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LOCUS FJ495842 3550 bp DNA linear VRL 03-JUN-2009
DEFINITION HIV-1 isolate CH40S_M2 from USA rev protein (rev) and tat protein
(tat) genes, partial cds; vpu protein (vpu) gene, complete cds;
envelope glycoprotein (env) pseudogene, complete sequence; and nef
protein (nef) gene, complete cds
ACCESSION FJ495842
VERSION FJ495842.1 GI:238633279
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 3550)
Show all sequences for reference 1
AUTHORS Salazar-Gonzalez,J.F., Salazar,M.G., Keele,B.F., Learn,G.H.,
Giorgi,E.E., Li,H., Decker,J.M., Wang,S., Baalwa,J., Kraus,M.H.,
Parrish,N.F., Shaw,K.S., Guffey,M.B., Bar,K.J., Davis,K.L.,
Ochsenbauer-Jambor,C., Kappes,J.C., Saag,M.S., Cohen,M.S.,
Mulenga,J., Derdeyn,C.A., Allen,S., Hunter,E., Markowitz,M.,
Hraber,P., Perelson,A.S., Bhattacharya,T., Haynes,B.F.,
Korber,B.T., Hahn,B.H. and Shaw,G.M.
TITLE Genetic identity, biological phenotype, and evolutionary pathways
of transmitted/founder viruses in acute and early HIV-1 infection.
JOURNAL J. Exp. Med.. 206(6); 1273-89 (2009)
PUBMED 19487424
REFERENCE 2 (bases 1 to 3550)
Show all sequences for reference 2
AUTHORS Hraber,P. and Hraber,P.T.
TITLE Direct Submission
JOURNAL Submitted (28-NOV-2008) Los Alamos National Laboratory, Theoretical
Biology and Biophysics (T10), MS K710, Los Alamos, NM 87545, USA
REFERENCE 3
Show all sequences for reference 3
AUTHORS Ferrari,G., Korber,B., Goonetilleke,N., Liu,M.K., Turnbull,E.L.,
Salazar-Gonzalez,J.F., Hawkins,N., Self,S., Watson,S., Betts,M.R.,
Gay,C., McGhee,K., Pellegrino,P., Williams,I., Tomaras,G.D.,
Haynes,B.F., Gray,C.M., Borrow,P., Roederer,M., McMichael,A.J. and
Weinhold,K.J.
TITLE Relationship between Functional Profile of HIV-1 Specific CD8 T
Cells and Epitope Variability with the Selection of Escape Mutants
in Acute HIV-1 Infection
JOURNAL PLoS Pathog. 7 (2), E1001273 (2011)
PUBMED 21347345
COMMENT Annotation information was provided by the author. Some of the
information does not have GenBank feature identifiers and is being
provided in the comment section. Information in this section is
searchable in HIV Database at Los Alamos (www.hiv.lanl.gov).;
##HIVDataBaseData-START## Sequence Name CH40S_M2 Patient code
700010040 Patient sex M Sample date 2006 Fiebig Stage 2 Viral Load
2197248 Sample city North Carolina Culture method uncultured Sample
tissue serum HLA type A*3101 A*0201 B*4402 B*4001 Cw*0302 Cw*0501
Subtype B DBID 4223180563 ##HIVDataBaseData-END##
FEATURES Location/Qualifiers
source 1..3550
/organism="Human immunodeficiency virus 1"
/proviral="Human immunodeficiency virus 1"
/mol_type="genomic DNA"
/isolate="CH40S_M2"
/host="Homo sapiens"
/db_xref="taxon:11676"
/country="USA"
/collection_date="2006"
/note="subtype: B"
gene <1..2597
/gene="rev"
CDS join(<1..62,2323..2597)
/gene="rev"
/codon_start="2"
/transl_table="1"
/product="rev protein"
/protein_id="ACR51338.1"
/db_xref="GI:238633281"
/translation="GDSDEELLKTVRLIKFLYQSNPPPSPEGTRQARRNRRRRWRERQ
RQIRSISERILSTYLERSTEPVPLQLPPLERLTLDCNEDCGTSGTQGVGSPQILVESP
TVLESGTKE"
gene <1..2413
/gene="tat"
CDS join(<1..62,2323..2413)
/gene="tat"
/codon_start="1"
/transl_table="1"
/product="tat protein"
/protein_id="ACR51337.1"
/db_xref="GI:238633280"
/translation="RRQRRRAPQDSQTHQVSLSKQPTSQPRGDPTGPKESEKKVERET
ETDPIH"
gene 79..324
/gene="vpu"
CDS 79..324
/gene="vpu"
/codon_start="1"
/transl_table="1"
/product="vpu protein"
/protein_id="ACR51339.1"
/db_xref="GI:238633282"
/translation="MNSLQISAIVALVVAGIIAIVVWSIVAIEYRKILRQRKIDRLID
RIRERAEDSGNESDGDQEELSALVERGHLALGDINDL"
gene 242..2739
/gene="env"
/pseudo="env"
CDS 242..2739
/gene="env"
/note="envelope glycoprotein"
/pseudo="envelope glycoprotein"
/codon_start="1"
/transl_table="1"
gene 2741..3361
/gene="nef"
CDS 2741..3361
/gene="nef"
/codon_start="1"
/transl_table="1"
/product="nef protein"
/protein_id="ACR51340.1"
/db_xref="GI:238633283"
/translation="MGGKWSKCSVVGWPSVRERMRRAEPAAEGVGAVSRDLEKHGAIT
SSNTAATNADCAWLEAQEEGEVGFPVRPQVPLRPMTFKGALDLSHFLKEKGGLEGLIY
SQKRQDILDLWVYHTQGYFPDWQNYTPGPGTRFPLTFGWCFKLVPVDPGKVEEANKGE
NNCLLHPMSQHGMDDPEREVLVWRFDSSLAFRHVARELHPEYYKNC"
BASE COUNT 1194 a 633 c 890 g 833 t
ORIGIN
1 cggagacagc gacgaagagc tcctcaagac agtcagactc atcaagtttc tctatcaaag
61 cagtaagtaa tatatgtaat gaactcttta caaatatcag caatagtagc attagtagta
121 gcaggaataa tagcaatagt tgtgtggtca atagtagcca tagaatatag gaaaatatta
181 aggcaaagaa aaatagacag gttaattgat agaataagag aaagagcaga agacagtggc
241 aatgagagtg atggggatca ggaagaatta tcagcacttg tggaaagagg gcatcttgct
301 cttggggata ttaatgatct gtagtgctgc agacaacttg tgggtcacag tctattatgg
361 ggtacctgtg tggagagaag caaccactac tctattttgt gcatcagatg ctaaagcata
421 tgatacagag gcacataatg tttgggccac acacgcctgt gtacccacag accccaaccc
481 acaagaagta gaattaaaaa atgtgacaga aaattttaat atgtgggaaa ataacatggt
541 agaacagatg catgaggata taatcagttt atgggatcaa agcttaaaac catgtgtaaa
601 attaactcca ctctgtgtta ctttaaattg cactgattta gggaatgtta ctaataccac
661 taatagtaac ggggaaatga tggagaaggg agaagtaaaa aactgttctt tcaagatcac
721 cacagacata aaagatagaa cgcggaagga atatgcactt ttttataaac ttgatgtagt
781 accaataaat gataccagat ataggttagt aagctgtaac acctcagtca ttacacaggc
841 ctgtccaaag gtatcctttg agccaattcc tatacattat tgtgccccgg ctggttttgc
901 gattctaaag tgtaatgata agcaattcat tggaacagga ccatgtacaa atgtcagcac
961 agtacaatgt acacatggaa ttaggccagt agtatcaact caactgctgt taaatggcag
1021 tttagcagaa gaagaggtag taattagatc agtcaatttc agtgacaatg ctaaaacaat
1081 aatagtacaa ctgaataaat ctgtagaaat tacttgcaca agacccaaca acaatacaag
1141 aaaaagtata cccatgggac cagggaaagc attttatgca agaggagaca taacaggaga
1201 cataagaaaa gcatattgtg aaattaatgg aacagaatgg catagcactt taaaactggt
1261 agttgaaaaa ttaagagaac aatataataa aacaatagtc tttaatcgct cctcaggagg
1321 ggacccagaa attgtaatgt acagtttcaa ttgcggaggg gaatttttct actgtaattc
1381 aacaaagctg tttaatagta cttggccttg gaatgatact aaagggtcac atgacactaa
1441 tggcacactc atactcccat gcaaaataaa acaaattata aacatgtggc agggagtagg
1501 aaaagcaatg tatgcccctc ccatcgaagg aaaaattaga tgctcatcaa acattacagg
1561 actgttatta acaagagatg gtggttacga gagcaatgag actgatgaga tcttcagacc
1621 tggaggagga gatatgaggg acaattggag gagtgaatta tataaatata aagtagtaaa
1681 aattgaacca ttgggagtag cacctaccaa ggcaaagagg agagtggtgc agagggaaaa
1741 aagagcattt ggactaggag ctgtgttcct tgggttcttg ggagcagcag gaagcactat
1801 gggcgcagca tcaataacgc tgacggtaca ggccagacaa ttattgtctg gtatagtgca
1861 acagcagaac aatttgctga gggctattga ggcgcaacag catctgttgc aactcacagt
1921 ctggggcatt aagcagctcc aggcaagagt cctggctgtg gaaagatacc taaaggatca
1981 acagctcccg tgccttggaa tactagttgg agtaataaat ctctggaaca gatttgggat
2041 aacatgacat ggatggagtg ggaaagagaa attgacaatt atacaggcta catataccaa
2101 ttaattgaag aatcgcagaa ccaacaagaa aagaatgaac aagaattatt ggcattggat
2161 aaatgggcaa gtttgtggaa ttggtttgac ataacaaact ggctgtggta tataaaaata
2221 ttcataatga tagtaggagg cttaataggt ttaagaatag tttttactgt actttctata
2281 gtgaatagag ttaggcaggg atactcacca ttatcatttc agacccacct cccagcccag
2341 aggggacccg acaggcccga aggaatcgga gaagaaggtg gagagagaga cagagacaga
2401 tccgatccat tagtgaacgg attcttagca cttatctgga gcgatctacg gagcctgtgc
2461 ctcttcagct accaccgctt gagagactta ctcttgattg taacgaggat tgtggaactt
2521 ctgggacgca gggggtggga agtcctcaaa tattggtgga atctcctaca gtattggagt
2581 caggaactaa agaatagtgc tgttagcttg ctcaacgcca cagccatagc agtagctgag
2641 gggacagata gggttataga agtagtacaa agagcttgta gagctattct ccacatacct
2701 agaagaataa gacagggctt ggaaagggct ttgctataag atgggtggca agtggtcaaa
2761 atgtagtgtg gttggatggc cttcagtaag ggaaagaatg agacgagctg agccagcagc
2821 agagggggta ggagcagtat ctcgagacct ggaaaaacat ggagcaatca caagtagcaa
2881 cacagcagct accaatgctg attgtgcctg gctagaagca caagaggagg gggaagtggg
2941 tttcccagtc agacctcagg tacctttaag accaatgacc ttcaagggag ctctggatct
3001 tagccacttt ttaaaagaaa aggggggact ggaagggtta atttactccc aaaaaagaca
3061 agatatcctt gatctgtggg tctaccacac gcaaggctac ttccctgatt ggcagaacta
3121 cacaccaggg ccagggacca gatttccact gacctttgga tggtgcttca agctagtacc
3181 agtggatcca gggaaagtag aagaggccaa taaaggagag aacaactgct tgttacaccc
3241 tatgagccag catgggatgg acgacccaga gagagaagtg ttagtgtgga ggtttgacag
3301 cagcctagca tttcgtcacg tggcccgaga gctgcatccg gagtactaca agaactgctg
3361 acatcgagct ttctacaagg gactttccgc tggggacttt ccagggaggc gtgacatggg
3421 cggaattggg gagtggcgag cccacagatg ctgcatataa gcagccgctt tctgcttgta
3481 ctgggtctct ctggttagac cagatctgag cctgggagct ctctggctag ctagggaacc
3541 cactgcttaa
//
last modified: Tue May 31 10:56 2022