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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