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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