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	    JN251850		    2983 bp    RNA     linear	VRL 12-SEP-2011
DEFINITION  HIV-1 isolate s5.522.3 from Sweden rev protein (rev) and tat
	    protein (tat) genes, partial cds; vpu protein (vpu) and envelope
	    glycoprotein (env) genes, complete cds; and nef protein (nef) gene,
	    partial cds
ACCESSION   JN251850
VERSION     JN251850.1 GI:346312587
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 2983)
            Show all sequences for reference 1
  AUTHORS   Skar,H., Gutenkunst,R.N., Wilbe Ramsay,K., Alaeus,A., Albert,J. and
	    Leitner,T.
  TITLE     Daily Sampling of an HIV-1 Patient with Slowly Progressing Disease
	    Displays Persistence of Multiple env Subpopulations Consistent with
	    Neutrality
  JOURNAL   PLoS ONE 6 (8), E21747 (2011)
  PUBMED    21829600
REFERENCE   2 (bases 1 to 2983)
            Show all sequences for reference 2
  AUTHORS   Leitner,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-JUL-2011) Theoretical Biology and Biophysics, Los
	    Alamos National Laboratory, MS K710, Los Alamos, NM 87545, USA
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 s5.522.3 Amplification
	    strategy limiting dilution PCR Culture method uncultured Drug naive
	    yes Patient health status asymptomatic Patient sex M Patient
	    progression LTNP Sample timepoint 522 Sample Date 6-Mar-00
	    ##HIVDataBaseData-END##
FEATURES             Location/Qualifiers
     source	     1..2983
		     /organism="Human immunodeficiency virus 1"
		     /mol_type="genomic RNA"
		     /isolate="s5.522.3"
		     /host="Homo sapiens"
		     /db_xref="taxon:11676"
		     /country="Sweden"
		     /collection_date="06-Mar-2000"
		     /note="subtype: B"
     gene	     <1..2663
		     /gene="rev"
     CDS	     join(<1..58,2380..2663)
		     /gene="rev"
		     /codon_start="1"
		     /transl_table="1"
		     /product="rev protein"
		     /protein_id="AEO22376.1"
		     /db_xref="GI:346312589"
		     /translation="DSDEELLKAVRLIKFLYQSNPLPSPEGTRQARRNRRRRWRERQR
		     QIRTISERILNTYLGRSAEPVPLQLPPLERLTLDCNEDCETSGTQGVGSPQILVESPA
		     VLETGTKEKCC"
     gene	     <1..2470
		     /gene="tat"
     CDS	     join(<1..58,2380..2470)
		     /gene="tat"
		     /codon_start="3"
		     /transl_table="1"
		     /product="tat protein"
		     /protein_id="AEO22375.1"
		     /db_xref="GI:346312588"
		     /translation="QRRRAPQGSPTHQVSLPKQPTSQPRGDPTGPKESKKKVERETET
		     DPDD"
     gene	     75..320
		     /gene="vpu"
     CDS	     75..320
		     /gene="vpu"
		     /codon_start="1"
		     /transl_table="1"
		     /product="vpu protein"
		     /protein_id="AEO22377.1"
		     /db_xref="GI:346312590"
		     /translation="MQSLHIVAIVALVVAAIIAIVVWTIVLIEYRKILRQRKIDRLVE
		     RISERAEDSGNESEGDQEELSALVGMGHHAPWNIDDL"
     gene	     238..2796
		     /gene="env"
     CDS	     238..2796
		     /gene="env"
		     /codon_start="1"
		     /transl_table="1"
		     /product="envelope glycoprotein"
		     /protein_id="AEO22378.1"
		     /db_xref="GI:346312591"
		     /translation="MKVREIRKSCQHLWGWGIMLLGILMICSTADKLWVTVYYGVPVW
		     KEATTTLFCASDAKSYDTEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQ
		     MHEDIISLWDQSLKPCVKLTPLCVTLNCTDLRNATNATNSSGGTMEGGEMKNCSFNIT
		     TNIRDKTKKKNEYALFYKLDVIPIDDDNTNTSYRLINCNTSVITQACPKVSFEPIPIH
		     YCAPAGFAIIKCNDKKFNGSGPCKNVSTVQCTHGIRPTVSTQLLLNGSLAEEEVVIRS
		     ENFTNNAKSIIVQLKKPVEIICARPNNNTRKGIHMGLGKTLYATGGIIGDIRQAHCNI
		     SKTDWNDTLQQIVTKLREQFRNKTIAFDQSSGGDPEVVMHMFNCGGEFFYCESSLLFN
		     NTWVNSTRNNSTKENSTLTLPCRIKQIINMWQEVGKAMYAPPIRGQIKCSSKITGLIL
		     TRDGGNSPNQSTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQREKR
		     TVIGAVFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQNNLLKAIEAQQHLLQLTV
		     WGIKQLQARVLAVERYLKDQQLLGIWGCSGKLICTTAVPWNTSWSNKSLNEIWNNMTW
		     MEWEREIHNYTSLIYTLIEESQNQQEKNEQELLELDKWASLWNWFDITKWLWYIKIFI
		     MIVGGLVGLRIVFAVLSIVNRVRQGYSPLSFQTHFPAPRGPDRPEGIEEEGGERDRDR
		     SGRLVNGFLTLIWDDLRSLCLFSYHRLRDLLLIVTKIVKLLGRRGWEALKYWWNLLQY
		     WRQELKKSAVSLFNAIAIAVAEGTDRIIEVLQRVYRAFIHIPRRIRQGLERILQ"
     gene	     2798..>2983
		     /gene="nef"
     CDS	     2798..>2983
		     /gene="nef"
		     /codon_start="1"
		     /transl_table="1"
		     /product="nef protein"
		     /protein_id="AEO22379.1"
		     /db_xref="GI:346312592"
		     /translation="MGGQWSKSSLVGWPAIRERMKRAEPAADGVGAASRDLERHGALT
		     SSNTVHNNAACAWLEAQE"
BASE COUNT     1064 a	 495 c	  715 g    709 t
ORIGIN
       1 gacagcgacg aagagctcct caaggcagtc cgactcatca agtttctcta ccaaagcagt 
      61 aagtagtaca tgtaatgcaa tctttacata tagtagcaat agtagcatta gtagtagcag 
     121 caataatagc aatagtagtg tggaccatag tactcataga atatagaaaa atattaagac 
     181 aaagaaaaat agacaggtta gttgaaagaa taagtgaaag agcagaagac agtggcaatg 
     241 aaagtgaggg agatcaggaa gagctgtcag cacttgtggg gatggggcat catgctcctt 
     301 ggaatattga tgatctgtag tactgcagac aaattgtggg tcacagttta ttatggggta 
     361 cctgtgtgga aagaagcaac taccactcta ttttgtgcat cagatgctaa atcatatgat 
     421 acagaagtac ataatgtctg ggctacacat gcctgtgtac ccacagaccc caacccacaa 
     481 gaagtagtat tggaaaatgt gacagaaaat tttaacatgt ggaaaaataa catggtagaa 
     541 caaatgcatg aggatataat cagtttatgg gatcaaagtt taaagccatg tgtaaaatta 
     601 accccactct gtgttacttt aaattgcact gatttgagaa atgctactaa tgccactaat 
     661 agtagcgggg gaacgatgga gggaggagaa atgaaaaact gttctttcaa tatcaccaca 
     721 aacataagag acaagacgaa gaagaagaac gaatatgcac ttttttataa acttgatgta 
     781 ataccaatag atgatgataa tactaatact agctataggt tgataaattg taacacctca 
     841 gtcattacac aggcctgtcc aaaggtatcc tttgaaccaa ttcccataca ttattgtgcc 
     901 ccggctggtt ttgcgattat aaagtgtaat gataagaagt tcaatggatc aggaccatgt 
     961 aaaaatgtca gcacagtaca atgtacacat ggaattaggc caacagtgtc aactcaactg 
    1021 ttattaaatg gcagtctagc agaagaagag gtagtaatta ggtctgaaaa tttcacaaat 
    1081 aatgctaaaa gcataatagt gcagctgaag aaacctgtag aaattatttg tgcaaggccc 
    1141 aacaacaata caagaaaagg gatacatatg ggactaggga aaacacttta tgcaacagga 
    1201 ggaataatag gagatataag acaagcacat tgtaacatta gtaaaacaga ctggaatgat 
    1261 actttacaac agatagttac aaaattaaga gaacaattta ggaataaaac aatagccttt 
    1321 gatcaatcct caggagggga cccagaagtt gtaatgcaca tgtttaattg tgggggggaa 
    1381 tttttctact gtgaatcatc actactgttt aataatactt gggttaatag tactagaaat 
    1441 aatagtacta aagaaaatag cacacttaca ctcccatgta gaataaaaca aattataaac 
    1501 atgtggcagg aggtaggaaa ggcaatgtat gcccctccca tcagaggaca aattaagtgt 
    1561 tcatcaaaga ttacagggct gatattaaca agagatgggg gtaatagccc gaaccaaagc 
    1621 acagagatct tcagaccggg aggaggagat atgagggaca attggagaag tgaactatat 
    1681 aaatacaaag tagtaaaaat tgaaccatta ggggtagcac ccaccaaggc aaagagacga 
    1741 gtggtgcaga gagaaaaaag aacagtaata ggagctgtgt tccttgggtt cttgggagca 
    1801 gcaggaagca ctatgggcgc agcgtcaatg acgctgacgg tacaggctag acaattattg 
    1861 tctggtatag tgcaacagca gaacaatttg ctgaaggcta ttgaagcgca acaacatctg 
    1921 ttgcaactca cagtctgggg catcaagcag ctccaggcaa gagtcctggc tgtggaaaga 
    1981 tacctaaagg atcaacagct cctggggatt tggggttgct ctggaaaact catttgcacc 
    2041 actgctgtgc cttggaatac tagttggagt aataaatctc tgaatgagat ctggaacaac 
    2101 atgacctgga tggagtggga aagagaaatt cacaattaca caagcttaat atacacttta 
    2161 attgaagaat cgcaaaacca acaagaaaag aatgaacaag aattattgga attagataag 
    2221 tgggcaagtt tgtggaattg gtttgacata acaaaatggc tgtggtatat aaaaatattc 
    2281 ataatgatag taggaggctt ggtaggttta agaatagttt ttgctgtact ttctatagtg 
    2341 aatagagtta ggcagggata ctcaccatta tcatttcaga cccacttccc agccccgagg 
    2401 ggacccgaca ggcccgaagg aatcgaagaa gaaggtggag agagagacag agacagatcc 
    2461 ggacgattag tgaacggatt cttaacactt atctgggacg atctgcggag cctgtgcctc 
    2521 ttcagctacc accgcttgag agacttactc ttgattgtaa cgaagattgt gaaacttctg 
    2581 ggacgcaggg ggtgggaagc cctcaaatat tggtggaatc tcctgcagta ttggagacag 
    2641 gaactaaaga aaagtgctgt tagcttgttc aatgccatag ccatagcagt agctgagggg 
    2701 acagatagga ttatagaagt attacaaaga gtttatagag cttttatcca catacctaga 
    2761 agaataagac agggcttgga aaggattttg caataagatg gggggccagt ggtcaaaaag 
    2821 tagtctggtt ggatggcctg ctataaggga aagaatgaaa cgagctgagc cagcagcaga 
    2881 tggggtggga gcagcatctc gagacctgga aagacatgga gcactcacaa gtagcaatac 
    2941 agtacataat aatgctgcat gtgcctggct agaagcacaa gag
//
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