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LOCUS	    JX446656		    4956 bp    RNA     linear	VRL 12-OCT-2012
DEFINITION  HIV-1 isolate AA001a01R 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   JX446656
VERSION     JX446656.1 GI:407731792
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 4956)
            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 4956)
            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..4956
		     /organism="Human immunodeficiency virus 1"
		     /mol_type="genomic RNA"
		     /isolate="AA001a01R"
		     /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="AFU25801.1"
		     /db_xref="GI:407731793"
		     /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="AFU25802.1"
		     /db_xref="GI:407731794"
		     /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="AFU25803.1"
		     /db_xref="GI:407731795"
		     /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="AFU25804.1"
		     /db_xref="GI:407731796"
		     /translation="MSPLEISAITGLVVALIAAIVVWTIVAIEFRKILKQRKIDRLVK
		     RIRERAEDSGNESEGDTDELAKLVEMGDFDPWVGDNV"
     misc_feature    <1591..1734
		     /gene="vpu"
		     /note="Vpu protein; Region: Vpu; pfam00558"
		     /db_xref="CDD:109608"
     gene	     1670..4255
		     /gene="env"
     CDS	     1670..4255
		     /gene="env"
		     /codon_start="1"
		     /transl_table="1"
		     /product="envelope glycoprotein"
		     /protein_id="AFU25805.1"
		     /db_xref="GI:407731797"
		     /translation="MRVKETQMNWLNLWRWGTLILGLVIMCSAADNLWVTVYYGVPVW
		     RDADTTLFCASDAKAHDTEVHNVWATYACVPTDPNPQEIHMVNVTENFNMWKNNMVEQ
		     MQEDVISLWDQSLKPCVKLTPLCVTLNCTNANLTHLNTTNLNTTTVSRDIGNITDEVR
		     NCTFNMTTVVSDKKQKVYALFYKLDLVPMKENQTNSEYRLINCNTSVIKQACPKISFD
		     PIPIHYCTPAGYAILKCNEKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEE
		     IIIRSENLTDNAKTIIVHLNKSVEINCTRPSNNTRTGITIGPGRTFYRTGDIIGDIRQ
		     AYCKINGTKWKETLKQVAKKLQEHFKNKTIKFQPHSGGDLEITMHHFNCKGEFFYCNT
		     TKLFNSTWTGNETIGNETIILPCRIKQIINMWQGVGQAMYAPPIRGVIRCVSNITGIL
		     LTRDGGNNGTNITETFRPGGGNIKDNWRSELYKYKVVQIEPLGVAPTRAKRRVVEREK
		     RAVGIGAMIFGFLGAAGSTMGAASITLTVQARQLLSGIVQQQSNLLRAIEAQQHMLQL
		     TVWGIKQLQARVLAVERYLKDQKFLGLWGCSGKIICTTAVPWNSTWSNKSYEEIWGNM
		     TWTEWEREIGNYTNQIYDILTKSQDQQDRNEKDLLELDKWASLWNWFDISNWLWYIKI
		     FIIIVGGLIGLRIIFAVLSIVNRVRQGYSPLSFQTPSHHQREPDRPERIEEGGGEQDR
		     DRSVRLVTGFLAIVWDDLRSLCLFSYHRLRDFILIATRAVELLGHSSLKGLRRGWEGL
		     KYLGNLLIYWGKELKISAISLFDAVAIAVAGWTDRVIEVAQGAWRAILHIPRRIRQGL
		     ERALL"
     misc_feature    1766..3160
		     /gene="env"
		     /note="Envelope glycoprotein GP120; Region: GP120;
		     pfam00516"
		     /db_xref="CDD:109567"
     misc_feature    3278..3658
		     /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(3278..3337,3344..3442)
		     /gene="env"
		     /note="HR1; other site"
		     /db_xref="CDD:197369"
     misc_feature    order(3284..3286,3290..3298,3302..3319,3323..3337,3344..33
		     61,3365..3382,3386..3394,3398..3403,3407..3412,3419..3424,
		     3428..3436,3440..3466,3479..3481,3485..3487,3491..3502,353
		     0..3535,3542..3547,3554..3556,3563..3568,3575..3580,3584..
		     3589,3596..3601,3605..3610,3617..3622,3638..3643,3650..365
		     2)
		     /gene="env"
		     /note="homotrimer interface [polypeptide binding]; other
		     site"
		     /db_xref="CDD:197369"
     misc_feature    order(3530..3589,3593..3628,3632..3658)
		     /gene="env"
		     /note="HR2; other site"
		     /db_xref="CDD:197369"
     gene	     4257..4874
		     /gene="nef"
     CDS	     4257..4874
		     /gene="nef"
		     /codon_start="1"
		     /transl_table="1"
		     /product="nef protein"
		     /protein_id="AFU25806.1"
		     /db_xref="GI:407731798"
		     /translation="MGGKWSKSSIVGWPQVRERIKQTPPAAEGVGAVSQDLDKHGAVT
		     SSSINNADSVWLRAQEEDEEVGFPVRPQVPLRPMTFKEAFDLSFFLKEKGGLDGLIYS
		     KKRQDILDLWVYNTQGFFPDWQNYTPGPGIRYPLCFGWCFKLVPVDPKEVEEDNKGEN
		     SCLLHPMNQHGVEDTEREVLMWKFDSALARTHIARELHPEFYKDC"
     misc_feature    4260..4868
		     /gene="nef"
		     /note="Negative factor, (F-Protein) or Nef; Region:
		     F-protein; pfam00469"
		     /db_xref="CDD:109523"
BASE COUNT     1765 a	 856 c	 1192 g   1143 t
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 cagagaccca atttggaaag gaccagcaaa actactctgg aaaggtgaag gggcagtagt 
     421 aatacaggac aatagtgaca taaaagtagt accaagaaga aaagcaaaga tcattaggga 
     481 ttatggaaaa cagatggcag gtgatgattg tgtggcaggt agacaggatg aggattagaa 
     541 catggaacag tttagtaaaa catcatatgt atatctcaaa gaaagcaaaa aattggtctt 
     601 ataaacatca 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 ccggggagtc 
    1321 agcctacaac tgcttgtagc aactgttact gtaaaaaatg cagctggcat tgtcaaatat 
    1381 gctttttgaa aaaaggctta ggcatctcct atggcaggaa gaagcggaag caccgacgag 
    1441 gaactcctca gagcagtaag gatcatcaaa 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 catggtaaat gtaacagaaa attttaacat gtggaaaaat aacatggtag aacagatgca 
    1981 ggaggatgta atcagtttat gggatcaaag tctaaagcca tgtgtaaaat 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 aaaatcaaac taatagtgag tataggttaa 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 ccaggacgaa cattctatag 
    2641 aacaggagac ataataggag atataagaca agcatattgt aagattaatg gaacaaaatg 
    2701 gaaggaaact ttaaaacagg tagctaaaaa attacaagag cactttaaga ataagacaat 
    2761 aaaattccag ccacactcag gaggagatct agaaattaca atgcatcatt ttaattgtaa 
    2821 aggggaattt ttctactgca atacaacaaa actgtttaat agtacttgga caggaaatga 
    2881 aaccatagga aatgaaacca tcatacttcc atgcagaata aagcaaatta taaacatgtg 
    2941 gcagggagta ggacaagcaa tgtatgctcc tcccatcagg ggagtaattc gatgtgtatc 
    3001 aaatattaca ggaatactat tgacaagaga tggtggtaat aatggaacta atataacaga 
    3061 gaccttcaga cctggaggag gaaatataaa ggacaattgg agaagtgaat tatataaata 
    3121 taaagtagta caaattgaac cactaggagt agcacccacc agggcaaaga gaagagtggt 
    3181 ggagagagaa aaaagagcag tgggaatagg agctatgatc tttgggttct taggagcagc 
    3241 aggaagcact atgggcgcgg cgtcaataac gctgacggta caggccagac aattattgtc 
    3301 tggtatagtg caacagcaaa gcaatttgct gagggctata gaggcgcagc agcatatgtt 
    3361 gcaactcaca gtctggggca ttaaacagct ccaggcaaga gtcctggctg tggaaagata 
    3421 cctaaaggat caaaagttcc taggactttg gggctgctct ggcaaaatca tctgcaccac 
    3481 tgctgtgccc tggaactcca cttggagtaa taaatcttat gaagagattt ggggcaacat 
    3541 gacatggaca gaatgggaga gagaaattgg caattacaca aaccaaatat atgacatact 
    3601 tacaaaatcg caggaccagc aagacagaaa tgaaaaagat ttgttagaat tggataaatg 
    3661 ggcaagtctg tggaattggt ttgacatatc aaattggctg tggtatataa aaatattcat 
    3721 aataatagta ggaggtttaa taggtttaag aataattttt gctgtgcttt ctatagtgaa 
    3781 tagagttagg cagggatact cacctttgtc tttccagacc ccttcccatc atcagaggga 
    3841 acccgacaga cccgaaagaa tcgaagaagg aggtggcgag caagacagag acagatccgt 
    3901 gcgattagtg accggattct tagcaattgt ctgggacgat ctcaggagcc tgtgcctctt 
    3961 cagctaccac cgcttgagag acttcatctt gattgcaaca agggctgtgg aacttttggg 
    4021 acacagcagt ctcaagggac tgagacgggg gtgggaaggc ctcaaatatc tggggaatct 
    4081 tctgatatat tggggcaagg aactaaaaat tagtgctatt tctttgtttg atgctgtggc 
    4141 aatagcagta gcggggtgga cagatagggt tatagaagta gcacaaggag cttggagagc 
    4201 cattctccac atacctagga gaatcagaca gggcttagaa agggctttgc tataacatgg 
    4261 gaggcaagtg gtcaaaaagt agcatagtgg gatggcctca ggtcagagaa agaataaagc 
    4321 aaactcctcc agcagcagaa ggagtaggag cagtatctca agatctagat aaacatggag 
    4381 cagtaacaag tagtagtata aataatgctg atagtgtctg gctgagagca caagaagagg 
    4441 atgaggaggt aggctttcca gtcaggccac aggtacctct aagaccaatg acttttaagg 
    4501 aagcttttga tcttagcttc tttttaaaag aaaagggggg actggatggg ctaatttact 
    4561 ccaagaaaag acaagatatc cttgacttat gggtttataa tacacaaggc ttcttccctg 
    4621 attggcagaa ctacacacca gggccaggga ttagataccc actatgtttt ggatggtgct 
    4681 tcaagttagt accagttgac ccaaaagaag tagaggagga caacaaggga gaaaacagct 
    4741 gcctgttaca ccccatgaac cagcatggag tagaagacac agaaagagaa gtgctgatgt 
    4801 ggaagtttga cagtgcccta gcacgaacac acatagcccg agaactgcat ccagagttct 
    4861 ataaagactg ctgacaacga agtttctaac taggacttcc gctggggact ttccagggga 
    4921 ggtgtggtcg gggcggagtt ggggagtggc taaccc
//
last modified: Tue May 31 10:56 2022


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