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NBRP Genome Information Upgrading Program in FY 2007

SNP information in laboratory strains of Drosophila melanogaster and its sibling species (ver. 1, 2008.3.31, English 2009.09.09)

Single nucleotide polymorphisms (SNPs) among the strains maintained in DGRC were searched for by partial sequencing of selected 100 genes that are equally distributed throughout the genome. A total of 40 strains were examined, that consist of 32 strains from D. melanogaster, five strains from D. simulans, two strains from D. sechellia and one strain from D. mauritiana.

Strains used

StrainDGRC No.Genotype
S01201218y[1] w[67c23] P{w[+mC]=GSV2}GS7375/Binsinscy
S02201414y[1] w[67c23] P{w[+mC]=GSV3}GS8136/Binsinscy
S03202495y[1] w[67c23]; P{w[+mC]=GSV6}GS10348/TM3, Sb[1] Ser[1]
S04103518y[*] w[*]; P{GawB}NP0080 / CyO, P{UAS-lacZ.UW14}UW14
S05105125y[*] w[*] P{GawB}NP6099 / FM7c
S06120218LA00218
S07120709LA00709
S08110606FlyTrap: G00147 III
S09105666Canton-S
S10109019Canton-S-brn
S11107655Harwich
S12103421Hikone-R
S13105669Oregon-R-C
S14107294Oregon-R-P2
S15107658Oregon-R-S
S16103453Staket
S17106267t[1] v[1] m[74f] wy[74i] sd[1] os[s]
S18106359y[1] cv[1] v[1] f[1] car[1]
S19107867y[1] pn[1] cv[1] v[1] f[1] B[1]
S20105790al[1] b[1] c[1] sp[2]
S21105837b[1] elA[1] rd[s] pr[1] cn[1] or[49h]
S22106283ast[1] dpp[d-ho] ed[1] dp[ov1] cl[1]
S23106383al[1] b[1] cn[1] sp[1]
S24105729ru[1] h[1] st[1] ry[506] e[1]
S25105998se[1] ss[1] k[1] e[s] ro[1]
S26106007st[1] Sb[sbd-1] e[s] ro[1] ca[1]
S27106315nub[1] b[1] rdo[1] hk[1] pr[1] cn[1]
S28106317ru[1] h[1] W[1] Sb[sbd-2] Tb[1]
S29106365ru[1] h[1] Ki[1] rn[roe-1] p[p] ro[1] ca[1]
S30106022ci[1] gvl[1] ey[R] sv[n]
S31102043y[1] Hw[1] v[1] Ubl[1] / FM7c
S32106681C(1)RA60g, y[1] B[1] w[a]/FM7c/Dp(1;Y)su(f)[+]
S33D.simulans Rak
S34D.simulans S2
S35D.simulans Lhr
S36D.simulans exf p
S37D.simulans L3
S38D. sechellia SS01
S39D. sechellia SS51
S40D. mauritiana jbw

Methods and Results

Coding region of each gene was amplified from genomic DNAs of each strain by PCR using a primer set shown in the table below. Each PCR-amplified fragment was then sequenced using the same primer set. The sequence information obtained was compared with a publicly available D. melanogaster genome sequence (ST) and SNPs were searched for using novoSNP(1).

Click each Position, e.g. P001, in the table. A new window or tab will open and show SNPs (not a sequenced genome, SNP sites only).

Genes studied

PositionGene symbolChromosome(arm)Cytogenetic mapPrimer(L)Primer(R)
P001ewgX1A1-1A1TCTGTTTGTCATCCTCTGAACGCAAAGGAGTTCGACTGGAAATG
P002CG14786X2A4-2A4GAACTCATGCGACACCTTCAGTCAGATTGACGAGCACAAAGTG
P003CG10260X3A8-3A8GTTCAGCTTCTGCTTGAACACCGTTTATTCTGCAGCTCCGTTTG
P004CG32779X3F2-3F2AAGTTCGACGATCAGGAGGATTGATCCGAGAGATTGATTTGTGC
P005rgX4F3-4F3AATCACAACAGCAACATGCAACATTTATGGCGCTCGTCTTGTAG
P006CG14446X5E1-5E1CATTTGGTTCGCTCCAGTGTATGTTCATCACCTCCCAGATTTTG
P007CG9657X7B2-7B2ATCCATATAGTGACGCCCATTGTTCTCCGGCAAACGTATAATTG
P008CG12125X7E9-7E9CAAGATCCTTGAACGAATCGAGCAGCTCGGTAGTCACACAACTG
P009nejX8F7-8F9TAGAGTCGCTCCACAAACTTGGCAAGATGCGTTACATGCAAATG
P010CG2145X9F11-9F12CTGGTTTGGTGGATTCAAGAAGTGGTGTACAGTAGCTCCGTCAG
P011CG1492X11A1-11A1CTTGACGAATCCAAACTTCATTGAAGTCCTGGAGAATGGAGGAAG
P012HDAC4X11E8-11E9GTAGTGCGTTTGGACCACATTCACTGCAACAGTACACCGGATTC
P013CG9411X12E10-12E10ACGAGCTGTTCGTCAGTGAGTCCACCCAAGCTGAACTTCCTG
P014CG15599X13E6-13E7GATCCAGCGGACACACTAATTCGTTTTGGAAGAAAGCAGCTGTG
P015CG9609X15A8-15A8TTTGGATAGCCTCGAATGTTTGCGACAAGACGTACTCGATTGTG
P016Dhc16FX16F6-16F6CTTAAGTTCACCACCCAGATGCGTGGATGGGTTCCCTCTTAATC
P017CG7876X18B1-18B1AGTGGATAACACACCCGACTTCAGTCGTAAGACGCTGAGCAAAC
P018RhoGAP19DX19D1-19D2TTAGCCTGCTGCTAGAGTCGTCCTGCCGGATATAGCCGAAGTA
P019mstX20A1-20A1GAGACCATCTGGCGAAACAATAATACTGCGAGTCTGCGTAAAGG
P020CG41642L21C2-21C2GGCCGGGACTTCTACAAAATACCTTGTCCTCCTCCGTAAGATCC
P021frtz2L22B1-22B1GGCTATCTTGTGCAGCGTAATCGCTGGAATCGATTGCCTATTG
P022CG88132L23B7-23B8TGCTATCAACCTATCAGCACGATCGAGATGCACTAGTCTTTGGAC
P023CG319612L24D8-24D8TAATCCTTGAGGAGGCTCCAGTCGAGCGTTTGAACAAAAGAAAC
P024Msp-3002L25C7-25C10CAACAGGTTAGCAAGGATCTCGCTCCTGCAGTTTGTCCTTGAGA
P025Tig2L26D1-26D1CTGCTCCACAGTGACATGGTAGGAACGGACAGTTTGAGATCGAG
P026CG137922L28B4-28C1GGGACGTATATTTCCGAAGGAGATATCAAGCGATTCGGAGGAAG
P027CG94652L29F1-29F1AAAAGTGCGAATTTGCATAGGACCAGAACTTTGGCGTTTACAAG
P028CG47092L30F2-30F2AAAGAACAATCTGCAGGAGCTGTTCCGTCGGCTTAAAGGTAAAC
P029RfC382L32D4-32D4AAAAATCATCCGTCATGTCCAGCAATCGGAAGGTAGAGGTGATG
P030CG63882L33E4-33E4CTCCGGAAGCTTGCTATGTAAATTCATCGAACTCGTAGACAGCA
P031CG318472L34C3-34C3AGCAGATTGCCAAACGTACAACTGACGGATGTGATTTTTGATGA
P032CG318352L35B5-35B5CAAATGACGATCTTCCAGGGTATCACTGACATGACCTTGACCAG
P033TepI2L35D6-35D6CGTTCGGTGGCATAGTAATCATCGCAATGCCTATAAAGTTCTGG
P034CG63042L36B6-36B6CCAATTGAGGCACTTTCAGTTCTACGCCCTCAAAAGTCCATTTA
P035kel2L36E5-36E6GCAAACTGGACTTGGAGATACGGAACAATGCGATACGAGAACATC
P036CG175442L37D4-37D5GAGTAACGAACTGCGATTACGGGAGAATGACCCCCTTTTTGC
P037phr6-42L38D2-38D2TGATTTCTCCTCGAAAGACGACGGAGGAATCCCTAAAGGATGAA
P038CG116342L40B4-40B4CACTGGATCATGTCGTCACCTAAAAAGAAGATAGCTGCGTGCTC
P039Atf62R41D4-41E1ACGCCATGTTTATTTTCAGACGTAGGGAATCGCATTCTTTTTCA
P040bin32R42A13-42A14ACCAATTAAAATGCTGCCAAAGCCCAGTTTTGGGCTTCAAGTAT
P041az22R43D1-43D1CAAGACTAACTCGCTCCGAGAAAGTTTCCCCAACTGTACGATCC
P042gcl2R44E3-44E3TATACAAGGCGCTCTTCAAGGAATCCATGTAGTGGTTGGTCAGG
P043CG129232R46C2-46C2GAGTTTCTGGACCCAAAGATCCACGTCAGACGCCAGTAACTTTC
P044Cyp12d1-p2R47D4-47D4ACGAACATGGTCTTGAATGGACCCAGACCTCGAGGGATATTTTC
P045CG339642R48E6-48E7CCTGCCTTGGAAAACTACAAGATATTGTTGCGTTTGCTGCTTTA
P046CG108142R50A3-50A3TGCCCTCCAGATATTGTGAAACTTAAGTTGGCTCTGCCAAAGG
P047RpI12R51B4-51B6CTAAAAGGTTTGCCAACGTCACTTCAGTTCCTATATGGCGAGGA
P048Poxn2R52C7-52C7AGCAGTTCTTCGATGGAGTACGAAGAAGATCATCCGGCTAAAGG
P049CG67962R53E4-53E4GGTTATCCCTTCAGTCCCAAACAAGCTGCAAGTAACGCTCAAAG
P050CG57262R55B12-55B12ATTCGCTTGATACGAGAGTCCAATGGAGTACCTGAACGACAAGG
P051CG100512R56D2-56D2CCTTGGTAAACCTGGATTCGACTATTTGCACCAGAACGGAAATC
P052Hil2R57A7-57A7AATCGAGAGTCCTGGAACTTGACAGGAGGAGGATGACCTATACCG
P053CG179222R57F9-57F9AGAGATCCACCACCTTCATGTCCTTTGCCCATCAATTTGAAAAC
P054CG38312R59B6-59B7TCCCCAGTGCTGTGAGATTTAGCATAGTGCCCAGTGGCTTTAAC
P055CG167862R60B8-60B9GTCACCTCAACCATTGAGAAGGGGAACGACAGAGGTTGAGAAGA
P056CG70283L61B2-61B2GCGCTTCTTTCTACGTAGCTCAATGCCGCCAGTCCTATTATTTT
P057CG24693L61F5-61F6CCTGCCAAGATCTTCTCTCTCATCGAGATCTTGAACGGGAACT
P058msn3L62E6-62E7CAGCACAATGACGGATTCAGAACATAAACCGCCTGCAAAAG
P059CG11203L63F1-63F1ACAAATGCCCTCAGAAATGAGACCTTTGGAACTGATCCGTATTG
P060Con3L64C2-64C4TCGTCTAGTTCCAGCTCACTCAGGCAACAACATGAACAATGGCTA
P061l(3)mbn3L65A6-65A6GGTGGTCTTGTCTTCGTATTGGTGTTCCGGTTGTTTCCTAAAAA
P062mus3123L65F4-65F5TTATAAATCTCTGGCGGTCCTGGAAGATGATCGTTCGCTAATGC
P063CG67653L66D5-66D5AATCCCAATGGAGTGCTGTATGAAGTGCCTGCTCCTCGTACTC
P064CG167193L67C4-67C5TAAAATCCGAAAACCCCAAATCAAATCCATCCGTTGGCTAAAAG
P065CG64093L67F1-67F1GATGTGGAGATTGTGGATGGACCACCTCTGGATGTCAAGGAGTC
P066Sema-5c3L68F2-68F2CATGGCACCATTTCACACTTCACCCAAGTGACGAACTGCAC
P067CG176873L70A5-70A5ACAACAATGGCGAAATCTATGCAAGTTGAGAAAACGGCAGATCA
P068CG79063L70D4-70D4CCTGATAACCAGCCACATCAATAGCAGTTCCACTGACTCAGCTC
P069RhoGAP71E3L71E1-71E2ATTGGAGAACAGTGTCCTGTCGCAGATACGAGAGGCTCTTGGTG
P070CG96743L73C4-73D1AGACTTGGCTATCTTGGCCTTCCGAGAAGGAGTTCGATGATCTG
P071Grd3L75A3-75A4GTCACATGGGCAACTTTCTGATGATGAATAGCAGTGGGAAGACG
P072BG6423783L75F9-75F9CGGCATCGAAGGAATTATACTGTTTGACAAAGCAACTGAGCAAG
P073CG56183L77B5-77B5CATCTGCAAGTTAGCGGGATACGAACCAAAAGCAGACATTGGAG
P074CG71773L78D5-78D6AAATGATTTGGAACTGCACCTGGCGTTTTAGTGTCAGTCGTGTG
P075CG112413L80A1-80A1CAGCCAGACCTTTGAGGAAGTAAAACATCTACATGCACCCCAAG
P076CG146563R82D5-82D5CGAGAGGTCTTCTTCCTCGATTCTTAGGTGCAGCAAGCTTTGAC
P077CG114593R83D2-83D2CCGACTAAAAGAACGGAGTGTGTAATCCTTCTGCTCCTTGTGGA
P078sas3R84C8-84D1AAGGACGAGGAGAAGAGACCACAGGATTGTCTGCTGCAAGTGTT
P079CG117183R84F15-84F15GGCGTACTTCTGTAGCGTCTTGGTGAGTTCCACGAGCACTATCC
P080RnpS13R85D24-85D24CTCCTCGAGCTCCTCATCATCGGTTCCTCATGGGTGACTGAC
P081Cap-H23R86C5-86C6AGTTGATCCCTATTTGCTCACGTTCCATACTGATCCCTGAATCG
P082Cad87A3R87A1-87A1GTGTGGAACAGGAGCTGGTAGTTCAGACAGGAGAACTGCGTACA
P083CG101483R87D13-87D13CACTGGCATCCAACTCCTTTAGATGGTGAAAATCGTGAACCAAC
P084trx3R88B1-88B1AAAGCGGCACTTATAGGAAAGGCTCCAAGTCGATCAACCGTAAG
P085Rh63R88F6-88F6GCATCATTGGCTTTGTGATTGTCAATCCGTACACAATGGGATT
P086CG149063R89D6-89D6CCTCCTGGTTGCAATGTTCTACCAAAGGCATTGAGGAAGACAAG
P087CG178023R90C5-90C5CAGAACTGGCAAGCGTATGGACCAACAATCGACTGACAATCC
P088gatA3R91E4-91E4GCCTTATACTGTTGCGAGTGCTCTTATTCCGCTGGTCAATTCC
P089CG159233R92F3-92F3ATGAGACGCTCTAGGGTCAGCGGCTGGTCATCTGTCCATCTAT
P090CG79563R93E4-93E4TGTAGACGAGCAAGAGGGCTACCTGTCATCAAATGCTTCGTGAG
P091CG311583R94B5-94B6GACTTATAATGCGCCACTCCAGACACATCGCTCTTCTTGAAACC
P092Nup983R95B1-95B5GAGAGTTTCTTCCAGGGAATGCTTCAGCTTAACGACTGCCTCTC
P093CG110893R96B2-96B2TCTTCTCAGTGTGTCGGACAAGTAATACCATCGGACACCTCTCG
P094CG145563R97A1-97A1CGTCGATGAGAAGGTCAGTTTCTAATTGGCGCTGTCTTCAAGTT
P095CG33393R97F1-97F2CCAGGGTCAGAATCTTGTTGTCGTCGGTCGGAATTTTTATCACC
P096Ppn3R98D3-98D4AATGCAGAAGTTTAGGCAATCGCGAGTGTGCCAACTACGTTACC
P097Kul3R99B9-99B9AAGAGGACAAGAGCGAGGAGTCGTAGTTACCGGGGAATCGGTAG
P098Aph-43R100B1-100B1TACAACGTGGACAAACAAGTGCTTAGCTGTCCCCAGGATATCAG
P099pan4102A4-102A4ATGAGCACGGAAGTCAGCTAAGGCGTTTGGAGGATTGCTAGATA
P100Dyrk34102F-102FACGTCCTTGTTGCTTGAGTAGCGACAAAAGATGTTCCTGGGTTG

Reference

(1) Weckx, S., Del-Favero, J., Rademaker, R., Claes, L., Cruts, M., De Jonghe, P., Van Broeckhove, C., & De Rijk, P., 2005. novoSNP, a novel computational tool for sequence variation discovery. Genome Research 15: 436-442.