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LOCUS JF320083 4957 bp RNA linear VRL 11-MAR-2011
DEFINITION HIV-1 isolate 502-0346_RH06 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 JF320083
VERSION JF320083.1 GI:325635117
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 4957)
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
502-0346 Patient sex M HLA type B*4403 CW*1601 A*2402 CW*0202
A*0201 B*1501 Sample date May-2006 Days from last seronegative
sample 38 Days between evidence of infection and sampling 0 Sample
tissue plasma Molecule RNA Viral Load 390000 Sequence name
502-0346_RH06 Subtype B ##HIVDataBaseData-END##
FEATURES Location/Qualifiers
source 1..4957
/organism="Human immunodeficiency virus 1"
/mol_type="genomic RNA"
/isolate="502-0346_RH06"
/isolation_source="plasma from male placebo recipient
502-0346"
/host="Homo sapiens"
/db_xref="taxon:11676"
/country="USA"
/collection_date="May-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="ADZ33028.1"
/db_xref="GI:325635118"
/translation="KTIHTDNGTNFTSTTVKAACWWAGVKQEFGIPYNPQSQGVVESM
NKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIASDIQTKE
LQKQITKIQNFRVYYRDSRDPLWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRD
YGKQMAGDDCVASRQDED"
gene 483..1061
/gene="vif"
CDS 483..1061
/gene="vif"
/codon_start="1"
/transl_table="1"
/product="vif protein"
/protein_id="ADZ33029.1"
/db_xref="GI:325635119"
/translation="MENRWQVMIVWQVDRMRISTWKSLVKHHMHISKKAKKWIYRHHY
ENTHPRISSEVYIPLGDAKLVVTTYWGLHTGERDWHLGQGVSIEWRKRRYSTQVDPGL
ADRLIHLYYFDCFSESAIRKAIVGRIVSPRCEYQAGHNKVGSLQYLALAALTTPQKTK
PPLPSVAKLTEDRWNKPQKTKGHRGSHTMNGH"
gene 1001..1294
/gene="vpr"
CDS 1001..1294
/gene="vpr"
/codon_start="1"
/transl_table="1"
/product="vpr protein"
/protein_id="ADZ33030.1"
/db_xref="GI:325635120"
/translation="MEQAPEDQGPQREPYNEWTLELLEELKREAVRHFPRPWLHGLGQ
HIYETYGDTWAGVEAIIRILQHLLFIHFRIGCQHSRIGIIQQRRARRNGASRS"
gene 1506..1745
/gene="vpu"
CDS 1506..1745
/gene="vpu"
/codon_start="1"
/transl_table="1"
/product="vpu protein"
/protein_id="ADZ33031.1"
/db_xref="GI:325635121"
/translation="MQPLQIAAIVALVVAAIIAIVVWTIVLIEYKKILRQRKIDRLID
RIRERAEDSGNESEGDQEELLVEMGHHAPWDVDDL"
gene 1669..4227
/gene="env"
CDS 1669..4227
/gene="env"
/codon_start="1"
/transl_table="1"
/product="envelope glycoprotein"
/protein_id="ADZ33032.1"
/db_xref="GI:325635122"
/translation="MRVKGTRKNYLWRWGTMLLGMLMICSATANLWVTVYYGVPVWKE
ANTTLFCASDAKAVNTEKHNVWATHACVPTDPNPQEVVMGNVTENFNAWKNNMVEQMQ
EDMISLWDQSLKPCVKLTPLCVTLECSNLNKTANLSDNGKEELKNCSFNVTTSIRDKV
RKEYALFYNLDIVQIDDKNNNTNNTKYRLTHCNTSVITQACPKASFEPIPIHYCAPAG
FAILKCNNESFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEKEIVIRSENISDN
AKTIIVQLKKPVQINCTRPNNNTRKSIPIGPGKAFFATGEIIGDIRQAHCILNRTQWN
NTLGEIAKKLGEIFGQNKTIVFNKSSGGDPEIVMHSFNCGGEFFYCNSTPLFNSTWNA
NGTWNGTGNLTTGNITLTCRIKQIINMWQEVGKAMYAPPIRGLISCSSNITGLLLTRD
GGEGNDTNNITEVFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQREKRA
VGIGALFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQNNLLRAIEAQQHLLQLTV
WGIKQLQARVLAVERYLKDQQLLGIWGCSGKLICTTAVPWNDSWSNKSMKDIWDNMTW
MQWDREITNYTKVIYSLIEESQNQQEKNEQELLALDKWDSLMNWFSITNWLWYIKIFI
MIVGGLVGLRIVFTVLSVVNRVRQGYSPLSFQTHLPIPREPDRPEGIEEEGGERDRDR
STRLVHGFLPLIWDDLRSLILFSYRRLRDLLLIAARIVELLGRRGWEILKYWWNLLQY
WSQELKNSAVSLLNATAIAVAEGTDRVIEAIQRILRAVLHVPRRIRQGLERILL"
gene 4229..4855
/gene="nef"
CDS 4229..4855
/gene="nef"
/codon_start="1"
/transl_table="1"
/product="nef protein"
/protein_id="ADZ33033.1"
/db_xref="GI:325635123"
/translation="MGGKWSKRRMPGWSDIRERMRRAEPAAEPAADGVGAVSRDLEKH
GAITSSNTAATNADCAWLEAQEEEEVGFPVRPQVPLRPMTYKGALDLSHFLREKGGLE
GLIYSQQRQDILDLWIYHTQGYFPDWQNYTPGPGVRYPLTFGWCFKLIPVEPEQIEEA
NEGENNILLHPMSQHGMDDPEKEVLMWKFDSTLAFHHRARELHPEYYK"
BASE COUNT 1736 a 874 c 1203 g 1144 t
ORIGIN
1 caaaacaata catacagaca atggcaccaa tttcaccagt actacggtga aggccgcctg
61 ttggtgggca ggggtcaagc aggaatttgg cattccctac aatccccaaa gtcaaggagt
121 agtagaatct atgaataaag aattaaagaa aattatagga caggtaagag accaggctga
181 acatcttaag acagcagtac aaatggcagt attcatccac aattttaaga gaaaaggggg
241 gattggggga tacagtgcag gggaaagaat agtagacata atagcatcag acatacaaac
301 taaagaatta caaaaacaaa ttacaaaaat tcaaaatttt cgggtttatt acagggacag
361 cagagatcca ctttggaaag gaccagcaaa gctcctctgg aaaggtgaag gggcagtagt
421 aatacaagat aatagtgaca taaaagtagt gccaagaaga aaagcaaaga tcattaggga
481 ttatggaaaa cagatggcag gtgatgattg tgtggcaagt agacaggatg aggattagca
541 catggaaaag tttagtaaaa caccatatgc acatttcaaa gaaagctaag aaatggattt
601 atagacatca ctatgaaaac actcatccaa gaataagctc agaagtatac atcccactag
661 gggatgctaa attggtagta acaacatatt ggggtctgca cacaggagaa agagactggc
721 acttgggcca gggagtttcc atagaatgga ggaaaaggag atatagcaca caagtagacc
781 ctggcctagc agaccgacta attcatctgt attattttga ttgtttttca gaatctgcta
841 taagaaaagc catagtagga cgtatagtta gtcctaggtg tgaatatcaa gcaggacata
901 ataaggtagg atctctacaa tacttggcat tagcagcatt aacaacacca caaaagacaa
961 agccaccttt gcctagtgtt gcgaagttga cagaggatag atggaacaag ccccagaaga
1021 ccaagggcca cagagggagc catacaatga atggacacta gagctgttag aggagcttaa
1081 gagagaagct gttaggcatt ttcctaggcc atggcttcat ggcttaggac aacatatcta
1141 tgaaacttat ggggatactt gggcaggagt ggaagccata ataagaattc tgcaacacct
1201 gctgtttatt catttcagaa ttgggtgtca acatagcaga ataggcatta ttcaacagag
1261 gagagcaaga agaaatggag ccagtagatc ctagactagc gccctgggag caaccaggaa
1321 gtcagcctag gactgcttgt accaagtgct attgtaaaaa atgttgcctt cattgccaag
1381 tttgtttcat gaaaaaaggc ttaggcatct cctatggcag gaagaagcgg aggcaacgac
1441 gaagatctcc tcaggacagt aagaatcatc aagatcctct accaaagcag taagtagtac
1501 atgtaatgca acctttacaa atagcagcaa tagtagcatt agtagtagca gcaataatag
1561 caatagttgt gtggaccata gtactcatag aatataagaa aatattaaga caaaggaaaa
1621 tagataggtt aattgataga ataagagaaa gagcagagga cagtggcaat gagagtgaag
1681 gggaccagga agaattactt gtggagatgg ggcaccatgc tccttgggat gttgatgatc
1741 tgtagtgcta cagccaattt gtgggtcaca gtctattatg gggtacctgt gtggaaagaa
1801 gcaaatacca ctctattttg tgcatcagat gctaaggcag ttaatacaga gaagcataat
1861 gtttgggcca cacatgcctg tgtacccaca gaccccaacc cacaagaagt ggtaatggga
1921 aatgtgacag aaaattttaa tgcatggaaa aataacatgg tagaacagat gcaggaggat
1981 atgatcagtc tatgggatca aagcctaaag ccatgtgtaa aattaacccc actctgtgtt
2041 actttagagt gctctaattt gaataagacc gctaacctta gtgataatgg gaaggaagaa
2101 ctaaaaaact gctctttcaa tgtcaccaca agtataagag ataaggttcg gaaagaatat
2161 gcactttttt ataatcttga tatagtacaa atagatgata agaataataa taccaataat
2221 actaaatata ggttgacaca ttgtaacacc tcagtcatta cacaggcctg tccaaaggca
2281 tcatttgagc caattcccat acattattgt gccccagctg gttttgcgat tctaaaatgt
2341 aacaatgaga gtttcaatgg aacaggaccc tgtacaaatg tcagtacagt acaatgtaca
2401 catggaatta gaccagtagt gtcaactcaa ctgctgttaa atggcagtct agcagaaaaa
2461 gagatagtga ttagatctga aaatatcagt gataatgcta aaaccataat agtacagctg
2521 aaaaaacctg tacaaattaa ttgtacaaga cccaacaaca atacaagaaa aagtatacct
2581 ataggaccag ggaaagcctt ctttgcaaca ggggaaataa taggagatat aagacaagca
2641 cattgtatcc ttaatagaac acaatggaat aacactttag gagagatagc taaaaaatta
2701 ggggaaatat ttggccaaaa taaaacaata gtctttaata aatcctcagg aggggaccca
2761 gaaattgtta tgcacagttt taattgtgga ggggaatttt tctactgtaa ttcaacacca
2821 ctgtttaata gtacttggaa tgctaatggt acttggaatg gtaccggaaa tttaactact
2881 ggaaacatca cactcacatg tagaataaaa caaattataa acatgtggca ggaagtagga
2941 aaagcaatgt acgcccctcc cataagagga ctaattagtt gttcatcaaa tattacagga
3001 ctgttattaa caagagatgg tggtgaaggt aatgacacca acaatatcac cgaggtcttt
3061 agacctggag gaggagatat gagggacaat tggagaagtg aattatataa atataaagta
3121 gtaaaaattg agccattagg agtagcaccc accaaggcaa agagaagagt ggtgcagaga
3181 gaaaaaagag cagtgggaat aggagctctg ttccttgggt tcttgggagc agcaggaagc
3241 actatgggcg cagcgtcgat gacgctgacg gtacaagcca gacaactatt gtctggtata
3301 gtgcaacagc agaacaatct gctgagagct attgaagcgc aacaacatct gttgcaactc
3361 acagtctggg gcatcaagca gctccaggca agagtcctgg ctgtggaaag atacctaaag
3421 gatcaacagc tcctgggaat ttggggttgc tctggaaaac tcatttgcac cactgctgtg
3481 ccttggaatg atagttggag taataaatct atgaaagata tttgggataa catgacctgg
3541 atgcagtggg acagggaaat taccaattac acaaaagtaa tatattcctt aattgaagaa
3601 tcgcagaacc aacaagaaaa gaatgaacaa gaattattgg cattagataa gtgggacagt
3661 ctgatgaatt ggttttccat aacaaactgg ctgtggtaca taaaaatatt cataatgata
3721 gtaggaggtt tggtaggttt aagaatagtt tttactgtac tttctgtagt gaatagagtt
3781 aggcagggat attcaccatt gtcatttcag acccacctcc caatcccgag ggaacccgac
3841 aggcccgaag gaatcgaaga agaaggtgga gaaagagaca gagacagatc cactcgatta
3901 gtgcacggat tcttgccact tatctgggac gatctgagga gcctgatcct attcagctac
3961 cgccgcttga gagacttact cttgattgca gcgaggattg tggaactact gggacgcagg
4021 gggtgggaaa tcctcaaata ttggtggaat ctcctgcagt attggagtca ggaactgaag
4081 aatagtgctg ttagtttgct caatgccaca gctatagcag tagctgaggg gacagatagg
4141 gttatagaag caatacaaag aattcttaga gctgttctcc acgtacctag aagaataaga
4201 cagggcttgg aaagaatttt gctataagat gggtggcaag tggtcaaaac gtaggatgcc
4261 aggatggtct gatataagag aaagaatgag aagagctgag ccagcagcag agccagcggc
4321 agatggggtg ggagcagtat ctcgagacct agaaaaacat ggagcaatca caagtagcaa
4381 tacagcagct actaatgctg attgtgcctg gctagaagca caagaagagg aagaggtggg
4441 ttttccagtc agacctcagg tacctttaag accaatgact tacaagggag ctttagatct
4501 tagccacttt ttaagagaaa aggggggact ggaagggtta atttactccc aacaaagaca
4561 agatatcctt gatctgtgga tctaccacac acaaggctac ttccctgatt ggcagaacta
4621 cacaccaggg ccaggggtca gatatcccct gacctttgga tggtgcttca agctaatacc
4681 agttgaacca gagcagatag aagaggccaa tgaaggagag aacaacatct tgttacaccc
4741 tatgagccag catgggatgg atgacccgga gaaagaagtg ttaatgtgga agtttgacag
4801 caccctggca tttcatcacc gagcccgaga gctgcatccg gagtactaca aataaatgct
4861 gacatttaaa actgctgaca tcgagctttc tacaagggac tttccgctgg ggactttcca
4921 ggggaggcgt ggcctgggcg ggactgggag tggcgag
//
last modified: Tue May 31 10:56 2022