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Landmark STSs Download table as text STS Identifier Location Multi-copy STS Start STS End STS Length Primer 1 Primer 2 PCR Conditions GenBank         Co-amplified Loci sY1247 Boundary between PAR1 and MSY   2709521 2709952 432 GAACTCTGCAAACCTCCTGG TTTTGAGGCGGAGTCTCG Standard PCR G75493   sY14 SRY exon 1   2715341 2715810 470 GAATATTCCCGCTCTCCGGA GCTGGTGCTCCATTCTTGAG Standard PCR G38356   sY274 RPS4Y1 intron 4   2781075 2781435 361 TTAAGGGGACAGTATTTCAACTTC CCACATTTAAACTGAGTACAGTCC Standard PCR G38351   sY238 ZFY intron 2   2906349 2906728 380 AACAAGTGAGTTCCACAGGG GCAAAGCAGCATTCAAAACA Standard PCR G38352   sY1254 TGIF2LY exon 1   3507551 3507931 381 GACCAATTTGTCTTTGTTGCG GCTGCTGAAGTCGGCGTA Standard PCR G75612   sY1240 PCDH11Y intron 3   5326058 5326442 385 GGGTCCTAGATAGGCTCCAAG TTCATGTTGGCAGTGATTGG Standard PCR G75486   sY1256 TSPY intron 5 * 6176391 6176650 260 CCCAGTGAAGAATCGTCCAT GCTAACAAGATGCACTGGGC Standard PCR G75613 9257539-9257798, 9277817-9278076, 9298163-9298422, 9916695-9916954, 9937027-9937286, 9957309-9957568, 9977622-9977881 sY276 AMELY exon 4/intron 4   6796679 6796894 216 CCTACCGCATCAGTGAATTTC TCTGTATGTGGAGTACACATGG Standard PCR G38362   sY1238 TBL1Y exon 11   6999460 6999834 375 GGTGTGCTAACATTGCATGG TTTGTTCCATTTCAGAGCGA Standard PCR G75611   sY637 PRKY 5' upstream of gene   7156520 7156812 293 CCTGCCTTTTTTAGTTTCCAGCA TACTGTGATAGGTAGAATAATGGC Standard PCR TranD in Schiebel et al, 1997   sY1319 PRKY 3' UTR   7305982 7306284 303 ACCTGTCTGGGAAACACCTC GAGCCCTACAACCAGCTTCA Standard PCR BV210882   sY1256 TSPY intron 5 * 9257539 9257798 260 CCCAGTGAAGAATCGTCCAT GCTAACAAGATGCACTGGGC Standard PCR G75613 6176391-6176650, 9277817-9278076, 9298163-9298422, 9916695-9916954, 9937027-9937286, 9957309-9957568, 9977622-9977881 sY1256 TSPY intron 5 * 9277817 9278076 260 CCCAGTGAAGAATCGTCCAT GCTAACAAGATGCACTGGGC Standard PCR G75613 6176391-6176650, 9257539-9257798, 9298163-9298422, 9916695-9916954, 9937027-9937286, 9957309-9957568, 9977622-9977881 sY1256 TSPY intron 5 * 9298163 9298422 260 CCCAGTGAAGAATCGTCCAT GCTAACAAGATGCACTGGGC Standard PCR G75613 6176391-6176650, 9257539-9257798, 9277817-9278076, 9916695-9916954, 9937027-9937286, 9957309-9957568, 9977622-9977881 sY1256 TSPY intron 5 * 9916695 9916954 260 CCCAGTGAAGAATCGTCCAT GCTAACAAGATGCACTGGGC Standard PCR G75613 6176391-6176650, 9257539-9257798, 9277817-9278076, 9298163-9298422, 9937027-9937286, 9957309-9957568, 9977622-9977881 sY1256 TSPY intron 5 * 9937027 9937286 260 CCCAGTGAAGAATCGTCCAT GCTAACAAGATGCACTGGGC Standard PCR G75613 6176391-6176650, 9257539-9257798, 9277817-9278076, 9298163-9298422, 9916695-9916954, 9957309-9957568, 9977622-9977881 sY1256 TSPY intron 5 * 9957309 9957568 260 CCCAGTGAAGAATCGTCCAT GCTAACAAGATGCACTGGGC Standard PCR G75613 6176391-6176650, 9257539-9257798, 9277817-9278076, 9298163-9298422, 9916695-9916954, 9937027-9937286, 9977622-9977881 sY1256 TSPY intron 5 * 9977622 9977881 260 CCCAGTGAAGAATCGTCCAT GCTAACAAGATGCACTGGGC Standard PCR G75613 6176391-6176650, 9257539-9257798, 9277817-9278076, 9298163-9298422, 9916695-9916954, 9937027-9937286, 9957309-9957568 sY1250 Proximal boundary of TSPY array   10009781 10010273 493 TTTTTCTAACCTTGCCTGCG TGCAGAGAAGCAGCCTACAA Standard PCR G75495   sY78 Alpha-satellite (DYZ3) sequences in centromeric heterochromatin * 10694559 10694732 174 TCCTTTTCCACAATAGACGTCA GGAAGTATCTTCCCTTAAAAGCTATG Standard PCR G38359 heterochromatic repeats in centromere sY1251 Boundary between centromere and Yq   12380015 12380436 422 GACTGGAGTGGAACGGTCTC TCACTTCCCTCCGATTTTCT Standard PCR G75496   sY1317 USP9Y exon 3   13330522 13331008 487 GAGATTACAGGCATGCACCA CCACACTTAGCCCACAGTCA Standard PCR BV210880   sY1316 USP9Y exon 26   13412695 13413157 463 AAGGCAGGTCTGATGCATGT AAAGAAAGCTGCCTCATAGCA Standard PCR BV210879   sY1234 DDX3Y (DBY) exon 9   13536063 13536412 350 TTACCCCTTTCACCCACTGA CCATAAACTACACAAGGACGAACT Standard PCR BV210873   sY1231 UTY exon 8   14015010 14015301 292 TTGCACCCGTAGTCAAATGT ACCCACAACTCAAATCGTCT Standard PCR BV210871   sY1230 TMSB4Y exon 1/intron 1   14325286 14325859 574 CTCTTCCAAGCCAGCCTTTA AACCTTTGCAAGCCACATTC Standard PCR BV210870   sY90 KALP intron 1   14376890 14377065 176 CAGTGCCCCATAACACTTTC ATGGTAATACAGCAGCTCGC Standard PCR G38357   sY1220 VCY exon 2 * 14607178 14607402 225 GAAGGGAGAAGCAGTTCGTG CTCAGTGGTTCCTCCAGCTC Standard PCR BV210869 14677874-14678098 sY1220 VCY exon 2 * 14677874 14678098 225 GAAGGGAGAAGCAGTTCGTG CTCAGTGGTTCCTCCAGCTC Standard PCR BV210869 14607178-14607402 sY1239 NLGN4Y exon 1   15143871 15144336 466 CCTAGCTCTCTTTTTCTTGCAG CAAATATCGCCAGTGAGGCT Standard PCR BV210876   sY210 STSP intron 5   16175655 16175919 265 ATCACTTGGCAGCTTTTCC GCACTGCAACTTTTATGCCT Standard PCR G38361   sY1235 XKRY exon 1 * 18390714 18390913 200 GACACCATGGCTGGAGTTTT GGATTGTATGTCCCACCTCG Standard PCR BV210874 18757642-18757841 sY1260 CDY2 exon 1 * 18500822 18501312 491 TTTCACTACACCAGTGGTGACC CTGGCAGCAAATAACTTGCA Standard PCR BV210877 18647241-18647731 sY1260 CDY2 exon 1 * 18647241 18647731 491 TTTCACTACACCAGTGGTGACC CTGGCAGCAAATAACTTGCA Standard PCR BV210877 18500822-18501312 sY1235 XKRY exon 1 * 18757642 18757841 200 GACACCATGGCTGGAGTTTT GGATTGTATGTCCCACCTCG Standard PCR BV210874 18390714-18390913 sY1237 HSFY exon 2 * 19169186 19169335 150 TAGAGCAGGGGCTAACATGG ATGGGGACAGATGAATTTGC Standard PCR BV210875 19393617-19393766 sY1237 HSFY exon 2 * 19393617 19393766 150 TAGAGCAGGGGCTAACATGG ATGGGGACAGATGAATTTGC Standard PCR BV210875 19169186-19169335 sY121 Immediately distal to palindrome P4   19511465 19511654 190 AGTTCACAGAATGGAGCCTG CCTGTGACTCCAGTTTGGTC Standard PCR G38341   sY1322 Between CYorf15A and CYorf15B   20211431 20211960 530 TGGAAACATTCTCAACAGGGA GGCATTTCTCGCATGAGTTT Standard PCR BV210883   sY280 JARID1D (SMCY) exon 9/intron 9   20353382 20353990 609 AACTGTACTCCTGGGTAGCCTG CTCCCGTGGGGATGAAGATAATA Standard PCR SH34Y/SH35Y in Agulnik et al, 1994   sY1233 EIF1AY exon 1   21146888 21147310 423 TCTCCGGTATCCTGATGGAG AAATAGGGCATTCCCAGCTC Standard PCR BV210872   sY1682 RPS4Y2 exon 1   21327391 21327827 437 GGTTGCACCGTAAAAGGAGA GTCTGTCAAGACAGCGTCCA Standard PCR BV444811   sY627 RBMY1 exon 12 * 22072997 22073100 104 GCACCTGCCACGCATATAGT GCAAACATGCTCACGATCAC Standard PCR G67175 22096537-22096640, 22120077-22120180, 22436029-22436132, 22459571-22459674, 22724495-22724598, 22972893-22972996 sY627 RBMY1 exon 12 * 22096537 22096640 104 GCACCTGCCACGCATATAGT GCAAACATGCTCACGATCAC Standard PCR G67175 22072997-22073100, 22120077-22120180, 22436029-22436132, 22459571-22459674, 22724495-22724598, 22972893-22972996 sY627 RBMY1 exon 12 * 22120077 22120180 104 GCACCTGCCACGCATATAGT GCAAACATGCTCACGATCAC Standard PCR G67175 22072997-22073100, 22096537-22096640, 22436029-22436132, 22459571-22459674, 22724495-22724598, 22972893-22972996 sY142 Proximal to AZFc   22387262 22387457 196 AGCTTCTATTCGAGGGCTTC CTCTCTGCAATCCCTGACAT Standard PCR G38345   sY627 RBMY1 exon 12 * 22436029 22436132 104 GCACCTGCCACGCATATAGT GCAAACATGCTCACGATCAC Standard PCR G67175 22072997-22073100, 22096537-22096640, 22120077-22120180, 22459571-22459674, 22724495-22724598, 22972893-22972996 sY627 RBMY1 exon 12 * 22459571 22459674 104 GCACCTGCCACGCATATAGT GCAAACATGCTCACGATCAC Standard PCR G67175 22072997-22073100, 22096537-22096640, 22120077-22120180, 22436029-22436132, 22724495-22724598, 22972893-22972996 sY1258 Boundary between unique sequence u1 and blue amplicon b1 in AZFc   22480301 22481268 968 AACCCCATCTCTAGCAAAAATATG TAGGTGACAGGGCAGGATTC Standard PCR G75499   sY1161 PRY intron 2 * 22648426 22648755 330 CGACACTTTTGGGAAGTTTCA TTGTGTCCAGTGGTGGCTTA Standard PCR G66148 23048718-23049047 sY627 RBMY1 exon 12 * 22724495 22724598 104 GCACCTGCCACGCATATAGT GCAAACATGCTCACGATCAC Standard PCR G67175 22072997-22073100, 22096537-22096640, 22120077-22120180, 22436029-22436132, 22459571-22459674, 22972893-22972996 sY1197 Internal boundary of palindrome P3   22933005 22933457 453 TCATTTGTGTCCTTCTCTTGGA CTAAGCCAGGAACTTGCCAC Standard PCR G67168   sY627 RBMY1 exon 12 * 22972893 22972996 104 GCACCTGCCACGCATATAGT GCAAACATGCTCACGATCAC Standard PCR G67175 22072997-22073100, 22096537-22096640, 22120077-22120180, 22436029-22436132, 22459571-22459674, 22724495-22724598 sY1161 PRY intron 2 * 23048718 23049047 330 CGACACTTTTGGGAAGTTTCA TTGTGTCCAGTGGTGGCTTA Standard PCR G66148 22648426-22648755 sY1191 Unique sequence u3 in AZFc   23285007 23285391 385 CCAGACGTTCTACCCTTTCG GAGCCGAGATCCAGTTACCA Standard PCR G73809   sY1035 BPY2 intron 5 * 23552607 23552954 348 TCAGTCCACCTATGTGCTGG ATTCCTTTCCTTGGGTGGAT Standard PCR BV210868 25186349-25186696, 25594480-25594827 sY1318 DAZ exon 11 * 23690490 23691020 531 TGATATCAGGTGATGCGTCC TGGCGTTAAGTAAACCTGGG Standard PCR BV210881 23840759-23841289, 25324214-25324744, 25456433-25456963 sY254 DAZ exon 3 * 23725582 23725961 380 GGGTGTTACCAGAAGGCAAA GAACCGTATCTACCAAAGCAGC Standard PCR G38349 23736422-23736801, 23747270-23747649, 23781963-23782342, 25361653-25362032, 25396350-25396729, 25407198-25407577 sY254 DAZ exon 3 * 23736422 23736801 380 GGGTGTTACCAGAAGGCAAA GAACCGTATCTACCAAAGCAGC Standard PCR G38349 23725582-23725961, 23747270-23747649, 23781963-23782342, 25361653-25362032, 25396350-25396729, 25407198-25407577 sY254 DAZ exon 3 * 23747270 23747649 380 GGGTGTTACCAGAAGGCAAA GAACCGTATCTACCAAAGCAGC Standard PCR G38349 23725582-23725961, 23736422-23736801, 23781963-23782342, 25361653-25362032, 25396350-25396729, 25407198-25407577 sY254 DAZ exon 3 * 23781963 23782342 380 GGGTGTTACCAGAAGGCAAA GAACCGTATCTACCAAAGCAGC Standard PCR G38349 23725582-23725961, 23736422-23736801, 23747270-23747649, 25361653-25362032, 25396350-25396729, 25407198-25407577 sY1318 DAZ exon 11 * 23840759 23841289 531 TGATATCAGGTGATGCGTCC TGGCGTTAAGTAAACCTGGG Standard PCR BV210881 23690490-23691020, 25324214-25324744, 25456433-25456963 sY1291 Red/gray boundary in AZFc   23914457 23914983 527 TAAAAGGCAGAACTGCCAGG GGGAGAAAAGTTCTGCAACG Standard PCR G72340   sY1125 Blue/gray boundaries in AZFc * 24029419 24029701 283 GTGGGGGTTTCACATTATGG GGTCACAGACTCACATTTAAGCA Standard PCR G67164 26751978-26752260 sY1054 Blue/yellow boundaries in AZFc * 24258107 24258446 340 ACCTAAGGGAACCCAGGAGA CGACACTTTTGGGAAGTTTCA Standard PCR G67163 26522696-26523035 sY1190 Yellow amplicon in AZFc * 24371542 24372207 666 TTGTGAAATGGTGGTGATGG CTGATTTGGAAACTCGTCCC Standard PCR G67165 26408950-26409615 sY1263 CDY1 exon 1/intron 1 * 24601321 24601787 467 TTAAGGAGCTTGCCTCATACAATC TAGAGCTTGCAAGAAGAGTCTGTT Standard PCR BV210878 26179412-26179878 sY1206 Yellow/green boundaries in AZFc * 24935833 24936226 394 ATTGATCTCCTTGGTTCCCC GACATGTGTGGCCAATTTGA Standard PCR G67171 25844981-25845374 sY1035 BPY2 intron 5 * 25186349 25186696 348 TCAGTCCACCTATGTGCTGG ATTCCTTTCCTTGGGTGGAT Standard PCR BV210868 23552607-23552954, 25594480-25594827 sY1318 DAZ exon 11 * 25324214 25324744 531 TGATATCAGGTGATGCGTCC TGGCGTTAAGTAAACCTGGG Standard PCR BV210881 23690490-23691020, 23840759-23841289, 25456433-25456963 sY254 DAZ exon 3 * 25361653 25362032 380 GGGTGTTACCAGAAGGCAAA GAACCGTATCTACCAAAGCAGC Standard PCR G38349 23725582-23725961, 23736422-23736801, 23747270-23747649, 23781963-23782342, 25396350-25396729, 25407198-25407577 sY254 DAZ exon 3 * 25396350 25396729 380 GGGTGTTACCAGAAGGCAAA GAACCGTATCTACCAAAGCAGC Standard PCR G38349 23725582-23725961, 23736422-23736801, 23747270-23747649, 23781963-23782342, 25361653-25362032, 25407198-25407577 sY254 DAZ exon 3 * 25407198 25407577 380 GGGTGTTACCAGAAGGCAAA GAACCGTATCTACCAAAGCAGC Standard PCR G38349 23725582-23725961, 23736422-23736801, 23747270-23747649, 23781963-23782342, 25361653-25362032, 25396350-25396729 sY1318 DAZ exon 11 * 25456433 25456963 531 TGATATCAGGTGATGCGTCC TGGCGTTAAGTAAACCTGGG Standard PCR BV210881 23690490-23691020, 23840759-23841289, 25324214-25324744 sY1035 BPY2 intron 5 * 25594480 25594827 348 TCAGTCCACCTATGTGCTGG ATTCCTTTCCTTGGGTGGAT Standard PCR BV210868 23552607-23552954, 25186349-25186696 sY1206 Yellow/green boundaries in AZFc * 25844981 25845374 394 ATTGATCTCCTTGGTTCCCC GACATGTGTGGCCAATTTGA Standard PCR G67171 24935833-24936226 sY1263 CDY1 exon 1/intron 1 * 26179412 26179878 467 TTAAGGAGCTTGCCTCATACAATC TAGAGCTTGCAAGAAGAGTCTGTT Standard PCR BV210878 24601321-24601787 sY1190 Yellow amplicon in AZFc * 26408950 26409615 666 TTGTGAAATGGTGGTGATGG CTGATTTGGAAACTCGTCCC Standard PCR G67165 24371542-24372207 sY1054 Blue/yellow boundaries in AZFc * 26522696 26523035 340 ACCTAAGGGAACCCAGGAGA CGACACTTTTGGGAAGTTTCA Standard PCR G67163 24258107-24258446 sY1125 Blue/gray boundaries in AZFc * 26751978 26752260 283 GTGGGGGTTTCACATTATGG GGTCACAGACTCACATTTAAGCA Standard PCR G67164 24029419-24029701 sY1201 Distal boundary of gray amplicon in AZFc   26866703 26867379 677 CCGACTTCCACAATGGCT GGGAGAAAAGTTCTGCAACG Standard PCR G67170   sY1246 Proximal portion of distal Yq heterochromatin * 27216146 27216314 169 ATCGTTTTGAATGGCGTCAA CTGCACCACTCCAATCCAA Standard PCR G75492 heterochromatic repeats in distal Yq sY160 Satellite-3 (DYZ1) sequences in distal Yq heterochromatin * 28219946 28220181 236 TACGGGTCTCGAATGGAATA TCATTGCATTCCTTTCCATT Standard PCR G38343 heterochromatic repeats in distal Yq sY1166 In MSY between distal Yq heterochromatin and PAR2   57390295 57390521 227 AGTCGGAGTCGGAGTGTGAT ATTCCATTGCTTTCCATTGC Standard PCR G66149   sY1273 Near boundary between MSY and PAR2   57442213 57442857 645 GAGCTGCAACATAACAGGCA AGGGGAACATCACACTCTGG Standard PCR G75500