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LOCUS EU579002 2785 bp RNA linear VRL 05-JUN-2009
DEFINITION HIV-1 isolate CH77S_B12 from USA rev protein (rev) and tat protein
(tat) genes, partial cds; vpu protein (vpu) gene, complete cds; and
env pseudogene, complete sequence
ACCESSION EU579002
VERSION EU579002.2 GI:238915324
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 2544)
Show all sequences for reference 1
AUTHORS Keele,B.F., Giorgi,E.E., Salazar-Gonzalez,J.F., Decker,J.M.,
Pham,K.T., Salazar,M.G., Sun,C., Grayson,T., Wang,S., Li,H.,
Wei,X., Jiang,C., Kirchherr,J.L., Gao,F., Anderson,J.A., Ping,L.H.,
Swanstrom,R., Tomaras,G.D., Blattner,W.A., Goepfert,P.A.,
Kilby,J.M., Saag,M.S., Delwart,E.L., Busch,M.P., Cohen,M.S.,
Montefiori,D.C., Haynes,B.F., Gaschen,B., Athreya,G.S., Lee,H.Y.,
Wood,N., Seoighe,C., Perelson,A.S., Bhattacharya,T., Korber,B.T.,
Hahn,B.H. and Shaw,G.M.
TITLE Identification and characterization of transmitted and early
founder virus envelopes in primary HIV-1 infection
JOURNAL Proc. Natl. Acad. Sci. U.S.A. 105 (21), 7552-7557 (2008)
PUBMED 18490657
REFERENCE 2 (bases 1 to 2544)
Show all sequences for reference 2
AUTHORS Keele,B.F. and Salazar-Gonzalez,J.
TITLE Direct Submission
JOURNAL Submitted (17-MAR-2008) Department of Medicine, Kaul 806,
University of Alabama at Birmingham, 720 20th Street South,
Birmingham, AL 35294, USA
REFERENCE 3
Show all sequences for reference 3
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 4
Show all sequences for reference 4
AUTHORS Gay,C., Dibben,O., Anderson,J.A., Stacey,A., Mayo,A.J.,
Norris,P.J., Kuruc,J.D., Salazar-Gonzalez,J.F., Li,H., Keele,B.F.,
Hicks,C., Margolis,D., Ferrari,G., Haynes,B., Swanstrom,R.,
Shaw,G.M., Hahn,B.H., Eron,J.J., Borrow,P. and Cohen,M.S.
TITLE Cross-Sectional Detection of Acute HIV Infection: Timing of
Transmission, Inflammation and Antiretroviral Therapy
JOURNAL PLoS ONE 6 (5), E19617 (2011)
PUBMED 21573003
COMMENT Annotation information was provided by the author. Some of
theinformation does not have GenBank feature identifiers and is
beingprovided in the comment section. Information in this section
issearchable in HIV Database at Los Alamos
(www.hiv.lanl.gov).##HIVDataBaseData-START##Patient cohort
CHAVI001Fiebig Stage 2Sequence Name CH77S_B12Sample tissue
plasmaViral Load 3565728Patient sex MSequence Number 6563Subtype
BSample Timepoint SSample date Aug-25-2006Patient code
700010077Sample city NorthCarolinaDBID 1081370390Subtype
B##HIVDataBaseData-END## This sequence was revised in GenBank;
HIVdb update 11/2010.
FEATURES Location/Qualifiers
source 1..2785
/organism="Human immunodeficiency virus 1"
/mol_type="genomic RNA"
/isolate="CH77S_B12"
/db_xref="taxon:11676"
/country="USA"
/note="subtype: B"
gene <1..2643
/gene="rev"
CDS join(<1..62,2369..2643)
/gene="rev"
/codon_start="2"
/transl_table="1"
/product="rev protein"
/protein_id="ACD41546.2"
/db_xref="GI:238915326"
/translation="GDSDEDLLKTVRLIKRLYQSNPPPSSEGTRQARRNRRRRWRERQ
RQIRTLSGWILDDFLGGPAEPVPLHLPPIERLTLDCNEDSGTSGTQGVGNPQILVEPP
TVLESGTKE"
gene <1..2459
/gene="tat"
CDS join(<1..62,2369..2459)
/gene="tat"
/codon_start="1"
/transl_table="1"
/product="tat protein"
/protein_id="ACD41545.2"
/db_xref="GI:238915325"
/translation="RRQRRRPAQDSKINQAPLPKQPTSQLRGDPTGPKESKKKVERET
ETDPNT"
gene 79..324
/gene="vpu"
CDS 79..324
/gene="vpu"
/codon_start="1"
/transl_table="1"
/product="vpu protein"
/protein_id="ACD41547.2"
/db_xref="GI:238915327"
/translation="MQSLYILGIVALVVAAILAIVVWTIVYIEYRKIVRQRKIDRLLD
RIIDRAEDSGNESEGDQEELSALMEMGHHAPWVIDDQ"
gene 242..2785
/gene="env"
CDS 242..2785
/gene="env"
/pseudo
/codon_start="1"
/transl_table="1"
BASE COUNT 983 a 468 c 650 g 684 t
ORIGIN
1 cggagacagc gacgaagacc tgctcaagac agtaagatta atcaagcgcc tctaccaaag
61 cagtaagtag catctgtaat gcaatcttta tatatattag gaatagtagc attagtagta
121 gcagcaatat tagcaatagt tgtgtggacc atagtataca tagaatatag gaaaatagta
181 agacaaagga aaatagacag attacttgat agaataatag acagagcaga agacagtggc
241 aatgagagcg agggtgatca ggaggaattg tcagcactta tggagatggg gcaccatgct
301 ccttgggtta ttgatgatca gtagtgctgc agaacaattg tgggtcacag tttattatgg
361 ggtgcctgtg tggaaagaag caaccaccaa tctattttgt gcatcagatg ctaaagtata
421 tgatacagag acacataatg tttgggccac ccacgcctgt gtacccacag accccaaccc
481 acaagaagta gaattggaaa atgtgacaga aaattttaac atgtggaaaa ataatatggt
541 agaacagatg catgaggatg taatcagttt atgggaccaa agcctaaagc catgtgtaaa
601 attaaccccg ctctgtgtta ctttaaattg cactgattct aatggtgata gtagcattgc
661 taatagtagc agcagtgagg cggtgaaaga aatgaaaaac tgctctttta atattaccac
721 aagcataaga gataagttgc aaaaagaata tgcacttttt tataaacttg atgtagtacc
781 aatagataca aaaactaata cttctaaata taggttaata agttgtaaca cctcagtcat
841 tacacaggcc tgtccaaagg tatcctttga gccaattccc atacattatt gtgccccggc
901 tggttttgcg atcctaaaat gtaaagataa aaagttcaat ggaacagggc catgtaaaaa
961 ggtcagcaca gtacaatgta cacatggaat taagccagta gtatcaacac agctgctgtt
1021 aaatggcagt ctagcagaag aagaggtagt aattagatct gaaaatttca caaacaatgc
1081 taaaaccata ctagtacagc tgaacacatc tgtagtaatc aaatgtatga gacccggcaa
1141 taatacaagc aaaagtatac atatgggagc attgagagct tttcatgcaa catcaagaat
1201 aataggagac acaaggcgag cacattgtaa tgttagtgga gaagattgga ataagacttt
1261 aagccatgta gttgacaaat taagagaaca atttaggaat aaaacaatag tctttaacca
1321 ttcctcagga ggggatccag aaattgtaat gcacactttt aattgtggag gagaattttt
1381 ctactgcgat tcaacagcgc tgtttaatag tacatggagg agaaataaca cttggactgg
1441 tactacagga aatatcacac tccaatgcag aataaaacaa attataaaca tgtggcagaa
1501 agtaggaaaa gcaatgtatg cccctcccat cagaggatac attaactgtt catcaaatat
1561 tacaggactg atattaacaa gagatggtgg taataatgat agtgaaaccg agatcttcag
1621 gcctggagga gggaatatga aggacaattg gagaagtgaa ttatataaat ataaagtaat
1681 aaaaattgaa ccattaggaa tagcacccac caaggcaaag agaagagtgg tgcaaagaga
1741 aaaaagagca ataggaatag gagctcttct ccttgggttc ttaggagcag caggaagcac
1801 tatgggcgca gcgtcagtga cgctgacggt acaagccaga caattattgt ctggtatagt
1861 gcaacagcag aacaatctgc tgagggctat tgaggcgcaa cagcatctgt tgcaactcac
1921 agtctggggc atcaagcagc tccaggcaag aatcctggct gtggaaagat acctacagga
1981 tcaacagctc ctagggattt ggggttgctc tggaagagtc atttgcacca ctactgtgcc
2041 ttggaatgtt agttggagta ataaatctct gaacgagatt tggaacaaca tgacatggat
2101 ggaatgggaa aaagaaatta acaattacac aggtataata tacaccttac ttgaacgatc
2161 gcaaagccag caagaaaaga atgaacaaga attattggaa ttggataaat gggcaagttt
2221 gtggaattgg tttgacataa caaattggct gtggtacata aaaatattca taatgatagt
2281 aggaggctta ataggtttaa gaatagtttt tactgtgctt tctatagtaa atagagttag
2341 gcagggatat tcacccttat cgtttcagac ccacctccca gctccgaggg gacccgacag
2401 gcccgaagga atcgaagaag aaggtggaga gagagacaga gacagatccg aacacttagt
2461 gggtggattc ttgacgattt tctgggtgga cctgcggaac ctgttcctct tcatctacca
2521 ccgattgaga gacttactct tgattgcaat gaggattctg gaacttctgg gacgcagggg
2581 gtgggaaatc ctcaaatact ggtggaacct cctactgtat tggagtcagg aactaaagaa
2641 tagtgctgtt agcttgctca atactatagc catagcagta gctgagggga cagatagggt
2701 tatagaagaa ttataaaggg cttggagagc tgttcttaac atacctacaa gaataagaca
2761 gggcttagaa agggctttgc tataa
//
last modified: Tue May 31 10:56 2022