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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


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