SNP sequencesWord格式文档下载.docx
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SNP sequencesWord格式文档下载.docx
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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'
=aatggaaaatacagctcccc
M3=DYS199(241bp)CtoTatposition181
taatcagtctcctcccagcaAGTGATATGCAACTGAGATTCCTTATGACACATCTGAACACTAGTGGATTTGCTTTGTAGTAGGAACAAGGTACATTCGCGGGATAAATGTGGCCAAGTTTTATCTGCTGCCAGGGCTTTCAAATAGGTTGACCTGACAATGGGTCACCTCTGGGACTGAYAATTAGGAAGAGCTGGTACCTAAAATGAAAGATGCccttaaatttcagattcacaatttt
=aaaattgtgaatctgaaatttaagg
M4=DYS234(273bp)AtoGatposition88
tcctaggttatgattacagagcgAGGATTATTATAATATTGGAATAAAGAATAATTGCTACAAACTAATGATTAATGATATTCATATRTAATCATATCTAAGATCTATATCTAGTATAACTATTCTTATTTTATATATTTTATTGTACTGGAACAGCTTGTGCCCTTGGTCTCTTGCCTCGGCACCTGGGTGGCTTGCCATCCACAGAAGTGTTTTAACAGCAAAAATTACTGTGAATTTTCTGCCCAAAAccttgtcatgtttacaagacgt
=acgtcttgtaaacatgacaagg
M5=DYS214a(322bp)CtoT
gggtttatactgacctgccaatgttAAAAGGGACCTAAATTCACTTTGGGGAAGTGGCCAGAAAGGAAGAAGYAGAAGGAGAAGAGTGCAAGAAACCTCCAGTTGTGGGGGTTGAGCCTCCAGGATAAGAAAGAAAGAAATCTCCAGTAGGGGGGATTGAGCCTAACACAAACCTTTGGTAATAGACAAGGCAAGACATTTCCAATAGGGGAGATTGAGTGTCACCTCAAAACTATTAAGATGGGAAATACCCCAGGTAAGATAGAGGGTAAAAAAGGATAAAGCTAGCAGCAATAACATTCcccctgaaagttcccaataa
=ttattgggaactttcagggg
DYS214complete.(656bp)ThisfragmentwasconvertedintotwoSTSs,a&
b,containingM4andM16respectively.ThetwonewSTSs(a&
b)omitanextrainternal68bpregionwithinthecompleteSTS.
gggtttatactgacctgccaatgttAAAAGGGACCTAAATTCACTTTGGGGAAGTGGCCAGAAAGGAAGAAGCAGAAGGAGAAGAGTGCAAGAAACCTCCAGTTGTGGGGGTTGAGCCTCCAGGATAAGAAAGAAAGAAATCTCCAGTAGGGGGGATTGAGCCTAACACAAACCTTTGGTAATAGACAAGGCAAGACATTTCCAATAGGGGAGATTGAGTGTCACCTCAAAACTATTAAGATGGGAAATACCCCAGGTAAGATAGAGGGTAAAAAAGGATAAAGCTAGCAGCAATAACATTCcccctgaaagttcccaataaTTTATGCTAAAATATTGGAAAGACAACGAAAGGACTAAGCACAAGAGAAAGCAACAGATGATAAATATtgttatgtcatttgaacccagGAACCAATCTTCGAACCCTCAGTTTTCTGGCCAAAGTTGGAGTCAAATGAGGATTGGATTTGTCAGCTTTTAATAGAACATATGATGACAAAACCTTCATCTCCCAGGAGGAGATAAATTATGCCCTATGTTGGTGGCAAGGACCTGTCCTCCTTTACCCTCTAAAAACTGGAGGGAGAAAGTCAAAGACTAACTCCTCTGAAAAAGATAAAGTCCCTATTCCTAgacagcccagcaacacacgg
=ccgtgtgttgctgggctgtc
M6=DYS198(218bp)TtoCatposition37
cactaccacatttctggttggCTTGTAGTTCTTTCTYGGAAAAATATTATTCTAATTTCCTTATAGTATTAGCCATCAAAGTAGGGGAAGCAGATCAAATCTACCATAAGACCAAGTCATAGGAAGAAGATCAAATTAAGATGCTAGGCAAAAGTCTCAGCACATATGGATTATGAGAAGCACATTCACACATCCAAActcaaagaatggactcagcg
=cgctgagtccattctttgag
M7=DYS253(300bp).CtoGatposition236
actgtgagcgagctgaaaatGCCTGATTTTCTCCCTTGGTTTAATGTAAAGGAAGGGATCCAAAGGCTTAGGGAGATTGGGATGGTGGATTAGTCACTTTAGACCTACTCATTCCAATAGGGAGGGTCCAGAAGATGTACCCTTGACCAATGCCTTGCAAAATAGATTCGTGAGGGCAGCACCTGCATCACCAAAGGGCATGTAATCATTCCTCTCTGTATGTCAGATCTAACAASAAGAAGAACAGTAACTCAACTACAAAATTTAAACACAATGGAAAtaattggttcacaaggctgc
=gcagccttgtgaaccaatta
M8=DYS263(267bp).GtoTatposition137
cccacccacttcagtatgaaTTTTGGGATCTGTTACCTATTTTTTGATATAAAATCAACTGCAAGTTTAGTGCCTCAGTATCACAAACACTGTATTTGCTCATATGTCTGTGAATCAATAACTTGGACTGGGTTCAKTTGGGCAGTTCTTCTATTGGTCTTGCCTGGGGTCTTTAATGCAGCTTCCATTTTCTGGCAGCTTGATGAGACTGGATGGTCTAAGGTACATTCATGAACACATCTGTTTGgtggacttgtctgtcagcct
=aggctgacagacaagtccac
M9(340bp)G10.35aCtoGsubstitutionatposition68
gcagcatataaaactttcaggACCCTGAAATACAGAACTGCAAAGAAACGGCCTAAGATGGTTGAATSCTCTTTATTTTTCTTTAATTTAGACATGTTCAAACGTTCAATGTCTTACATACTTAGTTATGTAAGTAAGGTAGCGCTTACTTCATTATGCATTTCAATACTCAAAAAAAATTCCTTTGTGAAATGTTGAAATATTTTTCTAATCTGTTTCACGAGCTTCAAAAATGAGGAAAAAAGATTCAGTTTACATTTCAGCAAAATGCCTCTTTTTAATCGGATTTATGTTTACTTAACATTTACAGTACATTTACgcttgagcaaagttaggtttt
=aaaacctaactttgctcaagc
M10=G10.10(343bp).TtoCatposition156
gcattgctataagttacctgcAATTTATAAAGTTGTGAAATAGTTCAAGACAATGAAGGGAGAGACTCTCTGGTAACTACAGAGTATGAGCTCATCATTGCTTAGTTTCCACAAGAGGTATCTCTGAATTTTTTTGTTTATTCCCAATGATCTTAYAGCACTTGTAAAGTTTTTACATTAGTTACAAAATGCAATTTGAAGTGAAAGAAACAGAAATACAAAATATTAGTTTCTCTTTTTCTCCTACATTCCTACATGGATTTGTAGAAGAGCTGACCTTTACTTATAAAATAAATCAGCAAATGAGTGTCTTTTCTAGAATGgggtgacccaatttttatta
=taataaaaattgggtcaccc
M11=G10.37(222p)AtoGatposition44.
tctctctgtctgtctctccctccCTCTCTCCTTGTATTCTAACRGAAAGGTTTAGAACTTGCATAATTGGGAAAGAAGCTGTTGCCTGAACTTACTGGGGGATTCAGCATTGTCATTTTGGACATGTCACTTATCCTCAGTATTTGCTTCCCCCAGGAGAGAGCTGTAATAAAAAAGCATTGCAATTTAATACATAAgctcagtaagttcttgtttatgctc
=gagcataaacaagaacttactgagc
M12=DYS260a(309bp)GtoTatposition286
actaaaacaccattagaaacaaaggACTTAAACTAGGAATTAATTATTTCTCTTTCTCTTTCCATGGCCAACAAACATTGAAAAAAAATTGCCATCTTTTTTTTTATTTGTTTGTTAGAGATGGGGATCTCACTCTGTTTCTTAGATTGTAGTGCCATGGCACAATAATGGCTCACTGCAGCCTCAAACTCCTGGGCTCAAGTGATCACCCCCATACAGACTCCCGAGTAGCTGGGAACACAGGCACATGCCACCACCCCTAGCTAATTTTTTATTATTTGTAGAKATGggggtcactatgttgctcag
=ctgagcaacatagtgacccc
M13=G10.06(233bp)GtoCatposition157
tcctaacctggtggtctttcATTGTTTTACAAAGGTGATTTAGTTTTGGGAAGGACTATTCTCCTTTAAACTATAGACTAAATTTTTCTCAAAGTTAGGTTAGTTTATGCCCAGGAATGAACAAGGGCAGTAGGTAGGTTAAGGGCAAGACGGTTASATCAGTTCTCTGTTACTGTTATAATTTTCTCATTGTTATATTTTTTGCAAATGTGgttggataaaatcatggctca
=tgagccatgattttatccaac
M14=G10.07(287bp)TtoCatposition180
agacggttagatcagttctctgTTACTGTTATAATTTTCTCATTGTTATATTTTTTGCAAATGTGGTTGGATAAAATCATGGCTCATACAAATATACAAAAAATACATATTAAAATTTTATTTAACATAAAACATTAAAATTTATTTAATAAATTATAAATGAAAAAATCAGTAACATGYTATAAGCAGTTTAAAAAAGTTAATGAAGCTCAGTTTTAACATGAAGTATAGGAATGGTGAAATTATATAAATGAAATTTGTAAATggtgtcaatgtgcttttatcta
=tagataaaagcacattgacacc
M15=G10.16(295bp=ancestralstate);
derivedallele=9bpinsertion(304bp)afterposition109;
NotethattherearealsotwoTtoGchangesimmediatelybeforethe9bpinsertion.
acaaatcctgaacaatcgcCATCACCTATTTGGTGGACGCATAGGCCTGGTCTCTGATCTGGTCGCATGTCCAGAGGGTCTGCTAACCCACTGCACCTAGGGAGACATTGTACAGAGACATTGTACCACCTTTTCTCTACTcttcccagactcaacacatttGATTGTATATGCGCATGAGGTAGAAATATAAGATGAAGCAGGGACAGAGTCAACAAGCCAGAACTAGATGCTTCTACCTGGACAGAAGACCTAGAATTCTTTTTTGGATCCTAAATTCACCAggaaattttaaccacatgca
=tgcatgtggttaaaatttcc
M15polymorphicregioninmoredetail
mutantsequence=GACATTGTACAGAGACA
ancestralsequence=GACAGG*********CA
TheM15primerspublished(1997GenomeResearch7:
996-1005)amplifyasmallerfragmentwhichhasabettersize(153bp=ancestralsize)forGeneScananalysis.Oneofthepublishedprimersformsahairpinwhichreducesamplificationefficiency.However,thepublishedprimersworkedwellenoughforGeneScanwithaFAMlabelontheFprimer.
M16=DYS214b(266bp)CtoA
tgttatgtcatttgaacccagGAACCAATCTTCGAACMCTCAGTTTTCTGGCCAAAGTTGGAGTCAAATGAGGATTGGATTTGTCAGCTTTTAATAGAACATATGATGACAAAACCTTCATCTCCCAGGAGGAGATAAATTATGCCCTATGTTGGTGGCAAGGACCTGTCCTCCTTTACCCTCTAAAAACTGGAGGGAGAAAGTCAAAGACTAACTCCTCTGAAAAAGATAAAGTCCCTATTCCTAgacagcccagcaacacacgg
=ccgtgtgttgctgggctgt
M17=G10.47a(333bp)
-1bpdeletion(4G'
sto3G'
s)atposition68
ctggtcataacactggaaatcAGATTCTGTCTACTCACCAGAGTTTGTGGTTGCTGGTTGTTACGGGGTTTTTTTAAGTGAATTTTGGGGTTTGTTAAGTGGCCAAACTATTTTTGTGAAGACTGTTGTATGTGGGTTTCAGATGTCTCTACATCAGTTTGTGGTCAGCTAGTGAGTTAAATTTTATGAAAAGCCTGGAGAAACAAGAATAGCAGTAAAAACTTCCAGTCTTTGTAGATTGGGTGTCTTCAGTGCTTAGCTGGGCAATTTAAAACTTACCTTAAGTAGTACAGTTGGCCCTTTGTGTCTGTgagtttcacatttgtaggttca
=tgaacctacaaatgtgaaact
M18=G10.47b(333bp=ancestralsize)+2bp(extraAA)insertionafterposition62
ctggtcataacactggaaatcAGATTCTGTCTACTCACCAGAGTTTGTGGTTGCTGGTTGTTAAACGGGGTTTTTTTAAGTGAATTTTGGGGTTTGTTAAGTGGCCAAACTATTTT
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