View NCBI entry Download GenBank file Graphics View Download GFF3 File
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