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LOCUS	    AY463224		    9066 bp    RNA     linear	VRL 18-SEP-2006
DEFINITION  HIV-1 isolate C.ZA.1162MB from South Africa, complete genome
ACCESSION   AY463224
VERSION     AY463224.1 GI:38892663
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 9066)
            Show all sequences for reference 1
  AUTHORS   Rousseau,C.M., Birditt,B.A., McKay,A.R., Stoddard,J.N., Lee,T.C.,
	    McLaughlin,S., Moore,S.W., Shindo,N., Learn,G.H., Korber,B.T.,
	    Brander,C., Goulder,P.J., Goulder,P.J.R., Kiepiela,P., Walker,B.D.
	    and Mullins,J.I.
  TITLE     Large-scale amplification, cloning and sequencing of near
	    full-length HIV-1 subtype C genomes
  JOURNAL   J. Virol. Methods 136 (1-2), 118-125 (2006)
  PUBMED    16701907
REFERENCE   2 (bases 1 to 9066)
            Show all sequences for reference 2
  AUTHORS   Korber,B.T., Mullins,J.I., Goulder,P.J., Brander,C., Kiepiela,P.,
	    Moore,S., Shindo,N. and Walker,B.
  CONSRTM   HIV HLA epitope mapping
  TITLE     Direct Submission
  JOURNAL   Submitted (12-NOV-2003) Theoretical Biology and Biophysics, Los
	    Alamos National Laboratory, T10 MS K710, Los Alamos, NM 87545, USA
REFERENCE   3
            Show all sequences for reference 3
  AUTHORS   Kiepiela,P., Leslie,A.J., Honeyborne,I., Ramduth,D., Thobakgale,C.,
	    Chetty,S., Rathnavalu,P., Moore,C., Pfafferott,K.J., Hilton,L.,
	    Zimbwa,P., Moore,S., Allen,T., Brander,C., Addo,M.M., Altfeld,M.,
	    James,I., Mallal,S., Bunce,M., Barber,L.D., Szinger,J., Day,C.,
	    Klenerman,P., Mullins,J., Korber,B., Coovadia,H.M., Walker,B.D. and
	    Goulder,P.J.
  TITLE     Dominant influence of HLA-B in mediating the potential co-evolution
	    of HIV and HLA
  JOURNAL   Nature 432 (7018), 769-775 (2004)
  PUBMED    15592417
COMMENT     Genome sequence lacks part of non-coding region.
FEATURES             Location/Qualifiers
     source	     1..9066
		     /organism="Human immunodeficiency virus 1"
		     /mol_type="genomic RNA"
		     /isolate="C.ZA.1162MB"
		     /isolation_source="woman with heterosexual transmission as
		     her primary risk factor; sample date 06/2000"
		     /db_xref="taxon:11676"
		     /country="South Africa: Durban"
		     /note="subtype: C"
     gene	     240..1717
		     /gene="gag"
     misc_feature    240..1717
		     /gene="gag"
		     /note="nonfunctional gag protein due to mutation"
     gene	     <1522..4520
		     /gene="pol"
     misc_feature    <1522..4520
		     /gene="pol"
		     /note="nonfunctional pol protein due to mutation"
     gene	     4465..5043
		     /gene="vif"
     CDS	     4465..5043
		     /gene="vif"
		     /codon_start="1"
		     /transl_table="1"
		     /product="vif protein"
		     /protein_id="AAR27667.1"
		     /db_xref="GI:38892664"
		     /translation="MENRWQVLIVWQVDRMKIRTWNSLVKHHMYISKKASGWFYRHHY
		     ESRHPRVSSEVHIPLGNARLVIKTYWGLLPGERDWHLGNGASIEWRLRRYSTQIDPGL
		     ADQLIHMHYFDCFADSAIRKAILGHIVIPRCDYQAGHNKVGSLQYLALTALIKPKKRK
		     PPLPSVRKLVEDRWNNPQKIRGRRGNHTMNGH"
     gene	     4983..5273
		     /gene="vpr"
     CDS	     4983..5273
		     /gene="vpr"
		     /codon_start="1"
		     /transl_table="1"
		     /product="vpr protein"
		     /protein_id="AAR27668.1"
		     /db_xref="GI:38892665"
		     /translation="MEQPPEDQGPQREPYNEWTLEILEELKQEAVRHFPRTWLHNLGQ
		     YIYETYGDTWTGVEAIIRILQQLLFIHFRIGCQHSRIGTLRQRRARNGASRS"
     gene	     5254..7873
		     /gene="tat"
     CDS	     join(5254..5468,7783..7873)
		     /gene="tat"
		     /codon_start="1"
		     /transl_table="1"
		     /product="tat protein"
		     /protein_id="AAR27669.1"
		     /db_xref="GI:38892666"
		     /translation="MEPVDPNLEPWNHPGSQPETSCNNCYSKHCSYHCLVCFQKKGLG
		     ISYGRKKRRQRRSTPPSSEDHQNHISKQPLSQTRGDPTGSEESKKKVESKTKTDQFD"
     gene	     5393..8030
		     /gene="rev"
     CDS	     join(5393..5468,7783..8030)
		     /gene="rev"
		     /codon_start="1"
		     /transl_table="1"
		     /product="rev protein"
		     /protein_id="AAR27670.1"
		     /db_xref="GI:38892667"
		     /translation="MAGRSGDSDEALLQAVKIIKIIYQSNPYPKPEGTRQARKNRRRR
		     WRARQRQINSISERILSTCLGRSAEPVPFQLPPIEKLHIGDSESSGTSGTQQSQGTTE
		     GMGSS"
     gene	     5482..5742
		     /gene="vpu"
     CDS	     5482..5742
		     /gene="vpu"
		     /codon_start="1"
		     /transl_table="1"
		     /product="vpu protein"
		     /protein_id="AAR27671.1"
		     /db_xref="GI:38892668"
		     /translation="MVNLLARVDYRLGVGALIIALSIAIIVWIIVYIEYRKLLRQKKI
		     DRLIKRIRERAEDSGNESEGDTEELATMVDMGYLRLLDDNNL"
     gene	     5660..8220
		     /gene="env"
     misc_feature    5660..8220
		     /gene="env"
		     /note="nonfunctional envelope protein due to mutation"
     gene	     8222..8845
		     /gene="nef"
     CDS	     8222..8845
		     /gene="nef"
		     /codon_start="1"
		     /transl_table="1"
		     /product="nef protein"
		     /protein_id="AAR27672.1"
		     /db_xref="GI:38892669"
		     /translation="MGGKWSKSSIVGWPAIRERIRQTKPAAEGVGAASQDLDKHGALT
		     TSDTAHNNADCAWLQAQEEEEEVGFPVRPQVPLRPMTFKGAFDLSFFLKEKGGLEGLV
		     YSRKRQEILDLWVYHTQGYFPDWQNYTPGPGVRYPLTFGWCFKLVPVDPREVEEANKG
		     ENNCLLHPMSLHGAEDEERGVLKWKFDSSLARRHMARELHPEYYKDC"
BASE COUNT     3299 a	1601 c	 2180 g   1986 t
ORIGIN
       1 agtagtgtgt gcccgtctgt tgtgtgactc tggtaactag agatccctca gaccctttgt 
      61 ggtagtgtgg aaaatctcta gcagtggcgc ccgaacaggg acccgaaagt gaaagtaaga 
     121 ccagaggagg tctctcgacg caggactcgg cttgctgaag tgcactcggc aagaggcgag 
     181 agcggcgact ggtgagtacg ccaaatttta tttgactagc ggaggctaga aggagagaga 
     241 tgggtgcgag agcgtcaata ttaagagggg aaaaattaga taaatgggaa aaaattaggt 
     301 taaggccagg gggaaagaaa cactatatgt taaaacacct agtatgggca agcagggagc 
     361 tggaaagatt tgcacttaac cctggcctgc tagaaacatc agaaggctgt aaacaaataa 
     421 tgaaacagct acaaccagct cttcagacag gaacagaaga acttagatcg ttattcaaca 
     481 cagtagcaac tctctattgt gtacatgaaa agatagaggt acgagacacc aaggaagcct 
     541 tagacaagat agaggaagaa caagacaaaa gtcagcaaaa aacacagtag gcaaaagcgg 
     601 ctgacgagaa ggtcagtcaa aattatccta tagtgcagaa tctccaaggg caaatggtac 
     661 accaagccat atcacctaga actttgaatg catgggtaaa agtaatagag gagaaggctt 
     721 ttagcccaga ggtaataccc atgttcacag cattatcaga aggagccacc cacaagattc 
     781 aaacaccatg ttgaatacag tggggggaca tcaagcagca atgcaaatgt taaaagatac 
     841 catcaatgaa gaggctgcgg aatgggatag attacatcca gtacatgcag ggcctattgc 
     901 accaggccaa gtaagagaac caaggggaag tgacatagca ggaactacta gtacccttca 
     961 ggaacaaata gcatggatga caagtaaccc acctatccca gtaggagaaa tctataaaag 
    1021 atggataatt ctggggctaa acaaaatagt gagaatgtat agccctgtca gcattttgga 
    1081 cataaaacaa gggccaaagg aaccttttag agactatgta gaccggttct ttaaatgttt 
    1141 aagagctgaa caagctacac aagatgtaaa aaattggatg acagacacct tgttggtcca 
    1201 aaatgcgaac ccagattgta aaaccatttt aagagcatta gggccagcgg cttcattaga 
    1261 agaaatgatg acagcatgtc agggagtggg aggacctagc cacaaagcaa gagtgttggc 
    1321 tgaggcaatg agccaggcaa atagtggaaa catactgatg cagagaagca attttaaagg 
    1381 ctctaaaaga attgttaaat gtttcaactg tggcaaggaa gggcacatag ccagaaattg 
    1441 cagggctcct aggaaaaagg gctgttggaa atgtggaaag gaaggacacc aaatgaaaga 
    1501 ctgtactgaa aggcaggcta attttttagg gaaaatttgg ccttcccaca aggggaggcc 
    1561 agggaatttc cttcagaaca gaccagagcc aacggcccca ccagcagaga gcttcaggtt 
    1621 cgaggagaca acccctgctc tgaagcagga gccgaaagac agggaaccct taacttccct 
    1681 caaatcactc tttggcagcg tccccttgtc tcaataaaaa tagggggcca ggtaagggag 
    1741 gctctcttag atacaggagc agatgataca gtattagaag aaataaattt accaggaaaa 
    1801 tggaaaccaa aaatgatagg aggaattgga ggttttatca aagtaagaca gtatgatcaa 
    1861 atacttatag aaatttgtgg aaaaaaggct ataggtacag tattagtagg acctacacct 
    1921 gtcaacacaa ttggaagaaa tatgttgact cagcttggat gcacactaaa ttttccaatt 
    1981 agtcctattg aaactatacc agtaaaactg aagccaggaa tggatggccc aaaggttaaa 
    2041 caatggccat tgacagaaga aaaaataaaa gcattaacag caatttgtaa agaaatggag 
    2101 aaggaaggaa aaattacaaa aattgggcct gaaaacccat ataatactcc agtatttgcc 
    2161 ataaaaaaga aggacagtac taagtggaga aaattagtag atttcaggga actcaataaa 
    2221 agaactcaag acttttggga ggttcaatta ggaataccac acccagcagg gttaaaaaag 
    2281 aaaaaatcag tgacagtact ggatgtgggg gatgcatatt tttcagtccc tttagatgaa 
    2341 gacttcagga aatatactgc attcaccata cctagtataa acaatgaaac accagggatt 
    2401 agatatcaat ataatgtgct tccacaggga tggaaaggat caccagcaat attccaaagt 
    2461 agcatgataa agatcttaga gccctttaga gcacaaaatc cagaaatagt catctatcaa 
    2521 tatatggatg acttgtatgt aggctctgac ttagaaatag ggcaacatag agcaaaaata 
    2581 gaggagttaa gagaacatct attaaggtgg ggacttacca caccagacaa gaaacaccag 
    2641 aaagaacccc cattcctttg gatggggtat gaactccatc cggacaaatg gacagtacag 
    2701 cctatacagc tgccagaaaa ggatagctgg actgtcaatg atatacagaa gttagtggga 
    2761 aaattaaact gggcaagcca gatttaccca gggattcagg taaggcaact ttgtaaactc 
    2821 cttagggggg ccaaagcact aacagacata gtaccactaa ctgaagaagc agaattagaa 
    2881 ttagcagaga acagggaaat tctaaaacaa ccagtacatg gagtatatta tgacccatca 
    2941 aaggacttaa tagctgaaat acagaaacag gggcatgacc aatggacgta tcaaatttac 
    3001 caagaaccat tcaaaaatct gaaaacaggg aagtatgcaa aaatgaggac tgcccacact 
    3061 aatgatgtaa aacagttaac agaggcagtg cagaaaatag ccttggaaag catagtaata 
    3121 tggggaaaga ctcctaaatt tagactgccc atccaaaaag aaacatggga gatatggtgg 
    3181 acagactatt ggcaagccac ctggattccc gagtgggagt ttgttaatac ccctccccta 
    3241 gtaaagttat ggtaccagct ggagaaagaa cccatagcag gagcagaaac tttttatgta 
    3301 gatggagcag ccaataggga tactaaaaag ggaaaagcag ggtatgttac tgacagagga 
    3361 aggcaaaaaa ttgtctctct aagtgaaaca acgaatcaga agactgaatt acaagcaatt 
    3421 cagctagctt tgcaagattc aggatcagaa gtaaacatag taacagactc acagtatgca 
    3481 ttaggaatca ttcaagcaca accagataag agtgaatcag agttagtcaa ccaaataata 
    3541 gaacaactaa taaaaaagga aaaggtctac ctgtcatggg taccagcaca caaaggaatt 
    3601 ggaggaagtg aacaagtaga caaattagta agtagtggaa tcaggaaagt gctgtttcta 
    3661 gatggaatag ataaggcaca agaagagcat gaaaagtatc acagcaattg gagagcaatg 
    3721 gctagtgagt ttaatctgcc acccatagta gcaaaagaaa tagtagcaag ctgtgataaa 
    3781 cgtcagttaa aaggggaagc catacatgga caagtagact gtagtccagg gatatggcaa 
    3841 ttagattgta cacatttaga agggaaagtc atcctggtag cagtccatgt agccagtggc 
    3901 tacatagagg cagaggttat cccagcagaa acaggacaag aaacagcata ctatatacca 
    3961 aaattagcag ggagatggcc agtcaaagta atacatacag acaatggcag taatttcact 
    4021 agtgctgcag ttaaggcagc ctgttggtgg gcaggaatcc aacaggaatt tggaattccc 
    4081 tacaatcccc aaagtcaagg agtagtagaa tccatgaata aagaattaaa gaaaatcata 
    4141 gggcaggtaa gagatcaagc tgagcacctt aagacagcag tacaaatggc agcattcatt 
    4201 cacaatttta aaagaaaagg ggggattggg agtacagtgc aggggaaaga ataatagaca 
    4261 taatagcaac agacatacaa actaaagaac tacaaaaaca aattataaaa attcaaaatt 
    4321 ttcgggttta ttacagagac agcagagacc ctatttggaa aggaccagcc aagctactct 
    4381 ggaaaggtga aggggcagta gtgatacaag ataacagtga cataaaggta gtaccaagga 
    4441 ggaaagtaaa aatcattaag gactatggaa aacagatggc aggtgctgat tgtgtggcag 
    4501 gtagacagga tgaagattag aacatggaat agtttagtaa agcaccatat gtacatttca 
    4561 aagaaagcta gtggatggtt ttacagacat cattatgaaa gcagacatcc aagagtaagt 
    4621 tcagaagtac acataccatt agggaatgct agattagtaa taaaaacata ttgggggttg 
    4681 ctaccaggag aaagagattg gcatttgggt aatggagcct ccatagaatg gagattgaga 
    4741 agatacagca cacaaataga ccctggcctg gcagaccagc taattcatat gcattatttt 
    4801 gattgttttg cagactctgc cataagaaaa gccatattag gacacatagt tattcctagg 
    4861 tgtgactatc aagcaggaca taataaggta ggatctctac aatatttggc actgacagca 
    4921 ttgataaagc caaaaaagag aaaaccacct ctgcctagtg ttagaaaatt agtagaggat 
    4981 cgatggaaca acccccagaa gatcaggggc cgcagaggga accatacaat gaatggacac 
    5041 tagagattct agaggaactc aagcaggaag ctgtcagaca ctttcctaga acatggctcc 
    5101 ataacttagg acagtatatc tatgaaacct atggggatac ttggacagga gttgaagcta 
    5161 taataagaat attgcaacaa ttactgttta ttcatttcag aattgggtgc cagcatagca 
    5221 ggataggaac cttgcgacag agaagagcca gaaatggagc cagtagatcc taacctagag 
    5281 ccctggaacc atccagggag tcagcctgaa acgtcttgta ataactgcta tagtaaacac 
    5341 tgtagctacc attgtctagt ttgctttcag aaaaaaggct taggcatttc ctatggcagg 
    5401 aagaagcgga gacagcgacg aagcactcct ccaagcagtg aagatcatca aaatcatata 
    5461 tcaaagcagt aagtagatgt aatggtgaat ttactagcaa gagtagatta tagattagga 
    5521 gtaggagctc tgataatagc attaagcata gcaataattg tgtggatcat agtatatata 
    5581 gaatatagga aattgttaag acaaaagaaa atagataggt taattaaaag aattagggaa 
    5641 agagcagaag acagtggcaa tgagagtgaa ggggataccg aggaattggc cacaatggtg 
    5701 gatatggggt atcttaggct tttggatgat aataatttgt agagtggtgg ggaacttgtg 
    5761 ggtcacagtt tattatgggg tacctgtgtg gaaagaagca aaggctactc tattctgtgc 
    5821 atcaaatgca aaagcatatg agagagaagt gcataatgtc tgggctacac atacctgtgt 
    5881 acccacagac cccgacccac aagaaatagt tttgaaaaat gtaacagaaa attttgacat 
    5941 gtggaaaaat tacatggtgg atcagatgca tgaggatata atcagtttat gggatcaaag 
    6001 cctaaaacca tgtgtaaagt tgaccccact ctgtgtcact ttaaactgta cacagtataa 
    6061 taataccaat aggggtaatg ttacctacag gagtgataat gatatttaca ttgagaacat 
    6121 aacggaagaa gtaagaaatt gctctttcaa tacaaccaca gaaataagag ataagaaaca 
    6181 aaaagggtat gcactttttt atagatctga tatagtacta cttaatgaga gtaagaattc 
    6241 tggtgagtat atattaataa actgcaatac ctcaaccata gcacaagcct gcccaaaggt 
    6301 ctcttttgac ccaattccca tacattattg tgctccagct ggttatgcga ttctaaagtg 
    6361 taataataag acattcagtg ggaagggacc atgcactaat gtcagcacag tacaatgtac 
    6421 acatggaatt aagccagtgg tatcaactca actactgtta aatggtagtc tagcagaaga 
    6481 aaagataata attagatctg aaaatctgac agacaatggc aaaacaataa tagtacacct 
    6541 taataaatct atagcaattg tgtgtacaag acctggcaat aatacaagaa aagtataagg 
    6601 ataggaccag gacaagcatt ttatgcaaca aatgacataa taggagacat aagacaagca 
    6661 tattgtaaca ttagtgctca ggactggacc acaaccttaa aaaatgtaaa gaaagaatta 
    6721 gaacactacc atcctactaa aacaatagaa tttaaaccac atccaggagg ggatctagaa 
    6781 gttacaacac atagctttaa ttgtagagga gaatttttct attgcaatac aacacaactg 
    6841 tttaataaaa atgttcaaag caacggaagc atcatactcc catgcaagat aaaacaaatt 
    6901 ataaacatgt ggcagggggt aggacgagca atgtatgccc ctcccatcgc aggaaacata 
    6961 acatgtaact caagtatcac aggactacta ttaacgaggg atggaggcat aagtgagaac 
    7021 atgacagaga cattcagacc tggaggggga aatatgaagg acaattggag aagtgaatta 
    7081 tataaatata aagtagtaga aattaagcca ttgggaatag cacccactaa ggcaaaaagg 
    7141 agagtggtgg agagagaaaa aagagcagca ataggagcta tgttccttgg gttcttggga 
    7201 gcagcaggaa gcactatggg cgtggcgtca ataacgctga cggtacaggc cagaaatctg 
    7261 ttgtctggta tagtgcaaca gcaaagcaat ttgctgagag ctgtagaagc gcaacaacat 
    7321 atgttgcaac tcacggtctg gggcattaag cagctccaga caagagtcct ggctatagaa 
    7381 agatacctaa aggatcaaca gctcctagga ctttggggct gctctggaaa actcatctgc 
    7441 aacactgccg tgccttggaa ctccacttgg agtaataaat ctgaaagata tatttgggag 
    7501 aacatgacct ggatgcagtg ggatagagaa attaataatt acacaggcat aatatatagg 
    7561 ttgcttgaaa aatcgcaaaa ccagcaggag gaaaatgaaa aagatttatt agcattggac 
    7621 aactggaaaa atctgtggaa ttggtttgac ataacaaact ggctgtggta tataaaaatg 
    7681 ttcatcatga tagtaggagg cttgataggt ttgagaataa tttttgctgt gctctctata 
    7741 gtgaaaagag ttaggcaggg atactcacct ttgtcgtttc agacccttat cccaaacccg 
    7801 aggggacccg acaggctcgg aagaatcgaa gaagaaggtg gagagcaaga caaagacaga 
    7861 tcaattcgat tagtgagcgg attcttagca cttgcctggg acgatctgcg gagcctgtgc 
    7921 cttttcagct accaccaatt gagaaacttc atattggtga cagcgagagc agtggaactt 
    7981 ctgggacgca gcagtctcag gggactacag aggggatggg aagctcttaa atatctggga 
    8041 aaccttgtgc agtattgggg tctggagcta aaaaagagtg ctactagtct gcttgatacc 
    8101 atagcaatag cagtagctga aggaacagat agaattatag aagtagtgca aggagtttgg 
    8161 agagctatcc gcaacatacc tactagaata agacagggct ttgaagcagc tttgctataa 
    8221 aatggggggc aaatggtcaa agagcagcat agttggatgg ccggctataa gagaaagaat 
    8281 aaggcaaact aagccagcag cggagggagt aggagcagca tctcaagact tagataaaca 
    8341 tggagcactt acaaccagtg acacagccca caataatgct gattgtgcct ggctgcaagc 
    8401 acaagaggag gaagaggaag tgggctttcc agtcagacct caggtgcctt taagaccaat 
    8461 gacatttaag ggagcattcg atctcagctt ctttttaaaa gaaaaggggg gactggaagg 
    8521 gttagtttac tctaggaaaa ggcaagaaat ccttgatttg tgggtctatc acacacaagg 
    8581 ctacttccct gattggcaaa actacacacc gggaccaggg gtcagatatc cactgacctt 
    8641 tggatggtgc ttcaagctag tgccagttga cccaagggaa gtagaagagg ccaacaaagg 
    8701 agaaaacaac tgtctgctac accctatgag cctacatgga gcagaggatg aagaaagagg 
    8761 agtattaaag tggaagtttg acagcagcct agcacgcaga cacatggccc gcgagctaca 
    8821 tccggaatat tacaaagact gctgacacag aagggacttt ccgcctggga ctttccactg 
    8881 gggcgttcca ggaggtgtgg tctgggaggg actagggagt ggtcaaccct cagatgctgc 
    8941 atataagcag ctgcttttcg cctgtactgg gtctctctag gtagaccaga tctgagcctg 
    9001 ggagctctct ggccacttag ggaacccact gcttaagcct caataaagct tgccttgagt 
    9061 gctcta
//
last modified: Tue May 31 10:56 2022


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