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LOCUS JX972230 4520 bp RNA linear VRL 16-MAR-2013
DEFINITION HIV-1 isolate B.700010040.w36.283dps.3_F2 from USA vif protein
(vif) gene, complete cds; pol protein (pol) gene, partial cds; and
vpr protein (vpr), tat protein (tat), rev protein (rev), vpu
protein (vpu), envelope glycoprotein (env), and nef protein (nef)
genes, complete cds
ACCESSION JX972230
VERSION JX972230.1 GI:459963273
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 4520)
Show all sequences for reference 1
AUTHORS Liu,M.K., Hawkins,N., Ritchie,A.J., Ganusov,V.V., Whale,V.,
Brackenridge,S., Li,H., Pavlicek,J.W., Cai,F., Rose-Abrahams,M.,
Treurnicht,F., Hraber,P., Riou,C., Gray,C., Ferrari,G., Tanner,R.,
Ping,L.H., Anderson,J.A., Swanstrom,R., B,C.C., Cohen,M.,
Karim,S.S., Haynes,B., Borrow,P., Perelson,A.S., Shaw,G.M.,
Hahn,B.H., Williamson,C., Korber,B.T., Gao,F., Self,S.,
McMichael,A. and Goonetilleke,N.
TITLE Vertical T cell immunodominance and epitope entropy determine HIV-1
escape
JOURNAL J. Clin. Invest. 123 (1), 380-393 (2013)
PUBMED 23221345
REFERENCE 2 (bases 1 to 4520)
Show all sequences for reference 2
AUTHORS Liu,M., Liu,M.K., Hawkins,N., Ritchie,A., Ritchie,A.J.,
Ganusov,V.V., Ganusov,V., Whale,V., Brackenridge,S., Li,H.,
Pavliceck,J., Pavlicek,J.W., Cai,F., Abrahams,M.-R., Treurnicht,F.,
Hraber,P., Hraber,P.T., Riou,C., Gray,C., Ferrari,G., Tanner,R.,
Ping,L.-H., Anderson,J.A., Anderson,J., Swanstrom,R., Cohen,M.S.,
Cohen,M., Abdool Karim,S., Abdool Karim,S.S., Haynes,B.,
Haynes,B.F., Borrow,P., Perelson,A., Shaw,G., Hahn,B., Hahn,B.H.,
Williamson,C., Korber,B., Korber,B.T., Gao,F., Self,S.,
McMichael,A., McMichael,A.J. and Goonetilleke,N.
CONSRTM CHAVI Core B
TITLE Direct Submission
JOURNAL Submitted (12-OCT-2012) T6 MS K710, LANL, PO Box 1663, Los Alamos,
NM 87545, USA
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-1 Database at Los Alamos (hiv.lanl.gov).;
##HIVDataBaseData-START## Patient code 700010040 Days
post-screening 283 Sample timepoint w36 Patient sex M Fiebig Stage
x Viral Load 7580 CD4 count 994 HLA type A*3101 A*0201 B*4402
B*4001 Cw*0302 Cw*0501 Infection date 2006 ##HIVDataBaseData-END##
FEATURES Location/Qualifiers
source 1..4520
/organism="Human immunodeficiency virus 1"
/mol_type="genomic RNA"
/isolate="B.700010040.w36.283dps.3_F2"
/host="Homo sapiens"
/db_xref="taxon:11676"
/country="USA"
/collection_date="2007"
/note="subtype: B"
gene 1..579
/gene="vif"
CDS 1..579
/gene="vif"
/codon_start="1"
/transl_table="1"
/product="vif protein"
/protein_id="AGG91848.1"
/db_xref="GI:459963275"
/translation="MENRWQVMIVWQVDRMRIRAWKSLVKHHMYVSGRARGWFYRHHY
ESTHPRISSEVHIPLGEGRLVVTTYWGLHTGERNWHLGQGVSIEWRKKRYSTQVDPNL
ADQLIHLYYFDCFSESAIREAILGRIVSPRCDYQAGHNKVGSLQYLALTALIKPKRTK
PPLPSVIKLTEDRWNKPQKTKGHRGSHTMNGH"
gene <1..56
/gene="pol"
CDS <1..56
/gene="pol"
/codon_start="3"
/transl_table="1"
/product="pol protein"
/protein_id="AGG91847.1"
/db_xref="GI:459963274"
/translation="GKQMAGDDCVASRQDED"
gene 519..809
/gene="vpr"
CDS 519..809
/gene="vpr"
/codon_start="1"
/transl_table="1"
/product="vpr protein"
/protein_id="AGG91849.1"
/db_xref="GI:459963276"
/translation="MEQAPEDQGPQREPYNEWTLELLEELKSEAVRHFPRIWLHGLGQ
HIYETYGDTWTGVEALIRILQQLLFVHFRIGCQHSRIGIRQRRRARNGASRS"
gene 790..3398
/gene="tat"
CDS join(790..1004,3308..3398)
/gene="tat"
/codon_start="1"
/transl_table="1"
/product="tat protein"
/protein_id="AGG91850.1"
/db_xref="GI:459963277"
/translation="MEPVDPRLEPWKHPGSQPRTACTNCYCKKCCFHCQVCFITKGLG
ISYGRKKRRPRRRAPQDSQTHQVSLSKQPTSQPRGDPTGPKESEKKVERETETDPIH"
gene 929..3582
/gene="rev"
CDS join(929..1004,3308..3582)
/gene="rev"
/codon_start="1"
/transl_table="1"
/product="rev protein"
/protein_id="AGG91851.1"
/db_xref="GI:459963278"
/translation="MAGRSGDRDEELLKTVRLIKFLYQSNPPPSPEGTRQARRNRRRR
WRERQRQIRSISERILNTYLERSTEPVPLQLPPLERLTLDCNEDCGTSGTQGVGSPQI
LVESPTVLESGTKE"
gene 1021..1266
/gene="vpu"
CDS 1021..1266
/gene="vpu"
/codon_start="1"
/transl_table="1"
/product="vpu protein"
/protein_id="AGG91852.1"
/db_xref="GI:459963279"
/translation="MNSLQISAIVALVVAGIIAIVVWSIVAIEYRKILRQRKIDRLID
RIRERAEDSGNESDGDQEELSALVERGHLALGDINDL"
gene 1184..3724
/gene="env"
CDS 1184..3724
/gene="env"
/codon_start="1"
/transl_table="1"
/product="envelope glycoprotein"
/protein_id="AGG91853.1"
/db_xref="GI:459963280"
/translation="MRVMGIRKNYQHLWREGILLLGILMICSAADNLWVTVYYGVPVW
REATTTLFCASDAKAYDTEAHNVWATHACVPTDPNPQEVELKNVTENFNMWENNMVEQ
MHEDIISLWDQSLKPCVKLTPLCVTLNCTDLGNVTNTTNSNGKMMEKGEVKNCSFKIT
TDIKDRTRKEYALFYKLDVVPINDTRYRLVSCNTSVITQACPKVSFEPIPIHYCAPAG
FAILKCNDKQFIGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRAVNFSDN
AKTIIVQLNKSVEINCTRPHNNTRKSIPMGPGKAFYARGDITGDIRKAYCEINGTEWH
STLKLVVEKLREQYNKTIVFNRSSGGDPEIVMYSFNCGGEFFYCNSTKLFNSTWPWND
TKGSHDTNDTLMLPCRIKQIINMWQGVGKAMYAPPIEGKIRCSSNITGLLLTRDGGYE
SNETDEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQREKRAFGLGAV
FLGFLGAAGSTMGAASITLTVQARQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQL
QARVLAVERYLKDQQLLGIWGCSGKLICTTTVPWNTSWSNKSLEQIWDNMTWMEWERE
IDNYTGYIYQLIEESQNQQEKNEQELLALDKWASLWNWFDITNWLWYIKIFIMIVGGL
IGLRIVFTVLSIVNRVRQGYSPLSFQTHLPAQRGPDRPEGIGEEGGERDRDRSDPLVN
GFLTLIWSDLRSLCLFSYHRLRDLLLIVTRIVELLGRRGWEVLKYWWNLLQYWSQELK
NSAVSLLNATATAVAEGTDRVIEVVQRACRAILHIPRRIRQGLERALL"
gene 3726..4346
/gene="nef"
CDS 3726..4346
/gene="nef"
/codon_start="1"
/transl_table="1"
/product="nef protein"
/protein_id="AGG91854.1"
/db_xref="GI:459963281"
/translation="MGGKWSKCSVVGWPSVRERMRRAEPAAEGVGAVSRDLEKHGAIT
SSNTAATNADCAWLEAQEEGEVGFPVRPQVPLRPMTFKGALDLSHFLKEKGGLEGLIY
SQKRQDILDLWVYHTQGYFPDWQNYTPGPGTRFPLTFGWCFKLVPVDPGKVEEANKGE
NNCLLHPMSQHGMDDPEREVLVWRFDSNLAFRHVARELHPEYYKNC"
BASE COUNT 1526 a 806 c 1129 g 1059 t
ORIGIN
1 atggaaaaca gatggcaggt gatgattgtg tggcaagtag acaggatgag gattagagca
61 tggaaaagtt tagtaaaaca ccatatgtat gtttcaggga gagctagggg atggttttat
121 agacatcact atgaaagcac tcatccaaga ataagttcag aagtacacat cccactaggg
181 gaaggtagat tggtagtaac aacatattgg ggtctgcata caggagaaag aaactggcat
241 ttgggtcaag gagtctccat agaatggaga aaaaagagat atagcacaca agtagaccct
301 aacctagcag accaactaat tcatctgtac tactttgact gtttttcaga atctgctata
361 agggaagcca tattaggacg aatagttagt cctaggtgtg actatcaagc aggacataac
421 aaggtaggat ctctgcagta cttggcacta acagcattaa taaaaccaaa aaggacaaag
481 ccacctttgc ctagtgtaat aaaactgaca gaagatagat ggaacaagcc ccagaagacc
541 aagggccaca gagggagcca tacaatgaat ggacactaga gcttttagag gagcttaaga
601 gtgaagctgt caggcacttt cctaggatat ggctccatgg tttagggcaa catatctatg
661 aaacttatgg agatacttgg acaggagtgg aagccttaat aagaattctg caacaactgc
721 tgtttgttca tttcagaatt gggtgtcaac atagcagaat aggcatcaga caacgaagga
781 gagcaagaaa tggagccagt agatcctaga ttagagccct ggaagcatcc aggaagtcaa
841 cctaggactg cttgtaccaa ttgctattgt aaaaagtgct gctttcattg ccaagtttgt
901 ttcataacaa aaggcttagg catctcctat ggcaggaaga agcggagacc gcgacgaaga
961 gctcctcaag acagtcagac tcatcaagtt tctctatcaa agcagtaagt aatatatgta
1021 atgaactctt tacaaatatc agcaatagta gcattagtag tagcaggaat aatagcaata
1081 gttgtgtggt caatagtagc catagaatat aggaaaatat taaggcaaag aaaaatagac
1141 aggttaattg atagaataag agaaagagca gaagacagtg gcaatgagag tgatggggat
1201 caggaagaat tatcagcact tgtggagaga gggcatcttg ctcttgggga tattaatgat
1261 ctgtagtgct gcagacaact tgtgggtcac agtctattat ggggtacctg tgtggagaga
1321 agcaaccact actctattct gtgcatcaga tgctaaagca tatgatacag aggcacataa
1381 tgtttgggcc acacacgcct gtgtacccac agaccccaac ccacaagaag tagaattaaa
1441 aaatgtgaca gaaaatttta atatgtggga aaataacatg gtagaacaga tgcatgagga
1501 tataatcagt ttatgggatc aaagcttaaa accatgtgta aaattaactc cactctgtgt
1561 tactttaaat tgcactgatt tagggaatgt tactaatacc actaatagta acgggaaaat
1621 gatggagaag ggagaagtaa aaaactgttc tttcaagatc accacagaca taaaagatag
1681 aacgcggaag gaatatgcac ttttttataa acttgatgta gtaccaataa atgataccag
1741 atataggtta gtaagctgta acacctcagt cattacacag gcctgtccaa aggtatcctt
1801 tgagccaatt cctatacatt attgtgcccc ggctggtttt gcgattctaa agtgtaatga
1861 taagcaattc attggaacag gaccatgtac aaatgtcagc acagtacaat gtacacatgg
1921 aattaggcca gtagtatcaa ctcaactgct gttaaatggc agtttagcag aagaagaggt
1981 agtaattaga gcagtcaatt tcagtgacaa tgctaaaaca ataatagtac aactgaataa
2041 atctgtagaa attaattgca caagacccca caacaataca agaaaaagta tacccatggg
2101 accagggaaa gcattttatg caagaggaga cataacagga gacataagaa aagcatattg
2161 tgaaattaat ggaacagaat ggcatagcac tttaaaactg gtagttgaaa aattaagaga
2221 acaatataat aaaacaatag tctttaatcg ctcctcagga ggggacccag aaattgtaat
2281 gtacagtttc aattgcggag gggaattttt ctactgtaat tcaacaaagc tgtttaatag
2341 tacttggcct tggaatgata ctaaagggtc acatgacact aatgacaccc tcatgctccc
2401 atgcagaata aaacaaatta taaacatgtg gcagggagta ggaaaagcaa tgtatgcccc
2461 tcccatcgaa ggaaaaatta gatgctcatc aaacattaca ggactgttat taacaagaga
2521 tggtggttac gagagcaatg agactgatga gatcttcaga cctggaggag gagatatgag
2581 ggacaattgg aggagtgaat tatataaata taaagtagta aaaattgaac cattgggagt
2641 agcacctacc aaggcaaaga ggagagtggt gcagagggaa aaaagagcat ttggactagg
2701 agctgtgttc cttgggttct tgggagcagc aggaagcact atgggcgcag catcaataac
2761 gctgacggta caggccagac aattattgtc tggtatagtg caacagcaga acaatttact
2821 gagggctatt gaggcgcaac agcatctgtt gcaactcaca gtctggggca ttaagcagct
2881 ccaggcaaga gtcctggctg tggaaagata cctaaaggat caacagctcc tggggatttg
2941 gggttgctct ggaaaactca tctgcaccac tactgtgcct tggaatacta gttggagtaa
3001 taaatctctg gaacagattt gggataacat gacatggatg gagtgggaaa gagaaattga
3061 caattataca ggctacatat accaattaat tgaagaatcg cagaaccaac aagaaaagaa
3121 tgaacaagaa ttattggcat tggataaatg ggcaagtttg tggaattggt ttgacataac
3181 aaactggctg tggtatataa aaatattcat aatgatagta ggaggcttaa taggtttaag
3241 aatagttttt actgtacttt ctatagtgaa tagagttagg cagggatact caccattatc
3301 atttcagacc cacctcccag cccagagggg acccgacagg cccgaaggaa tcggagaaga
3361 aggtggagag agagacagag acagatccga tccattagtg aacggattct taacacttat
3421 ctggagcgat ctacggagcc tgtgcctctt cagctaccac cgcttgagag acttactctt
3481 gattgtaacg aggattgtgg aacttctggg acgcaggggg tgggaagtcc tcaaatattg
3541 gtggaatctc ctacagtatt ggagtcagga actaaagaat agtgctgtta gcttgctcaa
3601 cgccacagcc acagcagtag ctgaggggac agatagggtt atagaagtag tacaaagagc
3661 ttgtagagct attctccaca tacctagaag aataagacag ggcttagaaa gggctttgct
3721 ataagatggg tggcaagtgg tcaaaatgta gtgtggttgg atggccttca gtaagggaaa
3781 gaatgagacg agctgagcca gcagcagagg gggtaggagc agtatctcga gacctggaaa
3841 aacatggagc aatcacaagt agcaacacag cagctaccaa tgctgattgt gcctggctag
3901 aagcacaaga ggagggggaa gtgggtttcc cagtcagacc tcaggtacct ttaagaccaa
3961 tgaccttcaa gggagctctg gatcttagcc actttttaaa agaaaagggg ggactggaag
4021 ggttaattta ctcccaaaaa agacaagata tccttgatct gtgggtctac cacacgcaag
4081 gctacttccc tgattggcag aactacacac cagggccagg gaccagattt ccactgacct
4141 ttggatggtg cttcaagcta gtaccagtgg atccagggaa agtagaagag gccaataaag
4201 gagagaacaa ctgcttgtta caccctatga gccagcatgg gatggacgac ccagagagag
4261 aagtgttagt gtggaggttt gacagcaacc tagcatttcg tcacgtggcc cgagagctgc
4321 atccggagta ctacaagaac tgctgacatc gagctttcta caagggactt tccgctgggg
4381 actttccagg gaggcgtgac atgggcggaa ttggggagtg gcgagcccac agatgctgca
4441 tataagcagc cgctttctgc ttgtactggg tctctctggt tagaccagat ctgagcctgg
4501 gagctctctg gctagctagg
//
last modified: Tue May 31 10:56 2022