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LOCUS JX972273 4596 bp RNA linear VRL 16-MAR-2013
DEFINITION HIV-1 isolate B.700010470.w04.41dps.3_B14 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 JX972273
VERSION JX972273.1 GI:459963630
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 4596)
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 4596)
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 700010470 Days
post-screening 41 Sample timepoint w4 Patient sex M Fiebig Stage x
Viral Load 27991 CD4 count 522 HLA type A*03 A*01 B*08 B*4901 Cw*07
Cw*07 Infection date 2008 ##HIVDataBaseData-END##
FEATURES Location/Qualifiers
source 1..4596
/organism="Human immunodeficiency virus 1"
/mol_type="genomic RNA"
/isolate="B.700010470.w04.41dps.3_B14"
/host="Homo sapiens"
/db_xref="taxon:11676"
/country="USA"
/collection_date="2008"
/note="subtype: B"
gene 1..579
/gene="vif"
CDS 1..579
/gene="vif"
/codon_start="1"
/transl_table="1"
/product="vif protein"
/protein_id="AGG92162.1"
/db_xref="GI:459963632"
/translation="MENRWQVMIVWQVDRMRIKTWKSLVKHHMHISKKARGWFYRHHY
ENTHPKISSEVHIPLREARLVITTYWGLHTGERDWHLGQGVSIEWRKRKYSTQVDPDL
ADQLIHLYYFDCFSESAIRNALLGHIVSPRCEYQAGHNKVGSLQYLALTALVAPKKTK
PPLPSVKKLTEDRWNKPQKTKGHRGSHTMSGH"
gene <1..56
/gene="pol"
CDS <1..56
/gene="pol"
/codon_start="3"
/transl_table="1"
/product="pol protein"
/protein_id="AGG92161.1"
/db_xref="GI:459963631"
/translation="GKQMAGDDCVASRQDED"
gene 519..809
/gene="vpr"
CDS 519..809
/gene="vpr"
/codon_start="1"
/transl_table="1"
/product="vpr protein"
/protein_id="AGG92163.1"
/db_xref="GI:459963633"
/translation="MEQAPEDQGPQREPYNEWTLELLEELKREAVRHFPRPWLQGLGQ
YIYETYGDTWAGVEAIIKILQQLLFIHFRIGCRHSRIGIIRQRRTRNGASRS"
gene 790..3445
/gene="tat"
CDS join(790..1004,3352..3445)
/gene="tat"
/codon_start="1"
/transl_table="1"
/product="tat protein"
/protein_id="AGG92164.1"
/db_xref="GI:459963634"
/translation="MEPVDPRLEPWKHPGSQPRTACTTCYCKKCCFHCQVCFITKGLG
ISYGRKKRRQRRRAPENSQTHQVSVSKQPDPQQRGDPTGPKKSKEEVERETETDPEDQ
"
gene 929..3626
/gene="rev"
CDS join(929..1004,3352..3626)
/gene="rev"
/codon_start="1"
/transl_table="1"
/product="rev protein"
/protein_id="AGG92165.1"
/db_xref="GI:459963635"
/translation="MAGRSGDSDEELLKTVRLIKFLYQSNPIPSSEGTRQARRNRRRR
WRERQRQIRKISDWIIRTHLGRPVEPVHLQLPPLERLSLDSSEGCGSSGTQGVGSPQV
LVESPAVLDSGTKE"
gene 1020..1262
/gene="vpu"
CDS 1020..1262
/gene="vpu"
/codon_start="1"
/transl_table="1"
/product="vpu protein"
/protein_id="AGG92166.1"
/db_xref="GI:459963636"
/translation="MIPLTILSIVALVVVVIIAIVVWSIAYIEYRKLLRQRKIDRLLD
RIRDRAEDSGNESDGDQEELSALELGHLAPWNVGDE"
gene 1183..3768
/gene="env"
CDS 1183..3768
/gene="env"
/codon_start="1"
/transl_table="1"
/product="envelope glycoprotein"
/protein_id="AGG92167.1"
/db_xref="GI:459963637"
/translation="MRVMGTKKNYQHLSWGILLLGMLAMSSAKKEEKWVTVYYGVPVW
KEAVTTLFCASDAKAYKAEAHNVWATHACVPTDPNPQEVKLENVTENFNMWKNKMVDQ
MHEDIISLWDQSLKPCVKFTPLCVTLNCTDASAGNGTDAIANNGTNATISLSENEMKN
CSFNVTKSVGNKLQKEYALFYKLDVASIDNSNTSYMLVHCNSSVVTQACPKISFQPIP
IHFCAPAGFAILKCNNKTFNGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEVVI
RAENFTDNAKTIIVQLNESVIINCTRPNNNTRKSIHLGPGSAIYATGQIIGDIRQAHC
NISEEKWNKTLRLIAEKLREQFREQLKNKTIIFSPHPGGDPEIEMHSFNCGGEFFYCN
TTRLFNNWTSNNTWNDTTGSNNSTITLPCRIKQIINRWQEIGKAMYAPPIAGQINCSS
NITGLLLTRDGGKTNNSNSSETFRPGGGNMKDNWRSELYKYKVVKIEPLGIAPTEARR
RVVQREKRTVTLGAMFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQSNLLRAIEA
QQHMLQLTVWGIKQLQARVLAVERYLKDQQLLGIWGCSGKLICTTNVPWNDSWSNRSI
QEIWNNMTWMQWEKEIDNYTELIYTLIEDSQNQQEKNELDLLKLDDWASLWNWFDITK
WLWYVKIFIMVIGGLVGLKIVFTVLSIVNRVRQGYSPLSFQTRSPAARGPDRPEEIEG
GGGERDRDRSGRSVIGLLGLIWDDLWNLCIFSYHRLRDFLLILVRVVEVLGHRGWEAL
KYWWSLLQYWIQELKNSAVSLLNATAIAVAEGTDRILEVLQRAGRAIIHIPRRIRQGL
ERALI"
gene 3770..4402
/gene="nef"
CDS 3770..4402
/gene="nef"
/codon_start="1"
/transl_table="1"
/product="nef protein"
/protein_id="AGG92168.1"
/db_xref="GI:459963638"
/translation="MGGKWSKRSGNGWAAVREKMEQAKPKVEPAAVGVGAASRDLEQH
GALTSSNTPANNADCAWLEAQEEEEVGFPVRPQVPLRPMTFKGALDLSHFLKEKGGLD
GLIYSKKRQEILDLWMYNTQGYFPDWQNYTPGPGIRYPLTFGWCFKLVPVDPEKVEEA
NTGENNCLLHPMSLHGMEDPEKEVLMWKFDSLLAYQHIAKEKHPEFYKNC"
BASE COUNT 1576 a 814 c 1120 g 1086 t
ORIGIN
1 atggaaaaca gatggcaggt gatgattgtg tggcaagtag acaggatgag gattaaaaca
61 tggaaaagtt tagtaaaaca ccacatgcat atttcaaaga aagctagagg atggttttat
121 agacatcact atgaaaatac tcatccaaaa ataagttcag aagtacacat cccactaagg
181 gaggctagat tggtaataac aacatattgg ggtctgcaca caggagaaag agactggcac
241 ttgggtcaag gggtctccat agaatggagg aagaggaaat atagcacaca agtagaccct
301 gacctagcag accaactaat tcacctgtat tactttgatt gtttttcaga atctgctata
361 aggaatgccc tattaggaca catagttagc cctaggtgtg agtatcaagc aggacataac
421 aaggtagggt ctctacagta cttggcacta acagcattag tagcaccaaa aaagacaaag
481 ccacctttgc ctagtgtcaa gaaactgaca gaggatagat ggaacaagcc ccagaagacc
541 aagggccaca gagggagcca tacaatgagt ggacactaga gcttttagag gaacttaaga
601 gagaagctgt tagacatttt cctaggccat ggctccaggg cttaggacaa tatatctatg
661 aaacttatgg agatacctgg gcaggagtgg aagctataat aaaaattctg caacaactgc
721 tgtttattca tttcagaatt ggatgtcgac atagcagaat aggcattatt cgacagagga
781 gaacaagaaa tggagccagt agatcctaga ctagagccct ggaagcatcc aggaagtcag
841 cctaggactg cttgtaccac atgctattgt aaaaagtgtt gctttcattg ccaagtgtgt
901 ttcataacaa aaggcttagg catctcctat ggcaggaaga agcggagaca gcgacgaaga
961 gctcctgaaa acagtcagac tcatcaagtt tctgtatcaa agcagtaagt gtatatgtaa
1021 tgataccctt aacaatatta tcaatagtag ctttagtagt agtagtaata atagcaatag
1081 ttgtgtggtc tatagcttac atagaatata ggaaattatt aagacaaaga aaaatagata
1141 ggttacttga taggataaga gacagagcag aagacagtgg caatgagagt gatggggacc
1201 aagaagaatt atcagcactt gagctggggc atcttgctcc ttggaatgtt ggcgatgagt
1261 agtgctaaaa aagaggaaaa gtgggtcaca gtctattatg gggtacctgt gtggaaagaa
1321 gcagtcacca ccctattttg tgcatcagat gctaaagcat ataaggcaga ggcacataat
1381 gtttgggcca cacatgcctg tgtacccaca gatcctaacc cacaagaagt aaaattggaa
1441 aatgtgacag aaaattttaa catgtggaaa aataaaatgg tagaccaaat gcatgaggac
1501 ataatcagtc tatgggatca aagcctaaag ccatgtgtaa aatttacccc actctgtgtt
1561 actctaaact gcactgatgc tagtgctggc aatggtactg atgctattgc taacaatggt
1621 actaatgcta caattagtct cagtgagaat gagatgaaaa actgctcttt caatgtcacc
1681 aaaagcgtag gaaataagtt acagaaagaa tatgcacttt tttataaact tgatgtagct
1741 tcaatagata atagtaatac tagctatatg ttggtacact gtaactcctc agtcgttaca
1801 caggcttgtc caaagatatc ctttcaacca attcccatac atttttgtgc cccagctggt
1861 tttgcgattc taaagtgtaa taataagaca ttcaacggaa caggaccatg taacaatgtc
1921 agcacagtac aatgcacaca tggaattaag ccagtagtgt caactcagct gttgttaaat
1981 ggcagtctag cagaagaaga agtagtaatt agagctgaaa atttcacaga caatgctaag
2041 accataatag tacagctaaa tgaatctgta ataattaatt gtacaagacc taacaataat
2101 acaagaaaaa gtatacattt aggaccaggg agtgcaattt atgcaacagg acaaataata
2161 ggagatataa gacaagcaca ttgtaacatt agtgaggaga aatggaataa aactttaaga
2221 ctgatagctg aaaaattaag agaacaattt agagaacaat tgaagaataa aacaataatc
2281 tttagtcccc acccaggagg ggacccagaa attgaaatgc atagttttaa ttgtggaggg
2341 gaatttttct attgtaacac aacacggctg tttaataatt ggacttctaa taatacttgg
2401 aatgatacta cagggtcaaa taacagcaca atcacactcc catgcagaat aaaacaaatt
2461 ataaataggt ggcaggaaat aggaaaagca atgtatgccc ctcccatcgc aggacaaatt
2521 aactgttcat caaatattac agggttgcta ttaacaagag atggtggtaa gaccaacaac
2581 agcaacagca gtgagacctt cagaccaggg ggaggaaata tgaaggacaa ttggagaagt
2641 gaattatata aatataaagt agtaaaaatt gaaccattag gaatagcacc caccgaggca
2701 aggagaagag tggtgcagag agaaaaaaga acagtaacat taggagctat gttccttggg
2761 ttcttgggag cagcaggaag cactatgggc gcagcatcaa tgacgctgac ggtacaggcc
2821 agacaattat tgtctggtat agtgcaacag cagagcaatc tgctgagggc tattgaggcg
2881 caacagcata tgttgcaact cacagtctgg ggcatcaagc agctccaggc aagagtcctg
2941 gctgtggaaa gatacctaaa ggatcaacag ctcctaggga tttggggttg ctctggaaaa
3001 ctcatctgca ccactaatgt gccttggaat gacagttgga gtaatagatc tatacaagag
3061 atttggaata acatgacctg gatgcaatgg gagaaagaaa ttgacaacta tacagagttg
3121 atatacacct taattgagga ctcgcaaaac caacaagaaa aaaatgaact agatttatta
3181 aaattggatg actgggcaag tttgtggaat tggtttgaca taacaaaatg gctgtggtat
3241 gtaaaaatat tcataatggt aataggaggt ttagtaggtt taaaaatagt ttttactgta
3301 ctttctatag tgaatagagt taggcaggga tactcaccat tgtcgtttca gacccgatcc
3361 ccagcagcga ggggacccga caggcccgaa gaaatcgaag gaggaggtgg agagagagac
3421 agagacagat ccggaagatc agtgattgga ttattaggac tcatctggga cgacctgtgg
3481 aacctgtgca tcttcagcta ccaccgcttg agagactttc tcttgattct agtgagggtt
3541 gtggaagttc tgggacacag ggggtgggaa gccctcaagt attggtggag tctcctgcag
3601 tattggattc aggaactaaa gaatagtgct gttagcttgc ttaatgccac agctatagca
3661 gtagctgagg ggacagatag gattttagag gtattacaaa gagctggtag agctattatc
3721 cacataccta gaagaataag acagggctta gaaagggctt taatataaga tgggtggcaa
3781 gtggtcaaaa cgtagtggaa atggatgggc tgctgtaaga gaaaaaatgg aacaggctaa
3841 gccaaaagtt gagccagcag cagttggggt gggagcagca tctcgagact tagaacaaca
3901 tggagcactc acaagtagca atacaccagc aaataatgct gattgtgcct ggctagaagc
3961 gcaagaggaa gaggaggtgg gttttccagt caggcctcag gtacctttaa gaccaatgac
4021 tttcaaggga gctctcgatc ttagccactt tttaaaagaa aaggggggac tggatgggtt
4081 aatttactct aaaaagagac aagagatcct tgatctgtgg atgtacaaca cacaaggcta
4141 cttccctgac tggcagaatt acacaccagg gccagggatt agatatcccc tgacctttgg
4201 atggtgcttc aagctagtac cagttgaccc agagaaggta gaagaggcca acacaggaga
4261 gaacaactgc ctgctacatc ctatgagcct gcatggaatg gaggacccgg agaaagaagt
4321 attaatgtgg aagtttgaca gcctcctagc atatcagcac atagccaaag agaagcatcc
4381 ggagttttac aagaactgct gacacctaca agaaatgctg acatagagat atctacaagg
4441 gactttccgc tggggacttt ccaggggagg tgtggcctgg gcgggaccgg ggagtggcga
4501 gccctcagat gctgcatata agcagctgct ttttgcctgt actgggtctc tctggttaga
4561 ccagatctga gcctgggagc tctctggcta gctagg
//
last modified: Tue May 31 10:56 2022