SNP sequences.docx

SNP sequences.docx

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SNPsequences

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Sequenceinformationforthe167Ychromosomemarkersdescribedin:

Underhilletal（2000）.Ychromosomesequencevariationandthehistoryofhumanpopulations.NatureGenet.Nov.issue

STSsequences（onestrandonly）forpolymorphicYsequences.

Primerregions=lowercase;Reversecomplimentmadetogenerate5'-3'ReversePCRprimersequenceforcomplimentarystrand.

IUBcodedefinespolymorphicsite

R=AorG（puRine）

Y=CorT（pYrimidine）

K=GorT（Keto）

M=AorC（aMino）

S=GorC（Strong-3Hbonds）

W=AorT（Weak-2Hbonds）

H=A,CorT

Markernumbersdiscontinuousbecauseofselectedremovalofnumberedmicrosatilliteandhomopolymerpolymorphisms

M1=DYS287=（YAP）Hammer&Horai1995Am.J.HumGenet.56:

951-962.YAPMINUSREGION=150bp.The•=Aluinsertionsite

caggggaagataaagaaataTA•ACATAAGAAGATCAAACCTGTTTTAACTTTAACTTGGTTGGAGTTGGCCCTGGAATAATTGTCCATGATTCTGGAGGGCGTCGTGTTCTTTTGATCCTAGTGTGATGAatccatccccttttagcagt

YAP.1:

5’-caggggaagataaagaaata-3’

YAP.2:

5’-actgctaaaaggggatggat-3’

ALUinsertionelement.（291bp）LargefontboldallelesarespecifictotheDYS287Aluelement.（Hammer1994Mol.Biol.Evol.11:

749-761）

GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGCGGGCGCCTGTATTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCATTGCAGTCCGCAGTCCGGCCTGGGCAACAGAGCGAGACTCCGTCTCAAA…polyA

YAPINSERTIONsitelocatedatposition253•withinfragmentfromR368toAR243withintheAluelement（italics）.LargefontboldallelesarespecifictotheDYS287Aluelement.

tcacataatttcattttcccTATTGCAGATATGTTTTCCTGCATTTGTTAAGGAACAAGGGTCTTGAGAGGGAGAGCTTTTTGTCTTAAAGGGGAAGAGATACTTCTGTGAGGCTAAGAGTTGCCTTTGACTTTGGAGATCTTCACAGGGTATAATAAGACAAGCATCAAAGGTAATAGTTTGGGGTCAACTTGACCTGGTTACGTTAATAAGGAGAGGACTAGCAATAGcaggggaagataaagaaataTA•GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGCGGGCGCCTGTATTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCATtgcagtccgcagtccggccGTCCGGCCTGGGCAACAGAGCGAGACTCCGTCTCAAA…polyAtail

R3685’-3’:

tcacataatttcattttccc

AR2435’-3’:

ggccggactgcggactgcaA（3’ntmatchesuniqueTwithinDYS287Aluforspecificity）

AR2375’-3’:

cgccattgcagtccgcagtc

YAP.15’-3’:

caggggaagataaagaaata

M2=DYS271（209bp）AtoGatposition168

aggcactggtcagaatgaagTGAATGGCACACAGGACAAGTCCAGACCCAGGAAGGTCCAGTAACATGGGAGAAGAACGGAAGGAGTTCTAAAATTCAGGGCTCCCTTGGGCTCCCCTGTTTAAAAATGTAGGTTTTATTATTATATTTCATTGTTAACAAAAGTCCRTGAGATCTGTGGAGGATAAAGggggagctgtattttccatt

Rev5'-3'=aatggaaaatacagctcccc

M3=DYS199（241bp）CtoTatposition181

taatcagtctcctcccagcaAGTGATATGCAACTGAGATTCCTTATGACACATCTGAACACTAGTGGATTTGCTTTGTAGTAGGAACAAGGTACATTCGCGGGATAAATGTGGCCAAGTTTTATCTGCTGCCAGGGCTTTCAAATAGGTTGACCTGACAATGGGTCACCTCTGGGACTGAYAATTAGGAAGAGCTGGTACCTAAAATGAAAGATGCccttaaatttcagattcacaatttt

Rev5'-3'=aaaattgtgaatctgaaatttaagg

M4=DYS234（273bp）AtoGatposition88

tcctaggttatgattacagagcgAGGATTATTATAATATTGGAATAAAGAATAATTGCTACAAACTAATGATTAATGATATTCATATRTAATCATATCTAAGATCTATATCTAGTATAACTATTCTTATTTTATATATTTTATTGTACTGGAACAGCTTGTGCCCTTGGTCTCTTGCCTCGGCACCTGGGTGGCTTGCCATCCACAGAAGTGTTTTAACAGCAAAAATTACTGTGAATTTTCTGCCCAAAAccttgtcatgtttacaagacgt

Rev5'-3'=acgtcttgtaaacatgacaagg

M5=DYS214a（322bp）CtoT

gggtttatactgacctgccaatgttAAAAGGGACCTAAATTCACTTTGGGGAAGTGGCCAGAAAGGAAGAAGYAGAAGGAGAAGAGTGCAAGAAACCTCCAGTTGTGGGGGTTGAGCCTCCAGGATAAGAAAGAAAGAAATCTCCAGTAGGGGGGATTGAGCCTAACACAAACCTTTGGTAATAGACAAGGCAAGACATTTCCAATAGGGGAGATTGAGTGTCACCTCAAAACTATTAAGATGGGAAATACCCCAGGTAAGATAGAGGGTAAAAAAGGATAAAGCTAGCAGCAATAACATTCcccctgaaagttcccaataa

Rev5'-3'=ttattgggaactttcagggg

DYS214complete.（656bp）ThisfragmentwasconvertedintotwoSTSs,a&b,containingM4andM16respectively.ThetwonewSTSs（a&b）omitanextrainternal68bpregionwithinthecompleteSTS.

gggtttatactgacctgccaatgttAAAAGGGACCTAAATTCACTTTGGGGAAGTGGCCAGAAAGGAAGAAGCAGAAGGAGAAGAGTGCAAGAAACCTCCAGTTGTGGGGGTTGAGCCTCCAGGATAAGAAAGAAAGAAATCTCCAGTAGGGGGGATTGAGCCTAACACAAACCTTTGGTAATAGACAAGGCAAGACATTTCCAATAGGGGAGATTGAGTGTCACCTCAAAACTATTAAGATGGGAAATACCCCAGGTAAGATAGAGGGTAAAAAAGGATAAAGCTAGCAGCAATAACATTCcccctgaaagttcccaataaTTTATGCTAAAATATTGGAAAGACAACGAAAGGACTAAGCACAAGAGAAAGCAACAGATGATAAATATtgttatgtcatttgaacccagGAACCAATCTTCGAACCCTCAGTTTTCTGGCCAAAGTTGGAGTCAAATGAGGATTGGATTTGTCAGCTTTTAATAGAACATATGATGACAAAACCTTCATCTCCCAGGAGGAGATAAATTATGCCCTATGTTGGTGGCAAGGACCTGTCCTCCTTTACCCTCTAAAAACTGGAGGGAGAAAGTCAAAGACTAACTCCTCTGAAAAAGATAAAGTCCCTATTCCTAgacagcccagcaacacacgg

Rev5'-3'=ccgtgtgttgctgggctgtc

M6=DYS198（218bp）TtoCatposition37

cactaccacatttctggttggCTTGTAGTTCTTTCTYGGAAAAATATTATTCTAATTTCCTTATAGTATTAGCCATCAAAGTAGGGGAAGCAGATCAAATCTACCATAAGACCAAGTCATAGGAAGAAGATCAAATTAAGATGCTAGGCAAAAGTCTCAGCACATATGGATTATGAGAAGCACATTCACACATCCAAActcaaagaatggactcagcg

Rev5'-3'=cgctgagtccattctttgag

M7=DYS253（300bp）.CtoGatposition236

actgtgagcgagctgaaaatGCCTGATTTTCTCCCTTGGTTTAATGTAAAGGAAGGGATCCAAAGGCTTAGGGAGATTGGGATGGTGGATTAGTCACTTTAGACCTACTCATTCCAATAGGGAGGGTCCAGAAGATGTACCCTTGACCAATGCCTTGCAAAATAGATTCGTGAGGGCAGCACCTGCATCACCAAAGGGCATGTAATCATTCCTCTCTGTATGTCAGATCTAACAASAAGAAGAACAGTAACTCAACTACAAAATTTAAACACAATGGAAAtaattggttcacaaggctgc

Rev5'-3'=gcagccttgtgaaccaatta

M8=DYS263（267bp）.GtoTatposition137

cccacccacttcagtatgaaTTTTGGGATCTGTTACCTATTTTTTGATATAAAATCAACTGCAAGTTTAGTGCCTCAGTATCACAAACACTGTATTTGCTCATATGTCTGTGAATCAATAACTTGGACTGGGTTCAKTTGGGCAGTTCTTCTATTGGTCTTGCCTGGGGTCTTTAATGCAGCTTCCATTTTCTGGCAGCTTGATGAGACTGGATGGTCTAAGGTACATTCATGAACACATCTGTTTGgtggacttgtctgtcagcct

Rev5'-3'=aggctgacagacaagtccac

M9（340bp）G10.35aCtoGsubstitutionatposition68

gcagcatataaaactttcaggACCCTGAAATACAGAACTGCAAAGAAACGGCCTAAGATGGTTGAATSCTCTTTATTTTTCTTTAATTTAGACATGTTCAAACGTTCAATGTCTTACATACTTAGTTATGTAAGTAAGGTAGCGCTTACTTCATTATGCATTTCAATACTCAAAAAAAATTCCTTTGTGAAATGTTGAAATATTTTTCTAATCTGTTTCACGAGCTTCAAAAATGAGGAAAAAAGATTCAGTTTACATTTCAGCAAAATGCCTCTTTTTAATCGGATTTATGTTTACTTAACATTTACAGTACATTTACgcttgagcaaagttaggtttt

Rev5'-3'=aaaacctaactttgctcaagc

M10=G10.10（343bp）.TtoCatposition156

gcattgctataagttacctgcAATTTATAAAGTTGTGAAATAGTTCAAGACAATGAAGGGAGAGACTCTCTGGTAACTACAGAGTATGAGCTCATCATTGCTTAGTTTCCACAAGAGGTATCTCTGAATTTTTTTGTTTATTCCCAATGATCTTAYAGCACTTGTAAAGTTTTTACATTAGTTACAAAATGCAATTTGAAGTGAAAGAAACAGAAATACAAAATATTAGTTTCTCTTTTTCTCCTACATTCCTACATGGATTTGTAGAAGAGCTGACCTTTACTTATAAAATAAATCAGCAAATGAGTGTCTTTTCTAGAATGgggtgacccaatttttatta

Rev5'-3'=taataaaaattgggtcaccc

M11=G10.37（222p）AtoGatposition44.

tctctctgtctgtctctccctccCTCTCTCCTTGTATTCTAACRGAAAGGTTTAGAACTTGCATAATTGGGAAAGAAGCTGTTGCCTGAACTTACTGGGGGATTCAGCATTGTCATTTTGGACATGTCACTTATCCTCAGTATTTGCTTCCCCCAGGAGAGAGCTGTAATAAAAAAGCATTGCAATTTAATACATAAgctcagtaagttcttgtttatgctc

Rev5'-3'=gagcataaacaagaacttactgagc

M12=DYS260a（309bp）GtoTatposition286

actaaaacaccattagaaacaaaggACTTAAACTAGGAATTAATTATTTCTCTTTCTCTTTCCATGGCCAACAAACATTGAAAAAAAATTGCCATCTTTTTTTTTATTTGTTTGTTAGAGATGGGGATCTCACTCTGTTTCTTAGATTGTAGTGCCATGGCACAATAATGGCTCACTGCAGCCTCAAACTCCTGGGCTCAAGTGATCACCCCCATACAGACTCCCGAGTAGCTGGGAACACAGGCACATGCCACCACCCCTAGCTAATTTTTTATTATTTGTAGAKATGggggtcactatgttgctcag

Rev5'-3'=ctgagcaacatagtgacccc

M13=G10.06（233bp）GtoCatposition157

tcctaacctggtggtctttcATTGTTTTACAAAGGTGATTTAGTTTTGGGAAGGACTATTCTCCTTTAAACTATAGACTAAATTTTTCTCAAAGTTAGGTTAGTTTATGCCCAGGAATGAACAAGGGCAGTAGGTAGGTTAAGGGCAAGACGGTTASATCAGTTCTCTGTTACTGTTATAATTTTCTCATTGTTATATTTTTTGCAAATGTGgttggataaaatcatggctca

Rev5'-3'=tgagccatgattttatccaac

M14=G10.07（287bp）TtoCatposition180

agacggttagatcagttctctgTTACTGTTATAATTTTCTCATTGTTATATTTTTTGCAAATGTGGTTGGATAAAATCATGGCTCATACAAATATACAAAAAATACATATTAAAATTTTATTTAACATAAAACATTAAAATTTATTTAATAAATTATAAATGAAAAAATCAGTAACATGYTATAAGCAGTTTAAAAAAGTTAATGAAGCTCAGTTTTAACATGAAGTATAGGAATGGTGAAATTATATAAATGAAATTTGTAAATggtgtcaatgtgcttttatcta

Rev5'-3'=tagataaaagcacattgacacc

M15=G10.16（295bp=ancestralstate）;derivedallele=9bpinsertion（304bp）afterposition109;NotethattherearealsotwoTtoGchangesimmediatelybeforethe9bpinsertion.

acaaatcctgaacaatcgcCATCACCTATTTGGTGGACGCATAGGCCTGGTCTCTGATCTGGTCGCATGTCCAGAGGGTCTGCTAACCCACTGCACCTAGGGAGACATTGTACAGAGACATTGTACCACCTTTTCTCTACTcttcccagactcaacacatttGATTGTATATGCGCATGAGGTAGAAATATAAGATGAAGCAGGGACAGAGTCAACAAGCCAGAACTAGATGCTTCTACCTGGACAGAAGACCTAGAATTCTTTTTTGGATCCTAAATTCACCAggaaattttaaccacatgca

Rev5'-3'=tgcatgtggttaaaatttcc

M15polymorphicregioninmoredetail

mutantsequence=GACATTGTACAGAGACA

ancestralsequence=GACAGG*********CA

TheM15primerspublished（1997GenomeResearch7:

996-1005）amplifyasmallerfragmentwhichhasabettersize（153bp=ancestralsize）forGeneScananalysis.Oneofthepublishedprimersformsahairpinwhichreducesamplificationefficiency.However,thepublishedprimersworkedwellenoughforGeneScanwithaFAMlabelontheFprimer.

M16=DYS214b（266bp）CtoA

tgttatgtcatttgaacccagGAACCAATCTTCGAACMCTCAGTTTTCTGGCCAAAGTTGGAGTCAAATGAGGATTGGATTTGTCAGCTTTTAATAGAACATATGATGACAAAACCTTCATCTCCCAGGAGGAGATAAATTATGCCCTATGTTGGTGGCAAGGACCTGTCCTCCTTTACCCTCTAAAAACTGGAGGGAGAAAGTCAAAGACTAACTCCTCTGAAAAAGATAAAGTCCCTATTCCTAgacagcccagcaacacacgg

Rev5'-3'=ccgtgtgttgctgggctgt

M17=G10.47a（333bp）

-1bpdeletion（4G'sto3G's）atposition68

ctggtcataacactggaaatcAGATTCTGTCTACTCACCAGAGTTTGTGGTTGCTGGTTGTTACGGGGTTTTTTTAAGTGAATTTTGGGGTTTGTTAAGTGGCCAAACTATTTTTGTGAAGACTGTTGTATGTGGGTTTCAGATGTCTCTACATCAGTTTGTGGTCAGCTAGTGAGTTAAATTTTATGAAAAGCCTGGAGAAACAAGAATAGCAGTAAAAACTTCCAGTCTTTGTAGATTGGGTGTCTTCAGTGCTTAGCTGGGCAATTTAAAACTTACCTTAAGTAGTACAGTTGGCCCTTTGTGTCTGTgagtttcacatttgtaggttca

Rev5'-3'=tgaacctacaaatgtgaaact

M18=G10.47b（333bp=ancestralsize）+2bp（extraAA）insertionafterposition62

ctggtcataacactggaaatcAGATTCTGTCTACTCACCAGAGTTTGTGGTTGCTGGTTGTTAAACGGGGTTTTTTTAAGTGAATTTTGGGGTTTGTTAAGTGGCCAAACTATTTT