HIV Databases HIV Databases home HIV Databases home
HIV Sequence Database



Download: ENTIRE SEQUENCE SEQUENCE FRAGMENT start end
Format:  
View NCBI entry		Download GenBank file		Graphics View		Download GFF3 File

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


Questions or comments? Contact us at seq-info@lanl.gov.

 
Operated by Triad National Security, LLC for the U.S. Department of Energy's National Nuclear Security Administration
© Copyright Triad National Security, LLC. All Rights Reserved | Disclaimer/Privacy

Dept of Health & Human Services Los Alamos National Institutes of Health