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LOCUS	    FJ495839		    3593 bp    DNA     linear	VRL 03-JUN-2009
DEFINITION  HIV-1 isolate CH40S_M17 from USA rev protein (rev) and tat protein
	    (tat) genes, partial cds; and vpu protein (vpu), envelope
	    glycoprotein (env), and nef protein (nef) genes, complete cds
ACCESSION   FJ495839
VERSION     FJ495839.1 GI:238633261
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 3593)
            Show all sequences for reference 1
  AUTHORS   Salazar-Gonzalez,J.F., Salazar,M.G., Keele,B.F., Learn,G.H.,
	    Giorgi,E.E., Li,H., Decker,J.M., Wang,S., Baalwa,J., Kraus,M.H.,
	    Parrish,N.F., Shaw,K.S., Guffey,M.B., Bar,K.J., Davis,K.L.,
	    Ochsenbauer-Jambor,C., Kappes,J.C., Saag,M.S., Cohen,M.S.,
	    Mulenga,J., Derdeyn,C.A., Allen,S., Hunter,E., Markowitz,M.,
	    Hraber,P., Perelson,A.S., Bhattacharya,T., Haynes,B.F.,
	    Korber,B.T., Hahn,B.H. and Shaw,G.M.
  TITLE     Genetic identity, biological phenotype, and evolutionary pathways
	    of transmitted/founder viruses in acute and early HIV-1 infection.
  JOURNAL   J. Exp. Med.. 206(6); 1273-89 (2009)
  PUBMED    19487424
REFERENCE   2 (bases 1 to 3593)
            Show all sequences for reference 2
  AUTHORS   Hraber,P. and Hraber,P.T.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-NOV-2008) Los Alamos National Laboratory, Theoretical
	    Biology and Biophysics (T10), MS K710, Los Alamos, NM 87545, USA
REFERENCE   3
            Show all sequences for reference 3
  AUTHORS   Ferrari,G., Korber,B., Goonetilleke,N., Liu,M.K., Turnbull,E.L.,
	    Salazar-Gonzalez,J.F., Hawkins,N., Self,S., Watson,S., Betts,M.R.,
	    Gay,C., McGhee,K., Pellegrino,P., Williams,I., Tomaras,G.D.,
	    Haynes,B.F., Gray,C.M., Borrow,P., Roederer,M., McMichael,A.J. and
	    Weinhold,K.J.
  TITLE     Relationship between Functional Profile of HIV-1 Specific CD8 T
	    Cells and Epitope Variability with the Selection of Escape Mutants
	    in Acute HIV-1 Infection
  JOURNAL   PLoS Pathog. 7 (2), E1001273 (2011)
  PUBMED    21347345
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## Sequence Name CH40S_M17 Patient code
	    700010040 Patient sex M Sample date 2006 Fiebig Stage 2 Viral Load
	    2197248 Sample city North Carolina Culture method uncultured Sample
	    tissue serum HLA type A*3101 A*0201 B*4402 B*4001 Cw*0302 Cw*0501
	    Subtype B DBID 3193676283 ##HIVDataBaseData-END##
FEATURES             Location/Qualifiers
     source	     1..3593
		     /organism="Human immunodeficiency virus 1"
		     /proviral="Human immunodeficiency virus 1"
		     /mol_type="genomic DNA"
		     /isolate="CH40S_M17"
		     /host="Homo sapiens"
		     /db_xref="taxon:11676"
		     /country="USA"
		     /collection_date="2006"
		     /note="subtype: B"
     gene	     <1..2640
		     /gene="rev"
     CDS	     join(<1..62,2366..2640)
		     /gene="rev"
		     /codon_start="2"
		     /transl_table="1"
		     /product="rev protein"
		     /protein_id="ACR51323.1"
		     /db_xref="GI:238633263"
		     /translation="GDSDEELLKTVRLIKFLYQSNPPPSPEGTRQARRNRRRRWRERQ
		     RQIRSISERILSTYLERSTEPVPLQLPPLERLTLDCNEDCGTSGTQGVGSPQILVESP
		     TVLESGTKE"
     gene	     <1..2456
		     /gene="tat"
     CDS	     join(<1..62,2366..2456)
		     /gene="tat"
		     /codon_start="1"
		     /transl_table="1"
		     /product="tat protein"
		     /protein_id="ACR51322.1"
		     /db_xref="GI:238633262"
		     /translation="RRQRRRAPQDSQTHQVSLSKQPTSQPRGDPTGPKESEKKVERET
		     ETDPIH"
     gene	     79..324
		     /gene="vpu"
     CDS	     79..324
		     /gene="vpu"
		     /codon_start="1"
		     /transl_table="1"
		     /product="vpu protein"
		     /protein_id="ACR51324.1"
		     /db_xref="GI:238633264"
		     /translation="MNSLQISAIVALVVAGIIAIVVWSIVAIEYRKILRQRKIDRLID
		     RIRERAEDSGNESDGDQEELSALVERGHLALGDINDL"
     gene	     242..2782
		     /gene="env"
     CDS	     242..2782
		     /gene="env"
		     /codon_start="1"
		     /transl_table="1"
		     /product="envelope glycoprotein"
		     /protein_id="ACR51325.1"
		     /db_xref="GI:238633265"
		     /translation="MRVMGIRKNYQHLWREGILLLGILMICSAADKLWVTVYYGVPVW
		     REATTTLFCASDAKAYDTEAHNVWATHACVPTDPNPQEVELKNVTENFNMWENNMVEQ
		     MHEDIISLWDQSLKPCVKLTPLCVTLNCTDLGNVTNTTNSNGEMMEKGEVKNCSFKIT
		     TDIKDRTRKEYALFYKLDVVPINDTRYRLVSCNTSVITQACPKVSFEPIPIHYCAPAG
		     FAILKCNDKQFIGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSVNFSDN
		     AKTIIVQLNKSVEITCTRPNNNTRKSIPMGPGKAFYARGDITGDIRKAYCEINGTEWH
		     STLKLVVEKLREQYNKTIVFNRSSGGDPEIVMYSFNCGGEFFYCNSTKLFNSTWPWND
		     TKGSHDTNGTLILPCKIKQIINMWQGVGKAMYAPPIEGKIRCSSNITGLLLTRDGGYE
		     SNETDEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQREKRAFGLGAV
		     FLGFLGAAGSTMGAASITLTVQARQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQL
		     QARVLAVERYLKDQQLLGIWGCSGKLICTTTVPWNTSWSNKSLEQIWDNMTWMEWERE
		     IDNYTGYIYQLIEESQNQQEKNEQELLALDKWASLWNWFDITNWLWYIKIFIMIVGGL
		     IGLRIVFTVLSIVNRVRQGYSPLSFQTHLPAQRGPDRPEGIGEEGGERDRDRSDPLVN
		     GFLALIWSDLRSLCLFSYHRLRDLLLIVTRIVELLGRRGWEVLKYWWNLLQYWSQELK
		     NSAVSLLNATAIAVAEGTDRVIEVVQRACRAILHIPRRIRQGLERALL"
     gene	     2784..3404
		     /gene="nef"
     CDS	     2784..3404
		     /gene="nef"
		     /codon_start="1"
		     /transl_table="1"
		     /product="nef protein"
		     /protein_id="ACR51326.1"
		     /db_xref="GI:238633266"
		     /translation="MGGKWSKCSVVGWPSVRERMRRAEPAAEGVGAVSRDLEKHGAIT
		     SSNTAATNADCAWLEAQEEGEVGFPVRPQVPLRPMTFKGALDLSHFLKEKGGLEGLIY
		     SQKRQDILDLWVYHTQGYFPDWQNYTPGPGTRFPLTFGWCFKLVPVDPGKVEEANKGE
		     NNCLLHPMSQHGMDDPEREVLVWRFDSSLAFRHVARELHPEYYKNC"
BASE COUNT     1202 a	 641 c	  904 g    846 t
ORIGIN
       1 cggagacagc gacgaagagc tcctcaagac agtcagactc atcaagtttc tctatcaaag 
      61 cagtaagtaa tatatgtaat gaactcttta caaatatcag caatagtagc attagtagta 
     121 gcaggaataa tagcaatagt tgtgtggtca atagtagcca tagaatatag gaaaatatta 
     181 aggcaaagaa aaatagacag gttaattgat agaataagag aaagagcaga agacagtggc 
     241 aatgagagtg atggggatca ggaagaatta tcagcacttg tggagagagg gcatcttgct 
     301 cttggggata ttaatgatct gtagtgctgc agacaaattg tgggtcacag tctattatgg 
     361 ggtacctgtg tggagagaag caaccactac tctattttgt gcatcagatg ctaaagcata 
     421 tgatacagag gcacataatg tttgggccac acacgcctgt gtacccacag accccaaccc 
     481 acaagaagta gaattaaaaa atgtgacaga aaattttaat atgtgggaaa ataacatggt 
     541 agaacagatg catgaggata taatcagttt atgggatcaa agcttaaaac catgtgtaaa 
     601 attaactcca ctctgtgtta ctttaaattg cactgattta gggaatgtta ctaataccac 
     661 taatagtaac ggggaaatga tggagaaggg agaagtaaaa aactgttctt tcaagatcac 
     721 cacagacata aaagatagaa cgcggaagga atatgcactt ttttataaac ttgatgtagt 
     781 accaataaat gataccagat ataggttagt aagctgtaac acctcagtca ttacacaggc 
     841 ctgtccaaag gtatcctttg agccaattcc tatacattat tgtgccccgg ctggttttgc 
     901 gattctaaag tgtaatgata agcaattcat tggaacagga ccatgtacaa atgtcagcac 
     961 agtacaatgt acacatggaa ttaggccagt agtatcaact caactgctgt taaatggcag 
    1021 tttagcagaa gaagaggtag taattagatc agtcaatttc agtgacaatg ctaaaacaat 
    1081 aatagtacaa ctgaataaat ctgtagaaat tacttgcaca agacccaaca acaatacaag 
    1141 aaaaagtata cccatgggac cagggaaagc attttatgca agaggagaca taacaggaga 
    1201 cataagaaaa gcatattgtg aaattaatgg aacagaatgg catagcactt taaaactggt 
    1261 agttgaaaaa ttaagagaac aatataataa aacaatagtc tttaatcgct cctcaggagg 
    1321 ggacccagaa attgtaatgt acagtttcaa ttgcggaggg gaatttttct actgtaattc 
    1381 aacaaagctg tttaatagta cttggccttg gaatgatact aaagggtcac atgacactaa 
    1441 tggcacactc atactcccat gcaaaataaa acaaattata aacatgtggc agggagtagg 
    1501 aaaagcaatg tatgcccctc ccatcgaagg aaaaattaga tgctcatcaa acattacagg 
    1561 actgttatta acaagagatg gtggttacga gagcaatgag actgatgaga tcttcagacc 
    1621 tggaggagga gatatgaggg acaattggag gagtgaatta tataaatata aagtagtaaa 
    1681 aattgaacca ttgggagtag cacctaccaa ggcaaagagg agagtggtgc agagggaaaa 
    1741 aagagcattt ggactaggag ctgtgttcct tgggttcttg ggagcagcag gaagcactat 
    1801 gggcgcagca tcaataacgc tgacggtaca ggccagacaa ttattgtctg gtatagtgca 
    1861 acagcagaac aatttgctga gggctattga ggcgcaacag catctgttgc aactcacagt 
    1921 ctggggcatt aagcagctcc aggcaagagt cctggctgtg gaaagatacc taaaggatca 
    1981 acagctcctg gggatttggg gttgctctgg aaaactcatc tgcaccacta ctgtgccttg 
    2041 gaatactagt tggagtaata aatctctgga acagatttgg gataacatga catggatgga 
    2101 gtgggaaaga gaaattgaca attatacagg ctacatatac caattaattg aagaatcgca 
    2161 gaaccaacaa gaaaagaatg aacaagaatt attggcattg gataaatggg caagtttgtg 
    2221 gaattggttt gacataacaa actggctgtg gtatataaaa atattcataa tgatagtagg 
    2281 aggcttaata ggtttaagaa tagtttttac tgtactttct atagtgaata gagttaggca 
    2341 gggatactca ccattatcat ttcagaccca cctcccagcc cagaggggac ccgacaggcc 
    2401 cgaaggaatc ggagaagaag gtggagagag agacagagac agatccgatc cattagtgaa 
    2461 cggattctta gcacttatct ggagcgatct acggagcctg tgcctcttca gctaccaccg 
    2521 cttgagagac ttactcttga ttgtaacgag gattgtggaa cttctgggac gcagggggtg 
    2581 ggaagtcctc aaatattggt ggaatctcct acagtattgg agtcaggaac taaagaatag 
    2641 tgctgttagc ttgctcaacg ccacagccat agcagtagct gaggggacag atagggttat 
    2701 agaagtagta caaagagctt gtagagctat tctccacata cctagaagaa taagacaggg 
    2761 cttggaaagg gctttgctat aagatgggtg gcaagtggtc aaaatgtagt gtggttggat 
    2821 ggccttcagt aagggaaaga atgagacgag ctgagccagc agcagagggg gtaggagcag 
    2881 tatctcgaga cctggaaaaa catggagcaa tcacaagtag caacacagca gctaccaatg 
    2941 ctgattgtgc ctggctagaa gcacaagagg agggggaagt gggtttccca gtcagacctc 
    3001 aggtgccttt aagaccaatg accttcaagg gagctctgga tcttagccac tttttaaaag 
    3061 aaaagggggg actggaaggg ttaatttact cccaaaaaag acaagatatc cttgatctgt 
    3121 gggtctacca cacgcaaggc tacttccctg attggcagaa ctacacacca gggccaggga 
    3181 ccagatttcc actgaccttt ggatggtgct tcaagctagt accagtggat ccagggaaag 
    3241 tagaagaggc caataaagga gagaacaact gcttgttaca ccctatgagc cagcatggga 
    3301 tggacgaccc agagagagaa gtgttagtgt ggaggtttga cagcagccta gcatttcgtc 
    3361 acgtggcccg agagctgcat ccggagtact acaagaactg ctgacatcga gctttctaca 
    3421 agggactttc cgctggggac tttccaggga ggcgtgacat gggcggaatt ggggagtggc 
    3481 gagcccacag atgctgcata taagcagccg ctttctgctt gtactgggtc tctctggtta 
    3541 gaccagatct gagcctggga gctctctggc tagctaggga acccactgct taa
//
last modified: Tue May 31 10:56 2022


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