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LOCUS JF320007 4930 bp RNA linear VRL 11-MAR-2011
DEFINITION HIV-1 isolate 502-1055_RH04 from USA pol protein (pol) gene,
partial cds; and vif protein (vif), vpr protein (vpr), vpu protein
(vpu), envelope glycoprotein (env), and nef protein (nef) genes,
complete cds
ACCESSION JF320007
VERSION JF320007.1 GI:325634549
KEYWORDS .
SOURCE Human immunodeficiency virus 1 (HIV-1)
ORGANISM Human immunodeficiency virus 1 Viruses; Retro-transcribing viruses;
Retroviridae; Orthoretrovirinae; Lentivirus; Primate lentivirus
group
REFERENCE 1 (bases 1 to 4930)
Show all sequences for reference 1
AUTHORS Rolland,M., Tovanabutra,S., deCamp,A.C., Frahm,N., Gilbert,P.B.,
Sanders-Buell,E., Heath,L., Magaret,C.A., Bose,M., Bradfield,A.,
O'Sullivan,A., Crossler,J., Jones,T., Nau,M., Wong,K., Zhao,H.,
Ragui,D.N., Sorensen,S., Stoddard,J.N., Maust,B.S., Deng,W.,
Hural,J., Dubey,S., Michael,N.L., Shiver,J., Corey,L., Li,F.,
Self,S.G., Kim,J., Buchbinder,S., Casimiro,D.R., Robertson,M.N.,
Duerr,A., McElrath,M.J., McCutchan,F.E. and Mullins,J.I.
TITLE Direct Submission
JOURNAL Submitted (08-FEB-2011) Microbiology, University of Washington, Box
358070, Seattle, WA 98195, USA
REFERENCE 2
Show all sequences for reference 2
AUTHORS Rolland,M., Tovanabutra,S., deCamp,A.C., Frahm,N., Gilbert,P.B.,
Sanders-Buell,E., Heath,L., Magaret,C.A., Bose,M., Bradfield,A.,
O'Sullivan,A., Crossler,J., Jones,T., Nau,M., Wong,K., Zhao,H.,
Raugi,D.N., Sorensen,S., Stoddard,J.N., Maust,B.S., Deng,W.,
Hural,J., Dubey,S., Michael,N.L., Shiver,J., Corey,L., Li,F.,
Self,S.G., Kim,J., Buchbinder,S., Casimiro,D.R., Robertson,M.N.,
Duerr,A., McElrath,M.J., McCutchan,F.E. and Mullins,J.I.
TITLE Genetic impact of vaccination on breakthrough HIV-1 sequences from
the STEP trial.
JOURNAL Nat. Med.. 17(3); 366-71 (2011)
PUBMED 21358627
COMMENT Annotation information was provided by the author. Some of the
information does not have GenBank feature identifiers and is being
provided in the comment section. Information in this section is
searchable in HIV Database at Los Alamos (www.hiv.lanl.gov).;
##HIVDataBaseData-START## Patient cohort HVTN 502 Patient code
502-1055 Patient sex M HLA type B*4011 CW*0702 A*3101 CW*0304
A*2901 B*0702 Sample date Jan-2006 Days from last seronegative
sample 28 Days between evidence of infection and sampling 0 Sample
tissue plasma Molecule RNA Viral Load 67000 Sequence name
502-1055_RH04 Subtype B ##HIVDataBaseData-END##
FEATURES Location/Qualifiers
source 1..4930
/organism="Human immunodeficiency virus 1"
/mol_type="genomic RNA"
/isolate="502-1055_RH04"
/isolation_source="plasma from male vaccine recipient
502-1055"
/host="Homo sapiens"
/db_xref="taxon:11676"
/country="USA"
/collection_date="Jan-2006"
/note="subtype: B"
gene <1..538
/gene="pol"
CDS <1..538
/gene="pol"
/codon_start="2"
/transl_table="1"
/product="pol protein"
/protein_id="ADZ32536.1"
/db_xref="GI:325634550"
/translation="KTVHTDNGSNFTSNAVKAACWWAGIKQEFGIPYNPQSQGVVESM
NKELKQIIGQIRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQTKE
LQKQITKIQNFRVYFRDSRDPLWKGPAKLLWKGEGAVVIQDNGDIKVVPRRKAKIIRD
YGKQMAGDDCVASRQDED"
gene 483..1061
/gene="vif"
CDS 483..1061
/gene="vif"
/codon_start="1"
/transl_table="1"
/product="vif protein"
/protein_id="ADZ32537.1"
/db_xref="GI:325634551"
/translation="MENRWQVMIVWQVDRMRIRTWKSLVKHHMHISGKAKKWSYRHHY
ESTNPRVSSEVHIPLGDARLVITTYWGLHTGERDWHLGQGVSIEWRKRRYSTQIDPGL
ADQLIHLYYFDCFSESAIRKAILGHIVSPRCEYQAGHNKVGSLQYLALAALITPKKRK
PPLPSVAKLIEDRWNKPQKTKGHKGSHTMSGH"
gene 1001..1291
/gene="vpr"
CDS 1001..1291
/gene="vpr"
/codon_start="1"
/transl_table="1"
/product="vpr protein"
/protein_id="ADZ32538.1"
/db_xref="GI:325634552"
/translation="MEQAPEDQGPQREPYNEWTLELLEELKHEAVRHFPRLWLHGLGQ
HIYETYGDTWAGVEALIRMLQQLIFVHFRIGCRHSRIGSLRRRRARNGASRS"
gene 1504..1755
/gene="vpu"
CDS 1504..1755
/gene="vpu"
/codon_start="1"
/transl_table="1"
/product="vpu protein"
/protein_id="ADZ32539.1"
/db_xref="GI:325634553"
/translation="MTHLVIYAIVALVVVGIIAIIVWSIVLIEYRKILRQRRIDRLID
RIRDREEDSGIESDGDREELSALVVEMGHHAPWDGNDDL"
gene 1667..4231
/gene="env"
CDS 1667..4231
/gene="env"
/codon_start="1"
/transl_table="1"
/product="envelope glycoprotein"
/protein_id="ADZ32540.1"
/db_xref="GI:325634554"
/translation="MRVMETGKNYQHWWWRWGTMLLGMVMMICSAAEKDQFWVTVYYG
VPVWKEATTTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIVMENVTEDFNMWKNN
MVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTNVTMANSMTNDTSDKITDGMKNCSF
EIATEIRDKMQKQYAVFYNLDIVPINDNTNSSATNYRLISCNTSAITQACPKVSFEPI
PIHYCTPAGFAILKCNDKKFNGTGPCKNVSTVQCTHGIRPVVSTQFLLNGSLAEEEVM
IRSANFSNNAKTIIVQLNQSVVINCTRPNNNTRKSIHIAPGRTFYATGEIIGDIRQAH
CNISRTAWNNTLKMVAEKLREQFNKTIIFNRSSGGDLETVTHSFNCGGEFFYCNTTAL
FNSTWGANSTWEITNDTEIILPCRIRQIINMWQEVGKAMYAPPISGNISCSSNITGLL
LTRDGGNGNGTKNETFRPTGGDMRDNWRSELYKYKVVRIEPLGVAPTKAKRRVVQREK
RAVGLGAXFLGFLGAAGSTMGAASVTLTVQARQLLSGIVQQQSNLLRAIEAQQHMLQL
TVWGIKQLQARVLAVERYLKDQQLLGIWGCSGKLICPTAVPWNISWSNKTQDEIWNNM
TWMQWEREIDNYTGLIYTLIEKSQSQQEKNEQELLELGKWASLWSWFDITNWLWYIRI
FIMIVGGLVGLRIVFTVLSIVNRVRKGYSPLSFQTHSPAPRGPDRPEGIEEEGGERDR
DRSGRLVTGFLAIIWVDLRSLILFLYHRLRDLLLIVTRIVELLGRRGREILKLWWNLL
QYWSQELKNSAVSLLNTTAIVVAEGTDRIIEFLQRAFRAILHIPTRIRQGFERALL"
gene 4233..4850
/gene="nef"
CDS 4233..4850
/gene="nef"
/codon_start="1"
/transl_table="1"
/product="nef protein"
/protein_id="ADZ32541.1"
/db_xref="GI:325634555"
/translation="MGGKWSKRKGDGWPAVRERMRQTEPAAVGVGAASRELEKHGAIT
SNTAANNPDCAWLEAQEEEEVGFPVRPQVPLRPMTYKEALDLSHFLKEKGGLEGLIHS
QKRQDILDLWVYHTQGFFPDWQNYTPGPGVRYPLTFGWCFKLVPVDPEKIEEANKGET
NCLLHPMSQHGIDDPEREVLQWKFDSRLAFHHMARELHPEYYKNC"
BASE COUNT 1716 a 861 c 1211 g 1141 t 1 other
ORIGIN
1 aaaaacagta catacagata atggcagcaa tttcaccagt aatgcagtta aggccgcctg
61 ttggtgggcg gggatcaagc aggaatttgg cattccctac aatccccaaa gtcaaggagt
121 agtagaatct atgaataaag aattaaagca aattatagga cagataagag atcaggctga
181 acatcttaaa acagcagtac aaatggcagt cttcatccac aattttaaaa gaaaaggggg
241 gattgggggg tacagtgcag gggaaagaat agtagacata atagcaacag acatacaaac
301 taaagaacta caaaaacaaa ttacaaaaat tcaaaatttt cgggtttatt tcagggacag
361 cagagatcca ctttggaaag gaccagcaaa gctgctctgg aaaggtgaag gggcagtagt
421 aatacaagat aatggtgata taaaagtagt gccaagaaga aaagcaaaga tcattaggga
481 ttatggaaaa cagatggcag gtgatgattg tgtggcaagt agacaggatg aggattagaa
541 catggaaaag tttagtaaaa caccatatgc atatctcagg gaaagctaag aaatggtctt
601 atagacatca ctatgaaagc actaatccaa gagtaagttc agaggtacac atcccactag
661 gggatgctag attggtaata acaacatatt ggggtctgca tacaggagaa agagactggc
721 atttgggtca gggagtctcc atagaatgga ggaaaagaag atatagcaca caaatagacc
781 ctggcctagc agaccaacta attcacctgt attactttga ttgtttttca gaatctgcta
841 taagaaaagc catattagga catatagtta gtcctaggtg tgaatatcaa gcaggacata
901 acaaggtagg atctctacag tacttggcac tagcagcatt aataacacca aaaaagagaa
961 agccaccttt gcctagtgtt gcaaaactga tagaggacag atggaacaag ccccagaaga
1021 ccaagggcca caaagggagc catacaatga gtggacacta gagcttttag aggaacttaa
1081 gcatgaagct gtcagacact ttcctaggct ttggctccat ggcttagggc aacatatcta
1141 tgaaacttat ggggatactt gggcaggagt ggaagcccta ataagaatgc tgcaacaact
1201 gatctttgtc catttcagaa ttggatgtcg acatagcagg ataggcagtt tgcgacggag
1261 gagagcaaga aatggagcca gtagatccta gactagagcc ctggaagcat ccaggaagtc
1321 agcctaaaac tgcttgtagc aagtgctatt gtaaacagtg ttgctttcat tgccaagttt
1381 gtttcataac aaaaggctta ggcatctcct atggcaggaa gaagcggaga cagcgacgaa
1441 gagctcatca aggcagtgag actcatcaag ttcctctatc aaagcagtaa gtaatacatg
1501 taaatgacac atttagtgat atatgcaata gtagcattgg tagtagtagg aataatagca
1561 ataattgtgt ggtccatagt actcatagaa tataggaaaa tattaagaca aaggagaata
1621 gacaggttaa ttgatagaat aagagataga gaagaagata gtggcattga gagtgatgga
1681 gaccgggaag aattatcagc actggtggtg gagatggggc accatgctcc ttgggatggt
1741 aatgatgatc tgtagtgctg cagaaaaaga tcaattttgg gtcacagtct attatggggt
1801 acctgtgtgg aaagaggcaa ccaccactct attttgtgca tctgatgcta aagcatatga
1861 aacagagaag cataatgtat gggccacaca tgcctgtgta cccacagacc ccaacccaca
1921 agaaatagta atggaaaatg tgacagaaga ttttaacatg tggaaaaata acatggtaga
1981 acagatgcat gaagatataa ttagtttatg ggatcaaagt ctaaagccat gtgtaaaatt
2041 aaccccactc tgtgttactt taaattgcac taatgttacc atggcaaata gcatgacgaa
2101 tgataccagt gacaagatta ccgatggaat gaaaaattgc tcattcgaaa tcgccacaga
2161 aataagagat aagatgcaga aacaatatgc agttttttat aatcttgata tagtaccaat
2221 aaatgataat actaatagta gtgctactaa ctataggttg ataagttgta acacctcagc
2281 cattacacaa gcctgcccaa aggtgtcctt tgaaccaatt cccatacatt attgtacccc
2341 ggctggtttt gcgattctaa aatgtaatga taaaaagttc aatggaacag gaccatgtaa
2401 aaatgttagc acagtacaat gtacacatgg aattaggcca gtggtatcaa cccaatttct
2461 gttaaatggc agcctagcag aggaagaggt aatgattaga tctgccaatt tctcgaataa
2521 tgctaaaacc ataatagtac agctgaatca atctgtagta attaattgta caagaccaaa
2581 caacaataca agaaaaagta tacatatagc accagggaga acattttatg caacaggaga
2641 aataatagga gatataagac aagcacattg caacattagt agaacagcat ggaataacac
2701 tttgaaaatg gtagctgaaa aattaagaga acaatttaat aaaacaataa tctttaatcg
2761 ttcctcagga ggggacctag aaactgtaac acacagtttt aactgtggag gggaattttt
2821 ctattgtaac acaacagcac tgtttaatag tacttggggg gctaacagta cttgggagat
2881 tacaaatgac actgaaatca tactcccatg cagaataaga caaatcataa acatgtggca
2941 ggaagtagga aaagcaatgt atgcccctcc cattagtgga aacattagtt gctcatcaaa
3001 tattacaggg ttactattaa caagagatgg gggtaatgga aatggtacca aaaacgagac
3061 cttcagacct acaggagggg atatgaggga caattggaga agtgaattgt ataaatataa
3121 agtagtaaga attgaaccat taggagtagc acccaccaag gcaaagagaa gagtggtgca
3181 gagagaaaaa agagcagtgg gactaggagc trtgttcctt gggttcttgg gagcagcagg
3241 aagcactatg ggcgcagcgt cggtaacgct gacggtacag gccagacaat tattgtctgg
3301 tatagtgcag cagcagagca atctgctgag agctattgag gcgcaacagc atatgttgca
3361 actcacagtc tggggcatca agcagctcca ggcaagagtc ctggctgtgg aaagatacct
3421 aaaggatcaa cagctcctgg ggatttgggg ttgctctgga aaactcatct gccccactgc
3481 tgtgccttgg aatattagtt ggagtaataa aactcaggat gaaatttgga ataacatgac
3541 ctggatgcag tgggaaagag aaattgacaa ttacacaggc ttaatataca ccttaattga
3601 aaaatcgcag agccaacaag aaaagaatga acaagaatta ttggaattgg gtaaatgggc
3661 aagtttgtgg agttggtttg atataacaaa ttggctgtgg tatataagaa tattcataat
3721 gatagtagga ggcttggtag gtttaagaat agtttttact gtgctttcta tagtaaatag
3781 agttaggaag ggatactcac cactatcgtt tcagacccac tccccagccc cgaggggacc
3841 cgacaggccc gaaggaatcg aagaagaagg tggagagaga gacagagaca gatccggacg
3901 attagtgact ggattcttag caatcatttg ggtcgaccta cggagcctga ttcttttcct
3961 ctaccaccgc ttgagagact tactcttgat tgtaacgagg attgtggaac ttctgggacg
4021 cagggggcgg gaaattctca aactttggtg gaatctcctg cagtattgga gtcaggaact
4081 aaagaatagt gctgttagct tgctcaatac cacagcaata gtagtagctg aggggacaga
4141 taggattata gaattcttac aaagagcttt tagagctatt ctccacatac ctacaagaat
4201 cagacagggc tttgaaaggg ctttgctata agatgggtgg caagtggtca aaacgcaagg
4261 gggatggatg gcctgctgta agagaaagaa tgagacaaac ggagccagca gcagttgggg
4321 taggggcagc ctctcgagag ctagaaaaac atggagcaat cacgagtaat acagcagcta
4381 acaatcctga ttgtgcctgg ctagaagcac aagaggaaga ggaagtgggt tttccagtca
4441 gacctcaggt acctctaaga ccaatgactt acaaggaagc tttagatctt agccactttt
4501 taaaagaaaa ggggggactg gaagggctaa ttcactcaca aaaaagacaa gatatccttg
4561 atctgtgggt ctaccacaca caaggcttct tccctgattg gcagaactac acaccagggc
4621 caggggtcag atacccattg acctttggat ggtgcttcaa gctagtacca gtagatccag
4681 agaagataga agaggccaat aaaggagaga ccaactgctt attacaccct atgagccagc
4741 atgggataga tgacccggag agagaagtgt tacagtggaa gtttgacagc cgcctagcat
4801 ttcatcacat ggcaagagag ctgcatccgg agtactacaa gaactgctga catcgagctt
4861 tctataaggg actttccgct ggggactttc caggggaggc gtggcctggg cgggacaggg
4921 gagtggcgag
//
last modified: Tue May 31 10:56 2022