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LOCUS FJ495851 3593 bp DNA linear VRL 03-JUN-2009
DEFINITION HIV-1 isolate CH40S_M8 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 FJ495851
VERSION FJ495851.1 GI:238633331
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 3593)
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 3593)
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_M8 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 19786657 ##HIVDataBaseData-END##
FEATURES Location/Qualifiers
source 1..3593
/organism="Human immunodeficiency virus 1"
/proviral="Human immunodeficiency virus 1"
/mol_type="genomic DNA"
/isolate="CH40S_M8"
/host="Homo sapiens"
/db_xref="taxon:11676"
/country="USA"
/collection_date="2006"
/note="subtype: B"
gene <1..2640
/gene="rev"
CDS join(<1..62,2366..2640)
/gene="rev"
/codon_start="2"
/transl_table="1"
/product="rev protein"
/protein_id="ACR51381.1"
/db_xref="GI:238633333"
/translation="GDSDEELLKTVRLIKFLYQSNPPPSPEGTRQARRNRRRRWRERQ
RQIRSISERILSTYLERSTEPVPLQLPPLERLTLDCNEDCGTSGTQGVGSPQILVESP
TVLESGTKE"
gene <1..2456
/gene="tat"
CDS join(<1..62,2366..2456)
/gene="tat"
/codon_start="1"
/transl_table="1"
/product="tat protein"
/protein_id="ACR51380.1"
/db_xref="GI:238633332"
/translation="RRQRRRAPQDSQTHQVSLSKQPTSQPRGDPTGPKESEKKVERET
ETDPIH"
gene 79..324
/gene="vpu"
CDS 79..324
/gene="vpu"
/codon_start="1"
/transl_table="1"
/product="vpu protein"
/protein_id="ACR51382.1"
/db_xref="GI:238633334"
/translation="MNSLQISAIVALVVAGIIAIVVWSIVAIEYRKILRQRKIDRLID
RIRERAEDSGNESDGDQEELSALVERGHLALGDINDL"
gene 242..2782
/gene="env"
/pseudo="env"
CDS 242..2782
/gene="env"
/note="envelope glycoprotein"
/pseudo="envelope glycoprotein"
/codon_start="1"
/transl_table="1"
gene 2784..3404
/gene="nef"
CDS 2784..3404
/gene="nef"
/codon_start="1"
/transl_table="1"
/product="nef protein"
/protein_id="ACR51383.1"
/db_xref="GI:238633335"
/translation="MGGKWSKCSVVGWPSVRERMRRAEPAAEGVGAVSRDLEKHGAIT
SSNTAATNADCAWLEAQEEGEVGFPVRPQVPLRPMTFKGALDLSHFLKEKGGLEGLIY
SQKRQDILDLWVYHTQGYFPDWQNYTPGPGTRFPLTFGWCFKLVPVDPGKVEEANKGE
NNCLLHPMSQHGMDDPEREVLVWRFDSSLAFRHVARELHPEYYKNC"
BASE COUNT 1203 a 642 c 902 g 846 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 tggagagagg 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 aacagaatga 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 acagctcctg gggatttggg gttgctctgg aaaactcatc tgcaccacta ctgtgccttg
2041 gaatactagt tggagtaata aatctctgga acagatttgg gataacatga catggatgga
2101 gtgggaaaga gaaattgaca attatacagg ctacatatac caattaattg aagaatcgca
2161 gaaccaacaa gaaaagaatg aacaagaatt attggcattg gataaatggg caagtttgtg
2221 gaattggttt gacataacaa actggctgtg gtatataaaa atattcataa tgatagtagg
2281 aggcttaata ggtttaagaa tagtttttac tgtactttct atagtgaata gagttaggca
2341 gggatactca ccattatcat ttcagaccca cctcccagcc cagaggggac ccgacaggcc
2401 cgaaggaatc ggagaagaag gtggagagag agacagagac agatccgatc cattagtgaa
2461 cggattctta gcacttatct ggagcgatct acggagcctg tgcctcttca gctaccaccg
2521 cttgagagac ttactcttga ttgtaacgag gattgtggaa cttctgggac gcagggggtg
2581 ggaagtcctc aaatattggt ggaatctcct acagtattgg agtcaggaac taaagaatag
2641 tgctgttagc ttgctcaacg ccacagccat agcagtagct gaggggacag atagggttat
2701 agaagtagta caaagagctt gtagagctat tctccacata cctagaagaa taagacaggg
2761 cttggaaagg gctttgctat aagatgggtg gcaagtggtc aaaatgtagt gtggttggat
2821 ggccttcagt aagggaaaga atgagacgag ctgagccagc agcagagggg gtaggagcag
2881 tatctcgaga cctggaaaaa catggagcaa tcacaagtag caacacagca gctaccaatg
2941 ctgattgtgc ctggctagaa gcacaagagg agggggaagt gggtttccca gtcagacctc
3001 aggtaccttt aagaccaatg accttcaagg gagctctgga tcttagccac tttttaaaag
3061 aaaagggggg actggaaggg ttaatttact cccaaaaaag acaagatatc cttgatctgt
3121 gggtctacca cacgcaaggc tacttccctg attggcagaa ctacacacca gggccaggga
3181 ccagatttcc actgaccttt ggatggtgct tcaagctagt accagtggat ccagggaaag
3241 tagaagaggc caataaagga gagaacaact gcttgttaca ccctatgagc cagcatggga
3301 tggacgaccc agagagagaa gtgttagtgt ggaggtttga cagcagccta gcatttcgtc
3361 acgtggcccg agagctgcat ccggagtact acaagaactg ctgacatcga gctttctaca
3421 agggactttc cgctggggac tttccaggga ggcgtgacat gggcggaatt ggggagtggc
3481 gagcccacag atgctgcata taagcagccg ctttctgctt gtactgggtc tctctggtta
3541 gaccagatct gagcctggga gctctctggc tagctaggga acccactgct taa
//
last modified: Tue May 31 10:56 2022