SNP sequences.docx

1、SNP sequencesNot for commercial use without permission from Stanford University.Sequence information for the 167 Y chromosome markers described in:Underhill et al (2000). Y chromosome sequence variation and the history of human populations. Nature Genet. Nov. issueSTS sequences (one strand only) for

2、 polymorphic Y sequences. Primer regions = lower case; Reverse compliment made to generate 5-3 Reverse PCR primer sequence for complimentary strand.IUB code defines polymorphic siteR = A or G (puRine)Y = C or T (pYrimidine)K = G or T (Keto)M = A or C (aMino)S = G or C (Strong-3H bonds)W = A or T (We

3、ak-2H bonds)H = A, C or TMarker numbers discontinuous because of selected removal of numbered microsatillite and homopolymer polymorphismsM1 = DYS287 = (YAP) Hammer & Horai 1995 Am. J. Hum Genet. 56:951-962. YAP MINUS REGION = 150 bp. The = Alu insertion sitecaggggaagataaagaaataTAACATAAGAAGATCAAACCT

4、GTTTTAACTTTAACTTGGTTGGAGTTGGCCCTGGAATAATTGTCCATGATTCTGGAGGGCGTCGTGTTCTTTTGATCCTAGTGTGATGAatccatccccttttagcagtYAP.1: 5-caggggaagataaagaaata-3YAP.2: 5-actgctaaaaggggatggat-3ALU insertion element. (291 bp) Large font bold alleles are specific to the DYS287 Alu element. (Hammer 1994 Mol. Biol. Evol. 11:

5、 749-761)GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGCGGGCGCCTGTATTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCATTGCAGTCCGCAGTCCGGCCTGGGCAACAGAGCGAGACTCCGTCTCAAA

6、poly AYAP INSERTION site located at position 253 within fragment from R368 to AR243 within the Alu element (italics). Large font bold alleles are specific to the DYS287 Alu element.tcacataatttcattttcccTATTGCAGATATGTTTTCCTGCATTTGTTAAGGAACAAGGGTCTTGAGAGGGAGAGCTTTTTGTCTTAAAGGGGAAGAGATACTTCTGTGAGGCTAAGA

7、GTTGCCTTTGACTTTGGAGATCTTCACAGGGTATAATAAGACAAGCATCAAAGGTAATAGTTTGGGGTCAACTTGACCTGGTTACGTTAATAAGGAGAGGACTAGCAATAGcaggggaagataaagaaataTAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGCGGGCGCCTGTATTCCCA

8、GCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCATtgcagtccgcagtccggccGTCCGGCCTGGGCAACAGAGCGAGACTCCGTCTCAAApolyA tailR368 5-3 : tcacataatttcattttcccAR243 5-3: ggccggactgcggactgcaA (3 nt matches unique T within DYS287 Alu for specificity)AR237 5-3: cgccattgcagtccgcagtcYAP.1 5

9、-3: caggggaagataaagaaataM2 = DYS271 (209 bp) A to G at position 168aggcactggtcagaatgaagTGAATGGCACACAGGACAAGTCCAGACCCAGGAAGGTCCAGTAACATGGGAGAAGAACGGAAGGAGTTCTAAAATTCAGGGCTCCCTTGGGCTCCCCTGTTTAAAAATGTAGGTTTTATTATTATATTTCATTGTTAACAAAAGTCCRTGAGATCTGTGGAGGATAAAGggggagctgtattttccattRev 5-3 = aatggaaaatacag

10、ctccccM3 = DYS199 (241 bp) C to T at position 181 taatcagtctcctcccagcaAGTGATATGCAACTGAGATTCCTTATGACACATCTGAACACTAGTGGATTTGCTTTGTAGTAGGAACAAGGTACATTCGCGGGATAAATGTGGCCAAGTTTTATCTGCTGCCAGGGCTTTCAAATAGGTTGACCTGACAATGGGTCACCTCTGGGACTGAYAATTAGGAAGAGCTGGTACCTAAAATGAAAGATGCccttaaatttcagattcacaattttRev 5-3 =

11、 aaaattgtgaatctgaaatttaaggM4 = DYS234 (273 bp) A to G at position 88tcctaggttatgattacagagcgAGGATTATTATAATATTGGAATAAAGAATAATTGCTACAAACTAATGATTAATGATATTCATATRTAATCATATCTAAGATCTATATCTAGTATAACTATTCTTATTTTATATATTTTATTGTACTGGAACAGCTTGTGCCCTTGGTCTCTTGCCTCGGCACCTGGGTGGCTTGCCATCCACAGAAGTGTTTTAACAGCAAAAATTACT

12、GTGAATTTTCTGCCCAAAAccttgtcatgtttacaagacgtRev 5-3 = acgtcttgtaaacatgacaaggM5 = DYS214a (322 bp) C to TgggtttatactgacctgccaatgttAAAAGGGACCTAAATTCACTTTGGGGAAGTGGCCAGAAAGGAAGAAGYAGAAGGAGAAGAGTGCAAGAAACCTCCAGTTGTGGGGGTTGAGCCTCCAGGATAAGAAAGAAAGAAATCTCCAGTAGGGGGGATTGAGCCTAACACAAACCTTTGGTAATAGACAAGGCAAGACAT

13、TTCCAATAGGGGAGATTGAGTGTCACCTCAAAACTATTAAGATGGGAAATACCCCAGGTAAGATAGAGGGTAAAAAAGGATAAAGCTAGCAGCAATAACATTCcccctgaaagttcccaataaRev 5-3 = ttattgggaactttcaggggDYS214 complete. (656 bp) This fragment was converted into two STSs, a & b, containing M4 and M16 respectively. The two new STSs (a & b) omit an ex

14、tra internal 68 bp region within the complete STS.gggtttatactgacctgccaatgttAAAAGGGACCTAAATTCACTTTGGGGAAGTGGCCAGAAAGGAAGAAGCAGAAGGAGAAGAGTGCAAGAAACCTCCAGTTGTGGGGGTTGAGCCTCCAGGATAAGAAAGAAAGAAATCTCCAGTAGGGGGGATTGAGCCTAACACAAACCTTTGGTAATAGACAAGGCAAGACATTTCCAATAGGGGAGATTGAGTGTCACCTCAAAACTATTAAGATGGGAAATA

15、CCCCAGGTAAGATAGAGGGTAAAAAAGGATAAAGCTAGCAGCAATAACATTCcccctgaaagttcccaataaTTTATGCTAAAATATTGGAAAGACAACGAAAGGACTAAGCACAAGAGAAAGCAACAGATGATAAATATtgttatgtcatttgaacccagGAACCAATCTTCGAACCCTCAGTTTTCTGGCCAAAGTTGGAGTCAAATGAGGATTGGATTTGTCAGCTTTTAATAGAACATATGATGACAAAACCTTCATCTCCCAGGAGGAGATAAATTATGCCCTATGTTGGTGGCA

16、AGGACCTGTCCTCCTTTACCCTCTAAAAACTGGAGGGAGAAAGTCAAAGACTAACTCCTCTGAAAAAGATAAAGTCCCTATTCCTAgacagcccagcaacacacggRev 5-3 = ccgtgtgttgctgggctgtcM6 = DYS198 (218 bp) T to C at position 37cactaccacatttctggttggCTTGTAGTTCTTTCTYGGAAAAATATTATTCTAATTTCCTTATAGTATTAGCCATCAAAGTAGGGGAAGCAGATCAAATCTACCATAAGACCAAGTCATAG

17、GAAGAAGATCAAATTAAGATGCTAGGCAAAAGTCTCAGCACATATGGATTATGAGAAGCACATTCACACATCCAAActcaaagaatggactcagcgRev 5-3 = cgctgagtccattctttgagM7 = DYS253 (300 bp). C to G at position 236actgtgagcgagctgaaaatGCCTGATTTTCTCCCTTGGTTTAATGTAAAGGAAGGGATCCAAAGGCTTAGGGAGATTGGGATGGTGGATTAGTCACTTTAGACCTACTCATTCCAATAGGGAGGGTCCA

18、GAAGATGTACCCTTGACCAATGCCTTGCAAAATAGATTCGTGAGGGCAGCACCTGCATCACCAAAGGGCATGTAATCATTCCTCTCTGTATGTCAGATCTAACAASAAGAAGAACAGTAACTCAACTACAAAATTTAAACACAATGGAAAtaattggttcacaaggctgcRev 5-3 = gcagccttgtgaaccaattaM8 = DYS263 (267 bp). G to T at position 137cccacccacttcagtatgaaTTTTGGGATCTGTTACCTATTTTTTGATATAAAATC

19、AACTGCAAGTTTAGTGCCTCAGTATCACAAACACTGTATTTGCTCATATGTCTGTGAATCAATAACTTGGACTGGGTTCAKTTGGGCAGTTCTTCTATTGGTCTTGCCTGGGGTCTTTAATGCAGCTTCCATTTTCTGGCAGCTTGATGAGACTGGATGGTCTAAGGTACATTCATGAACACATCTGTTTGgtggacttgtctgtcagcctRev 5-3 = aggctgacagacaagtccacM9 (340 bp) G10.35a C to G substitution at position 68gcagc

20、atataaaactttcaggACCCTGAAATACAGAACTGCAAAGAAACGGCCTAAGATGGTTGAATSCTCTTTATTTTTCTTTAATTTAGACATGTTCAAACGTTCAATGTCTTACATACTTAGTTATGTAAGTAAGGTAGCGCTTACTTCATTATGCATTTCAATACTCAAAAAAAATTCCTTTGTGAAATGTTGAAATATTTTTCTAATCTGTTTCACGAGCTTCAAAAATGAGGAAAAAAGATTCAGTTTACATTTCAGCAAAATGCCTCTTTTTAATCGGATTTATGTTTACTTAACATT

21、TACAGTACATTTACgcttgagcaaagttaggttttRev 5-3 = aaaacctaactttgctcaagcM10 = G10.10 (343bp). T to C at position 156gcattgctataagttacctgcAATTTATAAAGTTGTGAAATAGTTCAAGACAATGAAGGGAGAGACTCTCTGGTAACTACAGAGTATGAGCTCATCATTGCTTAGTTTCCACAAGAGGTATCTCTGAATTTTTTTGTTTATTCCCAATGATCTTAYAGCACTTGTAAAGTTTTTACATTAGTTACAAAAT

22、GCAATTTGAAGTGAAAGAAACAGAAATACAAAATATTAGTTTCTCTTTTTCTCCTACATTCCTACATGGATTTGTAGAAGAGCTGACCTTTACTTATAAAATAAATCAGCAAATGAGTGTCTTTTCTAGAATGgggtgacccaatttttattaRev 5-3 = taataaaaattgggtcacccM11 = G10.37 (222 p) A to G at position 44.tctctctgtctgtctctccctccCTCTCTCCTTGTATTCTAACRGAAAGGTTTAGAACTTGCATAATTGGGAAA

23、GAAGCTGTTGCCTGAACTTACTGGGGGATTCAGCATTGTCATTTTGGACATGTCACTTATCCTCAGTATTTGCTTCCCCCAGGAGAGAGCTGTAATAAAAAAGCATTGCAATTTAATACATAAgctcagtaagttcttgtttatgctcRev 5-3 = gagcataaacaagaacttactgagcM12=DYS260a (309 bp) G to T at position 286actaaaacaccattagaaacaaaggACTTAAACTAGGAATTAATTATTTCTCTTTCTCTTTCCATGGCCAACAA

24、ACATTGAAAAAAAATTGCCATCTTTTTTTTTATTTGTTTGTTAGAGATGGGGATCTCACTCTGTTTCTTAGATTGTAGTGCCATGGCACAATAATGGCTCACTGCAGCCTCAAACTCCTGGGCTCAAGTGATCACCCCCATACAGACTCCCGAGTAGCTGGGAACACAGGCACATGCCACCACCCCTAGCTAATTTTTTATTATTTGTAGAKATGggggtcactatgttgctcagRev 5-3 = ctgagcaacatagtgaccccM13 = G10.06 (233 bp) G to C at pos

25、ition 157tcctaacctggtggtctttcATTGTTTTACAAAGGTGATTTAGTTTTGGGAAGGACTATTCTCCTTTAAACTATAGACTAAATTTTTCTCAAAGTTAGGTTAGTTTATGCCCAGGAATGAACAAGGGCAGTAGGTAGGTTAAGGGCAAGACGGTTASATCAGTTCTCTGTTACTGTTATAATTTTCTCATTGTTATATTTTTTGCAAATGTGgttggataaaatcatggctcaRev 5-3 = tgagccatgattttatccaacM14 = G10.07 (287 bp) T to

26、C at position 180agacggttagatcagttctctgTTACTGTTATAATTTTCTCATTGTTATATTTTTTGCAAATGTGGTTGGATAAAATCATGGCTCATACAAATATACAAAAAATACATATTAAAATTTTATTTAACATAAAACATTAAAATTTATTTAATAAATTATAAATGAAAAAATCAGTAACATGYTATAAGCAGTTTAAAAAAGTTAATGAAGCTCAGTTTTAACATGAAGTATAGGAATGGTGAAATTATATAAATGAAATTTGTAAATggtgtcaatgtgctttta

27、tctaRev 5-3 = tagataaaagcacattgacaccM15 = G10.16 (295 bp = ancestral state); derived allele = 9 bp insertion (304 bp) after position 109; Note that there are also two T to G changes immediately before the 9 bp insertion.acaaatcctgaacaatcgcCATCACCTATTTGGTGGACGCATAGGCCTGGTCTCTGATCTGGTCGCATGTCCAGAGGGTC

28、TGCTAACCCACTGCACCTAGGGAGACATTGTACAGAGACATTGTACCACCTTTTCTCTACTcttcccagactcaacacatttGATTGTATATGCGCATGAGGTAGAAATATAAGATGAAGCAGGGACAGAGTCAACAAGCCAGAACTAGATGCTTCTACCTGGACAGAAGACCTAGAATTCTTTTTTGGATCCTAAATTCACCAggaaattttaaccacatgcaRev 5-3 = tgcatgtggttaaaatttccM15 polymorphic region in more detailmutant se

29、quence = GACA TT GTACAGAGA CAancestral sequence = GACA GG * * * * * * * * * CAThe M15 primers published (1997 Genome Research 7:996-1005) amplify a smaller fragment which has a better size (153 bp = ancestral size) for GeneScan analysis. One of the published primers forms a hairpin which reduces amp

30、lification efficiency. However, the published primers worked well enough for GeneScan with a FAM label on the F primer.M16 = DYS214b (266 bp) C to A tgttatgtcatttgaacccagGAACCAATCTTCGAACMCTCAGTTTTCTGGCCAAAGTTGGAGTCAAATGAGGATTGGATTTGTCAGCTTTTAATAGAACATATGATGACAAAACCTTCATCTCCCAGGAGGAGATAAATTATGCCCTATG

31、TTGGTGGCAAGGACCTGTCCTCCTTTACCCTCTAAAAACTGGAGGGAGAAAGTCAAAGACTAACTCCTCTGAAAAAGATAAAGTCCCTATTCCTAgacagcccagcaacacacggRev 5-3 = ccgtgtgttgctgggctgtM17 = G10.47a (333 bp)-1bp deletion (4Gs to 3Gs) at position 68ctggtcataacactggaaatcAGATTCTGTCTACTCACCAGAGTTTGTGGTTGCTGGTTGTTACGGGGTTTTTTTAAGTGAATTTTGGGGTTT

32、GTTAAGTGGCCAAACTATTTTTGTGAAGACTGTTGTATGTGGGTTTCAGATGTCTCTACATCAGTTTGTGGTCAGCTAGTGAGTTAAATTTTATGAAAAGCCTGGAGAAACAAGAATAGCAGTAAAAACTTCCAGTCTTTGTAGATTGGGTGTCTTCAGTGCTTAGCTGGGCAATTTAAAACTTACCTTAAGTAGTACAGTTGGCCCTTTGTGTCTGTgagtttcacatttgtaggttcaRev 5-3 = tgaacctacaaatgtgaaactM18 = G10.47b (333 bp = ancestral size) +2 bp (extra AA) insertion after position 62 ctggtcataacactggaaatcAGATTCTGTCTACTCACCAGAGTTTGTGGTTGCTGGTTGTTAAACGGGGTTTTTTTAAGTGAATTTTGGGGTTTGTTAAGTGGCCAAACTATTTT