157 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 14 21941431 21941646 1 2 chr14:21941431-21941526+, chr14:21941611-21941646+ 187 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 14 21990718 21990933 1 3 chr14:21990718-21990759+, chr14:21990763-21990810+, chr14:21990892-21990933+ 78 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 14 22003591 22003665 1 1 chr14:22003591-22003665+ 734 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 14 22071088 22071201 1 1 chr14:22071088-22071201+ 16 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 14 22086679 22096605 1 4 chr14:22086679-22086708+, chr14:22086736-22086804+, chr14:22086919-22086954+, chr14:22096564-22096605+ 401 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 14 22163645 22163866 1 2 chr14:22163645-22163713+, chr14:22163804-22163866+ 920 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 14 22462955 22464286 1 3 chr14:22462955-22463017+, chr14:22463066-22463155+, chr14:22464221-22464286+ 547 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 14 22478901 22550660 1 19 chr14:22478901-22478927+, chr14:22479534-22479563+, chr14:22482310-22482336+, chr14:22483036-22483062+, chr14:22486248-22486277+, chr14:22490520-22490546+, chr14:22493948-22493977+, chr14:22503760-22503798+, chr14:22509376-22509402+, chr14:22518478-22518504+, chr14:22520424-22520459+, chr14:22525643-22525708+, chr14:22531102-22531131+, chr14:22531965-22531991+, chr14:22532501-22532554+, chr14:22542228-22542254+, chr14:22544103-22544129+, chr14:22547517-22547543+, chr14:22550556-22550660+ 109 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 14 105584148 105601713 -1 15 chr14:105584148-105584318-, chr14:105586940-105587317-, chr14:105587591-105587872-, chr14:105588129-105588188-, chr14:105588231-105588338-, chr14:105597865-105597909-, chr14:105600084-105600140-, chr14:105600261-105600329-, chr14:105600354-105600398-, chr14:105600473-105600613-, chr14:105600695-105600799-, chr14:105600943-105600996-, chr14:105601093-105601188-, chr14:105601558-105601659-, chr14:105601684-105601713- 727 yes overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 14 105621918 105644790 -1 17 chr14:105621918-105621998-, chr14:105623062-105623190-, chr14:105624515-105624643-, chr14:105624689-105624730-, chr14:105624758-105624790-, chr14:105624903-105625031-, chr14:105625077-105625226-, chr14:105625773-105625820-, chr14:105625842-105626006-, chr14:105626031-105626066-, chr14:105629778-105629804-, chr14:105635807-105635878-, chr14:105640971-105641051-, chr14:105641761-105641898-, chr14:105643245-105643526-, chr14:105643630-105643935-, chr14:105644497-105644790- 914 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 14 105704391 105708662 -1 8 chr14:105704391-105704531-, chr14:105707189-105707299-, chr14:105707321-105707383-, chr14:105707432-105707548-, chr14:105707789-105707914-, chr14:105707957-105708079-, chr14:105708444-105708479-, chr14:105708567-105708662- 823 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 14 105737771 105743011 -1 6 chr14:105737771-105737851-, chr14:105740057-105740182-, chr14:105741497-105741646-, chr14:105741674-105741796-, chr14:105741900-105742202-, chr14:105742847-105743011- 829 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 22 22900978 22906658 1 3 chr22:22900978-22901292+, chr22:22906344-22906475+, chr22:22906491-22906658+ 375 no overlaps an immunoglobulin region immunoglobulin segment first 1000 PCCRs 9 61352022 61352123 1 1 chr9:61352022-61352123+ 1270 no protein similar to contactin associated protein-like 3 has a known sequence assembly problem; the CDS cannot yet be annotated known assembly issue previously unannotated PCCR 11 1074896 1110292 1 54 chr11:1074896-1074976+, chr11:1075653-1075919+, chr11:1077455-1077571+, chr11:1077949-1078041+, chr11:1078131-1078235+, chr11:1078312-1078521+, chr11:1081667-1081789+, chr11:1082284-1082403+, chr11:1082479-1082631+, chr11:1082884-1082976+, chr11:1083074-1083151+, chr11:1083424-1083564+, chr11:1083652-1083816+, chr11:1084290-1084394+, chr11:1084589-1084717+, chr11:1085067-1085324+, chr11:1085747-1085791+, chr11:1085807-1085842+, chr11:1086243-1086317+, chr11:1086330-1086407+, chr11:1086730-1086876+, chr11:1087755-1087877+, chr11:1087983-1088129+, chr11:1088255-1088500+, chr11:1089509-1089670+, chr11:1089941-1090072+, chr11:1090763-1090891+, chr11:1092397-1092429+, chr11:1092843-1092959+, chr11:1094180-1094410+, chr11:1094429-1094473+, chr11:1100753-1100782+, chr11:1100921-1100950+, chr11:1101231-1101371+, chr11:1101753-1101788+, chr11:1101810-1101929+, chr11:1102416-1102649+, chr11:1103271-1103456+, chr11:1103780-1103899+, chr11:1103972-1104007+, chr11:1104731-1104904+, chr11:1105302-1105364+, chr11:1105536-1105601+, chr11:1105855-1105893+, chr11:1107077-1107271+, chr11:1107649-1107753+, chr11:1108009-1108053+, chr11:1108173-1108220+, chr11:1108236-1108298+, chr11:1108548-1108613+, chr11:1109314-1109415+, chr11:1109647-1109697+, chr11:1109912-1110034+, chr11:1110137-1110292+ 26 yes MUC2 has a known sequence error; the CDS cannot yet be annotated known assembly issue first 1000 PCCRs 12 40565645 40570604 1 5 chr12:40565645-40565788+, chr12:40567598-40567642+, chr12:40567655-40567714+, chr12:40569707-40569799+, chr12:40570464-40570604+ 19 no MUC19 has a known sequence error; the CDS cannot yet be annotated known assembly issue first 1000 PCCRs 22 50674240 50684656 1 16 chr22:50674240-50674539+, chr22:50674292-50674579+, chr22:50674335-50674532+, chr22:50674582-50674707+, chr22:50674644-50674721+, chr22:50674758-50674865+, chr22:50674759-50674944+, chr22:50674760-50674930+, chr22:50675045-50675254+, chr22:50676622-50676693+, chr22:50678585-50678692+, chr22:50678768-50678926+, chr22:50679019-50679189+, chr22:50679312-50679431+, chr22:50683340-50683420+, chr22:50684585-50684656+ 61 yes SHANK3 has a known sequence error; the CDS cannot yet be annotated known assembly issue first 1000 PCCRs 1 19165221 19173121 1 2 chr1:19165221-19165247+, chr1:19173095-19173121+ 170 no potentially spurious not annotated first 1000 PCCRs 1 46466510 46466815 -1 6 chr1:46466510-46466557-, chr1:46466536-46466589-, chr1:46466621-46466689-, chr1:46466623-46466664-, chr1:46466695-46466784-, chr1:46466780-46466815- 1586 yes putative regulatory region not annotated previously unannotated PCCR 1 55775123 55775155 1 1 chr1:55775123-55775155+ 1616 no putative regulatory region not annotated previously unannotated PCCR 1 62997933 63000329 -1 9 chr1:62997933-62997977-, chr1:62998995-62999081-, chr1:62999128-62999199-, chr1:62999217-62999297-, chr1:62999293-62999403-, chr1:62999306-62999332-, chr1:62999370-62999405-, chr1:63000261-63000329-, chr1:63000280-63000312- 1026 no putative regulatory region not annotated previously unannotated PCCR 1 70039113 70043935 -1 3 chr1:70039113-70039160-, chr1:70039737-70039778-, chr1:70043885-70043935- 3 no potentially spurious not annotated first 1000 PCCRs 1 86505354 86506381 1 5 chr1:86505354-86505410+, chr1:86505617-86505736+, chr1:86505825-86505857+, chr1:86505903-86505965+, chr1:86506331-86506381+ 521 no fragments of a reteroviral ORF not annotated first 1000 PCCRs 1 89203293 89203370 -1 1 chr1:89203293-89203370- 1009 no putative regulatory region not annotated previously unannotated PCCR 1 90535213 90537888 1 2 chr1:90535213-90535269+, chr1:90537859-90537888+ 2040 no putative regulatory region not annotated previously unannotated PCCR 1 90832085 90840997 -1 14 chr1:90832085-90832138-, chr1:90833857-90834048-, chr1:90833963-90834049-, chr1:90834003-90834056-, chr1:90834182-90834265-, chr1:90834223-90834252-, chr1:90834458-90834541-, chr1:90835000-90835107-, chr1:90835001-90835108-, chr1:90835125-90835220-, chr1:90835296-90835352-, chr1:90835300-90835332-, chr1:90835627-90835662-, chr1:90840962-90840997- 3119 yes putative regulatory region not annotated lncRNA PCCR 1 111987704 111990382 1 7 chr1:111987704-111987784+, chr1:111989309-111989368+, chr1:111989394-111989429+, chr1:111989410-111989454+, chr1:111989694-111989729+, chr1:111990128-111990163+, chr1:111990263-111990382+ 4367 yes putative regulatory region not annotated lncRNA PCCR 1 116854681 116854716 -1 1 chr1:116854681-116854716- 1829 no putative regulatory region not annotated previously unannotated PCCR 1 150364575 150365278 -1 3 chr1:150364575-150364733-, chr1:150364589-150364813-, chr1:150365249-150365278- 648 yes putative regulatory region not annotated first 1000 PCCRs 1 153922296 153923335 1 8 chr1:153922296-153922592+, chr1:153922474-153922617+, chr1:153922517-153922612+, chr1:153922680-153922706+, chr1:153922773-153922814+, chr1:153922869-153922955+, chr1:153922886-153922999+, chr1:153923177-153923335+ 631 yes putative regulatory region not annotated first 1000 PCCRs 1 160262310 160262658 1 5 chr1:160262310-160262348+, chr1:160262388-160262504+, chr1:160262408-160262503+, chr1:160262416-160262472+, chr1:160262611-160262658+ 1078 yes putative regulatory region not annotated lncRNA PCCR 1 160722501 160723005 -1 3 chr1:160722501-160722575-, chr1:160722616-160722732-, chr1:160722922-160723005- 351 no putative regulatory region not annotated first 1000 PCCRs 1 161305675 161314396 -1 2 chr1:161305675-161305875-, chr1:161314361-161314396- 498 no MPZ known STOP codon readthrough event not annotated first 1000 PCCRs 1 171577592 171577645 -1 1 chr1:171577592-171577645- 2 no potentially spurious not annotated first 1000 PCCRs 1 199041659 199041770 1 2 chr1:199041659-199041694+, chr1:199041714-199041770+ 19990 no potentially spurious not annotated lncRNA PCCR 1 204359879 204378165 -1 7 chr1:204359879-204359944-, chr1:204359938-204359982-, chr1:204367798-204367854-, chr1:204371543-204371605-, chr1:204377576-204377671-, chr1:204377671-204377706-, chr1:204378133-204378165- 815 yes putative regulatory region not annotated first 1000 PCCRs 1 211941869 211941904 1 1 chr1:211941869-211941904+ 444 no potentially spurious not annotated first 1000 PCCRs 1 213987582 214019850 -1 15 chr1:213987582-213987650-, chr1:213987602-213987679-, chr1:213987831-213987896-, chr1:213988364-213988399-, chr1:213988691-213988825-, chr1:213995025-213995105-, chr1:213996442-213996534-, chr1:213996455-213996502-, chr1:213997166-213997207-, chr1:214002658-214002768-, chr1:214010044-214010097-, chr1:214016896-214016931-, chr1:214017262-214017288-, chr1:214019708-214019782-, chr1:214019740-214019850- 2229 no potentially spurious not annotated lncRNA PCCR 1 214030725 214031537 -1 2 chr1:214030725-214030778-, chr1:214031493-214031537- 20015 no potentially spurious not annotated lncRNA PCCR 1 216518138 216521946 1 3 chr1:216518138-216518203+, chr1:216518327-216518365+, chr1:216521872-216521946+ 2138 no putative regulatory region not annotated previously unannotated PCCR 1 221741882 221742912 1 3 chr1:221741882-221741914+, chr1:221742387-221742413+, chr1:221742886-221742912+ 1318 yes putative regulatory region not annotated previously unannotated PCCR 1 222815026 222815061 1 1 chr1:222815026-222815061+ 58910 no potentially spurious not annotated lncRNA PCCR 1 226159184 226159273 1 1 chr1:226159184-226159273+ 721 no putative regulatory region not annotated first 1000 PCCRs 1 230281750 230281782 -1 1 chr1:230281750-230281782- 1859 no potentially spurious not annotated lncRNA PCCR 1 244048122 244055468 -1 20 chr1:244048122-244048250-, chr1:244048135-244048215-, chr1:244048531-244048629-, chr1:244048547-244048600-, chr1:244048548-244048628-, chr1:244048639-244048866-, chr1:244048640-244048867-, chr1:244048641-244048865-, chr1:244048982-244049008-, chr1:244049244-244049453-, chr1:244049245-244049547-, chr1:244049246-244049530-, chr1:244049813-244049884-, chr1:244051185-244051352-, chr1:244051321-244051410-, chr1:244052131-244052187-, chr1:244052174-244052209-, chr1:244052230-244052295-, chr1:244054702-244054773-, chr1:244055436-244055468- 977 yes putative regulatory region not annotated first 1000 PCCRs 1 244272482 244272921 1 4 chr1:244272482-244272508+, chr1:244272533-244272562+, chr1:244272740-244272808+, chr1:244272868-244272921+ 1692 no putative regulatory region not annotated previously unannotated PCCR 2 16227044 16227106 -1 1 chr2:16227044-16227106- 4525 no potentially spurious not annotated lncRNA PCCR 2 19504683 19504721 1 1 chr2:19504683-19504721+ 950 no putative regulatory region not annotated first 1000 PCCRs 2 31376220 31376324 -1 1 chr2:31376220-31376324- 885 no low complexity region not annotated first 1000 PCCRs 2 41932436 41932471 -1 1 chr2:41932436-41932471- 63879 no potentially spurious not annotated lncRNA PCCR 2 42169275 42169579 -1 2 chr2:42169275-42169406-, chr2:42169514-42169579- 1811 yes putative regulatory region not annotated lncRNA PCCR 2 44167863 44168986 -1 2 chr2:44167863-44167892-, chr2:44168936-44168986- 2246 yes putative regulatory region not annotated lncRNA PCCR 2 62090379 62098552 -1 14 chr2:62090379-62090462-, chr2:62090493-62090531-, chr2:62090719-62090826-, chr2:62090851-62090922-, chr2:62091046-62091123-, chr2:62091202-62091267-, chr2:62091304-62091363-, chr2:62091817-62091858-, chr2:62094317-62094415-, chr2:62096382-62096510-, chr2:62097033-62097272-, chr2:62097506-62097562-, chr2:62097782-62097811-, chr2:62098472-62098552- 5807 no retrotransposon sequence not annotated lncRNA PCCR 2 62789658 62789699 -1 1 chr2:62789658-62789699- 2168 no putative regulatory region not annotated previously unannotated PCCR 2 66695564 66700411 1 4 chr2:66695564-66695638+, chr2:66698192-66698275+, chr2:66700277-66700309+, chr2:66700358-66700411+ 5616 no potentially spurious not annotated lncRNA PCCR 2 71578835 71579031 -1 3 chr2:71578835-71578879-, chr2:71578904-71578957-, chr2:71578963-71579031- 2011 no putative regulatory region not annotated previously unannotated PCCR 2 104430374 104434436 1 5 chr2:104430374-104430472+, chr2:104430605-104430634+, chr2:104431892-104431966+, chr2:104431923-104431958+, chr2:104434362-104434436+ 5767 no potentially spurious not annotated lncRNA PCCR 2 111429594 111429623 -1 1 chr2:111429594-111429623- 15824 no potentially spurious not annotated lncRNA PCCR 2 121382114 121382155 1 1 chr2:121382114-121382155+ 1948 no putative regulatory region not annotated previously unannotated PCCR 2 158795248 158795286 1 1 chr2:158795248-158795286+ 1306 no putative regulatory region not annotated previously unannotated PCCR 2 159232075 159232110 -1 1 chr2:159232075-159232110- 404 no potentially spurious not annotated first 1000 PCCRs 2 159396069 159397027 1 3 chr2:159396069-159396179+, chr2:159396918-159396992+, chr2:159396941-159397027+ 16402 no potentially spurious not annotated lncRNA PCCR 2 159712300 159712541 -1 3 chr2:159712300-159712326-, chr2:159712316-159712387-, chr2:159712512-159712541- 4866 yes putative regulatory region not annotated lncRNA PCCR 2 161266080 161266178 -1 2 chr2:161266080-161266178-, chr2:161266087-161266164- 19080 no potentially spurious not annotated lncRNA PCCR 2 163348314 163348757 1 3 chr2:163348314-163348352+, chr2:163348491-163348520+, chr2:163348731-163348757+ 1845 no putative regulatory region not annotated previously unannotated PCCR 2 173198177 173198791 -1 7 chr2:173198177-173198236-, chr2:173198385-173198504-, chr2:173198401-173198451-, chr2:173198521-173198559-, chr2:173198665-173198760-, chr2:173198730-173198786-, chr2:173198732-173198791- 11645 no potentially spurious not annotated lncRNA PCCR 2 175441462 175442589 1 7 chr2:175441462-175441497+, chr2:175441493-175441552+, chr2:175441588-175441614+, chr2:175441590-175441781+, chr2:175441592-175441768+, chr2:175441808-175441834+, chr2:175442563-175442589+ 3667 no potentially spurious not annotated lncRNA PCCR 2 216606912 216606938 -1 1 chr2:216606912-216606938- 25015 no potentially spurious not annotated lncRNA PCCR 2 225399685 225399729 1 1 chr2:225399685-225399729+ 26141 no potentially spurious not annotated lncRNA PCCR 3 67927434 67927787 1 2 chr3:67927434-67927625+, chr3:67927746-67927787+ 641 no potentially spurious not annotated first 1000 PCCRs 3 71003497 71007603 1 8 chr3:71003497-71003541+, chr3:71003704-71003769+, chr3:71004743-71004808+, chr3:71004793-71004858+, chr3:71005812-71005850+, chr3:71005901-71005975+, chr3:71006455-71006541+, chr3:71007577-71007603+ 1733 no putative regulatory region not annotated previously unannotated PCCR 3 101676348 101677166 1 2 chr3:101676348-101676410+, chr3:101677113-101677166+ 1953 yes putative regulatory region not annotated lncRNA PCCR 3 131050173 131050202 -1 1 chr3:131050173-131050202- 1592 no low complexity region not annotated previously unannotated PCCR 3 164020256 164021752 -1 7 chr3:164020256-164020414-, chr3:164020478-164020513-, chr3:164020569-164021051-, chr3:164021064-164021105-, chr3:164021175-164021216-, chr3:164021385-164021459-, chr3:164021465-164021752- 771 no fragments of a reteroviral ORF not annotated first 1000 PCCRs 3 173395998 173398001 1 4 chr3:173395998-173396024+, chr3:173396042-173396089+, chr3:173396510-173396539+, chr3:173397951-173398001+ 763 yes putative regulatory region not annotated first 1000 PCCRs 3 181534923 181535146 -1 3 chr3:181534923-181535018-, chr3:181535087-181535146-, chr3:181535097-181535141- 35860 no potentially spurious not annotated lncRNA PCCR 4 4735253 4735288 -1 1 chr4:4735253-4735288- 2192 no putative regulatory region not annotated previously unannotated PCCR 4 41745545 41752242 1 12 chr4:41745545-41745577+, chr4:41745734-41745796+, chr4:41745778-41745804+, chr4:41748331-41748378+, chr4:41748419-41748457+, chr4:41748687-41748743+, chr4:41748734-41748775+, chr4:41748901-41748954+, chr4:41748984-41749016+, chr4:41750262-41750303+, chr4:41752084-41752110+, chr4:41752210-41752242+ 2903 yes putative regulatory region not annotated lncRNA PCCR 4 41857345 41882783 -1 16 chr4:41857345-41857374-, chr4:41857471-41857566-, chr4:41857502-41857531-, chr4:41857625-41857651-, chr4:41857708-41857761-, chr4:41863913-41863960-, chr4:41867232-41867291-, chr4:41873311-41873361-, chr4:41873995-41874021-, chr4:41874098-41874193-, chr4:41879383-41879442-, chr4:41879454-41879489-, chr4:41881526-41881579-, chr4:41882497-41882553-, chr4:41882589-41882627-, chr4:41882745-41882783- 5013 yes putative regulatory region not annotated lncRNA PCCR 4 62454254 62454337 -1 1 chr4:62454254-62454337- 1975 no potentially spurious not annotated previously unannotated PCCR 4 79634275 79634310 1 1 chr4:79634275-79634310+ 1677 no potentially spurious not annotated previously unannotated PCCR 4 108483644 108483670 1 1 chr4:108483644-108483670+ 1256 no putative regulatory region not annotated previously unannotated PCCR 4 139889906 139890016 1 1 chr4:139889906-139890016+ 453 no low complexity region not annotated first 1000 PCCRs 4 144370278 144370319 -1 1 chr4:144370278-144370319- 1049 no putative regulatory region not annotated previously unannotated PCCR 4 144872963 144873004 1 1 chr4:144872963-144873004+ 8893 no potentially spurious not annotated lncRNA PCCR 4 154492320 154492352 1 1 chr4:154492320-154492352+ 8 no putative regulatory region not annotated first 1000 PCCRs 4 185071430 185071645 1 5 chr4:185071430-185071468+, chr4:185071450-185071518+, chr4:185071452-185071478+, chr4:185071567-185071605+, chr4:185071583-185071645+ 4626 no potentially spurious not annotated lncRNA PCCR 5 37834655 37842122 1 8 chr5:37834655-37834780+, chr5:37834722-37834784+, chr5:37839692-37839736+, chr5:37840022-37840051+, chr5:37840229-37840285+, chr5:37840558-37840587+, chr5:37840660-37840692+, chr5:37842081-37842122+ 1665 yes putative regulatory region not annotated lncRNA PCCR 5 77844392 77852299 1 7 chr5:77844392-77844562+, chr5:77847750-77847845+, chr5:77847920-77848051+, chr5:77850992-77851036+, chr5:77851017-77851100+, chr5:77851930-77851956+, chr5:77852273-77852299+ 1970 yes putative regulatory region not annotated previously unannotated PCCR 5 77946424 77946671 -1 2 chr5:77946424-77946450-, chr5:77946477-77946671- 20968 no potentially spurious not annotated lncRNA PCCR 5 78360504 78360619 -1 2 chr5:78360504-78360617-, chr5:78360515-78360619- 1744 yes putative regulatory region not annotated lncRNA PCCR 5 81851608 81852135 1 3 chr5:81851608-81851658+, chr5:81851895-81851960+, chr5:81851926-81852135+ 16747 no potentially spurious not annotated lncRNA PCCR 5 88943109 88943135 1 1 chr5:88943109-88943135+ 35315 no putative regulatory region not annotated lncRNA PCCR 5 93602010 93603078 1 6 chr5:93602010-93602036+, chr5:93602015-93602086+, chr5:93602278-93602367+, chr5:93602441-93602485+, chr5:93602455-93602484+, chr5:93603028-93603078+ 13238 no potentially spurious not annotated lncRNA PCCR 5 137305082 137305231 1 1 chr5:137305082-137305231+ 1334 no putative regulatory region not annotated previously unannotated PCCR 5 141413416 141417615 -1 2 chr5:141413416-141413442-, chr5:141417586-141417615- 620 yes putative regulatory region not annotated first 1000 PCCRs 6 12585160 12585219 -1 1 chr6:12585160-12585219- 22343 no potentially spurious not annotated lncRNA PCCR 6 15244943 15246114 -1 9 chr6:15244943-15244996-, chr6:15245105-15245179-, chr6:15245118-15245186-, chr6:15245158-15245196-, chr6:15245274-15245330-, chr6:15245294-15245326-, chr6:15245991-15246077-, chr6:15246020-15246046-, chr6:15246025-15246114- 2604 yes putative regulatory region not annotated lncRNA PCCR 6 19804719 19804943 -1 2 chr6:19804719-19804835-, chr6:19804902-19804943- 2401 yes putative regulatory region not annotated lncRNA PCCR 6 21523586 21523618 -1 1 chr6:21523586-21523618- 19832 no potentially spurious not annotated lncRNA PCCR 6 22149922 22149960 1 1 chr6:22149922-22149960+ 28811 no potentially spurious not annotated lncRNA PCCR 6 32387409 32387459 1 1 chr6:32387409-32387459+ 1762 no potentially spurious not annotated previously unannotated PCCR 6 41523976 41531924 -1 2 chr6:41523976-41524047-, chr6:41531895-41531924- 27214 no potentially spurious not annotated lncRNA PCCR 6 44387871 44387962 -1 2 chr6:44387871-44387909-, chr6:44387924-44387962- 2126 yes putative regulatory region not annotated previously unannotated PCCR 6 50093305 50093758 1 3 chr6:50093305-50093421+, chr6:50093473-50093514+, chr6:50093702-50093758+ 25810 no putative regulatory region not annotated lncRNA PCCR 6 73275832 73275909 1 1 chr6:73275832-73275909+ 48370 no potentially spurious not annotated lncRNA PCCR 6 84707256 84707297 1 1 chr6:84707256-84707297+ 25549 no potentially spurious not annotated lncRNA PCCR 6 97885333 97885567 1 3 chr6:97885333-97885542+, chr6:97885415-97885567+, chr6:97885506-97885541+ 10594 no potentially spurious not annotated lncRNA PCCR 6 99400282 99414614 1 4 chr6:99400282-99400314+, chr6:99409275-99409340+, chr6:99409306-99409359+, chr6:99414573-99414614+ 850 no putative regulatory region not annotated first 1000 PCCRs 6 108157665 108177636 1 14 chr6:108157665-108157802+, chr6:108157673-108157888+, chr6:108157678-108157842+, chr6:108158940-108158975+, chr6:108165947-108166069+, chr6:108165969-108166019+, chr6:108166012-108166092+, chr6:108166662-108166691+, chr6:108166664-108166765+, chr6:108166753-108166794+, chr6:108168640-108168666+, chr6:108170962-108171000+, chr6:108171115-108171165+, chr6:108177589-108177636+ 1015 yes putative regulatory region not annotated lncRNA PCCR 6 108945218 108945244 -1 1 chr6:108945218-108945244- 1621 no potentially spurious not annotated previously unannotated PCCR 6 133953198 133953686 1 3 chr6:133953198-133953224+, chr6:133953283-133953441+, chr6:133953657-133953686+ 259 yes putative regulatory region not annotated first 1000 PCCRs 7 5636614 5636676 1 1 chr7:5636614-5636676+ 2183 no putative regulatory region not annotated previously unannotated PCCR 7 10940506 10940532 1 1 chr7:10940506-10940532+ 23464 no potentially spurious not annotated lncRNA PCCR 7 25753491 25753602 -1 2 chr7:25753491-25753589-, chr7:25753552-25753602- 2133 no putative regulatory region not annotated previously unannotated PCCR 7 27130527 27185948 1 63 chr7:27130527-27130595+, chr7:27130619-27130705+, chr7:27130908-27130943+, chr7:27130913-27130945+, chr7:27130933-27131019+, chr7:27130983-27131030+, chr7:27133757-27133807+, chr7:27133875-27133922+, chr7:27140286-27140351+, chr7:27140287-27140349+, chr7:27141226-27141282+, chr7:27141245-27141277+, chr7:27141618-27141674+, chr7:27142045-27142092+, chr7:27143083-27143229+, chr7:27143124-27143276+, chr7:27143308-27143388+, chr7:27143331-27143657+, chr7:27143479-27143568+, chr7:27143617-27143883+, chr7:27143727-27143804+, chr7:27143750-27143776+, chr7:27143856-27143957+, chr7:27143906-27143932+, chr7:27143969-27144031+, chr7:27144037-27144075+, chr7:27147474-27147500+, chr7:27147648-27147710+, chr7:27147698-27147730+, chr7:27147815-27147994+, chr7:27147819-27148034+, chr7:27147820-27147990+, chr7:27150950-27150991+, chr7:27150955-27151002+, chr7:27152388-27152447+, chr7:27152504-27152563+, chr7:27152580-27152663+, chr7:27152765-27152791+, chr7:27156210-27156266+, chr7:27156417-27156605+, chr7:27156656-27156703+, chr7:27156672-27156755+, chr7:27156706-27156735+, chr7:27164984-27165055+, chr7:27165089-27165175+, chr7:27169442-27169546+, chr7:27169456-27169536+, chr7:27169491-27169565+, chr7:27170414-27170473+, chr7:27172881-27172946+, chr7:27172889-27172930+, chr7:27179873-27179908+, chr7:27184236-27184289+, chr7:27184249-27184311+, chr7:27184409-27184471+, chr7:27184530-27184613+, chr7:27184649-27184729+, chr7:27184781-27184855+, chr7:27184794-27184865+, chr7:27185013-27185081+, chr7:27185226-27185321+, chr7:27185432-27185509+, chr7:27185889-27185948+ 2422 yes putative regulatory region not annotated lncRNA PCCR 7 32428030 32428137 -1 1 chr7:32428030-32428137- 1895 yes putative regulatory region not annotated previously unannotated PCCR 7 32428082 32428135 1 1 chr7:32428082-32428135+ 1707 yes putative regulatory region not annotated previously unannotated PCCR 7 41705287 41705352 -1 1 chr7:41705287-41705352- 1990 no potentially spurious not annotated lncRNA PCCR 7 65770455 65770837 -1 3 chr7:65770455-65770517-, chr7:65770456-65770629-, chr7:65770685-65770837- 43654 yes putative regulatory region not annotated lncRNA PCCR 7 92916975 92917136 1 1 chr7:92916975-92917136+ 34578 no potentially spurious not annotated lncRNA PCCR 7 99032894 99032944 1 1 chr7:99032894-99032944+ 14256 no potentially spurious not annotated lncRNA PCCR 7 100793828 100793977 1 2 chr7:100793828-100793899+, chr7:100793906-100793977+ 846 no Frameshift within a ZAN coding exon that is due to a human specific 1bp deletion. This may suggest the locus is pseudogenic, although there is evidence to suggest that translation may proceed from other transcripts. not annotated first 1000 PCCRs 7 114085900 114086223 1 2 chr7:114085900-114085935+, chr7:114086182-114086223+ 1206 yes putative regulatory region not annotated previously unannotated PCCR 7 114629847 114631629 -1 5 chr7:114629847-114629963-, chr7:114630509-114630535-, chr7:114630748-114630840-, chr7:114631528-114631557-, chr7:114631594-114631629- 437 no low complexity region not annotated first 1000 PCCRs 7 115673834 115679526 -1 7 chr7:115673834-115673911-, chr7:115673893-115673949-, chr7:115673954-115674064-, chr7:115674576-115674626-, chr7:115679104-115679175-, chr7:115679172-115679219-, chr7:115679479-115679526- 7911 no potentially spurious not annotated lncRNA PCCR 7 115728598 115732308 -1 3 chr7:115728598-115728660-, chr7:115732188-115732247-, chr7:115732243-115732308- 2200 no putative regulatory region not annotated previously unannotated PCCR 7 136903193 136903228 -1 1 chr7:136903193-136903228- 6945 no potentially spurious not annotated lncRNA PCCR 7 152163143 152176287 1 4 chr7:152163143-152163178+, chr7:152168534-152168623+, chr7:152168572-152168607+, chr7:152176246-152176287+ 555 no potentially spurious not annotated first 1000 PCCRs 8 9555878 9556023 -1 2 chr8:9555878-9555970-, chr8:9555901-9556023- 1519 yes putative regulatory region not annotated lncRNA PCCR 8 22751075 22751104 -1 1 chr8:22751075-22751104- 987 no potentially spurious not annotated first 1000 PCCRs 8 48556218 48556379 -1 2 chr8:48556218-48556286-, chr8:48556353-48556379- 46797 no potentially spurious not annotated lncRNA PCCR 8 60792790 60793155 -1 4 chr8:60792790-60792825-, chr8:60792833-60792859-, chr8:60792954-60793118-, chr8:60793006-60793155- 943 no putative regulatory region not annotated first 1000 PCCRs 8 64368369 64380096 -1 7 chr8:64368369-64368398-, chr8:64368412-64368453-, chr8:64368897-64368947-, chr8:64377163-64377261-, chr8:64377334-64377378-, chr8:64379162-64379194-, chr8:64380061-64380096- 7413 no potentially spurious not annotated lncRNA PCCR 8 64377213 64379240 1 2 chr8:64377213-64377350+, chr8:64379211-64379240+ 15435 no potentially spurious not annotated lncRNA PCCR 8 76526118 76535635 1 3 chr8:76526118-76526198+, chr8:76526197-76526244+, chr8:76535588-76535635+ 2199 no putative regulatory region not annotated previously unannotated PCCR 8 78644641 78649262 1 14 chr8:78644641-78644835+, chr8:78645271-78645303+, chr8:78645309-78645443+, chr8:78645445-78645585+, chr8:78645685-78645891+, chr8:78646129-78646191+, chr8:78646425-78646454+, chr8:78647092-78647292+, chr8:78647394-78647492+, chr8:78647811-78647909+, chr8:78648665-78648721+, chr8:78648874-78648900+, chr8:78648982-78649011+, chr8:78649224-78649262+ 182 no putative regulatory region not annotated first 1000 PCCRs 8 105139340 105143726 -1 3 chr8:105139340-105139429-, chr8:105143574-105143726-, chr8:105143621-105143704- 7615 no potentially spurious not annotated lncRNA PCCR 8 124815655 124815693 -1 1 chr8:124815655-124815693- 4299 no potentially spurious not annotated lncRNA PCCR 8 133823295 133823321 -1 1 chr8:133823295-133823321- 2160 no potentially spurious not annotated previously unannotated PCCR 9 4850295 4850354 -1 1 chr9:4850295-4850354- 53115 no deeply conserved miRNA not annotated lncRNA PCCR 9 23821259 23831562 1 16 chr9:23821259-23821336+, chr9:23821632-23821694+, chr9:23821761-23821787+, chr9:23821762-23821851+, chr9:23821827-23821946+, chr9:23821850-23821924+, chr9:23822797-23822895+, chr9:23822901-23822927+, chr9:23824294-23824338+, chr9:23825871-23825930+, chr9:23826090-23826149+, chr9:23826226-23826372+, chr9:23826305-23826373+, chr9:23826333-23826377+, chr9:23826500-23826604+, chr9:23831500-23831562+ 4140 yes putative regulatory region not annotated lncRNA PCCR 9 35341754 35353800 1 7 chr9:35341754-35341885+, chr9:35351527-35351604+, chr9:35351926-35352132+, chr9:35352175-35352444+, chr9:35353009-35353068+, chr9:35353105-35353551+, chr9:35353636-35353800+ 597 no potentially spurious not annotated first 1000 PCCRs 9 37079962 37080054 1 1 chr9:37079962-37080054+ 48651 yes putative regulatory region not annotated lncRNA PCCR 9 41127083 41128234 -1 3 chr9:41127083-41127160-, chr9:41127236-41127439-, chr9:41128184-41128234- 417 yes FOXD4L6 contains a frameshift relative to its presumptive parent gene FOXD4, resulting in a terminal 55aa region that is potentially translated in a different frame. FOXD4L6 has been maintained as protein-coding at the present time due to published evidence for its functionality, although the evidence presented is not unequivocal and it is possible that the gene is pseudogenic. See also FOXD4L3. not annotated first 1000 PCCRs 9 68303101 68304252 1 3 chr9:68303101-68303151+, chr9:68303896-68304099+, chr9:68304175-68304252+ 416 yes FOXD4L3 contains a frameshift relative to its presumptive parent gene FOXD4, resulting in a terminal 55aa region that is potentially translated in a different frame. FOXD4L6 has been maintained as protein-coding at the present time due to published evidence for its functionality, although the evidence presented is not unequivocal and it is possible that the gene is pseudogenic. See also FOXD4L6. not annotated first 1000 PCCRs 9 95426721 95426765 -1 1 chr9:95426721-95426765- 30732 no potentially spurious not annotated lncRNA PCCR 9 99374155 99374214 -1 1 chr9:99374155-99374214- 13668 no potentially spurious not annotated lncRNA PCCR 9 106616132 106621609 1 2 chr9:106616132-106616185+, chr9:106621544-106621609+ 17354 no potentially spurious not annotated lncRNA PCCR 9 106697944 106698006 1 1 chr9:106697944-106698006+ 19970 no potentially spurious not annotated lncRNA PCCR 9 119526654 119526680 1 1 chr9:119526654-119526680+ 1650 no potentially spurious not annotated previously unannotated PCCR 9 122905081 122905417 -1 6 chr9:122905081-122905212-, chr9:122905089-122905184-, chr9:122905124-122905189-, chr9:122905217-122905261-, chr9:122905277-122905327-, chr9:122905370-122905417- 981 yes putative regulatory region not annotated first 1000 PCCRs 9 124693710 124693745 1 1 chr9:124693710-124693745+ 41375 no deeply conserved miRNA not annotated lncRNA PCCR 9 130712624 130713721 1 3 chr9:130712624-130712659+, chr9:130712976-130713005+, chr9:130713671-130713721+ 1714 yes putative regulatory region not annotated previously unannotated PCCR 9 136245441 136267514 -1 9 chr9:136245441-136245473-, chr9:136245586-136245636-, chr9:136245811-136245885-, chr9:136252721-136252795-, chr9:136253849-136253878-, chr9:136254542-136254577-, chr9:136254899-136254955-, chr9:136263703-136263756-, chr9:136267383-136267514- 774 yes putative regulatory region not annotated first 1000 PCCRs 10 8037394 8060257 -1 18 chr10:8037394-8037456-, chr10:8037423-8037467-, chr10:8040459-8040497-, chr10:8040741-8040773-, chr10:8040824-8041024-, chr10:8045434-8045466-, chr10:8050667-8050777-, chr10:8050943-8050981-, chr10:8051983-8052060-, chr10:8052002-8052070-, chr10:8052042-8052137-, chr10:8054446-8054505-, chr10:8054487-8054525-, chr10:8054525-8054572-, chr10:8054572-8054742-, chr10:8054618-8054710-, chr10:8055584-8055775-, chr10:8060192-8060257- 2791 yes putative regulatory region not annotated lncRNA PCCR 10 22475972 22476061 -1 1 chr10:22475972-22476061- 1008 yes putative regulatory region not annotated previously unannotated PCCR 10 23173215 23174753 1 7 chr10:23173215-23173259+, chr10:23173292-23173363+, chr10:23173311-23173397+, chr10:23173409-23173438+, chr10:23173438-23173509+, chr10:23174552-23174599+, chr10:23174706-23174753+ 1346 yes putative regulatory region not annotated previously unannotated PCCR 10 23223792 23223824 -1 1 chr10:23223792-23223824- 5043 no potentially spurious not annotated lncRNA PCCR 10 27741453 27745817 1 2 chr10:27741453-27741512+, chr10:27745779-27745817+ 290 yes putative regulatory region not annotated first 1000 PCCRs 10 33566078 33566119 -1 1 chr10:33566078-33566119- 995 no putative regulatory region not annotated first 1000 PCCRs 10 75401238 75417825 -1 10 chr10:75401238-75401273-, chr10:75401343-75401501-, chr10:75401420-75401503-, chr10:75401663-75401698-, chr10:75401685-75401795-, chr10:75401740-75401916-, chr10:75405182-75405280-, chr10:75405184-75405432-, chr10:75408408-75408497-, chr10:75417787-75417825- 4228 yes putative regulatory region not annotated lncRNA PCCR 10 75708158 75708438 -1 5 chr10:75708158-75708187-, chr10:75708193-75708225-, chr10:75708229-75708324-, chr10:75708261-75708368-, chr10:75708406-75708438- 1870 no putative regulatory region not annotated previously unannotated PCCR 10 97865716 97865787 1 1 chr10:97865716-97865787+ 929 no GOLGA7B suspected STOP-codon readthrough event not annotated first 1000 PCCRs 10 100864660 100882989 1 14 chr10:100864660-100864824+, chr10:100866615-100866641+, chr10:100866713-100866769+, chr10:100866801-100866902+, chr10:100866880-100866948+, chr10:100870348-100870389+, chr10:100876667-100876708+, chr10:100877208-100877246+, chr10:100877282-100877428+, chr10:100877406-100877441+, chr10:100879886-100879924+, chr10:100882236-100882271+, chr10:100882255-100882281+, chr10:100882945-100882989+ 1983 no putative regulatory region not annotated previously unannotated PCCR 10 101050227 101050298 1 1 chr10:101050227-101050298+ 1961 no putative regulatory region not annotated previously unannotated PCCR 10 101322790 101331146 -1 3 chr10:101322790-101323044-, chr10:101331011-101331115-, chr10:101331018-101331146- 8363 no potentially spurious not annotated lncRNA PCCR 10 113118964 113126911 -1 10 chr10:113118964-113119083-, chr10:113119136-113119180-, chr10:113119982-113120011-, chr10:113120036-113120113-, chr10:113121307-113121456-, chr10:113123127-113123228-, chr10:113125658-113125720-, chr10:113125826-113125891-, chr10:113126694-113126849-, chr10:113126858-113126911- 1110 no putative regulatory region not annotated previously unannotated PCCR 10 117534530 117554766 -1 25 chr10:117534530-117534580-, chr10:117534647-117534691-, chr10:117541393-117541419-, chr10:117542440-117542478-, chr10:117542498-117542647-, chr10:117542538-117542606-, chr10:117542569-117542634-, chr10:117542643-117542714-, chr10:117542656-117542823-, chr10:117542879-117542914-, chr10:117543188-117543226-, chr10:117543413-117543442-, chr10:117543523-117543615-, chr10:117543674-117543715-, chr10:117546674-117546760-, chr10:117546684-117546764-, chr10:117551337-117551450-, chr10:117551366-117551437-, chr10:117551425-117551457-, chr10:117551523-117551600-, chr10:117551543-117551602-, chr10:117551697-117551747-, chr10:117553506-117553565-, chr10:117554621-117554689-, chr10:117554728-117554766- 1320 yes putative regulatory region not annotated lncRNA PCCR 10 123517645 123517671 1 1 chr10:123517645-123517671+ 17598 no potentially spurious not annotated lncRNA PCCR 10 124510196 124510294 -1 1 chr10:124510196-124510294- 1684 no putative regulatory region not annotated previously unannotated PCCR 10 124988918 124988947 -1 1 chr10:124988918-124988947- 965 no potentially spurious not annotated first 1000 PCCRs 10 128537129 128539816 1 2 chr10:128537129-128537164+, chr10:128539775-128539816+ 1257 no putative regulatory region not annotated previously unannotated PCCR 10 129211045 129211095 1 1 chr10:129211045-129211095+ 1794 no putative regulatory region not annotated previously unannotated PCCR 10 129833677 129871400 1 32 chr10:129833677-129833715+, chr10:129835481-129835516+, chr10:129837705-129837734+, chr10:129839157-129839207+, chr10:129840820-129840864+, chr10:129841018-129841053+, chr10:129842299-129842328+, chr10:129844645-129844689+, chr10:129844834-129844884+, chr10:129844929-129844955+, chr10:129845282-129845329+, chr10:129845406-129845477+, chr10:129845618-129845698+, chr10:129846338-129846370+, chr10:129846610-129846663+, chr10:129849946-129849990+, chr10:129850278-129850307+, chr10:129852034-129852078+, chr10:129854097-129854132+, chr10:129854658-129854684+, chr10:129854788-129854823+, chr10:129855388-129855426+, chr10:129860677-129860739+, chr10:129863194-129863220+, chr10:129868509-129868535+, chr10:129868548-129868586+, chr10:129869778-129869819+, chr10:129869952-129869981+, chr10:129871007-129871105+, chr10:129871012-129871086+, chr10:129871132-129871194+, chr10:129871350-129871400+ 1459 no potentially spurious not annotated lncRNA PCCR 11 253470 253517 -1 1 chr11:253470-253517- 1851 no potentially spurious not annotated previously unannotated PCCR 11 1991242 1991307 1 1 chr11:1991242-1991307+ 22455 no potentially spurious not annotated lncRNA PCCR 11 2652195 2652680 -1 2 chr11:2652195-2652224-, chr11:2652636-2652680- 3436 no potentially spurious not annotated lncRNA PCCR 11 20274456 20277249 -1 5 chr11:20274456-20274497-, chr11:20276489-20276515-, chr11:20276775-20276828-, chr11:20277101-20277139-, chr11:20277217-20277249- 1144 no putative regulatory region not annotated previously unannotated PCCR 11 28566878 28566937 -1 2 chr11:28566878-28566937-, chr11:28566891-28566932- 1963 no putative regulatory region not annotated previously unannotated PCCR 11 32380093 32380125 1 1 chr11:32380093-32380125+ 1950 no putative regulatory region not annotated previously unannotated PCCR 11 32436892 32436921 1 1 chr11:32436892-32436921+ 11415 no potentially spurious not annotated lncRNA PCCR 11 65487766 65500691 1 3 chr11:65487766-65487825+, chr11:65497502-65497534+, chr11:65500659-65500691+ 2793 yes putative regulatory region not annotated lncRNA PCCR 11 85662411 85665175 1 10 chr11:85662411-85662491+, chr11:85663213-85663278+, chr11:85663239-85663277+, chr11:85663486-85663515+, chr11:85663503-85663583+, chr11:85663820-85663888+, chr11:85663979-85664038+, chr11:85664258-85664293+, chr11:85664647-85664706+, chr11:85665113-85665175+ 984 yes putative regulatory region not annotated first 1000 PCCRs 11 114076681 114083125 -1 2 chr11:114076681-114076707-, chr11:114083087-114083125- 2013 no putative regulatory region not annotated previously unannotated PCCR 11 114160174 114164042 -1 6 chr11:114160174-114160233-, chr11:114162901-114162981-, chr11:114162936-114163040-, chr11:114163838-114163867-, chr11:114163901-114163954-, chr11:114163983-114164042- 933 no putative regulatory region not annotated first 1000 PCCRs 11 115645239 115645283 1 1 chr11:115645239-115645283+ 11189 no potentially spurious not annotated lncRNA PCCR 11 122309284 122309334 -1 1 chr11:122309284-122309334- 27401 no potentially spurious not annotated lncRNA PCCR 11 124411362 124411427 1 1 chr11:124411362-124411427+ 1810 no putative regulatory region not annotated previously unannotated PCCR 11 126101394 126101435 -1 1 chr11:126101394-126101435- 20553 no putative regulatory region not annotated lncRNA PCCR 11 132347304 132347330 1 1 chr11:132347304-132347330+ 1769 no putative regulatory region not annotated previously unannotated PCCR 12 6667963 6678792 1 5 chr12:6667963-6668028+, chr12:6672245-6672349+, chr12:6672418-6672450+, chr12:6672822-6672869+, chr12:6678691-6678792+ 12 no potentially spurious not annotated first 1000 PCCRs 12 16786700 16786822 1 1 chr12:16786700-16786822+ 72566 no putative regulatory region not annotated lncRNA PCCR 12 45610611 45610655 -1 1 chr12:45610611-45610655- 38968 no potentially spurious not annotated lncRNA PCCR 12 49020566 49033910 1 10 chr12:49020566-49020658+, chr12:49021006-49021035+, chr12:49024063-49024134+, chr12:49030371-49030424+, chr12:49032447-49032473+, chr12:49032882-49033007+, chr12:49033104-49033145+, chr12:49033428-49033496+, chr12:49033650-49033679+, chr12:49033869-49033910+ 27 no potentially spurious not annotated first 1000 PCCRs 12 53675817 53677539 1 6 chr12:53675817-53675870+, chr12:53675846-53675878+, chr12:53676010-53676039+, chr12:53677141-53677539+, chr12:53677193-53677399+, chr12:53677284-53677511+ 760 yes putative regulatory region not annotated first 1000 PCCRs 12 54259577 54262648 1 3 chr12:54259577-54259669+, chr12:54262535-54262648+, chr12:54262548-54262583+ 4874 no potentially spurious not annotated lncRNA PCCR 12 69353147 69360016 1 3 chr12:69353147-69353173+, chr12:69359661-69359687+, chr12:69359981-69360016+ 958 yes putative regulatory region not annotated first 1000 PCCRs 12 70445357 70448659 -1 12 chr12:70445357-70445419-, chr12:70445450-70445530-, chr12:70445631-70445687-, chr12:70445721-70445807-, chr12:70445910-70445942-, chr12:70446123-70446164-, chr12:70446218-70446253-, chr12:70447636-70447662-, chr12:70448007-70448036-, chr12:70448073-70448201-, chr12:70448546-70448587-, chr12:70448633-70448659- 185 no potentially spurious not annotated first 1000 PCCRs 12 79934559 79935332 1 4 chr12:79934559-79934609+, chr12:79935096-79935122+, chr12:79935163-79935243+, chr12:79935303-79935332+ 2233 yes putative regulatory region not annotated lncRNA PCCR 12 89351989 89353104 1 7 chr12:89351989-89352087+, chr12:89352475-89352528+, chr12:89352498-89352596+, chr12:89352548-89352610+, chr12:89352621-89352752+, chr12:89352641-89352730+, chr12:89353060-89353104+ 2898 yes putative regulatory region not annotated lncRNA PCCR 12 103699066 103699095 1 1 chr12:103699066-103699095+ 931 no potentially spurious not annotated first 1000 PCCRs 12 106681962 106681991 -1 1 chr12:106681962-106681991- 835 no potentially spurious not annotated first 1000 PCCRs 12 114441286 114448738 -1 2 chr12:114441286-114441336-, chr12:114448691-114448738- 1628 yes putative regulatory region not annotated previously unannotated PCCR 12 114895933 114896645 -1 3 chr12:114895933-114895968-, chr12:114896133-114896162-, chr12:114896598-114896645- 2030 no putative regulatory region not annotated previously unannotated PCCR 12 117099377 117099481 1 1 chr12:117099377-117099481+ 40862 yes putative regulatory region not annotated lncRNA PCCR 12 130424479 130424565 1 1 chr12:130424479-130424565+ 1401 yes putative regulatory region not annotated previously unannotated PCCR 13 51451954 51453308 1 6 chr13:51451954-51452061+, chr13:51452057-51452302+, chr13:51452169-51452312+, chr13:51452260-51452412+, chr13:51452409-51452513+, chr13:51453246-51453308+ 2509 yes putative regulatory region not annotated lncRNA PCCR 13 63746801 63746998 1 2 chr13:63746801-63746863+, chr13:63746939-63746998+ 21750 no potentially spurious not annotated lncRNA PCCR 13 74554805 74554858 1 1 chr13:74554805-74554858+ 55269 no potentially spurious not annotated lncRNA PCCR 13 97110055 97110108 -1 1 chr13:97110055-97110108- 1494 no putative regulatory region not annotated previously unannotated PCCR 13 98519173 98519211 1 1 chr13:98519173-98519211+ 1706 no putative regulatory region not annotated previously unannotated PCCR 13 99723905 99724160 -1 3 chr13:99723905-99723991-, chr13:99723982-99724020-, chr13:99724077-99724160- 1756 no putative regulatory region not annotated previously unannotated PCCR 14 22928522 22929775 1 3 chr14:22928522-22928593+, chr14:22929697-22929774+, chr14:22929716-22929775+ 2247 no potentially spurious not annotated lncRNA PCCR 14 28760181 28778530 1 16 chr14:28760181-28760210+, chr14:28765760-28765786+, chr14:28766575-28766604+, chr14:28766577-28766723+, chr14:28766778-28766942+, chr14:28766800-28767030+, chr14:28767102-28767275+, chr14:28767116-28767259+, chr14:28767480-28767605+, chr14:28767687-28767881+, chr14:28768053-28768085+, chr14:28768155-28768259+, chr14:28768359-28768469+, chr14:28770640-28770681+, chr14:28778332-28778418+, chr14:28778378-28778530+ 2163 yes putative regulatory region not annotated lncRNA PCCR 14 29380951 29390501 1 5 chr14:29380951-29381079+, chr14:29389901-29389954+, chr14:29390181-29390243+, chr14:29390288-29390314+, chr14:29390460-29390501+ 23607 no potentially spurious not annotated lncRNA PCCR 14 74188570 74194217 -1 2 chr14:74188570-74188680-, chr14:74194173-74194217- 2058 no putative regulatory region not annotated previously unannotated PCCR 14 74552396 74552425 1 1 chr14:74552396-74552425+ 72482 no potentially spurious not annotated lncRNA PCCR 14 75277155 75281681 1 9 chr14:75277155-75277238+, chr14:75278460-75278492+, chr14:75278528-75278563+, chr14:75279526-75279609+, chr14:75279543-75279578+, chr14:75281216-75281245+, chr14:75281425-75281454+, chr14:75281463-75281513+, chr14:75281589-75281681+ 653 yes putative regulatory region not annotated first 1000 PCCRs 14 76131383 76139120 -1 9 chr14:76131383-76131418-, chr14:76134284-76134358-, chr14:76134398-76134424-, chr14:76134426-76134452-, chr14:76136692-76136841-, chr14:76138651-76138761-, chr14:76138806-76138985-, chr14:76138915-76138950-, chr14:76139094-76139120- 1818 no putative regulatory region not annotated previously unannotated PCCR 14 79417471 79417497 1 1 chr14:79417471-79417497+ 967 no potentially spurious not annotated first 1000 PCCRs 14 80211350 80211457 1 1 chr14:80211350-80211457+ 1561 no putative regulatory region not annotated lncRNA PCCR 14 93926359 93927414 -1 5 chr14:93926359-93926385-, chr14:93926482-93926517-, chr14:93926669-93926725-, chr14:93927189-93927302-, chr14:93927274-93927414- 4529 no potentially spurious not annotated lncRNA PCCR 14 97230200 97230331 1 1 chr14:97230200-97230331+ 2120 no putative regulatory region not annotated previously unannotated PCCR 14 102052554 102052995 -1 3 chr14:102052554-102052634-, chr14:102052637-102052690-, chr14:102052969-102052995- 3470 no potentially spurious not annotated lncRNA PCCR 15 24165553 24165603 -1 1 chr15:24165553-24165603- 39860 no retrotransposon sequence not annotated lncRNA PCCR 15 24212291 24212452 -1 2 chr15:24212291-24212368-, chr15:24212417-24212452- 2027 no putative regulatory region not annotated previously unannotated PCCR 15 38072940 38073050 -1 2 chr15:38072940-38072993-, chr15:38073018-38073050- 9650 no potentially spurious not annotated lncRNA PCCR 15 40313687 40324514 1 10 chr15:40313687-40313767+, chr15:40323638-40323778+, chr15:40323681-40323779+, chr15:40323700-40323777+, chr15:40323786-40323944+, chr15:40323787-40323825+, chr15:40323842-40324024+, chr15:40324014-40324514+, chr15:40324058-40324210+, chr15:40324355-40324381+ 2488 yes putative regulatory region not annotated lncRNA PCCR 15 41048231 41048266 1 1 chr15:41048231-41048266+ 650 no putative regulatory region not annotated first 1000 PCCRs 15 42208311 42208337 1 1 chr15:42208311-42208337+ 450 yes putative regulatory region not annotated first 1000 PCCRs 15 45198578 45201222 -1 8 chr15:45198578-45198643-, chr15:45198579-45198653-, chr15:45198586-45198678-, chr15:45200411-45200485-, chr15:45200419-45200460-, chr15:45201131-45201160-, chr15:45201141-45201221-, chr15:45201172-45201222- 1685 yes 3 tRNAs not annotated lncRNA PCCR 15 58538488 58538523 -1 1 chr15:58538488-58538523- 975 no potentially spurious not annotated first 1000 PCCRs 15 61034459 61034494 1 1 chr15:61034459-61034494+ 1893 no putative regulatory region not annotated previously unannotated PCCR 15 95454977 95464832 -1 4 chr15:95454977-95455015-, chr15:95455034-95455162-, chr15:95464621-95464710-, chr15:95464791-95464832- 6935 no potentially spurious not annotated lncRNA PCCR 15 95497806 95497850 1 1 chr15:95497806-95497850+ 70265 no potentially spurious not annotated lncRNA PCCR 15 95929520 95940999 1 3 chr15:95929520-95929558+, chr15:95931143-95931169+, chr15:95940961-95940999+ 1117 no putative regulatory region not annotated previously unannotated PCCR 16 3004217 3004832 1 2 chr16:3004217-3004609+, chr16:3004608-3004832+ 1301 yes putative regulatory region not annotated previously unannotated PCCR 16 14186604 14186633 -1 1 chr16:14186604-14186633- 1986 no putative regulatory region not annotated previously unannotated PCCR 16 24609769 24610266 1 2 chr16:24609769-24609810+, chr16:24610186-24610266+ 24254 no potentially spurious not annotated lncRNA PCCR 16 25086330 25086377 -1 1 chr16:25086330-25086377- 38842 no potentially spurious not annotated lncRNA PCCR 16 28974152 28974178 -1 1 chr16:28974152-28974178- 33611 no potentially spurious not annotated lncRNA PCCR 16 30775877 30776062 -1 2 chr16:30775877-30775978-, chr16:30776030-30776062- 1077 yes putative regulatory region not annotated lncRNA PCCR 16 50386980 50391447 -1 4 chr16:50386980-50387009-, chr16:50391136-50391195-, chr16:50391357-50391410-, chr16:50391418-50391447- 9104 no potentially spurious not annotated lncRNA PCCR 16 52439420 52439641 1 1 chr16:52439420-52439641+ 980 no potentially spurious not annotated first 1000 PCCRs 16 54632610 54632996 1 2 chr16:54632610-54632741+, chr16:54632967-54632996+ 1582 no putative regulatory region not annotated previously unannotated PCCR 16 54928752 54938880 1 12 chr16:54928752-54928817+, chr16:54928778-54928900+, chr16:54928795-54928854+, chr16:54930707-54930775+, chr16:54930741-54930845+, chr16:54931143-54931196+, chr16:54931929-54931970+, chr16:54933435-54933485+, chr16:54934765-54934824+, chr16:54934815-54934844+, chr16:54938702-54938746+, chr16:54938845-54938880+ 736 yes putative regulatory region not annotated first 1000 PCCRs 16 56191313 56194112 -1 10 chr16:56191313-56191441-, chr16:56191326-56191424-, chr16:56191504-56191677-, chr16:56191649-56191702-, chr16:56191699-56191809-, chr16:56191731-56191805-, chr16:56191799-56191870-, chr16:56192139-56192234-, chr16:56193740-56193781-, chr16:56194047-56194112- 1942 yes putative regulatory region not annotated lncRNA PCCR 16 72284703 72284771 -1 1 chr16:72284703-72284771- 9953 no potentially spurious not annotated lncRNA PCCR 16 72425643 72428006 1 14 chr16:72425643-72425732+, chr16:72425686-72425724+, chr16:72425759-72425863+, chr16:72425830-72425943+, chr16:72425907-72426035+, chr16:72426157-72426189+, chr16:72426167-72426235+, chr16:72427086-72427190+, chr16:72427094-72427168+, chr16:72427371-72427454+, chr16:72427573-72427605+, chr16:72427777-72427803+, chr16:72427940-72427978+, chr16:72427959-72428006+ 2536 no potentially spurious not annotated lncRNA PCCR 16 72425674 72429311 -1 11 chr16:72425674-72425721-, chr16:72425861-72425953-, chr16:72425869-72425898-, chr16:72425938-72425979-, chr16:72426154-72426234-, chr16:72426363-72426410-, chr16:72426579-72426608-, chr16:72427437-72427466-, chr16:72428000-72428038-, chr16:72428246-72428278-, chr16:72429285-72429311- 7419 no potentially spurious not annotated lncRNA PCCR 16 72786749 72802320 1 9 chr16:72786749-72786784+, chr16:72787179-72787319+, chr16:72787392-72787517+, chr16:72787623-72787727+, chr16:72787667-72787699+, chr16:72787740-72788033+, chr16:72793442-72793480+, chr16:72797459-72797515+, chr16:72802213-72802320+ 1595 yes putative regulatory region not annotated lncRNA PCCR 16 73227024 73232264 1 2 chr16:73227024-73227098+, chr16:73232217-73232264+ 11316 no putative regulatory region not annotated lncRNA PCCR 16 73871387 73890893 1 4 chr16:73871387-73871452+, chr16:73877344-73877439+, chr16:73885110-73885160+, chr16:73890867-73890893+ 1245 no putative regulatory region not annotated previously unannotated PCCR 16 75434051 75434393 1 3 chr16:75434051-75434122+, chr16:75434165-75434221+, chr16:75434355-75434393+ 16322 no potentially spurious not annotated lncRNA PCCR 16 86476526 86476564 -1 1 chr16:86476526-86476564- 21941 no potentially spurious not annotated lncRNA PCCR 16 88884148 88887214 1 2 chr16:88884148-88884180+, chr16:88887170-88887214+ 25779 no potentially spurious not annotated lncRNA PCCR 17 1713893 1724692 -1 7 chr17:1713893-1713988-, chr17:1714648-1714797-, chr17:1714671-1714760-, chr17:1716190-1716261-, chr17:1716219-1716269-, chr17:1716294-1716320-, chr17:1724654-1724692- 1472 yes putative regulatory region not annotated lncRNA PCCR 17 2213699 2215813 1 3 chr17:2213699-2213749+, chr17:2215594-2215656+, chr17:2215697-2215813+ 10766 no potentially spurious not annotated lncRNA PCCR 17 2392678 2402115 1 19 chr17:2392678-2392707+, chr17:2392688-2392759+, chr17:2393803-2393928+, chr17:2399714-2399746+, chr17:2399997-2400035+, chr17:2400001-2400075+, chr17:2400231-2400275+, chr17:2400606-2400638+, chr17:2400683-2400835+, chr17:2400714-2400851+, chr17:2400736-2400792+, chr17:2400996-2401112+, chr17:2401001-2401036+, chr17:2401060-2401173+, chr17:2401131-2401172+, chr17:2401142-2401189+, chr17:2401712-2401762+, chr17:2401732-2401776+, chr17:2402086-2402115+ 468 yes putative regulatory region not annotated first 1000 PCCRs 17 3846277 3846312 1 1 chr17:3846277-3846312+ 2178 yes putative regulatory region not annotated previously unannotated PCCR 17 6637185 6640241 -1 4 chr17:6637185-6637253-, chr17:6639636-6639995-, chr17:6640131-6640157-, chr17:6640188-6640241- 237 yes putative regulatory region not annotated first 1000 PCCRs 17 8221594 8227025 -1 10 chr17:8221594-8221620-, chr17:8222235-8222276-, chr17:8222239-8222295-, chr17:8222267-8222305-, chr17:8222832-8222900-, chr17:8222833-8222889-, chr17:8226236-8226301-, chr17:8226609-8226686-, chr17:8226611-8226688-, chr17:8226990-8227025- 2014 yes 6 tRNAs not annotated lncRNA PCCR 17 8311412 8311480 -1 1 chr17:8311412-8311480- 1909 no low complexity region not annotated previously unannotated PCCR 17 13496410 13496577 1 2 chr17:13496410-13496469+, chr17:13496512-13496577+ 828 no potentially spurious not annotated first 1000 PCCRs 17 28729026 28729058 -1 1 chr17:28729026-28729058- 2079 yes putative regulatory region not annotated previously unannotated PCCR 17 39402672 39410654 1 5 chr17:39402672-39402701+, chr17:39410286-39410357+, chr17:39410303-39410383+, chr17:39410436-39410654+, chr17:39410507-39410590+ 809 yes putative regulatory region not annotated first 1000 PCCRs 17 41909234 41909269 1 1 chr17:41909234-41909269+ 1758 no potentially spurious not annotated previously unannotated PCCR 17 45161411 45169317 -1 3 chr17:45161411-45161530-, chr17:45161412-45161495-, chr17:45169288-45169317- 2238 yes putative regulatory region not annotated lncRNA PCCR 17 47896176 47896544 -1 8 chr17:47896176-47896316-, chr17:47896177-47896233-, chr17:47896187-47896285-, chr17:47896295-47896321-, chr17:47896365-47896391-, chr17:47896388-47896519-, chr17:47896413-47896544-, chr17:47896456-47896524- 633 yes putative regulatory region not annotated first 1000 PCCRs 17 48294084 48294260 1 2 chr17:48294084-48294110+, chr17:48294207-48294260+ 1593 no putative regulatory region not annotated previously unannotated PCCR 17 48307328 48313286 1 5 chr17:48307328-48307372+, chr17:48310888-48310998+, chr17:48311030-48311227+, chr17:48311217-48311264+, chr17:48313233-48313286+ 16723 no potentially spurious not annotated lncRNA PCCR 17 48590257 48633940 1 48 chr17:48590257-48590364+, chr17:48590312-48590386+, chr17:48593271-48593312+, chr17:48593317-48593505+, chr17:48593541-48593609+, chr17:48593629-48593838+, chr17:48593684-48593755+, chr17:48593709-48593873+, chr17:48593872-48593979+, chr17:48593931-48593957+, chr17:48594060-48594086+, chr17:48595772-48595801+, chr17:48596023-48596055+, chr17:48596924-48596953+, chr17:48597102-48597170+, chr17:48597884-48597925+, chr17:48598040-48598228+, chr17:48598152-48598301+, chr17:48598270-48598392+, chr17:48600552-48600614+, chr17:48603947-48603982+, chr17:48604920-48604988+, chr17:48604928-48605077+, chr17:48605028-48605066+, chr17:48610556-48610633+, chr17:48610729-48610767+, chr17:48610745-48610780+, chr17:48610955-48611023+, chr17:48611229-48611258+, chr17:48613046-48613084+, chr17:48614468-48614626+, chr17:48614569-48614853+, chr17:48614941-48614991+, chr17:48614972-48615094+, chr17:48615200-48615283+, chr17:48615234-48615278+, chr17:48615465-48615539+, chr17:48615568-48615615+, chr17:48621307-48621348+, chr17:48625697-48625723+, chr17:48625886-48625948+, chr17:48626063-48626104+, chr17:48626191-48626220+, chr17:48626275-48626385+, chr17:48626282-48626326+, chr17:48626433-48626546+, chr17:48626716-48626760+, chr17:48633911-48633940+ 2307 yes putative regulatory region not annotated lncRNA PCCR 17 58324435 58331258 -1 5 chr17:58324435-58324464-, chr17:58324558-58324593-, chr17:58328649-58328684-, chr17:58328869-58328919-, chr17:58331205-58331258- 1430 yes putative regulatory region not annotated lncRNA PCCR 17 59001524 59001562 -1 1 chr17:59001524-59001562- 371 no low complexity region not annotated first 1000 PCCRs 17 62966188 62966607 -1 2 chr17:62966188-62966223-, chr17:62966575-62966607- 54817 yes putative regulatory region not annotated lncRNA PCCR 17 64146333 64146431 -1 1 chr17:64146333-64146431- 2052 yes putative regulatory region not annotated previously unannotated PCCR 17 71828229 71828264 -1 1 chr17:71828229-71828264- 1393 no putative regulatory region not annotated previously unannotated PCCR 17 78048844 78051364 1 2 chr17:78048844-78049062+, chr17:78051335-78051364+ 563 no potentially spurious not annotated first 1000 PCCRs 18 26035069 26035971 1 4 chr18:26035069-26035119+, chr18:26035323-26035367+, chr18:26035825-26035971+, chr18:26035892-26035957+ 832 no putative regulatory region not annotated first 1000 PCCRs 18 39841629 39841658 -1 1 chr18:39841629-39841658- 14458 no potentially spurious not annotated lncRNA PCCR 18 47594360 47602035 1 7 chr18:47594360-47594419+, chr18:47594690-47594737+, chr18:47594763-47594801+, chr18:47594835-47594957+, chr18:47594846-47594971+, chr18:47595035-47595070+, chr18:47602000-47602035+ 13245 no potentially spurious not annotated lncRNA PCCR 18 56083383 56083445 -1 1 chr18:56083383-56083445- 47446 no potentially spurious not annotated lncRNA PCCR 18 56873607 56873950 -1 4 chr18:56873607-56873714-, chr18:56873698-56873754-, chr18:56873785-56873823-, chr18:56873924-56873950- 31192 no potentially spurious not annotated lncRNA PCCR 18 78294316 78294424 1 2 chr18:78294316-78294342+, chr18:78294329-78294424+ 1610 no putative regulatory region not annotated previously unannotated PCCR 19 3762915 3762956 -1 1 chr19:3762915-3762956- 2031 yes putative regulatory region not annotated previously unannotated PCCR 19 8390328 8390435 -1 1 chr19:8390328-8390435- 1138 yes putative regulatory region not annotated lncRNA PCCR 19 12775496 12806530 1 11 chr19:12775496-12775525+, chr19:12782520-12782573+, chr19:12782533-12782595+, chr19:12786693-12786737+, chr19:12791282-12791410+, chr19:12791308-12791382+, chr19:12791718-12791744+, chr19:12793666-12793767+, chr19:12802147-12802203+, chr19:12804115-12804279+, chr19:12806492-12806530+ 113 yes putative regulatory region not annotated first 1000 PCCRs 19 15398227 15398985 1 4 chr19:15398227-15398283+, chr19:15398559-15398801+, chr19:15398588-15398809+, chr19:15398905-15398985+ 3366 no potentially spurious not annotated lncRNA PCCR 19 21454201 21454233 -1 1 chr19:21454201-21454233- 37629 no potentially spurious not annotated lncRNA PCCR 19 28608133 28611285 1 8 chr19:28608133-28608351+, chr19:28608547-28608783+, chr19:28608785-28608826+, chr19:28609336-28609524+, chr19:28609647-28610027+, chr19:28610631-28610771+, chr19:28611016-28611195+, chr19:28611202-28611285+ 36033 no potentially spurious not annotated lncRNA PCCR 19 28700946 28711165 -1 5 chr19:28700946-28701020-, chr19:28704300-28704374-, chr19:28706953-28707024-, chr19:28708008-28708211-, chr19:28711082-28711165- 8891 no potentially spurious not annotated lncRNA PCCR 19 29840491 29840517 1 1 chr19:29840491-29840517+ 2057 no putative regulatory region not annotated previously unannotated PCCR 19 31118515 31118553 1 1 chr19:31118515-31118553+ 1478 no putative regulatory region not annotated previously unannotated PCCR 19 31961652 31966868 -1 4 chr19:31961652-31961678-, chr19:31962199-31962255-, chr19:31962598-31962678-, chr19:31966815-31966868- 2226 no potentially spurious not annotated lncRNA PCCR 19 43575565 43575612 1 1 chr19:43575565-43575612+ 2050 no potentially spurious not annotated lncRNA PCCR 19 49639968 49642300 -1 4 chr19:49639968-49640123-, chr19:49642180-49642245-, chr19:49642181-49642300-, chr19:49642197-49642280- 868 yes putative regulatory region not annotated first 1000 PCCRs 19 49839159 49839191 -1 1 chr19:49839159-49839191- 64534 no potentially spurious not annotated lncRNA PCCR 20 31722888 31724001 1 3 chr20:31722888-31722932+, chr20:31722928-31722960+, chr20:31723960-31724001+ 2432 yes putative regulatory region not annotated lncRNA PCCR 20 50233512 50243267 1 2 chr20:50233512-50233541+, chr20:50243193-50243267+ 1568 no low complexity region not annotated previously unannotated PCCR 20 50662116 50662166 1 1 chr20:50662116-50662166+ 5900 no potentially spurious not annotated lncRNA PCCR 20 52493458 52501022 1 2 chr20:52493458-52493499+, chr20:52500942-52501022+ 737 no putative regulatory region not annotated first 1000 PCCRs 20 53171298 53178229 -1 2 chr20:53171298-53171339-, chr20:53178194-53178229- 8709 no potentially spurious not annotated lncRNA PCCR 20 58840432 58840488 -1 1 chr20:58840432-58840488- 1791 yes putative regulatory region not annotated lncRNA PCCR 20 59146082 59146369 1 2 chr20:59146082-59146132+, chr20:59146337-59146369+ 4380 no potentially spurious not annotated lncRNA PCCR 20 63931001 63931027 -1 1 chr20:63931001-63931027- 21 no potentially spurious not annotated first 1000 PCCRs 21 8209806 8218947 1 42 chr21:8209806-8210150+, chr21:8209807-8209845+, chr21:8209936-8210082+, chr21:8209958-8210251+, chr21:8210306-8210689+, chr21:8210319-8210429+, chr21:8210320-8211207+, chr21:8210559-8211248+, chr21:8210837-8210911+, chr21:8211002-8211430+, chr21:8211352-8211432+, chr21:8211372-8211437+, chr21:8211477-8211527+, chr21:8213982-8214167+, chr21:8214038-8214121+, chr21:8214073-8214147+, chr21:8214594-8214653+, chr21:8214902-8214937+, chr21:8215101-8215373+, chr21:8215133-8215264+, chr21:8215162-8215530+, chr21:8215385-8215591+, chr21:8215542-8215589+, chr21:8215677-8215808+, chr21:8215685-8215822+, chr21:8215696-8215980+, chr21:8215899-8215979+, chr21:8215916-8215978+, chr21:8216129-8216581+, chr21:8216131-8216598+, chr21:8216268-8216624+, chr21:8217041-8217106+, chr21:8217397-8217639+, chr21:8217398-8217568+, chr21:8217837-8218205+, chr21:8217871-8218071+, chr21:8217956-8218333+, chr21:8218478-8218678+, chr21:8218495-8218668+, chr21:8218560-8218667+, chr21:8218712-8218774+, chr21:8218783-8218947+ 1489 yes SSU-rRNA_Hsa repeat sequence not annotated lncRNA PCCR 21 8391812 8402305 -1 61 chr21:8391812-8391850-, chr21:8392450-8392494-, chr21:8392609-8392656-, chr21:8392611-8392643-, chr21:8392664-8393185-, chr21:8392843-8394579-, chr21:8392920-8394464-, chr21:8393249-8393464-, chr21:8393588-8394562-, chr21:8394567-8394653-, chr21:8394599-8394739-, chr21:8394613-8394717-, chr21:8394828-8394878-, chr21:8394829-8394894-, chr21:8394898-8394999-, chr21:8394899-8395000-, chr21:8395054-8395176-, chr21:8395180-8395452-, chr21:8395182-8395328-, chr21:8395331-8395426-, chr21:8395332-8395394-, chr21:8395484-8395522-, chr21:8395599-8395880-, chr21:8395600-8395782-, chr21:8395601-8395879-, chr21:8395987-8396022-, chr21:8396106-8396165-, chr21:8396169-8396216-, chr21:8396170-8396217-, chr21:8396420-8396461-, chr21:8396468-8396584-, chr21:8396469-8396597-, chr21:8396485-8396583-, chr21:8396934-8397278-, chr21:8397010-8397522-, chr21:8397014-8397484-, chr21:8397360-8397521-, chr21:8397526-8397690-, chr21:8397527-8397658-, chr21:8397528-8397659-, chr21:8397815-8397973-, chr21:8397831-8397974-, chr21:8397835-8397975-, chr21:8398064-8398129-, chr21:8398149-8398619-, chr21:8398150-8398617-, chr21:8398262-8398618-, chr21:8398636-8399025-, chr21:8398715-8399026-, chr21:8398719-8399027-, chr21:8399164-8399919-, chr21:8399165-8399917-, chr21:8399166-8399918-, chr21:8401510-8401716-, chr21:8401744-8401986-, chr21:8401745-8401945-, chr21:8401746-8401985-, chr21:8401994-8402026-, chr21:8402078-8402170-, chr21:8402083-8402268-, chr21:8402276-8402305- 2472 yes SSU-rRNA_Hsa not annotated lncRNA PCCR 21 8392730 8401986 1 42 chr21:8392730-8393185+, chr21:8392837-8393172+, chr21:8392842-8393213+, chr21:8393338-8394465+, chr21:8393349-8394242+, chr21:8393354-8393464+, chr21:8393588-8394562+, chr21:8394363-8394467+, chr21:8394774-8394812+, chr21:8394828-8394878+, chr21:8394898-8394936+, chr21:8395264-8395395+, chr21:8395331-8395453+, chr21:8395599-8395880+, chr21:8395600-8395881+, chr21:8395897-8395974+, chr21:8396933-8397523+, chr21:8396934-8397251+, chr21:8396977-8397522+, chr21:8397526-8397690+, chr21:8397527-8397658+, chr21:8397528-8397659+, chr21:8397813-8397974+, chr21:8397814-8397975+, chr21:8397815-8397967+, chr21:8398064-8398129+, chr21:8398148-8398564+, chr21:8398150-8398617+, chr21:8398182-8398619+, chr21:8398673-8399008+, chr21:8398711-8398854+, chr21:8398719-8399027+, chr21:8398960-8399025+, chr21:8399165-8399917+, chr21:8399166-8399918+, chr21:8399326-8399919+, chr21:8401516-8401716+, chr21:8401533-8401715+, chr21:8401598-8401717+, chr21:8401744-8401986+, chr21:8401746-8401868+, chr21:8401751-8401984+ 2662 yes LSU-rRNA_Hsa not annotated lncRNA PCCR 21 8433673 8446534 -1 87 chr21:8433673-8433759-, chr21:8433811-8434005-, chr21:8433812-8434006-, chr21:8434648-8434698-, chr21:8434793-8434963-, chr21:8434801-8434962-, chr21:8434833-8434925-, chr21:8434967-8435080-, chr21:8435280-8435408-, chr21:8435537-8435572-, chr21:8435577-8435726-, chr21:8435702-8435809-, chr21:8435860-8435916-, chr21:8436030-8436098-, chr21:8436061-8436099-, chr21:8436112-8436219-, chr21:8436182-8436220-, chr21:8436229-8436291-, chr21:8436245-8436292-, chr21:8436295-8436372-, chr21:8436353-8436493-, chr21:8436376-8436618-, chr21:8436399-8436530-, chr21:8436557-8436619-, chr21:8436629-8436727-, chr21:8436630-8436728-, chr21:8436819-8436866-, chr21:8436821-8436853-, chr21:8436874-8437395-, chr21:8437053-8438792-, chr21:8437130-8438866-, chr21:8437459-8437674-, chr21:8437798-8438952-, chr21:8438826-8438930-, chr21:8439041-8439109-, chr21:8439113-8439214-, chr21:8439114-8439215-, chr21:8439269-8439391-, chr21:8439395-8439667-, chr21:8439397-8439543-, chr21:8439546-8439641-, chr21:8439547-8439609-, chr21:8439699-8439767-, chr21:8439815-8440096-, chr21:8439816-8439998-, chr21:8439817-8440095-, chr21:8440203-8440238-, chr21:8440322-8440381-, chr21:8440388-8440435-, chr21:8440389-8440436-, chr21:8440566-8440601-, chr21:8440639-8440680-, chr21:8440687-8440803-, chr21:8440688-8440816-, chr21:8440704-8440802-, chr21:8441092-8441118-, chr21:8441129-8441704-, chr21:8441130-8441498-, chr21:8441230-8441742-, chr21:8441580-8441741-, chr21:8441746-8441910-, chr21:8441747-8441911-, chr21:8441748-8441909-, chr21:8442045-8442203-, chr21:8442061-8442204-, chr21:8442065-8442205-, chr21:8442294-8442371-, chr21:8442295-8442372-, chr21:8442378-8442848-, chr21:8442379-8442846-, chr21:8442491-8442847-, chr21:8442865-8443254-, chr21:8442944-8443255-, chr21:8442948-8443256-, chr21:8443399-8444154-, chr21:8443400-8444152-, chr21:8443401-8444153-, chr21:8445742-8445948-, chr21:8445976-8446044-, chr21:8445977-8446045-, chr21:8446052-8446216-, chr21:8446053-8446217-, chr21:8446054-8446176-, chr21:8446225-8446257-, chr21:8446309-8446497-, chr21:8446337-8446399-, chr21:8446505-8446534- 2451 yes SSU-rRNA_Hsa not annotated lncRNA PCCR 21 8436296 8446217 1 42 chr21:8436296-8436619+, chr21:8436376-8436618+, chr21:8436940-8437395+, chr21:8437047-8437382+, chr21:8437052-8437423+, chr21:8437548-8438675+, chr21:8437559-8438452+, chr21:8437564-8437674+, chr21:8437798-8438838+, chr21:8438573-8438677+, chr21:8438987-8439037+, chr21:8439113-8439151+, chr21:8439479-8439610+, chr21:8439546-8439668+, chr21:8439815-8440096+, chr21:8439816-8440097+, chr21:8440113-8440190+, chr21:8441129-8441743+, chr21:8441130-8441471+, chr21:8441197-8441742+, chr21:8441746-8441910+, chr21:8441747-8441911+, chr21:8441748-8441909+, chr21:8442043-8442204+, chr21:8442044-8442205+, chr21:8442045-8442197+, chr21:8442294-8442371+, chr21:8442377-8442793+, chr21:8442379-8442846+, chr21:8442411-8442848+, chr21:8442902-8443237+, chr21:8442940-8443083+, chr21:8442948-8443256+, chr21:8443189-8443254+, chr21:8443400-8444152+, chr21:8443401-8444153+, chr21:8443561-8444154+, chr21:8445748-8445948+, chr21:8445765-8445938+, chr21:8445830-8445937+, chr21:8445982-8446044+, chr21:8446053-8446217+ 2663 yes LSU-rRNA_Hsa not annotated lncRNA PCCR 21 15051690 15051725 1 1 chr21:15051690-15051725+ 39145 no potentially spurious not annotated lncRNA PCCR 21 16534450 16539161 1 3 chr21:16534450-16534743+, chr21:16535305-16535376+, chr21:16539102-16539161+ 7083 no ancient miRNA not annotated lncRNA PCCR 21 26169453 26170881 1 4 chr21:26169453-26169515+, chr21:26169669-26169713+, chr21:26170753-26170881+, chr21:26170800-26170868+ 2228 yes putative regulatory region not annotated lncRNA PCCR 21 31160930 31160956 1 1 chr21:31160930-31160956+ 2164 no putative regulatory region not annotated previously unannotated PCCR 21 33064756 33064800 1 1 chr21:33064756-33064800+ 66848 no potentially spurious not annotated lncRNA PCCR 21 35072749 35072925 1 2 chr21:35072749-35072784+, chr21:35072890-35072925+ 1565 no putative regulatory region not annotated previously unannotated PCCR 21 43363840 43363914 1 1 chr21:43363840-43363914+ 50578 no potentially spurious not annotated lncRNA PCCR 22 23034170 23037838 1 2 chr22:23034170-23034211+, chr22:23037785-23037838+ 1589 no putative regulatory region not annotated previously unannotated PCCR 22 26672136 26672180 -1 1 chr22:26672136-26672180- 15741 no potentially spurious not annotated lncRNA PCCR 22 27023184 27023252 1 1 chr22:27023184-27023252+ 5176 no potentially spurious not annotated lncRNA PCCR 22 29080202 29080576 -1 2 chr22:29080202-29080234-, chr22:29080550-29080576- 1857 no putative regulatory region not annotated previously unannotated PCCR 22 29480974 29481069 -1 1 chr22:29480974-29481069- 1900 yes putative regulatory region not annotated lncRNA PCCR 22 29825619 29825825 1 2 chr22:29825619-29825681+, chr22:29825799-29825825+ 956 no potentially spurious not annotated first 1000 PCCRs 22 38506019 38506525 1 4 chr22:38506019-38506195+, chr22:38506111-38506194+, chr22:38506295-38506363+, chr22:38506493-38506525+ 940 yes putative regulatory region not annotated first 1000 PCCRs 22 40636406 40636954 1 3 chr22:40636406-40636465+, chr22:40636864-40636890+, chr22:40636919-40636954+ 1941 yes putative regulatory region not annotated previously unannotated PCCR 22 42079657 42079683 1 1 chr22:42079657-42079683+ 1648 yes putative regulatory region not annotated previously unannotated PCCR 22 42615270 42615341 1 1 chr22:42615270-42615341+ 2376 no RNU12 snRNA not annotated lncRNA PCCR X 40418610 40418660 1 1 chrX:40418610-40418660+ 2197 no putative regulatory region not annotated previously unannotated PCCR X 50607740 50607787 1 1 chrX:50607740-50607787+ 7 no potentially spurious not annotated first 1000 PCCRs X 133538257 133538331 1 1 chrX:133538257-133538331+ 1987 no potentially spurious not annotated previously unannotated PCCR X 137860420 137860482 1 1 chrX:137860420-137860482+ 1184 no putative regulatory region not annotated previously unannotated PCCR 1 13893666 13893752 1 1 chr1:13893666-13893752+ 500 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 1 120557034 120558959 -1 4 chr1:120557034-120557159-, chr1:120557193-120558149-, chr1:120558303-120558365-, chr1:120558900-120558959- 455 yes PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 1 120641608 120641754 -1 1 chr1:120641608-120641754- 148 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 1 204274737 204277667 -1 2 chr1:204274737-204274811-, chr1:204277638-204277667- 865 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 2 130914079 130914189 1 1 chr2:130914079-130914189+ 775 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 2 200764538 200764715 1 2 chr2:200764538-200764567+, chr2:200764620-200764715+ 347 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 3 28576036 28576517 1 6 chr3:28576036-28576071+, chr3:28576068-28576235+, chr3:28576153-28576206+, chr3:28576312-28576392+, chr3:28576332-28576517+, chr3:28576349-28576411+ 1505 yes PhyloCSF signals are accounted for elsewhere on the list redundant lncRNA PCCR 3 28865227 28865292 1 1 chr3:28865227-28865292+ 1066 no PhyloCSF signals are accounted for elsewhere on the list redundant previously unannotated PCCR 3 88059269 88059508 1 3 chr3:88059269-88059412+, chr3:88059298-88059360+, chr3:88059467-88059508+ 300 yes PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 3 88113116 88113196 1 1 chr3:88113116-88113196+ 936 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 3 88126134 88139310 1 6 chr3:88126134-88126265+, chr3:88128808-88129011+, chr3:88129687-88129836+, chr3:88135077-88135202+, chr3:88138705-88139073+, chr3:88139275-88139310+ 388 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 3 128965505 128965690 -1 1 chr3:128965505-128965690- 612 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 3 141663155 141666935 1 2 chr3:141663155-141663280+, chr3:141666819-141666935+ 80 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 3 141713327 141738361 1 5 chr3:141713327-141713374+, chr3:141721005-141721052+, chr3:141721068-141721094+, chr3:141729293-141729376+, chr3:141738332-141738361+ 281 yes PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 4 2596075 2596335 1 1 chr4:2596075-2596335+ 700 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 4 55831348 55837348 1 2 chr4:55831348-55831464+, chr4:55837085-55837348+ 431 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 4 149351990 149433516 -1 3 chr4:149351990-149352067-, chr4:149433391-149433453-, chr4:149433469-149433516- 957 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 4 149351990 149352067 -1 1 chr4:149351990-149352067- 1155 no PhyloCSF signals are accounted for elsewhere on the list redundant lncRNA PCCR 4 149563803 149563850 -1 1 chr4:149563803-149563850- 10164 no PhyloCSF signals are accounted for elsewhere on the list redundant lncRNA PCCR 5 127798109 127798153 1 1 chr5:127798109-127798153+ 1389 no PhyloCSF signals are accounted for elsewhere on the list redundant lncRNA PCCR 5 140570090 140575575 -1 6 chr5:140570090-140570182-, chr5:140570282-140570401-, chr5:140573821-140573976-, chr5:140573989-140574033-, chr5:140575498-140575524-, chr5:140575546-140575575- 188 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 5 170245967 170246011 1 1 chr5:170245967-170246011+ 1438 no PhyloCSF signals are accounted for elsewhere on the list redundant lncRNA PCCR 6 9610632 9610706 -1 1 chr6:9610632-9610706- 883 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 6 9697636 9705441 -1 4 chr6:9697636-9697725-, chr6:9697744-9697779-, chr6:9705205-9705381-, chr6:9705391-9705441- 603 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 6 9819156 9819329 -1 2 chr6:9819156-9819287-, chr6:9819297-9819329- 587 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 6 9840243 9840436 -1 2 chr6:9840243-9840284-, chr6:9840377-9840436- 979 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 6 60425413 60430572 1 2 chr6:60425413-60425445+, chr6:60430396-60430572+ 507 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 6 60499345 60504670 1 2 chr6:60499345-60499458+, chr6:60504611-60504670+ 194 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 6 60531226 60531288 1 1 chr6:60531226-60531288+ 1471 no PhyloCSF signals are accounted for elsewhere on the list redundant previously unannotated PCCR 6 60544725 60544940 1 1 chr6:60544725-60544940+ 982 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 6 109254451 109270128 1 10 chr6:109254451-109254624+, chr6:109255380-109255409+, chr6:109255437-109255466+, chr6:109257544-109257630+, chr6:109257655-109257777+, chr6:109261886-109261966+, chr6:109262000-109262089+, chr6:109264823-109264954+, chr6:109267806-109267898+, chr6:109270051-109270128+ 241 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 6 109284468 109286489 1 3 chr6:109284468-109284560+, chr6:109285988-109286026+, chr6:109286355-109286489+ 218 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 7 7877341 7877535 1 1 chr7:7877341-7877535+ 702 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 7 135288238 135288396 -1 1 chr7:135288238-135288396- 339 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 8 822158 822193 1 1 chr8:822158-822193+ 10674 no PhyloCSF signals are accounted for elsewhere on the list redundant lncRNA PCCR 8 10474912 10483234 -1 3 chr8:10474912-10474953-, chr8:10474966-10475007-, chr8:10483193-10483234- 2083 no PhyloCSF signals are accounted for elsewhere on the list redundant lncRNA PCCR 8 54678466 54679932 1 3 chr8:54678466-54678531+, chr8:54679418-54679477+, chr8:54679819-54679932+ 939 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 8 54701510 54706652 1 3 chr8:54701510-54701596+, chr8:54701612-54701653+, chr8:54706440-54706652+ 525 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 8 54720129 54720308 1 1 chr8:54720129-54720308+ 898 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 8 54734595 54734741 1 1 chr8:54734595-54734741+ 779 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 8 143771490 143772485 1 4 chr8:143771490-143771621+, chr8:143771795-143771968+, chr8:143772040-143772258+, chr8:143772357-143772485+ 87 yes PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 9 27245683 27250106 -1 2 chr9:27245683-27245742-, chr9:27250074-27250106- 13799 no PhyloCSF signals are accounted for elsewhere on the list redundant lncRNA PCCR 9 61096906 61113907 -1 6 chr9:61096906-61096959-, chr9:61096975-61097037-, chr9:61104490-61104579-, chr9:61108221-61108253-, chr9:61108263-61108325-, chr9:61113782-61113907- 579 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 9 92157355 92157444 -1 1 chr9:92157355-92157444- 14212 no PhyloCSF signals are accounted for elsewhere on the list redundant lncRNA PCCR 10 23250457 23250664 -1 2 chr10:23250457-23250516-, chr10:23250629-23250664- 968 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 10 24367131 24367199 1 1 chr10:24367131-24367199+ 959 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 10 26577734 26577838 -1 1 chr10:26577734-26577838- 13580 no PhyloCSF signals are accounted for elsewhere on the list redundant lncRNA PCCR 10 38199286 38199408 1 1 chr10:38199286-38199408+ 24334 no PhyloCSF signals are accounted for elsewhere on the list redundant lncRNA PCCR 10 38210652 38210798 1 1 chr10:38210652-38210798+ 8695 no PhyloCSF signals are accounted for elsewhere on the list redundant lncRNA PCCR 10 38310049 38310231 1 1 chr10:38310049-38310231+ 2413 no PhyloCSF signals are accounted for elsewhere on the list redundant lncRNA PCCR 10 38333047 38333124 1 1 chr10:38333047-38333124+ 8338 no PhyloCSF signals are accounted for elsewhere on the list redundant lncRNA PCCR 10 113118930 113129936 1 19 chr10:113118930-113119019+, chr10:113119039-113119089+, chr10:113119058-113119087+, chr10:113119086-113119169+, chr10:113119150-113119224+, chr10:113119187-113119237+, chr10:113119764-113119907+, chr10:113120070-113120102+, chr10:113121389-113121433+, chr10:113123109-113123141+, chr10:113125290-113125319+, chr10:113125550-113125609+, chr10:113125570-113125617+, chr10:113125689-113125751+, chr10:113125850-113125888+, chr10:113126645-113126686+, chr10:113126822-113126866+, chr10:113126838-113126873+, chr10:113129859-113129936+ 464 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 10 122568594 122568902 1 3 chr10:122568594-122568653+, chr10:122568666-122568800+, chr10:122568831-122568902+ 210 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 10 122729428 122734656 1 2 chr10:122729428-122729454+, chr10:122734345-122734656+ 222 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 10 130079554 130079598 -1 1 chr10:130079554-130079598- 3222 no PhyloCSF signals are accounted for elsewhere on the list redundant lncRNA PCCR 11 94512607 94517677 1 2 chr11:94512607-94512645+, chr11:94517582-94517677+ 244 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 11 123591392 123591550 1 2 chr11:123591392-123591460+, chr11:123591518-123591550+ 983 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 12 3323318 3323512 -1 1 chr12:3323318-3323512- 712 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 12 3337119 3337208 -1 1 chr12:3337119-3337208- 955 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 12 25017177 25017290 1 1 chr12:25017177-25017290+ 242 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 12 40419182 40446630 1 29 chr12:40419182-40419217+, chr12:40420206-40420388+, chr12:40421228-40421254+, chr12:40421264-40421302+, chr12:40421837-40421896+, chr12:40422103-40422198+, chr12:40426419-40426505+, chr12:40426521-40426616+, chr12:40427385-40427504+, chr12:40427969-40428100+, chr12:40429537-40429677+, chr12:40431632-40431721+, chr12:40432393-40432431+, chr12:40432716-40432763+, chr12:40433763-40433909+, chr12:40436117-40436185+, chr12:40436614-40436736+, chr12:40438127-40438378+, chr12:40440572-40440622+, chr12:40440723-40440815+, chr12:40441073-40441207+, chr12:40441870-40442010+, chr12:40443073-40443174+, chr12:40443266-40443388+, chr12:40443395-40443451+, chr12:40444077-40444319+, chr12:40444389-40444547+, chr12:40445518-40445643+, chr12:40446487-40446630+ 178 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 12 48727481 48727516 1 1 chr12:48727481-48727516+ 4128 no PhyloCSF signals are accounted for elsewhere on the list redundant lncRNA PCCR 12 95377268 95382508 -1 2 chr12:95377268-95377297-, chr12:95382461-95382508- 5778 no PhyloCSF signals are accounted for elsewhere on the list redundant lncRNA PCCR 12 132115194 132134115 1 16 chr12:132115194-132115298+, chr12:132118828-132118872+, chr12:132118885-132118950+, chr12:132118961-132119104+, chr12:132119122-132119163+, chr12:132119853-132120002+, chr12:132120411-132120500+, chr12:132120500-132120604+, chr12:132121440-132121526+, chr12:132121508-132121588+, chr12:132125194-132125310+, chr12:132125313-132125408+, chr12:132125854-132125991+, chr12:132126011-132126052+, chr12:132127088-132127177+, chr12:132134005-132134115+ 696 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 13 51110832 51111907 -1 4 chr13:51110832-51111002-, chr13:51111024-51111131-, chr13:51111144-51111203-, chr13:51111878-51111907- 177 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 13 51816907 51817074 -1 2 chr13:51816907-51816966-, chr13:51817024-51817074- 13029 no PhyloCSF signals are accounted for elsewhere on the list redundant lncRNA PCCR 14 34982422 34982517 -1 1 chr14:34982422-34982517- 353 yes PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 15 86907112 86907228 1 1 chr15:86907112-86907228+ 94 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 15 98485898 98485978 -1 1 chr15:98485898-98485978- 710 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 15 98520256 98520381 -1 2 chr15:98520256-98520291-, chr15:98520310-98520381- 869 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 16 67223826 67227004 -1 2 chr16:67223826-67223924-, chr16:67226972-67227004- 758 yes PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 16 73792837 73792923 -1 1 chr16:73792837-73792923- 1261 no PhyloCSF signals are accounted for elsewhere on the list redundant previously unannotated PCCR 16 85357463 85357594 1 1 chr16:85357463-85357594+ 538 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 17 1228806 1229657 -1 3 chr17:1228806-1229189-, chr17:1229220-1229327-, chr17:1229472-1229657- 196 yes PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 17 27621191 27621271 1 1 chr17:27621191-27621271+ 659 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 17 43303149 43303256 -1 1 chr17:43303149-43303256- 229 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 19 6396383 6400239 1 3 chr19:6396383-6396484+, chr19:6400105-6400146+, chr19:6400159-6400239+ 152 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 19 28683074 28687844 -1 3 chr19:28683074-28683247-, chr19:28683249-28683329-, chr19:28687812-28687844- 962 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 21 16588460 16588760 1 4 chr21:16588460-16588516+, chr21:16588518-16588619+, chr21:16588649-16588756+, chr21:16588653-16588760+ 7260 no PhyloCSF signals are accounted for elsewhere on the list redundant lncRNA PCCR 21 36962033 36966698 -1 2 chr21:36962033-36962167-, chr21:36966429-36966698- 179 yes PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 22 21661475 21661561 -1 1 chr22:21661475-21661561- 684 no PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 22 30968833 30969812 1 4 chr22:30968833-30968889+, chr22:30969223-30969282+, chr22:30969349-30969519+, chr22:30969363-30969812+ 994 yes PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs 22 50694774 50731692 1 18 chr22:50694774-50695001+, chr22:50697426-50697539+, chr22:50697523-50697726+, chr22:50697681-50697710+, chr22:50698689-50698802+, chr22:50703859-50703939+, chr22:50704164-50704247+, chr22:50704737-50704865+, chr22:50704964-50705104+, chr22:50705497-50705532+, chr22:50705900-50706157+, chr22:50714916-50715056+, chr22:50715666-50715743+, chr22:50720183-50722438+, chr22:50730704-50731315+, chr22:50730831-50730905+, chr22:50731406-50731438+, chr22:50731633-50731692+ 251 yes PhyloCSF signals are accounted for elsewhere on the list redundant first 1000 PCCRs