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Landmark STSs             (NCBI Build 38)
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STS IdentifierLocationMulti-copySTS StartSTS EndSTS LengthPrimer 1Primer 2PCR ConditionsGenBank         Co-amplified Loci
sY1247Boundary between PAR1 and MSY
 
27813332781765433GAACTCTGCAAACCTCCTGGTTTTGAGGCGGAGTCTCGStandard PCRG75493 
sY14SRY exon 1
 
27870662787535470GAATATTCCCGCTCTCCGGAGCTGGTGCTCCATTCTTGAGStandard PCRG38356 
sY274RPS4Y1 intron 4
 
28530342853394361TTAAGGGGACAGTATTTCAACTTCCCACATTTAAACTGAGTACAGTCCStandard PCRG38351 
sY238ZFY intron 2
 
29780762978433358AACAAGTGAGTTCCACAGGGGCAAAGCAGCATTCAAAACAStandard PCRG38352 
sY1254TGIF2LY exon 1
 
35795113579891381GACCAATTTGTCTTTGTTGCGGCTGCTGAAGTCGGCGTAStandard PCRG75612 
sY1240PCDH11Y intron 3
 
53980185398402385GGGTCCTAGATAGGCTCCAAGTTCATGTTGGCAGTGATTGGStandard PCRG75486 
sY1256TSPY intron 5
*
62483516248610260CCCAGTGAAGAATCGTCCATGCTAACAAGATGCACTGGGCStandard PCRG756139359931-9360190, 9380209-9380468, 9400555-9400814, 9469087-9469346, 9489419-9489678, 9509701-9509960, 9530014-9530273
sY276AMELY exon 4/intron 4
 
68686386868853216CCTACCGCATCAGTGAATTTCTCTGTATGTGGAGTACACATGGStandard PCRG38362 
sY1238TBL1Y exon 11
 
70714207071794375GGTGTGCTAACATTGCATGGTTTGTTCCATTTCAGAGCGAStandard PCRG75611 
sY637PRKY 5' upstream of gene
 
72284807228772293CCTGCCTTTTTTAGTTTCCAGCATACTGTGATAGGTAGAATAATGGCStandard PCRTranD in Schiebel et al, 1997 
sY1319PRKY 3' UTR
 
73779427378244303ACCTGTCTGGGAAACACCTCGAGCCCTACAACCAGCTTCAStandard PCRBV210882 
sY1256TSPY intron 5
*
93599319360190260CCCAGTGAAGAATCGTCCATGCTAACAAGATGCACTGGGCStandard PCRG756136248351-6248610, 9380209-9380468, 9400555-9400814, 9469087-9469346, 9489419-9489678, 9509701-9509960, 9530014-9530273
sY1256TSPY intron 5
*
93802099380468260CCCAGTGAAGAATCGTCCATGCTAACAAGATGCACTGGGCStandard PCRG756136248351-6248610, 9359931-9360190, 9400555-9400814, 9469087-9469346, 9489419-9489678, 9509701-9509960, 9530014-9530273
sY1256TSPY intron 5
*
94005559400814260CCCAGTGAAGAATCGTCCATGCTAACAAGATGCACTGGGCStandard PCRG756136248351-6248610, 9359931-9360190, 9380209-9380468, 9469087-9469346, 9489419-9489678, 9509701-9509960, 9530014-9530273
sY1256TSPY intron 5
*
94690879469346260CCCAGTGAAGAATCGTCCATGCTAACAAGATGCACTGGGCStandard PCRG756136248351-6248610, 9359931-9360190, 9380209-9380468, 9400555-9400814, 9489419-9489678, 9509701-9509960, 9530014-9530273
sY1256TSPY intron 5
*
94894199489678260CCCAGTGAAGAATCGTCCATGCTAACAAGATGCACTGGGCStandard PCRG756136248351-6248610, 9359931-9360190, 9380209-9380468, 9400555-9400814, 9469087-9469346, 9509701-9509960, 9530014-9530273
sY1256TSPY intron 5
*
95097019509960260CCCAGTGAAGAATCGTCCATGCTAACAAGATGCACTGGGCStandard PCRG756136248351-6248610, 9359931-9360190, 9380209-9380468, 9400555-9400814, 9469087-9469346, 9489419-9489678, 9530014-9530273
sY1256TSPY intron 5
*
95300149530273260CCCAGTGAAGAATCGTCCATGCTAACAAGATGCACTGGGCStandard PCRG756136248351-6248610, 9359931-9360190, 9380209-9380468, 9400555-9400814, 9469087-9469346, 9489419-9489678, 9509701-9509960
sY1250Proximal boundary of TSPY array
 
95621739562665493TTTTTCTAACCTTGCCTGCGTGCAGAGAAGCAGCCTACAAStandard PCRG75495 
sY78Alpha-satellite (DYZ3) sequences in centromeric heterochromatin
*
1059426810594441174TCCTTTTCCACAATAGACGTCAGGAAGTATCTTCCCTTAAAAGCTATGStandard PCRG38359heterochromatic repeats in centromere
sY1251Boundary between centromere and Yq
 
1174931011749731422GACTGGAGTGGAACGGTCTCTCACTTCCCTCCGATTTTCTStandard PCRG75496 
sY1317USP9Y exon 3
 
1270919612709682487GAGATTACAGGCATGCACCACCACACTTAGCCCACAGTCAStandard PCRBV210880 
sY1316USP9Y exon 26
 
1279136912791831463AAGGCAGGTCTGATGCATGTAAAGAAAGCTGCCTCATAGCAStandard PCRBV210879 
sY1234DDX3Y (DBY) exon 9
 
1291475812915107350TTACCCCTTTCACCCACTGACCATAAACTACACAAGGACGAACTStandard PCRBV210873 
sY1231UTY exon 8
 
1339373713394028292TTGCACCCGTAGTCAAATGTACCCACAACTCAAATCGTCTStandard PCRBV210871 
sY1230TMSB4Y exon 1/intron 1
 
1370401313704586574CTCTTCCAAGCCAGCCTTTAAACCTTTGCAAGCCACATTCStandard PCRBV210870 
sY90KALP intron 1
 
1375561613755791176CAGTGCCCCATAACACTTTCATGGTAATACAGCAGCTCGCStandard PCRG38357 
sY1220VCY exon 2
*
1398590513986129225GAAGGGAGAAGCAGTTCGTGCTCAGTGGTTCCTCCAGCTCStandard PCRBV21086914056601-14056825
sY1220VCY exon 2
*
1405660114056825225GAAGGGAGAAGCAGTTCGTGCTCAGTGGTTCCTCCAGCTCStandard PCRBV21086913985905-13986129
sY1239NLGN4Y exon 1
 
1452259814523063466CCTAGCTCTCTTTTTCTTGCAGCAAATATCGCCAGTGAGGCTStandard PCRBV210876 
sY210STSP intron 5
 
1555425015554514265ATCACTTGGCAGCTTTTCCGCACTGCAACTTTTATGCCTStandard PCRG38361 
sY1235XKRY exon 1
*
1776944117769640200GACACCATGGCTGGAGTTTTGGATTGTATGTCCCACCTCGStandard PCRBV21087418136369-18136568
sY1260CDY2 exon 1
*
1787954917880039491TTTCACTACACCAGTGGTGACCCTGGCAGCAAATAACTTGCAStandard PCRBV21087718025968-18026458
sY1260CDY2 exon 1
*
1802596818026458491TTTCACTACACCAGTGGTGACCCTGGCAGCAAATAACTTGCAStandard PCRBV21087717879549-17880039
sY1235XKRY exon 1
*
1813636918136568200GACACCATGGCTGGAGTTTTGGATTGTATGTCCCACCTCGStandard PCRBV21087417769441-17769640
sY1237HSFY exon 2
*
1854791318548062150TAGAGCAGGGGCTAACATGGATGGGGACAGATGAATTTGCStandard PCRBV21087518772344-18772493
sY1237HSFY exon 2
*
1877234418772493150TAGAGCAGGGGCTAACATGGATGGGGACAGATGAATTTGCStandard PCRBV21087518547913-18548062
sY121Immediately distal to palindrome P4
 
1889019218890381190AGTTCACAGAATGGAGCCTGCCTGTGACTCCAGTTTGGTCStandard PCRG38341 
sY1322Between CYorf15A and CYorf15B
 
1959015819590687530TGGAAACATTCTCAACAGGGAGGCATTTCTCGCATGAGTTTStandard PCRBV210883 
sY280JARID1D (SMCY) exon 9/intron 9
 
1973210819732716609AACTGTACTCCTGGGTAGCCTGCTCCCGTGGGGATGAAGATAATAStandard PCRSH34Y/SH35Y in Agulnik et al, 1994 
sY1233EIF1AY exon 1
 
2057561520576037423TCTCCGGTATCCTGATGGAGAAATAGGGCATTCCCAGCTCStandard PCRBV210872 
sY1682RPS4Y2 exon 1
 
2075611720756553437GGTTGCACCGTAAAAGGAGAGTCTGTCAAGACAGCGTCCAStandard PCRBV444811 
sY627RBMY1 exon 12
*
2150172421501827104GCACCTGCCACGCATATAGTGCAAACATGCTCACGATCACStandard PCRG6717521525264-21525367, 21548804-21548907, 22417359-22417462, 21880495-21880598, 21904037-21904140, 22168961-22169064
sY627RBMY1 exon 12
*
2152526421525367104GCACCTGCCACGCATATAGTGCAAACATGCTCACGATCACStandard PCRG6717521501724-21501827, 21548804-21548907, 22417359-22417462, 21880495-21880598, 21904037-21904140, 22168961-22169064
sY627RBMY1 exon 12
*
2154880421548907104GCACCTGCCACGCATATAGTGCAAACATGCTCACGATCACStandard PCRG6717521501724-21501827, 21525264-21525367, 22417359-22417462, 21880495-21880598, 21904037-21904140, 22168961-22169064
sY142Proximal to AZFc
 
2183172821831923196AGCTTCTATTCGAGGGCTTCCTCTCTGCAATCCCTGACATStandard PCRG38345 
sY627RBMY1 exon 12
*
2188049521880598104GCACCTGCCACGCATATAGTGCAAACATGCTCACGATCACStandard PCRG6717521501724-21501827, 21525264-21525367, 21548804-21548907, 22417359-22417462, 21904037-21904140, 22168961-22169064
sY627RBMY1 exon 12
*
2190403721904140104GCACCTGCCACGCATATAGTGCAAACATGCTCACGATCACStandard PCRG6717521501724-21501827, 21525264-21525367, 21548804-21548907, 22417359-22417462, 21880495-21880598, 22168961-22169064
sY1258Boundary between unique sequence u1 and blue amplicon b1 in AZFc
 
2192476721925734968AACCCCATCTCTAGCAAAAATATGTAGGTGACAGGGCAGGATTCStandard PCRG75499 
sY1161PRY intron 2
*
2209289222093221330CGACACTTTTGGGAAGTTTCATTGTGTCCAGTGGTGGCTTAStandard PCRG6614822493184-22493513
sY627RBMY1 exon 12
*
2216896122169064104GCACCTGCCACGCATATAGTGCAAACATGCTCACGATCACStandard PCRG6717521501724-21501827, 21525264-21525367, 21548804-21548907, 22417359-22417462, 21880495-21880598, 21904037-21904140
sY1197Internal boundary of palindrome P3
 
2237747122377923453TCATTTGTGTCCTTCTCTTGGACTAAGCCAGGAACTTGCCACStandard PCRG67168 
sY627RBMY1 exon 12
*
2241735922417462104GCACCTGCCACGCATATAGTGCAAACATGCTCACGATCACStandard PCRG6717521501724-21501827, 21525264-21525367, 21548804-21548907, 21880495-21880598, 21904037-21904140, 22168961-22169064
sY1161PRY intron 2
*
2249318422493513330CGACACTTTTGGGAAGTTTCATTGTGTCCAGTGGTGGCTTAStandard PCRG6614822092892-22093221
sY1191Unique sequence u3 in AZFc
 
2272947322729857385CCAGACGTTCTACCCTTTCGGAGCCGAGATCCAGTTACCAStandard PCRG73809 
sY1035BPY2 intron 5
*
2299707322997420348TCAGTCCACCTATGTGCTGGATTCCTTTCCTTGGGTGGATStandard PCRBV21086825038946-25039293, 24630815-24631162
sY1318DAZ exon 11
*
2313495623135486531TGATATCAGGTGATGCGTCCTGGCGTTAAGTAAACCTGGGStandard PCRBV21088123285225-23285755, 24900899-24901429, 24768680-24769210
sY254DAZ exon 3
*
2317004623170425380GGGTGTTACCAGAAGGCAAAGAACCGTATCTACCAAAGCAGCStandard PCRG3834923226429-23226808, 24840816-24841195, 24851664-24852043, 23180886-23181265, 23191734-23192113, 24806117-24806496
sY254DAZ exon 3
*
2318088623181265380GGGTGTTACCAGAAGGCAAAGAACCGTATCTACCAAAGCAGCStandard PCRG3834923226429-23226808, 24840816-24841195, 24851664-24852043, 23170046-23170425, 23191734-23192113, 24806117-24806496
sY254DAZ exon 3
*
2319173423192113380GGGTGTTACCAGAAGGCAAAGAACCGTATCTACCAAAGCAGCStandard PCRG3834923226429-23226808, 24840816-24841195, 24851664-24852043, 23170046-23170425, 23180886-23181265, 24806117-24806496
sY254DAZ exon 3
*
2322642923226808380GGGTGTTACCAGAAGGCAAAGAACCGTATCTACCAAAGCAGCStandard PCRG3834924840816-24841195, 24851664-24852043, 23170046-23170425, 23180886-23181265, 23191734-23192113, 24806117-24806496
sY1318DAZ exon 11
*
2328522523285755531TGATATCAGGTGATGCGTCCTGGCGTTAAGTAAACCTGGGStandard PCRBV21088124900899-24901429, 23134956-23135486, 24768680-24769210
sY1291Red/gray boundary in AZFc
 
2335892323359449527TAAAAGGCAGAACTGCCAGGGGGAGAAAAGTTCTGCAACGStandard PCRG72340 
sY1125Blue/gray boundaries in AZFc
*
2347388523474167283GTGGGGGTTTCACATTATGGGGTCACAGACTCACATTTAAGCAStandard PCRG6716426196444-26196726
sY1054Blue/yellow boundaries in AZFc
*
2370257323702912340ACCTAAGGGAACCCAGGAGACGACACTTTTGGGAAGTTTCAStandard PCRG6716325967162-25967501
sY1190Yellow amplicon in AZFc
*
2381600823816673666TTGTGAAATGGTGGTGATGGCTGATTTGGAAACTCGTCCCStandard PCRG6716525853416-25854081
sY1263CDY1 exon 1/intron 1
*
2404578724046253467TTAAGGAGCTTGCCTCATACAATCTAGAGCTTGCAAGAAGAGTCTGTTStandard PCRBV21087825623878-25624344
sY1206Yellow/green boundaries in AZFc
*
2438029924380692394ATTGATCTCCTTGGTTCCCCGACATGTGTGGCCAATTTGAStandard PCRG6717125289447-25289840
sY1035BPY2 intron 5
*
2463081524631162348TCAGTCCACCTATGTGCTGGATTCCTTTCCTTGGGTGGATStandard PCRBV21086825038946-25039293, 22997073-22997420
sY1318DAZ exon 11
*
2476868024769210531TGATATCAGGTGATGCGTCCTGGCGTTAAGTAAACCTGGGStandard PCRBV21088123285225-23285755, 24900899-24901429, 23134956-23135486
sY254DAZ exon 3
*
2480611724806496380GGGTGTTACCAGAAGGCAAAGAACCGTATCTACCAAAGCAGCStandard PCRG3834923226429-23226808, 24840816-24841195, 24851664-24852043, 23170046-23170425, 23180886-23181265, 23191734-23192113
sY254DAZ exon 3
*
2484081624841195380GGGTGTTACCAGAAGGCAAAGAACCGTATCTACCAAAGCAGCStandard PCRG3834923226429-23226808, 24851664-24852043, 23170046-23170425, 23180886-23181265, 23191734-23192113, 24806117-24806496
sY254DAZ exon 3
*
2485166424852043380GGGTGTTACCAGAAGGCAAAGAACCGTATCTACCAAAGCAGCStandard PCRG3834923226429-23226808, 24840816-24841195, 23170046-23170425, 23180886-23181265, 23191734-23192113, 24806117-24806496
sY1318DAZ exon 11
*
2490089924901429531TGATATCAGGTGATGCGTCCTGGCGTTAAGTAAACCTGGGStandard PCRBV21088123285225-23285755, 23134956-23135486, 24768680-24769210
sY1035BPY2 intron 5
*
2503894625039293348TCAGTCCACCTATGTGCTGGATTCCTTTCCTTGGGTGGATStandard PCRBV21086822997073-22997420, 24630815-24631162
sY1206Yellow/green boundaries in AZFc
*
2528944725289840394ATTGATCTCCTTGGTTCCCCGACATGTGTGGCCAATTTGAStandard PCRG6717124380299-24380692
sY1263CDY1 exon 1/intron 1
*
2562387825624344467TTAAGGAGCTTGCCTCATACAATCTAGAGCTTGCAAGAAGAGTCTGTTStandard PCRBV21087824045787-24046253
sY1190Yellow amplicon in AZFc
*
2585341625854081666TTGTGAAATGGTGGTGATGGCTGATTTGGAAACTCGTCCCStandard PCRG6716523816008-23816673
sY1054Blue/yellow boundaries in AZFc
*
2596716225967501340ACCTAAGGGAACCCAGGAGACGACACTTTTGGGAAGTTTCAStandard PCRG6716323702573-23702912
sY1125Blue/gray boundaries in AZFc
*
2619644426196726283GTGGGGGTTTCACATTATGGGGTCACAGACTCACATTTAAGCAStandard PCRG6716423473885-23474167
sY1201Distal boundary of gray amplicon in AZFc
 
2631116926311845677CCGACTTCCACAATGGCTGGGAGAAAAGTTCTGCAACGStandard PCRG67170 
sY1246Proximal portion of distal Yq heterochromatin
*
2666061226660780169ATCGTTTTGAATGGCGTCAACTGCACCACTCCAATCCAAStandard PCRG75492heterochromatic repeats in distal Yq
sY160Satellite-3 (DYZ1) sequences in distal Yq heterochromatin
*
5000000050000235236TACGGGTCTCGAATGGAATATCATTGCATTCCTTTCCATTStandard PCRG38343heterochromatic repeats in distal Yq
sY1166In MSY between distal Yq heterochromatin and PAR2
 
5683476156834987227AGTCGGAGTCGGAGTGTGATATTCCATTGCTTTCCATTGCStandard PCRG66149 
sY1273Near boundary between MSY and PAR2
 
5688667956887323645GAGCTGCAACATAACAGGCAAGGGGAACATCACACTCTGGStandard PCRG75500