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LOCUS	    JX972273		    4596 bp    RNA     linear	VRL 16-MAR-2013
DEFINITION  HIV-1 isolate B.700010470.w04.41dps.3_B14 from USA vif protein
	    (vif) gene, complete cds; pol protein (pol) gene, partial cds; and
	    vpr protein (vpr), tat protein (tat), rev protein (rev), vpu
	    protein (vpu), envelope glycoprotein (env), and nef protein (nef)
	    genes, complete cds
ACCESSION   JX972273
VERSION     JX972273.1 GI:459963630
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 4596)
            Show all sequences for reference 1
  AUTHORS   Liu,M.K., Hawkins,N., Ritchie,A.J., Ganusov,V.V., Whale,V.,
	    Brackenridge,S., Li,H., Pavlicek,J.W., Cai,F., Rose-Abrahams,M.,
	    Treurnicht,F., Hraber,P., Riou,C., Gray,C., Ferrari,G., Tanner,R.,
	    Ping,L.H., Anderson,J.A., Swanstrom,R., B,C.C., Cohen,M.,
	    Karim,S.S., Haynes,B., Borrow,P., Perelson,A.S., Shaw,G.M.,
	    Hahn,B.H., Williamson,C., Korber,B.T., Gao,F., Self,S.,
	    McMichael,A. and Goonetilleke,N.
  TITLE     Vertical T cell immunodominance and epitope entropy determine HIV-1
	    escape
  JOURNAL   J. Clin. Invest. 123 (1), 380-393 (2013)
  PUBMED    23221345
REFERENCE   2 (bases 1 to 4596)
            Show all sequences for reference 2
  AUTHORS   Liu,M., Liu,M.K., Hawkins,N., Ritchie,A., Ritchie,A.J.,
	    Ganusov,V.V., Ganusov,V., Whale,V., Brackenridge,S., Li,H.,
	    Pavliceck,J., Pavlicek,J.W., Cai,F., Abrahams,M.-R., Treurnicht,F.,
	    Hraber,P., Hraber,P.T., Riou,C., Gray,C., Ferrari,G., Tanner,R.,
	    Ping,L.-H., Anderson,J.A., Anderson,J., Swanstrom,R., Cohen,M.S.,
	    Cohen,M., Abdool Karim,S., Abdool Karim,S.S., Haynes,B.,
	    Haynes,B.F., Borrow,P., Perelson,A., Shaw,G., Hahn,B., Hahn,B.H.,
	    Williamson,C., Korber,B., Korber,B.T., Gao,F., Self,S.,
	    McMichael,A., McMichael,A.J. and Goonetilleke,N.
  CONSRTM   CHAVI Core B
  TITLE     Direct Submission
  JOURNAL   Submitted (12-OCT-2012) T6 MS K710, LANL, PO Box 1663, 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-1 Database at Los Alamos (hiv.lanl.gov).;
	    ##HIVDataBaseData-START## Patient code 700010470 Days
	    post-screening 41 Sample timepoint w4 Patient sex M Fiebig Stage x
	    Viral Load 27991 CD4 count 522 HLA type A*03 A*01 B*08 B*4901 Cw*07
	    Cw*07 Infection date 2008 ##HIVDataBaseData-END##
FEATURES             Location/Qualifiers
     source	     1..4596
		     /organism="Human immunodeficiency virus 1"
		     /mol_type="genomic RNA"
		     /isolate="B.700010470.w04.41dps.3_B14"
		     /host="Homo sapiens"
		     /db_xref="taxon:11676"
		     /country="USA"
		     /collection_date="2008"
		     /note="subtype: B"
     gene	     1..579
		     /gene="vif"
     CDS	     1..579
		     /gene="vif"
		     /codon_start="1"
		     /transl_table="1"
		     /product="vif protein"
		     /protein_id="AGG92162.1"
		     /db_xref="GI:459963632"
		     /translation="MENRWQVMIVWQVDRMRIKTWKSLVKHHMHISKKARGWFYRHHY
		     ENTHPKISSEVHIPLREARLVITTYWGLHTGERDWHLGQGVSIEWRKRKYSTQVDPDL
		     ADQLIHLYYFDCFSESAIRNALLGHIVSPRCEYQAGHNKVGSLQYLALTALVAPKKTK
		     PPLPSVKKLTEDRWNKPQKTKGHRGSHTMSGH"
     gene	     <1..56
		     /gene="pol"
     CDS	     <1..56
		     /gene="pol"
		     /codon_start="3"
		     /transl_table="1"
		     /product="pol protein"
		     /protein_id="AGG92161.1"
		     /db_xref="GI:459963631"
		     /translation="GKQMAGDDCVASRQDED"
     gene	     519..809
		     /gene="vpr"
     CDS	     519..809
		     /gene="vpr"
		     /codon_start="1"
		     /transl_table="1"
		     /product="vpr protein"
		     /protein_id="AGG92163.1"
		     /db_xref="GI:459963633"
		     /translation="MEQAPEDQGPQREPYNEWTLELLEELKREAVRHFPRPWLQGLGQ
		     YIYETYGDTWAGVEAIIKILQQLLFIHFRIGCRHSRIGIIRQRRTRNGASRS"
     gene	     790..3445
		     /gene="tat"
     CDS	     join(790..1004,3352..3445)
		     /gene="tat"
		     /codon_start="1"
		     /transl_table="1"
		     /product="tat protein"
		     /protein_id="AGG92164.1"
		     /db_xref="GI:459963634"
		     /translation="MEPVDPRLEPWKHPGSQPRTACTTCYCKKCCFHCQVCFITKGLG
		     ISYGRKKRRQRRRAPENSQTHQVSVSKQPDPQQRGDPTGPKKSKEEVERETETDPEDQ
		     "
     gene	     929..3626
		     /gene="rev"
     CDS	     join(929..1004,3352..3626)
		     /gene="rev"
		     /codon_start="1"
		     /transl_table="1"
		     /product="rev protein"
		     /protein_id="AGG92165.1"
		     /db_xref="GI:459963635"
		     /translation="MAGRSGDSDEELLKTVRLIKFLYQSNPIPSSEGTRQARRNRRRR
		     WRERQRQIRKISDWIIRTHLGRPVEPVHLQLPPLERLSLDSSEGCGSSGTQGVGSPQV
		     LVESPAVLDSGTKE"
     gene	     1020..1262
		     /gene="vpu"
     CDS	     1020..1262
		     /gene="vpu"
		     /codon_start="1"
		     /transl_table="1"
		     /product="vpu protein"
		     /protein_id="AGG92166.1"
		     /db_xref="GI:459963636"
		     /translation="MIPLTILSIVALVVVVIIAIVVWSIAYIEYRKLLRQRKIDRLLD
		     RIRDRAEDSGNESDGDQEELSALELGHLAPWNVGDE"
     gene	     1183..3768
		     /gene="env"
     CDS	     1183..3768
		     /gene="env"
		     /codon_start="1"
		     /transl_table="1"
		     /product="envelope glycoprotein"
		     /protein_id="AGG92167.1"
		     /db_xref="GI:459963637"
		     /translation="MRVMGTKKNYQHLSWGILLLGMLAMSSAKKEEKWVTVYYGVPVW
		     KEAVTTLFCASDAKAYKAEAHNVWATHACVPTDPNPQEVKLENVTENFNMWKNKMVDQ
		     MHEDIISLWDQSLKPCVKFTPLCVTLNCTDASAGNGTDAIANNGTNATISLSENEMKN
		     CSFNVTKSVGNKLQKEYALFYKLDVASIDNSNTSYMLVHCNSSVVTQACPKISFQPIP
		     IHFCAPAGFAILKCNNKTFNGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEVVI
		     RAENFTDNAKTIIVQLNESVIINCTRPNNNTRKSIHLGPGSAIYATGQIIGDIRQAHC
		     NISEEKWNKTLRLIAEKLREQFREQLKNKTIIFSPHPGGDPEIEMHSFNCGGEFFYCN
		     TTRLFNNWTSNNTWNDTTGSNNSTITLPCRIKQIINRWQEIGKAMYAPPIAGQINCSS
		     NITGLLLTRDGGKTNNSNSSETFRPGGGNMKDNWRSELYKYKVVKIEPLGIAPTEARR
		     RVVQREKRTVTLGAMFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQSNLLRAIEA
		     QQHMLQLTVWGIKQLQARVLAVERYLKDQQLLGIWGCSGKLICTTNVPWNDSWSNRSI
		     QEIWNNMTWMQWEKEIDNYTELIYTLIEDSQNQQEKNELDLLKLDDWASLWNWFDITK
		     WLWYVKIFIMVIGGLVGLKIVFTVLSIVNRVRQGYSPLSFQTRSPAARGPDRPEEIEG
		     GGGERDRDRSGRSVIGLLGLIWDDLWNLCIFSYHRLRDFLLILVRVVEVLGHRGWEAL
		     KYWWSLLQYWIQELKNSAVSLLNATAIAVAEGTDRILEVLQRAGRAIIHIPRRIRQGL
		     ERALI"
     gene	     3770..4402
		     /gene="nef"
     CDS	     3770..4402
		     /gene="nef"
		     /codon_start="1"
		     /transl_table="1"
		     /product="nef protein"
		     /protein_id="AGG92168.1"
		     /db_xref="GI:459963638"
		     /translation="MGGKWSKRSGNGWAAVREKMEQAKPKVEPAAVGVGAASRDLEQH
		     GALTSSNTPANNADCAWLEAQEEEEVGFPVRPQVPLRPMTFKGALDLSHFLKEKGGLD
		     GLIYSKKRQEILDLWMYNTQGYFPDWQNYTPGPGIRYPLTFGWCFKLVPVDPEKVEEA
		     NTGENNCLLHPMSLHGMEDPEKEVLMWKFDSLLAYQHIAKEKHPEFYKNC"
BASE COUNT     1576 a	 814 c	 1120 g   1086 t
ORIGIN
       1 atggaaaaca gatggcaggt gatgattgtg tggcaagtag acaggatgag gattaaaaca 
      61 tggaaaagtt tagtaaaaca ccacatgcat atttcaaaga aagctagagg atggttttat 
     121 agacatcact atgaaaatac tcatccaaaa ataagttcag aagtacacat cccactaagg 
     181 gaggctagat tggtaataac aacatattgg ggtctgcaca caggagaaag agactggcac 
     241 ttgggtcaag gggtctccat agaatggagg aagaggaaat atagcacaca agtagaccct 
     301 gacctagcag accaactaat tcacctgtat tactttgatt gtttttcaga atctgctata 
     361 aggaatgccc tattaggaca catagttagc cctaggtgtg agtatcaagc aggacataac 
     421 aaggtagggt ctctacagta cttggcacta acagcattag tagcaccaaa aaagacaaag 
     481 ccacctttgc ctagtgtcaa gaaactgaca gaggatagat ggaacaagcc ccagaagacc 
     541 aagggccaca gagggagcca tacaatgagt ggacactaga gcttttagag gaacttaaga 
     601 gagaagctgt tagacatttt cctaggccat ggctccaggg cttaggacaa tatatctatg 
     661 aaacttatgg agatacctgg gcaggagtgg aagctataat aaaaattctg caacaactgc 
     721 tgtttattca tttcagaatt ggatgtcgac atagcagaat aggcattatt cgacagagga 
     781 gaacaagaaa tggagccagt agatcctaga ctagagccct ggaagcatcc aggaagtcag 
     841 cctaggactg cttgtaccac atgctattgt aaaaagtgtt gctttcattg ccaagtgtgt 
     901 ttcataacaa aaggcttagg catctcctat ggcaggaaga agcggagaca gcgacgaaga 
     961 gctcctgaaa acagtcagac tcatcaagtt tctgtatcaa agcagtaagt gtatatgtaa 
    1021 tgataccctt aacaatatta tcaatagtag ctttagtagt agtagtaata atagcaatag 
    1081 ttgtgtggtc tatagcttac atagaatata ggaaattatt aagacaaaga aaaatagata 
    1141 ggttacttga taggataaga gacagagcag aagacagtgg caatgagagt gatggggacc 
    1201 aagaagaatt atcagcactt gagctggggc atcttgctcc ttggaatgtt ggcgatgagt 
    1261 agtgctaaaa aagaggaaaa gtgggtcaca gtctattatg gggtacctgt gtggaaagaa 
    1321 gcagtcacca ccctattttg tgcatcagat gctaaagcat ataaggcaga ggcacataat 
    1381 gtttgggcca cacatgcctg tgtacccaca gatcctaacc cacaagaagt aaaattggaa 
    1441 aatgtgacag aaaattttaa catgtggaaa aataaaatgg tagaccaaat gcatgaggac 
    1501 ataatcagtc tatgggatca aagcctaaag ccatgtgtaa aatttacccc actctgtgtt 
    1561 actctaaact gcactgatgc tagtgctggc aatggtactg atgctattgc taacaatggt 
    1621 actaatgcta caattagtct cagtgagaat gagatgaaaa actgctcttt caatgtcacc 
    1681 aaaagcgtag gaaataagtt acagaaagaa tatgcacttt tttataaact tgatgtagct 
    1741 tcaatagata atagtaatac tagctatatg ttggtacact gtaactcctc agtcgttaca 
    1801 caggcttgtc caaagatatc ctttcaacca attcccatac atttttgtgc cccagctggt 
    1861 tttgcgattc taaagtgtaa taataagaca ttcaacggaa caggaccatg taacaatgtc 
    1921 agcacagtac aatgcacaca tggaattaag ccagtagtgt caactcagct gttgttaaat 
    1981 ggcagtctag cagaagaaga agtagtaatt agagctgaaa atttcacaga caatgctaag 
    2041 accataatag tacagctaaa tgaatctgta ataattaatt gtacaagacc taacaataat 
    2101 acaagaaaaa gtatacattt aggaccaggg agtgcaattt atgcaacagg acaaataata 
    2161 ggagatataa gacaagcaca ttgtaacatt agtgaggaga aatggaataa aactttaaga 
    2221 ctgatagctg aaaaattaag agaacaattt agagaacaat tgaagaataa aacaataatc 
    2281 tttagtcccc acccaggagg ggacccagaa attgaaatgc atagttttaa ttgtggaggg 
    2341 gaatttttct attgtaacac aacacggctg tttaataatt ggacttctaa taatacttgg 
    2401 aatgatacta cagggtcaaa taacagcaca atcacactcc catgcagaat aaaacaaatt 
    2461 ataaataggt ggcaggaaat aggaaaagca atgtatgccc ctcccatcgc aggacaaatt 
    2521 aactgttcat caaatattac agggttgcta ttaacaagag atggtggtaa gaccaacaac 
    2581 agcaacagca gtgagacctt cagaccaggg ggaggaaata tgaaggacaa ttggagaagt 
    2641 gaattatata aatataaagt agtaaaaatt gaaccattag gaatagcacc caccgaggca 
    2701 aggagaagag tggtgcagag agaaaaaaga acagtaacat taggagctat gttccttggg 
    2761 ttcttgggag cagcaggaag cactatgggc gcagcatcaa tgacgctgac ggtacaggcc 
    2821 agacaattat tgtctggtat agtgcaacag cagagcaatc tgctgagggc tattgaggcg 
    2881 caacagcata tgttgcaact cacagtctgg ggcatcaagc agctccaggc aagagtcctg 
    2941 gctgtggaaa gatacctaaa ggatcaacag ctcctaggga tttggggttg ctctggaaaa 
    3001 ctcatctgca ccactaatgt gccttggaat gacagttgga gtaatagatc tatacaagag 
    3061 atttggaata acatgacctg gatgcaatgg gagaaagaaa ttgacaacta tacagagttg 
    3121 atatacacct taattgagga ctcgcaaaac caacaagaaa aaaatgaact agatttatta 
    3181 aaattggatg actgggcaag tttgtggaat tggtttgaca taacaaaatg gctgtggtat 
    3241 gtaaaaatat tcataatggt aataggaggt ttagtaggtt taaaaatagt ttttactgta 
    3301 ctttctatag tgaatagagt taggcaggga tactcaccat tgtcgtttca gacccgatcc 
    3361 ccagcagcga ggggacccga caggcccgaa gaaatcgaag gaggaggtgg agagagagac 
    3421 agagacagat ccggaagatc agtgattgga ttattaggac tcatctggga cgacctgtgg 
    3481 aacctgtgca tcttcagcta ccaccgcttg agagactttc tcttgattct agtgagggtt 
    3541 gtggaagttc tgggacacag ggggtgggaa gccctcaagt attggtggag tctcctgcag 
    3601 tattggattc aggaactaaa gaatagtgct gttagcttgc ttaatgccac agctatagca 
    3661 gtagctgagg ggacagatag gattttagag gtattacaaa gagctggtag agctattatc 
    3721 cacataccta gaagaataag acagggctta gaaagggctt taatataaga tgggtggcaa 
    3781 gtggtcaaaa cgtagtggaa atggatgggc tgctgtaaga gaaaaaatgg aacaggctaa 
    3841 gccaaaagtt gagccagcag cagttggggt gggagcagca tctcgagact tagaacaaca 
    3901 tggagcactc acaagtagca atacaccagc aaataatgct gattgtgcct ggctagaagc 
    3961 gcaagaggaa gaggaggtgg gttttccagt caggcctcag gtacctttaa gaccaatgac 
    4021 tttcaaggga gctctcgatc ttagccactt tttaaaagaa aaggggggac tggatgggtt 
    4081 aatttactct aaaaagagac aagagatcct tgatctgtgg atgtacaaca cacaaggcta 
    4141 cttccctgac tggcagaatt acacaccagg gccagggatt agatatcccc tgacctttgg 
    4201 atggtgcttc aagctagtac cagttgaccc agagaaggta gaagaggcca acacaggaga 
    4261 gaacaactgc ctgctacatc ctatgagcct gcatggaatg gaggacccgg agaaagaagt 
    4321 attaatgtgg aagtttgaca gcctcctagc atatcagcac atagccaaag agaagcatcc 
    4381 ggagttttac aagaactgct gacacctaca agaaatgctg acatagagat atctacaagg 
    4441 gactttccgc tggggacttt ccaggggagg tgtggcctgg gcgggaccgg ggagtggcga 
    4501 gccctcagat gctgcatata agcagctgct ttttgcctgt actgggtctc tctggttaga 
    4561 ccagatctga gcctgggagc tctctggcta gctagg
//
last modified: Tue May 31 10:56 2022


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