MSY Breakpoint Mapper -- Landmark STSs (NCBI Build 38) http://breakpointmapper.wi.mit.edu/STS_table.txt sY1247 Boundary between PAR1 and MSY 2781333 2781765 433 GAACTCTGCAAACCTCCTGG TTTTGAGGCGGAGTCTCG Standard PCR G75493 sY14 SRY exon 1 2787066 2787535 470 GAATATTCCCGCTCTCCGGA GCTGGTGCTCCATTCTTGAG Standard PCR G38356 sY274 RPS4Y1 intron 4 2853034 2853394 361 TTAAGGGGACAGTATTTCAACTTC CCACATTTAAACTGAGTACAGTCC Standard PCR G38351 sY238 ZFY intron 2 2978076 2978433 358 AACAAGTGAGTTCCACAGGG GCAAAGCAGCATTCAAAACA Standard PCR G38352 sY1254 TGIF2LY exon 1 3579511 3579891 381 GACCAATTTGTCTTTGTTGCG GCTGCTGAAGTCGGCGTA Standard PCR G75612 sY1240 PCDH11Y intron 3 5398018 5398402 385 GGGTCCTAGATAGGCTCCAAG TTCATGTTGGCAGTGATTGG Standard PCR G75486 sY1256 TSPY intron 5 * 6248351 6248610 260 CCCAGTGAAGAATCGTCCAT GCTAACAAGATGCACTGGGC Standard PCR G75613 9359931-9360190, 9380209-9380468, 9400555-9400814, 9469087-9469346, 9489419-9489678, 9509701-9509960, 9530014-9530273 sY276 AMELY exon 4/intron 4 6868638 6868853 216 CCTACCGCATCAGTGAATTTC TCTGTATGTGGAGTACACATGG Standard PCR G38362 sY1238 TBL1Y exon 11 7071420 7071794 375 GGTGTGCTAACATTGCATGG TTTGTTCCATTTCAGAGCGA Standard PCR G75611 sY637 PRKY 5' upstream of gene 7228480 7228772 293 CCTGCCTTTTTTAGTTTCCAGCA TACTGTGATAGGTAGAATAATGGC Standard PCR TranD in Schiebel et al, 1997 sY1319 PRKY 3' UTR 7377942 7378244 303 ACCTGTCTGGGAAACACCTC GAGCCCTACAACCAGCTTCA Standard PCR BV210882 sY1256 TSPY intron 5 * 9359931 9360190 260 CCCAGTGAAGAATCGTCCAT GCTAACAAGATGCACTGGGC Standard PCR G75613 6248351-6248610, 9380209-9380468, 9400555-9400814, 9469087-9469346, 9489419-9489678, 9509701-9509960, 9530014-9530273 sY1256 TSPY intron 5 * 9380209 9380468 260 CCCAGTGAAGAATCGTCCAT GCTAACAAGATGCACTGGGC Standard PCR G75613 6248351-6248610, 9359931-9360190, 9400555-9400814, 9469087-9469346, 9489419-9489678, 9509701-9509960, 9530014-9530273 sY1256 TSPY intron 5 * 9400555 9400814 260 CCCAGTGAAGAATCGTCCAT GCTAACAAGATGCACTGGGC Standard PCR G75613 6248351-6248610, 9359931-9360190, 9380209-9380468, 9469087-9469346, 9489419-9489678, 9509701-9509960, 9530014-9530273 sY1256 TSPY intron 5 * 9469087 9469346 260 CCCAGTGAAGAATCGTCCAT GCTAACAAGATGCACTGGGC Standard PCR G75613 6248351-6248610, 9359931-9360190, 9380209-9380468, 9400555-9400814, 9489419-9489678, 9509701-9509960, 9530014-9530273 sY1256 TSPY intron 5 * 9489419 9489678 260 CCCAGTGAAGAATCGTCCAT GCTAACAAGATGCACTGGGC Standard PCR G75613 6248351-6248610, 9359931-9360190, 9380209-9380468, 9400555-9400814, 9469087-9469346, 9509701-9509960, 9530014-9530273 sY1256 TSPY intron 5 * 9509701 9509960 260 CCCAGTGAAGAATCGTCCAT GCTAACAAGATGCACTGGGC Standard PCR G75613 6248351-6248610, 9359931-9360190, 9380209-9380468, 9400555-9400814, 9469087-9469346, 9489419-9489678, 9530014-9530273 sY1256 TSPY intron 5 * 9530014 9530273 260 CCCAGTGAAGAATCGTCCAT GCTAACAAGATGCACTGGGC Standard PCR G75613 6248351-6248610, 9359931-9360190, 9380209-9380468, 9400555-9400814, 9469087-9469346, 9489419-9489678, 9509701-9509960 sY1250 Proximal boundary of TSPY array 9562173 9562665 493 TTTTTCTAACCTTGCCTGCG TGCAGAGAAGCAGCCTACAA Standard PCR G75495 sY78 Alpha-satellite (DYZ3) sequences in centromeric heterochromatin * 10594268 10594441 174 TCCTTTTCCACAATAGACGTCA GGAAGTATCTTCCCTTAAAAGCTATG Standard PCR G38359 heterochromatic repeats in centromere sY1251 Boundary between centromere and Yq 11749310 11749731 422 GACTGGAGTGGAACGGTCTC TCACTTCCCTCCGATTTTCT Standard PCR G75496 sY1317 USP9Y exon 3 12709196 12709682 487 GAGATTACAGGCATGCACCA CCACACTTAGCCCACAGTCA Standard PCR BV210880 sY1316 USP9Y exon 26 12791369 12791831 463 AAGGCAGGTCTGATGCATGT AAAGAAAGCTGCCTCATAGCA Standard PCR BV210879 sY1234 DDX3Y (DBY) exon 9 12914758 12915107 350 TTACCCCTTTCACCCACTGA CCATAAACTACACAAGGACGAACT Standard PCR BV210873 sY1231 UTY exon 8 13393737 13394028 292 TTGCACCCGTAGTCAAATGT ACCCACAACTCAAATCGTCT Standard PCR BV210871 sY1230 TMSB4Y exon 1/intron 1 13704013 13704586 574 CTCTTCCAAGCCAGCCTTTA AACCTTTGCAAGCCACATTC Standard PCR BV210870 sY90 KALP intron 1 13755616 13755791 176 CAGTGCCCCATAACACTTTC ATGGTAATACAGCAGCTCGC Standard PCR G38357 sY1220 VCY exon 2 * 13985905 13986129 225 GAAGGGAGAAGCAGTTCGTG CTCAGTGGTTCCTCCAGCTC Standard PCR BV210869 14056601-14056825 sY1220 VCY exon 2 * 14056601 14056825 225 GAAGGGAGAAGCAGTTCGTG CTCAGTGGTTCCTCCAGCTC Standard PCR BV210869 13985905-13986129 sY1239 NLGN4Y exon 1 14522598 14523063 466 CCTAGCTCTCTTTTTCTTGCAG CAAATATCGCCAGTGAGGCT Standard PCR BV210876 sY210 STSP intron 5 15554250 15554514 265 ATCACTTGGCAGCTTTTCC GCACTGCAACTTTTATGCCT Standard PCR G38361 sY1235 XKRY exon 1 * 17769441 17769640 200 GACACCATGGCTGGAGTTTT GGATTGTATGTCCCACCTCG Standard PCR BV210874 18136369-18136568 sY1260 CDY2 exon 1 * 17879549 17880039 491 TTTCACTACACCAGTGGTGACC CTGGCAGCAAATAACTTGCA Standard PCR BV210877 18025968-18026458 sY1260 CDY2 exon 1 * 18025968 18026458 491 TTTCACTACACCAGTGGTGACC CTGGCAGCAAATAACTTGCA Standard PCR BV210877 17879549-17880039 sY1235 XKRY exon 1 * 18136369 18136568 200 GACACCATGGCTGGAGTTTT GGATTGTATGTCCCACCTCG Standard PCR BV210874 17769441-17769640 sY1237 HSFY exon 2 * 18547913 18548062 150 TAGAGCAGGGGCTAACATGG ATGGGGACAGATGAATTTGC Standard PCR BV210875 18772344-18772493 sY1237 HSFY exon 2 * 18772344 18772493 150 TAGAGCAGGGGCTAACATGG ATGGGGACAGATGAATTTGC Standard PCR BV210875 18547913-18548062 sY121 Immediately distal to palindrome P4 18890192 18890381 190 AGTTCACAGAATGGAGCCTG CCTGTGACTCCAGTTTGGTC Standard PCR G38341 sY1322 Between CYorf15A and CYorf15B 19590158 19590687 530 TGGAAACATTCTCAACAGGGA GGCATTTCTCGCATGAGTTT Standard PCR BV210883 sY280 JARID1D (SMCY) exon 9/intron 9 19732108 19732716 609 AACTGTACTCCTGGGTAGCCTG CTCCCGTGGGGATGAAGATAATA Standard PCR SH34Y/SH35Y in Agulnik et al, 1994 sY1233 EIF1AY exon 1 20575615 20576037 423 TCTCCGGTATCCTGATGGAG AAATAGGGCATTCCCAGCTC Standard PCR BV210872 sY1682 RPS4Y2 exon 1 20756117 20756553 437 GGTTGCACCGTAAAAGGAGA GTCTGTCAAGACAGCGTCCA Standard PCR BV444811 sY627 RBMY1 exon 12 * 21501724 21501827 104 GCACCTGCCACGCATATAGT GCAAACATGCTCACGATCAC Standard PCR G67175 21525264-21525367, 21548804-21548907, 22417359-22417462, 21880495-21880598, 21904037-21904140, 22168961-22169064 sY627 RBMY1 exon 12 * 21525264 21525367 104 GCACCTGCCACGCATATAGT GCAAACATGCTCACGATCAC Standard PCR G67175 21501724-21501827, 21548804-21548907, 22417359-22417462, 21880495-21880598, 21904037-21904140, 22168961-22169064 sY627 RBMY1 exon 12 * 21548804 21548907 104 GCACCTGCCACGCATATAGT GCAAACATGCTCACGATCAC Standard PCR G67175 21501724-21501827, 21525264-21525367, 22417359-22417462, 21880495-21880598, 21904037-21904140, 22168961-22169064 sY142 Proximal to AZFc 21831728 21831923 196 AGCTTCTATTCGAGGGCTTC CTCTCTGCAATCCCTGACAT Standard PCR G38345 sY627 RBMY1 exon 12 * 21880495 21880598 104 GCACCTGCCACGCATATAGT GCAAACATGCTCACGATCAC Standard PCR G67175 21501724-21501827, 21525264-21525367, 21548804-21548907, 22417359-22417462, 21904037-21904140, 22168961-22169064 sY627 RBMY1 exon 12 * 21904037 21904140 104 GCACCTGCCACGCATATAGT GCAAACATGCTCACGATCAC Standard PCR G67175 21501724-21501827, 21525264-21525367, 21548804-21548907, 22417359-22417462, 21880495-21880598, 22168961-22169064 sY1258 Boundary between unique sequence u1 and blue amplicon b1 in AZFc 21924767 21925734 968 AACCCCATCTCTAGCAAAAATATG TAGGTGACAGGGCAGGATTC Standard PCR G75499 sY1161 PRY intron 2 * 22092892 22093221 330 CGACACTTTTGGGAAGTTTCA TTGTGTCCAGTGGTGGCTTA Standard PCR G66148 22493184-22493513 sY627 RBMY1 exon 12 * 22168961 22169064 104 GCACCTGCCACGCATATAGT GCAAACATGCTCACGATCAC Standard PCR G67175 21501724-21501827, 21525264-21525367, 21548804-21548907, 22417359-22417462, 21880495-21880598, 21904037-21904140 sY1197 Internal boundary of palindrome P3 22377471 22377923 453 TCATTTGTGTCCTTCTCTTGGA CTAAGCCAGGAACTTGCCAC Standard PCR G67168 sY627 RBMY1 exon 12 * 22417359 22417462 104 GCACCTGCCACGCATATAGT GCAAACATGCTCACGATCAC Standard PCR G67175 21501724-21501827, 21525264-21525367, 21548804-21548907, 21880495-21880598, 21904037-21904140, 22168961-22169064 sY1161 PRY intron 2 * 22493184 22493513 330 CGACACTTTTGGGAAGTTTCA TTGTGTCCAGTGGTGGCTTA Standard PCR G66148 22092892-22093221 sY1191 Unique sequence u3 in AZFc 22729473 22729857 385 CCAGACGTTCTACCCTTTCG GAGCCGAGATCCAGTTACCA Standard PCR G73809 sY1035 BPY2 intron 5 * 22997073 22997420 348 TCAGTCCACCTATGTGCTGG ATTCCTTTCCTTGGGTGGAT Standard PCR BV210868 25038946-25039293, 24630815-24631162 sY1318 DAZ exon 11 * 23134956 23135486 531 TGATATCAGGTGATGCGTCC TGGCGTTAAGTAAACCTGGG Standard PCR BV210881 23285225-23285755, 24900899-24901429, 24768680-24769210 sY254 DAZ exon 3 * 23170046 23170425 380 GGGTGTTACCAGAAGGCAAA GAACCGTATCTACCAAAGCAGC Standard PCR G38349 23226429-23226808, 24840816-24841195, 24851664-24852043, 23180886-23181265, 23191734-23192113, 24806117-24806496 sY254 DAZ exon 3 * 23180886 23181265 380 GGGTGTTACCAGAAGGCAAA GAACCGTATCTACCAAAGCAGC Standard PCR G38349 23226429-23226808, 24840816-24841195, 24851664-24852043, 23170046-23170425, 23191734-23192113, 24806117-24806496 sY254 DAZ exon 3 * 23191734 23192113 380 GGGTGTTACCAGAAGGCAAA GAACCGTATCTACCAAAGCAGC Standard PCR G38349 23226429-23226808, 24840816-24841195, 24851664-24852043, 23170046-23170425, 23180886-23181265, 24806117-24806496 sY254 DAZ exon 3 * 23226429 23226808 380 GGGTGTTACCAGAAGGCAAA GAACCGTATCTACCAAAGCAGC Standard PCR G38349 24840816-24841195, 24851664-24852043, 23170046-23170425, 23180886-23181265, 23191734-23192113, 24806117-24806496 sY1318 DAZ exon 11 * 23285225 23285755 531 TGATATCAGGTGATGCGTCC TGGCGTTAAGTAAACCTGGG Standard PCR BV210881 24900899-24901429, 23134956-23135486, 24768680-24769210 sY1291 Red/gray boundary in AZFc 23358923 23359449 527 TAAAAGGCAGAACTGCCAGG GGGAGAAAAGTTCTGCAACG Standard PCR G72340 sY1125 Blue/gray boundaries in AZFc * 23473885 23474167 283 GTGGGGGTTTCACATTATGG GGTCACAGACTCACATTTAAGCA Standard PCR G67164 26196444-26196726 sY1054 Blue/yellow boundaries in AZFc * 23702573 23702912 340 ACCTAAGGGAACCCAGGAGA CGACACTTTTGGGAAGTTTCA Standard PCR G67163 25967162-25967501 sY1190 Yellow amplicon in AZFc * 23816008 23816673 666 TTGTGAAATGGTGGTGATGG CTGATTTGGAAACTCGTCCC Standard PCR G67165 25853416-25854081 sY1263 CDY1 exon 1/intron 1 * 24045787 24046253 467 TTAAGGAGCTTGCCTCATACAATC TAGAGCTTGCAAGAAGAGTCTGTT Standard PCR BV210878 25623878-25624344 sY1206 Yellow/green boundaries in AZFc * 24380299 24380692 394 ATTGATCTCCTTGGTTCCCC GACATGTGTGGCCAATTTGA Standard PCR G67171 25289447-25289840 sY1035 BPY2 intron 5 * 24630815 24631162 348 TCAGTCCACCTATGTGCTGG ATTCCTTTCCTTGGGTGGAT Standard PCR BV210868 25038946-25039293, 22997073-22997420 sY1318 DAZ exon 11 * 24768680 24769210 531 TGATATCAGGTGATGCGTCC TGGCGTTAAGTAAACCTGGG Standard PCR BV210881 23285225-23285755, 24900899-24901429, 23134956-23135486 sY254 DAZ exon 3 * 24806117 24806496 380 GGGTGTTACCAGAAGGCAAA GAACCGTATCTACCAAAGCAGC Standard PCR G38349 23226429-23226808, 24840816-24841195, 24851664-24852043, 23170046-23170425, 23180886-23181265, 23191734-23192113 sY254 DAZ exon 3 * 24840816 24841195 380 GGGTGTTACCAGAAGGCAAA GAACCGTATCTACCAAAGCAGC Standard PCR G38349 23226429-23226808, 24851664-24852043, 23170046-23170425, 23180886-23181265, 23191734-23192113, 24806117-24806496 sY254 DAZ exon 3 * 24851664 24852043 380 GGGTGTTACCAGAAGGCAAA GAACCGTATCTACCAAAGCAGC Standard PCR G38349 23226429-23226808, 24840816-24841195, 23170046-23170425, 23180886-23181265, 23191734-23192113, 24806117-24806496 sY1318 DAZ exon 11 * 24900899 24901429 531 TGATATCAGGTGATGCGTCC TGGCGTTAAGTAAACCTGGG Standard PCR BV210881 23285225-23285755, 23134956-23135486, 24768680-24769210 sY1035 BPY2 intron 5 * 25038946 25039293 348 TCAGTCCACCTATGTGCTGG ATTCCTTTCCTTGGGTGGAT Standard PCR BV210868 22997073-22997420, 24630815-24631162 sY1206 Yellow/green boundaries in AZFc * 25289447 25289840 394 ATTGATCTCCTTGGTTCCCC GACATGTGTGGCCAATTTGA Standard PCR G67171 24380299-24380692 sY1263 CDY1 exon 1/intron 1 * 25623878 25624344 467 TTAAGGAGCTTGCCTCATACAATC TAGAGCTTGCAAGAAGAGTCTGTT Standard PCR BV210878 24045787-24046253 sY1190 Yellow amplicon in AZFc * 25853416 25854081 666 TTGTGAAATGGTGGTGATGG CTGATTTGGAAACTCGTCCC Standard PCR G67165 23816008-23816673 sY1054 Blue/yellow boundaries in AZFc * 25967162 25967501 340 ACCTAAGGGAACCCAGGAGA CGACACTTTTGGGAAGTTTCA Standard PCR G67163 23702573-23702912 sY1125 Blue/gray boundaries in AZFc * 26196444 26196726 283 GTGGGGGTTTCACATTATGG GGTCACAGACTCACATTTAAGCA Standard PCR G67164 23473885-23474167 sY1201 Distal boundary of gray amplicon in AZFc 26311169 26311845 677 CCGACTTCCACAATGGCT GGGAGAAAAGTTCTGCAACG Standard PCR G67170 sY1246 Proximal portion of distal Yq heterochromatin * 26660612 26660780 169 ATCGTTTTGAATGGCGTCAA CTGCACCACTCCAATCCAA Standard PCR G75492 heterochromatic repeats in distal Yq sY160 Satellite-3 (DYZ1) sequences in distal Yq heterochromatin * 50000000 50000235 236 TACGGGTCTCGAATGGAATA TCATTGCATTCCTTTCCATT Standard PCR G38343 heterochromatic repeats in distal Yq sY1166 In MSY between distal Yq heterochromatin and PAR2 56834761 56834987 227 AGTCGGAGTCGGAGTGTGAT ATTCCATTGCTTTCCATTGC Standard PCR G66149 sY1273 Near boundary between MSY and PAR2 56886679 56887323 645 GAGCTGCAACATAACAGGCA AGGGGAACATCACACTCTGG Standard PCR G75500