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LOCUS JX972467 4657 bp RNA linear VRL 16-MAR-2013
DEFINITION HIV-1 isolate C.703010131.S.0dps.e015 from Malawi pol protein (pol)
gene, partial cds; and vif protein (vif), vpr protein (vpr), tat
protein (tat), rev protein (rev), vpu protein (vpu), envelope
glycoprotein (env), and nef protein (nef) genes, complete cds
ACCESSION JX972467
VERSION JX972467.1 GI:459965342
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 4657)
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 4657)
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
REFERENCE 3
Show all sequences for reference 3
AUTHORS Parrish,N.F., Gao,F., Li,H., Giorgi,E.E., Barbian,H.J.,
Parrish,E.H., Zajic,L., Iyer,S.S., Decker,J.M., Kumar,A., Hora,B.,
Berg,A., Cai,F., Hopper,J., Denny,T.N., Ding,H., Ochsenbauer,C.,
Kappes,J.C., Galimidi,R.P., West,A.P.J., Bjorkman,P.J., Wilen,C.B.,
Doms,R.W., O'Brien,M., Bhardwaj,N., Borrow,P., Haynes,B.F.,
Muldoon,M., Theiler,J.P., Korber,B., Shaw,G.M. and Hahn,B.H.
TITLE Phenotypic properties of transmitted founder HIV-1.
JOURNAL Proc. Natl. Acad. Sci. U. S. A.. 110(17); 6626-33 (2013)
PUBMED 23542380
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 703010131 Days
post-screening 0 Sample timepoint s Patient sex M Fiebig Stage I-II
Viral Load 411873 CD4 count NA HLA type A*29 A*23/A*24 B*45 B*15
Cw*02 Cw*06 Infection date 2007 ##HIVDataBaseData-END##
FEATURES Location/Qualifiers
source 1..4657
/organism="Human immunodeficiency virus 1"
/mol_type="genomic RNA"
/isolate="C.703010131.S.0dps.e015"
/host="Homo sapiens"
/db_xref="taxon:11676"
/country="Malawi"
/collection_date="2007"
/note="subtype: C"
gene <1..173
/gene="pol"
CDS <1..173
/gene="pol"
/codon_start="3"
/transl_table="1"
/product="pol protein"
/protein_id="AGG93679.1"
/db_xref="GI:459965343"
/translation="PIWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIKDYGKQMA
GADCVAGRQDED"
gene 118..696
/gene="vif"
CDS 118..696
/gene="vif"
/codon_start="1"
/transl_table="1"
/product="vif protein"
/protein_id="AGG93680.1"
/db_xref="GI:459965344"
/translation="MENRWQVLIVWQVDRMKIRTWNSLVKHHIWASKKASGWFYRHHY
ESRHPKVSSEVHIPLGDARLIITTYWGLQTGERDWHLGHGVSIEWRLKRYSTQVDPGL
ADQLIHMHYFDCFADSAIRNAILGHIVFPRCDYQAGHNKVGSLQYLALIALIKPKRIK
PPLPSVRKLVEDRWNKPQKTRGRRGNHTMNGH"
gene 636..926
/gene="vpr"
CDS 636..926
/gene="vpr"
/codon_start="1"
/transl_table="1"
/product="vpr protein"
/protein_id="AGG93681.1"
/db_xref="GI:459965345"
/translation="MEQAPEDQGPQREPYNEWTLELLEELKQEAVRHFPRPWLHNLGQ
HIYETYGDTWTGVEVIIRILQQLLFIHFRIGCQHSRIGILRQRRARNGANRS"
gene 907..3528
/gene="tat"
CDS join(907..1121,3438..3528)
/gene="tat"
/codon_start="1"
/transl_table="1"
/product="tat protein"
/protein_id="AGG93682.1"
/db_xref="GI:459965346"
/translation="MEPIDPELDPWNHPGSQPKTACNNCYCKGCSYHCLVCFQKKGLG
ISYGRKKRRQRRSAPPSSEDHQNPIPKQPLSQTRGDSTGSKESKKKVESKTETDPFD"
gene 1046..3664
/gene="rev"
CDS join(1046..1121,3438..3664)
/gene="rev"
/codon_start="1"
/transl_table="1"
/product="rev protein"
/protein_id="AGG93683.1"
/db_xref="GI:459965347"
/translation="MAGRSGDSDEALLQAVRIIKILYQSNPYPKPEGTRQARKNRRRR
WRARQRQIHSISERILSTCLGRPTEPVPFQLPPLERLCIDCDKSGGTPGTQGVGNP"
gene 1145..1399
/gene="vpu"
CDS 1145..1399
/gene="vpu"
/codon_start="1"
/transl_table="1"
/product="vpu protein"
/protein_id="AGG93684.1"
/db_xref="GI:459965348"
/translation="MIELLARVDYRIGVGAFIIALIIAIVVWTIVYIEYRKLVRQRKI
DWLVERIRERAEDSGNESDGDTEELSTMVDMGHLRLLDDI"
gene 1323..3854
/gene="env"
CDS 1323..3854
/gene="env"
/codon_start="1"
/transl_table="1"
/product="envelope glycoprotein"
/protein_id="AGG93685.1"
/db_xref="GI:459965349"
/translation="MRVMGIQRNCQQWWIWGILGFWMIYSGMGQLWVTVYYGVPVWKE
AKTTLFCASDAKAYSQEAHNIWATHACVPTDPNPQEMVLENVTENFNMWKNDMVDQMH
EDIISLWDQSLKPCVKLTPLCVTLNCTTVNITQENNPLNDSDSNYMKNCSFNMTTELK
DKKKEERALFHRLDLVPLNENSSKYENSNKYILTNCRTSTIAQACPKISFDPIPIHYC
APAGYAILKCNNKAFNGSGPCTNVSTVQCTHGIKPVVSTQLLLNGSLAEEIIIRFENL
TNNVKTIIVHLNESVEISCTRPNNNTRKSVRIGPGQTFYATGEIIGDIRQAYCTINEG
KWNKTLERIRNKLAEYFPNKTIQFQSASGGDLEITTHSFNCGGEFFYCNTSRLFNHTF
NETSDEDITLQCRIKQIINMWQGVGRAIYAPPIAGNITCNSNITGLLLTRDGGKSNSS
NQTEIFRPAGGNMRDNWRSELYKYKVVEIKPLGIAPTKAKRRVVEREKRAAIGAMFLG
FLGAAGSTMGAASITLTVQARQLLSGIVQQQSNLLRAIEAQQHMLQLTVWGIKQLQAR
VLAIERYLKDQQLLGIWGCSGKLICTTNVPWNSSWSNKPEEEIWGNMTWMQWEREIDN
YTDTIYSLLEKSQNQQEQNEQDLLALDSWKNLWNWFSITKWLWYIKIFIMIVGGLIGL
RIIFAVLSIVNRVRQGYSPLSFQTLIPNPRGLDRLERIEEEGGEQDRDRSIRLVNGFL
ALAWDDLRSLCLFSYHRLRDCVLIVTRVVELLGHRGWEILKYLGSLAQYWGLELKQSA
INLLDTIAIAVAEGTDRIIEVIQRICRAICNIPTRIRQGFEAALQ"
gene 3856..4485
/gene="nef"
CDS 3856..4485
/gene="nef"
/codon_start="1"
/transl_table="1"
/product="nef protein"
/protein_id="AGG93686.1"
/db_xref="GI:459965350"
/translation="MGGKWSKSSIVGWPAVRERIRQARPEPAAEGVGAASQDLDKHGA
LTTSNTVYNNAACAWIEAQEEGEEVGFPVKPQVPLRPMTYKGAFDLSFFLKEKGGLDG
LIYSQQRQDILDLWVYNTQGYFPDWQNYTPGPGIRYPLTFGWCYKLVPVDPRTVEEAN
SGENSCLLHPMSQHGMEDADREVLIWKFDSSLARRHLARELHPEYYKDC"
BASE COUNT 1627 a 816 c 1123 g 1091 t
ORIGIN
1 accctatttg gaaaggacca gccaaactac tctggaaagg tgaaggggca gtagtaatac
61 aagataacag tgacataaag gtagtaccaa ggaggaaagc aaaaatcatt aaggactatg
121 gaaaacagat ggcaggtgct gattgtgtgg caggtagaca ggatgaagat tagaacatgg
181 aatagtttag taaagcacca tatatgggcc tcaaagaaag ctagtggatg gttttacaga
241 catcattatg aaagcagaca tccaaaagta agttcagaag tacacatccc attaggggat
301 gctagattaa taataacaac atattggggt ttgcaaacag gagaaagaga ttggcatttg
361 ggtcatggag tctccataga atggagattg aaaagatata gcacacaagt agaccctggc
421 ctggcagacc agctaattca tatgcattat tttgattgtt ttgcagactc tgccataaga
481 aatgccatat taggacacat agtttttcct aggtgtgact atcaagcagg acataataag
541 gtaggatctc tacaatattt ggcactgata gcattgataa aaccaaaaag gataaagcct
601 cctctgccta gtgttaggaa attagtagag gatagatgga acaagcccca gaagaccagg
661 ggccgcagag ggaaccatac aatgaatgga cactagagct tttagaggaa ctcaagcagg
721 aagctgtcag acactttcct agaccatggc tccataactt aggacaacat atctatgaaa
781 cctatgggga tacttggaca ggagtcgaag tgataataag aattctgcaa caactactgt
841 ttatccattt cagaattggg tgccagcata gcagaatagg catcttgaga cagagaagag
901 caagaaatgg agccaataga tcctgaacta gatccctgga accatccagg aagtcagcct
961 aagactgctt gtaataattg ttattgtaaa ggctgcagct atcattgtct agtttgcttt
1021 cagaaaaaag gcttaggcat ttcctatggc aggaagaagc ggagacagcg acgaagcgct
1081 cctccaagca gtgaggatca tcaaaatcct ataccaaagc agtaagtatt aaatactgga
1141 tgtaatgata gaattactag caagagtaga ttatagaata ggagtaggag cattcataat
1201 agcattaatt atagcaatag ttgtgtggac catagtatat atagaatata ggaaattggt
1261 aaggcaaaga aaaatagact ggttggttga aagaattagg gaaagagcag aagacagtgg
1321 caatgagagt gatggggata cagaggaatt gtcaacaatg gtggatatgg ggcatcttag
1381 gcttttggat gatatatagt gggatggggc aattgtgggt cacagtctat tatggggtac
1441 ctgtatggaa ggaagcaaaa actactctat tttgtgcatc agatgctaaa gcatattccc
1501 aagaagcaca taatatctgg gctacacatg cctgcgtacc tacagacccc aacccacaag
1561 aaatggtttt agaaaatgta acagaaaatt ttaacatgtg gaaaaatgac atggtagatc
1621 agatgcatga ggatataatc agtttatggg atcaaagcct aaagccatgt gtaaagttga
1681 ccccactctg tgtcacttta aactgtacta ctgttaatat tacccaggaa aataatccac
1741 ttaatgatag tgatagtaat tacatgaaaa actgctcttt caatatgacc acagaactaa
1801 aagataaaaa gaaggaagag agggcattgt ttcatagact tgatctagta ccacttaatg
1861 agaatagtag caagtatgag aatagtaaca agtatatatt aacaaattgt aggacctcaa
1921 ccatagcaca ggcctgtcca aagatctcgt ttgatccgat tcctatacat tattgtgctc
1981 cagctggtta tgcgattcta aaatgtaata ataaggcatt caatggatca ggaccatgca
2041 ctaatgtcag cacagtacaa tgtacacatg gaattaagcc agtggtatca actcagctac
2101 tgttaaatgg tagcctagca gaagagataa taatcagatt tgaaaatctg acaaacaatg
2161 tcaaaacaat aatagtacac cttaatgaat ctgtagaaat ttcgtgtaca agacccaaca
2221 ataatacaag aaaaagtgtg aggataggac caggacaaac attctatgca acaggagaaa
2281 taataggaga tataagacaa gcatattgta ccattaatga aggaaaatgg aataaaactt
2341 tagaaaggat aaggaacaaa ttagcagagt acttccctaa taaaacaata caatttcaaa
2401 gcgcctcagg aggggaccta gaaattacaa cacatagctt taattgtgga ggagaatttt
2461 tctattgcaa cacatcaaga ttgtttaatc atacatttaa tgagacatca gacgaagaca
2521 tcacactcca atgtaggata aaacaaatta taaacatgtg gcagggggta ggacgagcaa
2581 tatatgcccc tcccattgca ggaaacataa catgtaactc aaatatcaca ggactactat
2641 tgacacgtga tggagggaag agtaatagta gtaatcagac agagatattc agacctgcag
2701 gaggaaatat gagggacaat tggagaagtg aattatataa atataaagtg gtagaaatta
2761 aaccattagg aatagcaccc actaaggcga aaaggagagt ggtggagaga gaaaaaagag
2821 cggcaatagg agctatgttc cttgggttct tgggagcagc aggaagcact atgggcgcgg
2881 cgtcaataac gctgacggta caggccagac aattattgtc tggtatagtg caacagcaaa
2941 gcaatttgct gagagctata gaggcgcaac agcatatgtt gcaactcacg gtctggggca
3001 ttaaacagct ccaggcaaga gtcctggcta tagaaagata cctaaaggat caacagctcc
3061 taggaatttg gggctgctct ggaaaactca tctgcaccac taatgtgcct tggaactcta
3121 gttggagtaa taaacctgaa gaagaaattt gggggaacat gacctggatg caatgggaga
3181 gagaaattga taattataca gacacaatat acagtttgct tgaaaaatcg caaaaccagc
3241 aggaacaaaa tgaacaagat ttactagcat tggacagttg gaaaaacctg tggaattggt
3301 ttagcataac aaaatggttg tggtatataa aaatattcat aatgatagta ggaggcttaa
3361 taggtttaag aataattttt gctgtgcttt ctatagtgaa tagagttagg cagggatact
3421 cacctttatc gttccagacc cttatcccaa acccgagggg actcgacagg ctcgaaagaa
3481 tcgaagaaga aggtggagag caagacagag acagatccat tcgattagtg aacggattct
3541 tagcacttgc ctgggacgac ctacggagcc tgtgcctttt cagctaccac cgcttgagag
3601 actgtgtatt gattgtgaca agagtggtgg aactcctggg acacaggggg tgggaaatcc
3661 ttaagtatct aggaagtctt gcgcagtatt ggggtctgga actaaaacaa agtgctatta
3721 acctgcttga taccatagca atagcagtag ctgaaggaac agataggatc atagaagtaa
3781 tacaaagaat ttgtagagct atctgcaata tacctacaag aataagacag ggctttgaag
3841 cagctttgca ataaaatggg gggcaagtgg tcaaaaagca gtatagttgg atggcctgct
3901 gtaagagaaa gaataagaca agctaggcca gagccagcag cagagggagt aggagcagcg
3961 tctcaagacc tagataaaca tggggcactt acaaccagca acacagttta taacaatgct
4021 gcttgtgcct ggatagaagc gcaagaggag ggagaagagg taggctttcc agtcaaaccc
4081 caggtgcctt taagaccaat gacttataaa ggagcattcg atctcagctt ctttttaaaa
4141 gaaaaggggg gactggatgg gttaatttac tcccagcaaa gacaggatat ccttgatttg
4201 tgggtctata acacacaagg ctacttccct gattggcaaa actacacacc aggaccaggg
4261 atcagatatc cactgacctt tggatggtgc tacaagttag tgccagttga cccaaggaca
4321 gtagaagagg ccaacagtgg agaaaacagc tgcttgctcc accctatgag ccagcatgga
4381 atggaggatg cagacagaga agtattaata tggaagtttg acagcagcct agcacgcaga
4441 cacctggccc gcgagctaca tccggagtat tacaaagatt gctgacacag aagggacttt
4501 ccgctgggac tttccactgg gcgttccagg aggtgtggtc tgggcgggac ggggagtggc
4561 cagccctcag atgctgcata taagcagctg cttttcgcct gtactgggtc tctctaggta
4621 gaccagatct gagcctggga gctctctggc tatctgg
//
last modified: Tue May 31 10:56 2022