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LOCUS	    JX446663		    4971 bp    RNA     linear	VRL 12-OCT-2012
DEFINITION  HIV-1 isolate AA001a10R from Thailand pol protein (pol) gene,
	    partial cds; and vif protein (vif), vpr protein (vpr), vpu protein
	    (vpu), envelope glycoprotein (env), and nef protein (nef) genes,
	    complete cds
ACCESSION   JX446663
VERSION     JX446663.1 GI:407731841
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 4971)
            Show all sequences for reference 1
  AUTHORS   Rolland,M., Edlefsen,P.T., Larsen,B.B., Tovanabutra,S.,
	    Sanders-Buell,E., Hertz,T., deCamp,A.C., Carrico,C., Menis,S.,
	    Magaret,C.A., Ahmed,H., Juraska,M., Chen,L., Konopa,P., Nariya,S.,
	    Stoddard,J.N., Wong,K., Zhao,H., Deng,W., Maust,B.S., Bose,M.,
	    Howell,S., Bates,A., Lazzaro,M., O'Sullivan,A., Lei,E.,
	    Bradfield,A., Ibitamuno,G., Assawadarachai,V., O'Connell,R.J.,
	    deSouza,M.S., Nitayaphan,S., RERKS-NGARM,S., Robb,M.L.,
	    McLellan,J.S., Georgiev,I., Kwong,P.D., Carlson,J.M., Michael,N.L.,
	    Schief,W.R., Gilbert,P.B., Mullins,J.I. and Kim,J.H.
  TITLE     Increased HIV-1 vaccine efficacy against viruses with genetic
	    signatures in Env V2.
  JOURNAL   Nature.. 490(7420); 417-20 (2012)
  PUBMED    22960785
REFERENCE   2 (bases 1 to 4971)
            Show all sequences for reference 2
  AUTHORS   Rolland,M., Edlefsen,P.T., Larsen,B.B., Tovanabutra,S.,
	    Sanders-Buell,E., Hertz,T., de Camp,A.C., Carrico,C., Menis,S.,
	    Magaret,C.A., Ahmed,H., Juraska,M., Chen,L., Konopa,P., Nariya,S.,
	    Stoddard,J.N., Wong,K., Zhao,H., Deng,W., Maust,B.S., Bose,M.,
	    Howell,S., Bates,A., Lazzaro,M., O'Sullivan,A., Lei,E.,
	    Bradfield,A., Ibitamuno,G., Assawadarachai,V., O'Connell,R.J., de
	    Souza,M.S., Nitayaphan,S., RERKS-NGARM,S., Robb,M.L.,
	    McLellan,J.S., Georgiev,I., Kwong,P.D., Carlson,J.M., Michael,N.L.,
	    Schief,W.R., Gilbert,P.B., Mullins,J.I. and Kim,J.H.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-AUG-2012) US Military HIV Research Program, 503
	    Robert Grant Ave, Silver Spring, MD 20910, USA
COMMENT     ##Assembly-Data-START## Sequencing Technology Sanger dideoxy
	    sequencing ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source	     1..4971
		     /organism="Human immunodeficiency virus 1"
		     /mol_type="genomic RNA"
		     /isolate="AA001a10R"
		     /isolation_source="plasma AA001a"
		     /host="Homo sapiens; RV144 trial participant AA001"
		     /db_xref="taxon:11676"
		     /country="Thailand"
		     /collection_date="2008"
		     /note="subtype: CRF01_AE"
     gene	     <1..538
		     /gene="pol"
     CDS	     <1..538
		     /gene="pol"
		     /codon_start="2"
		     /transl_table="1"
		     /product="pol protein"
		     /protein_id="AFU25843.1"
		     /db_xref="GI:407731842"
		     /translation="KVIHTDNGSNFTSAAVKAACWWANVRQEFGIPYNPQSQGVVESM
		     NKELKKIIGQVREQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIIDIIATDIQTKE
		     LQKQITKIQNFRVYYRDSRDPIWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRD
		     YGKQMAGDDCVAGRQDED"
     misc_feature    <1..157
		     /gene="pol"
		     /note="Integrase core domain; Region: rve; pfam00665"
		     /db_xref="CDD:201381"
     misc_feature    329..481
		     /gene="pol"
		     /note="Integrase DNA binding domain; Region: IN_DBD_C;
		     pfam00552"
		     /db_xref="CDD:144223"
     gene	     483..1061
		     /gene="vif"
     CDS	     483..1061
		     /gene="vif"
		     /codon_start="1"
		     /transl_table="1"
		     /product="vif protein"
		     /protein_id="AFU25844.1"
		     /db_xref="GI:407731843"
		     /translation="MENRWQVMIVWQVDRMRIRTWNSLVKHHMYISKKAKNWSYKHHY
		     DSQHPKVSSEVHIPIREARLVIRTYWGLQTGEKDWHLGHGVSIEWRQRNYSTQIDPDL
		     ADQLIHIQYFECFSDSAIRRAILGQVVRSRCDYPSGHNKVGSLQYLALKALTTSKRKG
		     PPLPSVKKLTEDRWNKPQRIRDHRGNPSMNGH"
     misc_feature    483..1058
		     /gene="vif"
		     /note="Retroviral Vif (Viral infectivity) protein; Region:
		     Vif; pfam00559"
		     /db_xref="CDD:109609"
     gene	     1001..1291
		     /gene="vpr"
     CDS	     1001..1291
		     /gene="vpr"
		     /codon_start="1"
		     /transl_table="1"
		     /product="vpr protein"
		     /protein_id="AFU25845.1"
		     /db_xref="GI:407731844"
		     /translation="MEQAPEDQGPQREPFNEWTLELLEELKHEAVRHFPRPWLHGLGQ
		     HIYNTYGDTWEGVEAIIRILQQLLFVHFRIGCQHSRIGIIPGRRGRNGAGRS"
     misc_feature    1001..1237
		     /gene="vpr"
		     /note="VPR/VPX protein; Region: VPR; pfam00522"
		     /db_xref="CDD:109573"
     gene	     1507..1752
		     /gene="vpu"
     CDS	     1507..1752
		     /gene="vpu"
		     /codon_start="1"
		     /transl_table="1"
		     /product="vpu protein"
		     /protein_id="AFU25846.1"
		     /db_xref="GI:407731845"
		     /translation="MSPLEISAITGLVVALIAAIVVWTIVAIEFRKILKQRKIDRLVK
		     RIRERAEDSGNESEGDTDELAKLVEMGDFDPWVGDNV"
     misc_feature    <1591..1734
		     /gene="vpu"
		     /note="Vpu protein; Region: Vpu; pfam00558"
		     /db_xref="CDD:109608"
     gene	     1670..4270
		     /gene="env"
     CDS	     1670..4270
		     /gene="env"
		     /codon_start="1"
		     /transl_table="1"
		     /product="envelope glycoprotein"
		     /protein_id="AFU25847.1"
		     /db_xref="GI:407731846"
		     /translation="MRVKETQMNWLNLWRWGTLILGLVIMCSAADNLWVTVYYGVPVW
		     RDADTTLFCASDAKAHDTEVHNVWATYACVPTDPNPQEIHLVNVTENFNMWKNNMVEQ
		     MQEDVISLWDQSLKPCVKLTPLCVTLNCTNANLTHLNTTNLNTTTVSRDIGNITDEVR
		     NCTFNMTTVVSDKKQKVYALFYKLDLVPMKENPNNSEYRLINCNTSVIKQACPKISFD
		     PIPIHYCTPAGYAILKCNEKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEE
		     IIIRSENLTDNAKTIIVHLNKSVEINCTRPSNNTRTGITIGPGQTFYRTGDIIGDIRQ
		     AYCKINGTKWNETLKQVAKKLQEHFKNKTIKFQPHSGGDLEITMHHFNCKGEFFYCNT
		     TKLFNSTWTGNETIGNKTIGNDTIILPCRIKQIINLWQGVGQAMYAPPIRGVIQCVSN
		     ITGILLTRDGGNNGTNITETFRPGGGNIKDNWRSELYKYKVVQIEPLGVAPTRAKRRV
		     VEREKRAVGIGAMIFGFLGAAGSTMGAASITLTVQARQLLSGIVQQQSNLLRAIEAQQ
		     HMLQLTVWGIKQLQARVLAVERYLKDQKFLGLWGCSGKIICTTAVPWNSTWSNKSYEE
		     IWGNMTWIEWEREIGNYTNQIYDILTKSQDQQDRNEKDLLELDKWASLWNWFDISNWL
		     WYIKIFIIIVGGLIGLRIIFAVLSIVNRVRQGYSPLSFQTPSHHQREPDRPERIEEGG
		     GEQDRDRSVRLVTGFLAVVWDDLRNLCLFSYHRLRDFILIATRAVELLGHSSLKGLRR
		     GWEGLKYLGNLLIYWGKELKISAISLFDAGAIAVAGWTDRVIEIAQGAWRAILHIPRR
		     IRQGLERALL"
     misc_feature    1766..3175
		     /gene="env"
		     /note="Envelope glycoprotein GP120; Region: GP120;
		     pfam00516"
		     /db_xref="CDD:109567"
     misc_feature    3293..3673
		     /gene="env"
		     /note="heptad repeat 1-heptad repeat 2 region (ectodomain)
		     of the gp41 subunit of human immunodeficiency virus
		     (HIV-1), and related domains; Region: HIV-1-like_HR1-HR2;
		     cd09909"
		     /db_xref="CDD:197369"
     misc_feature    order(3293..3352,3359..3457)
		     /gene="env"
		     /note="HR1; other site"
		     /db_xref="CDD:197369"
     misc_feature    order(3299..3301,3305..3313,3317..3334,3338..3352,3359..33
		     76,3380..3397,3401..3409,3413..3418,3422..3427,3434..3439,
		     3443..3451,3455..3481,3494..3496,3500..3502,3506..3517,354
		     5..3550,3557..3562,3569..3571,3578..3583,3590..3595,3599..
		     3604,3611..3616,3620..3625,3632..3637,3653..3658,3665..366
		     7)
		     /gene="env"
		     /note="homotrimer interface [polypeptide binding]; other
		     site"
		     /db_xref="CDD:197369"
     misc_feature    order(3545..3604,3608..3643,3647..3673)
		     /gene="env"
		     /note="HR2; other site"
		     /db_xref="CDD:197369"
     gene	     4272..4889
		     /gene="nef"
     CDS	     4272..4889
		     /gene="nef"
		     /codon_start="1"
		     /transl_table="1"
		     /product="nef protein"
		     /protein_id="AFU25848.1"
		     /db_xref="GI:407731847"
		     /translation="MGGKWSKSSIVGWPQVRERIRQTPPATEGVGAVSQDLAKHGAVT
		     SSNINNADSVWLRAQEEDEEVGFPVRPQVPLRPMTFKGAFDLSFFLKEKGGLDGLIYS
		     KKRQDILDLWVYNTQGFFPDWQNYTPGPGIRYPLCFGWCFKLVPVDPKEVEEDNKGEN
		     SCLLHPMNQQGIEDTEREVLMWKFDSALARTHRARELHPEYYKDC"
     misc_feature    4275..4883
		     /gene="nef"
		     /note="Negative factor, (F-Protein) or Nef; Region:
		     F-protein; pfam00469"
		     /db_xref="CDD:109523"
BASE COUNT     1771 a	 858 c	 1194 g   1147 t      1 other
ORIGIN
       1 aaaagtaata cacacagaca atggtagcaa tttcaccagc gctgcagtta aagcagcctg 
      61 ttggtgggcc aatgtccgac aggaatttgg gatcccctac aatccccaaa gccaaggagt 
     121 agtagaatct atgaataagg aattaaagaa aatcataggg caggtaagag agcaagctga 
     181 acaccttaag acagcagtac aaatggcagt attcattcac aattttaaaa gaaaaggggg 
     241 gattgggggg tacagtgcag gggaaagaat aatagacata atagcaacag acatacaaac 
     301 caaagaatta caaaaacaaa ttacaaaaat tcaaaatttt cgggtttatt acagggacag 
     361 cagagatcca atttggaaag gaccagcaaa actactctgg aaaggtgaag gggcagtagt 
     421 aatacaggac aatagtgaca taaaagtagt accaagaaga aaagcaaaga tcattaggga 
     481 ttatggaaaa cagatggcag gtgatgattg tgtggcaggt agacaggatg aggattagaa 
     541 catggaacag tttagtaaaa catcatatgt atatctcaaa gaaagctaaa aattggtctt 
     601 ataarcatca ttatgatagc cagcatccaa aggtaagttc agaagtacat atcccaataa 
     661 gagaggctag attagtaata agaacatatt ggggtctgca gacaggagaa aaggactggc 
     721 acttgggtca tggagtctcc atagaatgga ggcagagaaa ctatagcaca caaatagacc 
     781 ctgacctagc agaccaactg attcatatac aatattttga atgtttttca gactctgcca 
     841 taaggagagc catattagga caagtagtta ggagtaggtg tgactacccg tcaggacata 
     901 acaaggtagg atccctacaa tatttggcac tgaaagcatt aacaacatca aaaaggaaag 
     961 ggccacctct gcctagtgtt aagaaattaa cagaagatag atggaacaag ccccagagga 
    1021 tcagggacca cagagggaac ccttcaatga atggacatta gaattgttag aagagcttaa 
    1081 acatgaagct gttagacatt ttcctaggcc ctggctccat ggcttaggac agcacatcta 
    1141 taacacttat ggggatactt gggaaggggt tgaagctata ataaggatat tgcaacaact 
    1201 actgtttgtt catttcagaa ttgggtgtca acatagcaga ataggcatta taccagggag 
    1261 aagaggcagg aatggagccg gtagatccta acctagagcc ctggaatcat ccagggagtc 
    1321 agcctacaac tgcttgtagc aactgttact gtaaaaaatg cagctggcat tgtcaactat 
    1381 gctttctgaa aaaaggctta ggcatctcct atggcaggaa gaagcggaag caccgacgag 
    1441 gaactcctca gagcagtaag gaccatcaaa atcctatacg agagcagtaa gtactaaata 
    1501 catgtaatgt cacctttgga aattagtgca ataacaggac tggtagtagc gctaatcgca 
    1561 gcaatagtag tgtggactat agtagctata gaatttagga aaatactaaa gcaaaggaaa 
    1621 atagacaggt tagttaagag aataagagaa agagcagaag acagtggaaa tgagagtgaa 
    1681 ggagacacag atgaattggc taaacttgtg gagatggggg actttgatcc ttgggttggt 
    1741 gataatgtgt agtgccgcag acaatttgtg ggttacagtt tattatgggg ttcctgtgtg 
    1801 gagagatgca gataccaccc tattttgtgc atcagatgcc aaagcacatg atacagaagt 
    1861 gcacaatgtc tgggccacat atgcctgtgt acccacagat cccaacccgc aagaaataca 
    1921 cctggtaaat gtaacagaaa attttaacat gtggaaaaat aacatggtag agcagatgca 
    1981 ggaggatgta atcagtttat gggatcaaag tctaaagcca tgtgtaaagt taactcctct 
    2041 ctgcgttact ctaaattgta ctaatgctaa tttgacccat ctcaacacga ccaatctcaa 
    2101 cacgaccact gtctctaggg acataggaaa tataacagat gaagtaagaa actgtacttt 
    2161 taatatgacc acagtagtat cagataagaa gcagaaggtc tatgcacttt tttataagct 
    2221 tgatttagta ccaatgaaag aaaatccaaa taatagtgag tatagattaa taaattgtaa 
    2281 tacttcagtc attaagcagg cttgtccaaa gatatccttt gatccaattc ctatacatta 
    2341 ttgtactcca gctggttatg cgattttaaa gtgtaatgag aagaatttca atggaacagg 
    2401 gccatgtaaa aatgtcagct cagtacaatg cacacatgga attaagccag tagtatcaac 
    2461 tcaattgctg ttaaatggca gtctagcaga agaagagata ataatcagat ctgaaaatct 
    2521 cacagacaat gccaaaacca taatagtgca ccttaataaa tctgtagaaa tcaattgtac 
    2581 cagaccctcc aacaatacaa gaacaggcat aactatagga ccaggacaaa cattctatag 
    2641 aacaggagac ataataggag atataagaca agcatattgt aagattaatg gaacaaaatg 
    2701 gaatgaaact ttaaaacagg tagctaaaaa attacaagag cactttaaga ataagacaat 
    2761 aaaattccag ccacactcag gaggagatct agaaattaca atgcatcatt ttaattgtaa 
    2821 aggggaattt ttctactgca atacaacaaa actgtttaat agtacttgga caggaaatga 
    2881 aaccatagga aataaaacca taggtaatga tactatcata cttccatgca gaataaagca 
    2941 aattataaac ttgtggcagg gagtaggaca agcaatgtat gctcctccca tcaggggagt 
    3001 aattcaatgt gtatcaaata ttacaggaat actattgaca agagatggtg gtaataatgg 
    3061 aactaatata acagagacct tcagacctgg aggaggaaat ataaaggaca attggagaag 
    3121 tgaattatat aaatataaag tagtacaaat tgaaccacta ggagtagcac ccaccagggc 
    3181 aaagagaaga gtggtggaga gagaaaaaag agcagtggga ataggagcta tgatctttgg 
    3241 gttcttagga gcagcaggaa gcactatggg cgcggcgtca ataacgctga cggtacaggc 
    3301 cagacaatta ttgtctggta tagtgcaaca gcaaagcaat ttgctgaggg ctatagaggc 
    3361 gcagcagcat atgttgcaac tcacagtctg gggcattaaa cagctccagg caagagtcct 
    3421 ggctgtggaa agatacctaa aggatcaaaa gttcctagga ctttggggct gctctggcaa 
    3481 aatcatctgc accactgctg tgccctggaa ctccacttgg agtaataaat cttatgaaga 
    3541 gatttggggc aacatgacat ggatagaatg ggagagagaa attggcaatt acacaaacca 
    3601 aatatatgac atacttacaa aatcgcagga ccagcaggac agaaatgaaa aagatttgtt 
    3661 agaattggat aaatgggcaa gtctgtggaa ttggtttgac atatcaaatt ggctgtggta 
    3721 tataaaaata ttcataataa tagtaggagg tttaataggt ttaagaataa tttttgctgt 
    3781 gctttctata gtgaatagag ttaggcaggg atactcacct ttgtctttcc agaccccttc 
    3841 ccatcatcag agggaacccg acagacccga aagaatcgaa gaaggaggtg gcgagcaaga 
    3901 cagagacaga tccgtgcgat tagtgaccgg attcttagca gttgtctggg acgatctcag 
    3961 gaacctgtgc ctcttcagct accaccgctt gagagacttc atcttgattg caacgagggc 
    4021 tgtggaactt ctgggacaca gcagtctcaa gggattgaga cgggggtggg aaggcctcaa 
    4081 atatctgggg aatcttctga tatattgggg caaggaacta aaaattagtg ctatttcttt 
    4141 gtttgatgct ggggcaatag cagtagcggg gtggacagat agggttatag aaatagcaca 
    4201 aggagcttgg agagccattc tccacatacc taggagaatc agacagggct tagaaagggc 
    4261 tttgctataa catgggaggc aagtggtcaa aaagtagcat agtgggatgg cctcaggtca 
    4321 gagaaagaat aaggcaaact cctccagcaa cagaaggagt aggagcagta tctcaagatc 
    4381 tagctaaaca tggagcagta acaagtagta atataaataa tgctgatagt gtctggctga 
    4441 gagcacaaga agaggatgag gaggtaggct ttccagtcag gccacaggta cctctaagac 
    4501 caatgacttt taagggagct tttgatctta gcttcttttt aaaagaaaag gggggactgg 
    4561 atgggctaat ttactccaag aaaagacaag atatccttga cttatgggtt tataatacac 
    4621 aaggcttctt ccctgattgg cagaactaca caccagggcc agggattaga tacccactat 
    4681 gttttggatg gtgcttcaag ttagtaccag ttgacccaaa agaagtagag gaggacaaca 
    4741 agggagaaaa cagctgcctg ttacacccca tgaaccagca gggaatagaa gacacagaaa 
    4801 gagaagtgct gatgtggaag tttgacagtg ccctagcacg aacacacaga gcccgagaac 
    4861 tgcatccaga gtactataaa gactgctgac aaagaagttt ctaactagga cttccgctgg 
    4921 ggactttcca ggggaggtgt ggtaggggcg gagttgggga gtggctaacc c
//
last modified: Tue May 31 10:56 2022


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