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LOCUS	    HIVHXB2CG		    9719 bp    RNA     linear	VRL 21-OCT-2002
DEFINITION  Human immunodeficiency virus type 1 (HXB2), complete genome;
	    HIV1/HTLV-III/LAV reference genome
ACCESSION   K03455
VERSION     K03455.1 GI:1906382
KEYWORDS    TAR protein; acquired immune deficiency syndrome; complete genome;
	    env protein; gag protein; long terminal repeat (LTR); pol protein;
	    polyprotein; proviral gene; reverse transcriptase; transactivator.
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 493 to 674; 9577 to 9718)
            Show all sequences for reference 1
  AUTHORS   Wong-Staal,F., Gallo,R.C., Haseltine,W., Chang,N.T., Ghrayeb,J.,
	    Papas,T.S., Josephs,S.F., Lautenberger,J.A., Pearson,M.L.,
	    Petteway,S.R. Jr.., Ivanoff,L., Baumeister,K., Whitehorn,E.A.,
	    Petteway,S.R. Jr.., Rafalski,J.A., Doran,E.R., Josephs,S.J.,
	    Starcich,B., Livak,K.J., Patarca,R., Haseltine,W.A. and Ratner,L.
  TITLE     Complete nucleotide sequence of the AIDS virus, HTLV-III
  JOURNAL   Nature 313 (6000), 277-284 (1985)
  PUBMED    2578615
REFERENCE   2 (bases 1 to 653)
            Show all sequences for reference 2
  AUTHORS   Starcich,B., Ratner,L., Josephs,S.F., Okamoto,T., Gallo,R.C. and
	    Wong-Staal,F.
  TITLE     Characterization of long terminal repeat sequences of HTLV-III
  JOURNAL   Science 227 (4686), 538-540 (1985)
  PUBMED    2981438
REFERENCE   3 (sites)
            Show all sequences for reference 3
  AUTHORS   Allan,J.S., Coligan,J.E., Barin,F., McLane,M.F., Sodroski,J.G.,
	    Rosen,C.A., Haseltine,W.A., Lee,T.H. and Essex,M.
  TITLE     Major glycoprotein antigens that induce antibodies in AIDS patients
	    are encoded by HTLV-III
  JOURNAL   Science 228 (4703), 1091-1094 (1985)
  PUBMED    2986290
REFERENCE   4 (sites)
            Show all sequences for reference 4
  AUTHORS   Rosen,C.A., Sodroski,J.G. and Haseltine,W.A.
  TITLE     The location of cis-acting regulatory sequences in the human T cell
	    lymphotropic virus type III (HTLV-III/LAV) long terminal repeat
  JOURNAL   Cell 41 (3), 813-823 (1985)
  PUBMED    2988790
REFERENCE   5 (sites)
            Show all sequences for reference 5
  AUTHORS   Arya,S.K., Guo,C., Josephs,S.F. and Wong-Staal,F.
  TITLE     Trans-activator gene of human T-lymphotropic virus type III
	    (HTLV-III)
  JOURNAL   Science 229 (4708), 69-73 (1985)
  PUBMED    2990040
REFERENCE   6 (sites)
            Show all sequences for reference 6
  AUTHORS   Sodroski,J., Patarca,R., Rosen,C., Wong-Staal,F. and Haseltine,W.
  TITLE     Location of the trans-activating region on the genome of human
	    T-cell lymphotropic virus type III
  JOURNAL   Science 229 (4708), 74-77 (1985)
  PUBMED    2990041
REFERENCE   7 (sites)
            Show all sequences for reference 7
  AUTHORS   Rabson,A.B., Daugherty,D.F., Venkatesan,S., Boulukos,K.E.,
	    Benn,S.I., Folks,T.M., Feorino,P. and Martin,M.A.
  TITLE     Transcription of novel open reading frames of AIDS retrovirus
	    during infection of lymphocytes
  JOURNAL   Science 229 (4720), 1388-1390 (1985)
  PUBMED    2994220
REFERENCE   8 (sites)
            Show all sequences for reference 8
  AUTHORS   Allan,J.S., Coligan,J.E., Lee,T.H., McLane,M.F., Kanki,P.J.,
	    Groopman,J.E. and Essex,M.
  TITLE     A new HTLV-III/LAV encoded antigen detected by antibodies from AIDS
	    patients
  JOURNAL   Science 230 (4727), 810-813 (1985)
  PUBMED    2997921
REFERENCE   9 (sites)
            Show all sequences for reference 9
  AUTHORS   Rosen,C.A., Sodroski,J.G., Goh,W.C., Dayton,A.I., Lippke,J. and
	    Haseltine,W.A.
  TITLE     Post-transcriptional regulation accounts for the trans-activation
	    of the human T-lymphotropic virus type III
  JOURNAL   Nature 319 (6054), 555-559 (1986)
  PUBMED    3003584
REFERENCE   10 (sites)
            Show all sequences for reference 10
  AUTHORS   di Marzo Veronese,F., Copeland,T.D., DeVico,A.L., Rahman,R.,
	    Oroszlan,S., Gallo,R.C. and Sarngadharan,M.G.
  TITLE     Characterization of highly immunogenic p66/p51 as the reverse
	    transcriptase of HTLV-III/LAV
  JOURNAL   Science 231 (4743), 1289-1291 (1986)
  PUBMED    2418504
REFERENCE   11 (sites)
            Show all sequences for reference 11
  AUTHORS   Kramer,R.A., Schaber,M.D., Skalka,A.M., Ganguly,K., Wong-Staal,F.
	    and Reddy,E.P.
  TITLE     HTLV-III gag protein is processed in yeast cells by the virus
	    pol-protease
  JOURNAL   Science 231 (4745), 1580-1584 (1986)
  PUBMED    2420008
REFERENCE   12 (sites)
            Show all sequences for reference 12
  AUTHORS   Dayton,A.I., Sodroski,J.G., Rosen,C.A., Goh,W.C. and Haseltine,W.A.
  TITLE     The trans-activator gene of the human T cell lymphotropic virus
	    type III is required for replication
  JOURNAL   Cell 44 (6), 941-947 (1986)
  PUBMED    2420471
REFERENCE   13 (sites)
            Show all sequences for reference 13
  AUTHORS   Lee,T.H., Coligan,J.E., Allan,J.S., McLane,M.F., Groopman,J.E. and
	    Essex,M.
  TITLE     A new HTLV-III/LAV protein encoded by a gene found in cytopathic
	    retroviruses
  JOURNAL   Science 231 (4745), 1546-1549 (1986)
  PUBMED    3006243
REFERENCE   14 (sites)
            Show all sequences for reference 14
  AUTHORS   Sodroski,J., Goh,W.C., Rosen,C., Tartar,A., Portetelle,D., Burny,A.
	    and Haseltine,W.
  TITLE     Replicative and cytopathic potential of HTLV-III/LAV with sor gene
	    deletions
  JOURNAL   Science 231 (4745), 1549-1553 (1986)
  PUBMED    3006244
REFERENCE   15 (sites)
            Show all sequences for reference 15
  AUTHORS   Kan,N.C., Franchini,G., Wong-Staal,F., DuBois,G.C., Robey,W.G.,
	    Lautenberger,J.A. and Papas,T.S.
  TITLE     Identification of HTLV-III/LAV sor gene product and detection of
	    antibodies in human sera
  JOURNAL   Science 231 (4745), 1553-1555 (1986)
  PUBMED    3006245
REFERENCE   16 (sites)
            Show all sequences for reference 16
  AUTHORS   Arya,S.K. and Gallo,R.C.
  TITLE     Three novel genes of human T-lymphotropic virus type III: immune
	    reactivity of their products with sera from acquired immune
	    deficiency syndrome patients
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 83 (7), 2209-2213 (1986)
  PUBMED    3008154
REFERENCE   17 (sites)
            Show all sequences for reference 17
  AUTHORS   Jones,K.A., Kadonaga,J.T., Luciw,P.A. and Tjian,R.
  TITLE     Activation of the AIDS retrovirus promoter by the cellular
	    transcription factor, Sp1
  JOURNAL   Science 232 (4751), 755-759 (1986)
  PUBMED    3008338
REFERENCE   18 (sites)
            Show all sequences for reference 18
  AUTHORS   Sodroski,J., Goh,W.C., Rosen,C., Dayton,A., Terwilliger,E. and
	    Haseltine,W.
  TITLE     A second post-transcriptional trans-activator gene required for
	    HTLV-III replication
  JOURNAL   Nature 321 (6068), 412-417 (1986)
  PUBMED    3012355
REFERENCE   19 (sites)
            Show all sequences for reference 19
  AUTHORS   Starcich,B.R., Hahn,B.H., Shaw,G.M., McNeely,P.D., Modrow,S.,
	    Wolf,H., Parks,E.S., Parks,W.P., Josephs,S.F., Gallo,R.C. and
	    Wong-Staal,F.
  TITLE     Identification and characterization of conserved and variable
	    regions in the envelope gene of HTLV-III/LAV, the retrovirus of
	    AIDS
  JOURNAL   Cell 45 (5), 637-648 (1986)
  PUBMED    2423250
REFERENCE   20 (sites)
            Show all sequences for reference 20
  AUTHORS   Willey,R.L., Rutledge,R.A., Dias,S., Folks,T., Theodore,T.,
	    Buckler,C.E. and Martin,M.A.
  TITLE     Identification of conserved and divergent domains within the
	    envelope gene of the acquired immunodeficiency syndrome retrovirus
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 83 (14), 5038-5042 (1986)
  PUBMED    3014529
REFERENCE   21 (bases 8761 to 9060)
            Show all sequences for reference 21
  AUTHORS   Fisher,A.G., Ratner,L., Mitsuya,H., Marselle,L.M., Harper,M.E.,
	    Broder,S., Gallo,R.C. and Wong-Staal,F.
  TITLE     Infectious mutants of HTLV-III with changes in the 3' region and
	    markedly reduced cytopathic effects
  JOURNAL   Science 233 (4764), 655-659 (1986)
  PUBMED    3014663
REFERENCE   22 (sites)
            Show all sequences for reference 22
  AUTHORS   Feinberg,M.B., Jarrett,R.F., Aldovini,A., Gallo,R.C. and
	    Wong-Staal,F.
  TITLE     HTLV-III expression and production involve complex regulation at
	    the levels of splicing and translation of viral RNA
  JOURNAL   Cell 46 (6), 807-817 (1986)
  PUBMED    3638988
REFERENCE   23 (sites)
            Show all sequences for reference 23
  AUTHORS   Lightfoote,M.M., Coligan,J.E., Folks,T.M., Fauci,A.S., Martin,M.A.
	    and Venkatesan,S.
  TITLE     Structural characterization of reverse transcriptase and
	    endonuclease polypeptides of the acquired immunodeficiency syndrome
	    retrovirus
  JOURNAL   J. Virol. 60 (2), 771-775 (1986)
  PUBMED    2430111
REFERENCE   24 (sites)
            Show all sequences for reference 24
  AUTHORS   Terwilliger,E., Sodroski,J.G., Rosen,C.A. and Haseltine,W.A.
  TITLE     Effects of mutations within the 3' orf open reading frame region of
	    human T-cell lymphotropic virus type III (HTLV-III/LAV) on
	    replication and cytopathogenicity
  JOURNAL   J. Virol. 60 (2), 754-760 (1986)
  PUBMED    3490583
REFERENCE   25 (sites)
            Show all sequences for reference 25
  AUTHORS   Wright,C.M., Felber,B.K., Paskalis,H. and Pavlakis,G.N.
  TITLE     Expression and characterization of the trans-activator of
	    HTLV-III/LAV virus
  JOURNAL   Science 234 (4779), 988-992 (1986)
  PUBMED    3490693
REFERENCE   26 (bases 1 to 9635)
            Show all sequences for reference 26
  AUTHORS   Ratner,L., Fisher,A., Jagodzinski,L.L., Mitsuya,H., Liou,R.S.,
	    Gallo,R.C. and Wong-Staal,F.
  TITLE     Complete nucleotide sequences of functional clones of the AIDS
	    virus
  JOURNAL   AIDS Res. Hum. Retroviruses 3 (1), 57-69 (1987)
  PUBMED    3040055
REFERENCE   27 (sites)
            Show all sequences for reference 27
  AUTHORS   Modrow,S., Hahn,B.H., Shaw,G.M., Gallo,R.C., Wong-Staal,F. and
	    Wolf,H.
  TITLE     Computer-assisted analysis of envelope protein sequences of seven
	    human immunodeficiency virus isolates: prediction of antigenic
	    epitopes in conserved and variable regions
  JOURNAL   J. Virol. 61 (2), 570-578 (1987)
  PUBMED    2433466
REFERENCE   28 (sites)
            Show all sequences for reference 28
  AUTHORS   Goh,W.C., Sodroski,J.G., Rosen,C.A. and Haseltine,W.A.
  TITLE     Expression of the art gene protein of human T-lymphotropic virus
	    type III (HTLV-III/LAV) in bacteria
  JOURNAL   J. Virol. 61 (2), 633-637 (1987)
  PUBMED    3543401
REFERENCE   29 (sites)
            Show all sequences for reference 29
  AUTHORS   Muesing,M.A., Smith,D.H. and Capon,D.J.
  TITLE     Regulation of mRNA accumulation by a human immunodeficiency virus
	    trans-activator protein
  JOURNAL   Cell 48 (4), 691-701 (1987)
  PUBMED    3643816
REFERENCE   30 (sites)
            Show all sequences for reference 30
  AUTHORS   Nabel,G. and Baltimore,D.
  TITLE     An inducible transcription factor activates expression of human
	    immunodeficiency virus in T cells
  JOURNAL   Nature 326 (6114), 711-713 (1987)
  PUBMED    3031512
REFERENCE   31 (sites)
            Show all sequences for reference 31
  AUTHORS   Fisher,A.G., Ensoli,B., Ivanoff,L., Chamberlain,M., Petteway,S.,
	    Ratner,L., Gallo,R.C. and Wong-Staal,F.
  TITLE     The sor gene of HIV-1 is required for efficient virus transmission
	    in vitro
  JOURNAL   Science 237 (4817), 888-893 (1987)
  PUBMED    3497453
REFERENCE   32 (sites)
            Show all sequences for reference 32
  AUTHORS   Patarca,R., Heath,C., Goldenberg,G.J., Rosen,C.A., Sodroski,J.G.,
	    Haseltine,W.A. and Hansen,U.M.
  TITLE     Transcription directed by the HIV long terminal repeat in vitro
  JOURNAL   AIDS Res. Hum. Retroviruses 3 (1), 41-55 (1987)
  PUBMED    3040054
REFERENCE   33 (sites)
            Show all sequences for reference 33
  AUTHORS   Wong-Staal,F., Chanda,P.K. and Ghrayeb,J.
  TITLE     Human immunodeficiency virus: the eighth gene
  JOURNAL   AIDS Res. Hum. Retroviruses 3 (1), 33-39 (1987)
  PUBMED    3476127
REFERENCE   34 (bases 6225 to 8795)
            Show all sequences for reference 34
  AUTHORS   Reitz,M.S. Jr.., Wilson,C., Naugle,C., Gallo,R.C. and
	    Robert-Guroff,M.
  TITLE     Generation of a neutralization-resistant variant of HIV-1 is due to
	    selection for a point mutation in the envelope gene
  JOURNAL   Cell 54 (1), 57-63 (1988)
  PUBMED    2838179
REFERENCE   35 (bases 790 to 2292)
            Show all sequences for reference 35
  AUTHORS   Pal,R., Reitz,M.S. Jr.., Tschachler,E., Gallo,R.C.,
	    Sarngadharan,M.G. and Veronese,F.D.
  TITLE     Myristoylation of gag proteins of HIV-1 plays an important role in
	    virus assembly
  JOURNAL   AIDS Res. Hum. Retroviruses 6 (6), 721-730 (1990)
  PUBMED    2194551
REFERENCE   36 (sites)
            Show all sequences for reference 36
  AUTHORS   Ido,E., Han,H.P., Kezdy,F.J. and Tang,J.
  TITLE     Kinetic studies of human immunodeficiency virus type 1 protease and
	    its active-site hydrogen bond mutant A28S
  JOURNAL   J. Biol. Chem. 266 (36), 24359-24366 (1991)
  PUBMED    1761538
REFERENCE   37
            Show all sequences for reference 37
  AUTHORS   Kantor,R., Katzenstein,D.A., Efron,B., Carvalho,A.P., Wynhoven,B.,
	    Cane,P., Clarke,J., Sirivichayakul,S., Soares,M.A., Snoeck,J.,
	    Pillay,C., Rudich,H., Rodrigues,R., Holguin,A., Ariyoshi,K.,
	    Bouzas,M.B., Cahn,P., Sugiura,W., Soriano,V., Brigido,L.F.,
	    Grossman,Z., Morris,L., Vandamme,A.M., Tanuri,A., Phanuphak,P.,
	    Weber,J.N., Pillay,D., Harrigan,P.R., Camacho,R., Schapiro,J.M. and
	    Shafer,R.W.
  TITLE     Impact of HIV-1 Subtype and Antiretroviral Therapy on Protease and
	    Reverse Transcriptase Genotype: Results of a Global Collaboration
  JOURNAL   PLoS Med 2 (4), E112 (2005)
  PUBMED    15839752
REFERENCE   38
            Show all sequences for reference 38
  AUTHORS   van Beveren,C.P., Coffin,J. and Hughes,S.
  TITLE     Appendix B: HTLV-3/LAV genome
  JOURNAL   (in) Weiss,R.L., Teich,N., Varmus,H. and Coffin,J. (Eds.); RNA
	    TUMOR VIRUSES, MOLECULAR BIOLOGY OF TUMOR VIRUSES, SECOND EDITION,
	    2: Supplements and Appendixes: 1106-1123; Cold Spring Harbor
	    Laboratory, CSH, NY (1985)
REFERENCE   39
            Show all sequences for reference 39
  AUTHORS   Wain-Hobson,S., Vartanian,J.P., Henry,M., Chenciner,N.,
	    Cheynier,R., Delassus,S., Martins,L.P., Sala,M., Nugeyre,M.T. and
	    Guetard,D.
  TITLE     LAV revisited: origins of the early HIV-1 isolates from Institut
	    Pasteur.
  JOURNAL   Science.. 252(5008); 961-5 (1991)
  PUBMED    2035026
REFERENCE   40
            Show all sequences for reference 40
  AUTHORS   Baesi,K., Moallemi,S., Farrokhi,M., Alinaghi,S.A.S. and
	    Truong,H.-H.M.
  TITLE     Subtype classification of Iranian HIV-1 sequences registered in the
	    HIV databases, 2006-2013.
  JOURNAL   PLoS. One.. 9(9); e105098 (2014)
  PUBMED    25188443
COMMENT     This sequence is used as the primary reference genome for HIV-1 at
	    the Los Alamos HIV Databases. HXB2 is a specific clone from the
	    French isolate LAI (formerly BRU), which is also referred to as
	    IIIB or LAV. It was one of the first published nucleotide sequences
	    of HIV-1. The present sequence (HXB2R) is a revised version of the
	    originally-published sequence. Since the LAI isolate is a
	    widely-used laboratory strain, it is associated with many
	    publications; not all of the references linked to this entry are
	    concerned with this specific clone. This sequence contains a
	    mutation of the vpu start codon (bases 6062-6064; ACG instead of
	    ATG). It contains a frameshift at 5772, resulting in premature
	    termination of Vpr. Despite these mutations, the clone
	    corresponding to this sequence is demonstrably infectious. The
	    database contains a number of other full-length and partial
	    sequences derived from the same patient as the HXB2 clone. Other
	    related clones include BH1-BH10, N1T, and PV22. The clone NL43 (or
	    NL4-3) is spliced from the envelope of HXB2 and gag-pol from NY5.
	    Other sequences from the same isolate as HXB2 include: PV22
	    (K08083), MFA (M33943), F12CG (Z11530), TH4 (L31963), MCK1
	    (D86068), PM213 (D86069), BH10 (M15654), and LAI (M14100, K02013,
	    X01762). Other GenBank entries with IIIB-LAI sequences include many
	    patent sequences and cloning vectors. Note that occasionally
	    laboratory samples become contaminated by the LAI/HXB2 lab strain,
	    resulting in sequences with a high degree of similarity to HXB2;
	    such sequences may be labeled as C ('contaminant') in the HIV
	    database 'problematic' field; however, not all such contaminants
	    are detected and labeled. The NCBI REFSEQ for HIV-1 is also a clone
	    of HXB2, but it lacks the first 454 bases of this sequence, and has
	    the Vpu start codon (defective ACG in this sequence) corrected to
	    ATG. See entries with accession numbers NC_001802 and AF033819.
	    Some annotation data from Seaman 2010 [PMID 19939925] or Virus
	    Registry
	    [http://www.hiv.lanl.gov/content/nab-reference-strains/html/home.ht
	    m].
FEATURES             Location/Qualifiers
     source	     1..9719
		     /organism="Human immunodeficiency virus 1"
		     /proviral="Human immunodeficiency virus 1"
		     /mol_type="genomic RNA"
		     /isolate="HXB2"
		     /db_xref="taxon:11676"
		     /note="HTLV-III/LAV"
     LTR	     1..634
		     /note="5'' LTR"
     repeat_region   454..551
		     /note="R repeat 5'' copy"
     mRNA	     455..9635
		     /product="HXB2 genomic mRNA"
     prim_transcript 455..9635
		     /note="tat, trs, 27K subgenomic mRNA"
     intron	     744..5777
		     /note="tat, trs, 27K mRNA intron 1"
     CDS	     790..2292
		     /note="gag polyprotein"
		     /codon_start="1"
		     /transl_table="1"
		     /protein_id="AAB50258.1"
		     /db_xref="GI:327745"
		     /translation="MGARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERF
		     AVNPGLLETSEGCRQILGQLQPSLQTGSEELRSLYNTVATLYCVHQRIEIKDTKEALD
		     KIEEEQNKSKKKAQQAAADTGHSNQVSQNYPIVQNIQGQMVHQAISPRTLNAWVKVVE
		     EKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPV
		     HAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRM
		     YSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTIL
		     KALGPAATLEEMMTACQGVGGPGHKARVLAEAMSQVTNSATIMMQRGNFRNQRKIVKC
		     FNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWPSYKGRPGNFLQ
		     SRPEPTAPPEESFRSGVETTTPPQKQEPIDKELYPLTSLRSLFGNDPSSQ"
     CDS	     2358..5096
		     /note="pol polyprotein (NH2-terminus uncertain)"
		     /codon_start="1"
		     /transl_table="1"
		     /protein_id="AAB50259.1"
		     /db_xref="GI:1906384"
		     /translation="MSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGP
		     TPVNIIGRNLLTQIGCTLNFPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEIC
		     TEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPH
		     PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWK
		     GSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRW
		     GLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQI
		     YPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAE
		     IQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKT
		     PKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDG
		     AANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYA
		     LGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVL
		     FLDGIDKAQDEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSP
		     GIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTIHTD
		     NGSNFTGATVRAACWWAGIKQEFGIPYNPQSQGVVESMNKELKKIIGQVRDQAEHLKT
		     AVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRVYYRDSRN
		     PLWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED"
     CDS	     5041..5619
		     /note="sor 23K protein"
		     /codon_start="1"
		     /transl_table="1"
		     /protein_id="AAB50260.1"
		     /db_xref="GI:327747"
		     /translation="MENRWQVMIVWQVDRMRIRTWKSLVKHHMYVSGKARGWFYRHHY
		     ESPHPRISSEVHIPLGDARLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPEL
		     ADQLIHLYYFDCFSDSAIRKALLGHIVSPRCEYQAGHNKVGSLQYLALAALITPKKIK
		     PPLPSVTKLTEDRWNKPQKTKGHRGSHTMNGH"
     CDS	     5559..5795
		     /note="R (ORF) protein"
		     /codon_start="1"
		     /transl_table="1"
		     /protein_id="AAB50261.1"
		     /db_xref="GI:327748"
		     /translation="MEQAPEDQGPQREPHNEWTLELLEELKNEAVRHFPRIWLHGLGQ
		     HIYETYGDTWAGVEAIIRILQQLLFIHFQNWVST"
     CDS	     join(5831..6045,8379..8424)
		     /note="tat protein"
		     /codon_start="1"
		     /transl_table="1"
		     /protein_id="AAB50256.1"
		     /db_xref="GI:1906383"
		     /translation="MEPVDPRLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKALG
		     ISYGRKKRRQRRRAHQNSQTHQASLSKQPTSQPRGDPTGPKE"
     exon	     5831..6045
		     /note="tat protein, first expressed exon"
		     /number="2"
     CDS	     join(5970..6045,8379..8653)
		     /note="trs protein"
		     /codon_start="1"
		     /transl_table="1"
		     /protein_id="AAB50257.1"
		     /db_xref="GI:327744"
		     /translation="MAGRSGDSDEELIRTVRLIKLLYQSNPPPNPEGTRQARRNRRRR
		     WRERQRQIHSISERILGTYLGRSAEPVPLQLPPLERLTLDCNEDCGTSGTQGVGSPQI
		     LVESPTVLESGTKE"
     exon	     5970..6045
		     /note="trs protein, first expressed exon"
		     /number="2"
     intron	     6046..8378
		     /note="tat, trs, 27K mRNA intron 2"
     CDS	     6225..8795
		     /note="envelope polyprotein"
		     /codon_start="1"
		     /transl_table="1"
		     /protein_id="AAB50262.1"
		     /db_xref="GI:1906385"
		     /translation="MRVKEKYQHLWRWGWRWGTMLLGMLMICSATEKLWVTVYYGVPV
		     WKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLVNVTENFNMWKNDMVE
		     QMHEDIISLWDQSLKPCVKLTPLCVSLKCTDLKNDTNTNSSSGRMIMEKGEIKNCSFN
		     ISTSIRGKVQKEYAFFYKLDIIPIDNDTTSYKLTSCNTSVITQACPKVSFEPIPIHYC
		     APAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSVN
		     FTDNAKTIIVQLNTSVEINCTRPNNNTRKRIRIQRGPGRAFVTIGKIGNMRQAHCNIS
		     RAKWNNTLKQIASKLREQFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCNSTQLFN
		     STWFNSTWSTEGSNNTEGSDTITLPCRIKQIINMWQKVGKAMYAPPISGQIRCSSNIT
		     GLLLTRDGGNSNNESEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQR
		     EKRAVGIGALFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQNNLLRAIEAQQHLL
		     QLTVWGIKQLQARILAVERYLKDQQLLGIWGCSGKLICTTAVPWNASWSNKSLEQIWN
		     HTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWFNITNWLWYI
		     KLFIMIVGGLVGLRIVFAVLSIVNRVRQGYSPLSFQTHLPTPRGPDRPEGIEEEGGER
		     DRDRSIRLVNGSLALIWDDLRSLCLFSYHRLRDLLLIVTRIVELLGRRGWEALKYWWN
		     LLQYWSQELKNSAVSLLNATAIAVAEGTDRVIEVVQGACRAIRHIPRRIRQGLERILL
		     "
     exon	     8379..8652
		     /note="trs protein"
		     /number="3"
     exon	     8379..8424
		     /note="tat protein"
		     /number="3"
     CDS	     8797..9168
		     /note="27K protein (premature termination)"
		     /codon_start="1"
		     /transl_table="1"
		     /protein_id="AAB50263.1"
		     /db_xref="GI:1906386"
		     /translation="MGGKWSKSSVIGWPTVRERMRRAEPAADRVGAASRDLEKHGAIT
		     SSNTAATNAACAWLEAQEEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIH
		     SQRRQDILDLWIYHTQGYFPD"
     LTR	     9086..9719
		     /note="3'' LTR"
     repeat_region   9540..9636
		     /note="R repeat 3'' copy"
     polyA_signal    9612..9617
		     /note="HXB2 mRNA polyadenyation signal"
BASE COUNT     3411 a	1772 c	 2373 g   2163 t
ORIGIN
       1 tggaagggct aattcactcc caacgaagac aagatatcct tgatctgtgg atctaccaca 
      61 cacaaggcta cttccctgat tagcagaact acacaccagg gccagggatc agatatccac 
     121 tgacctttgg atggtgctac aagctagtac cagttgagcc agagaagtta gaagaagcca 
     181 acaaaggaga gaacaccagc ttgttacacc ctgtgagcct gcatggaatg gatgacccgg 
     241 agagagaagt gttagagtgg aggtttgaca gccgcctagc atttcatcac atggcccgag 
     301 agctgcatcc ggagtacttc aagaactgct gacatcgagc ttgctacaag ggactttccg 
     361 ctggggactt tccagggagg cgtggcctgg gcgggactgg ggagtggcga gccctcagat 
     421 cctgcatata agcagctgct ttttgcctgt actgggtctc tctggttaga ccagatctga 
     481 gcctgggagc tctctggcta actagggaac ccactgctta agcctcaata aagcttgcct 
     541 tgagtgcttc aagtagtgtg tgcccgtctg ttgtgtgact ctggtaacta gagatccctc 
     601 agaccctttt agtcagtgtg gaaaatctct agcagtggcg cccgaacagg gacctgaaag 
     661 cgaaagggaa accagaggag ctctctcgac gcaggactcg gcttgctgaa gcgcgcacgg 
     721 caagaggcga ggggcggcga ctggtgagta cgccaaaaat tttgactagc ggaggctaga 
     781 aggagagaga tgggtgcgag agcgtcagta ttaagcgggg gagaattaga tcgatgggaa 
     841 aaaattcggt taaggccagg gggaaagaaa aaatataaat taaaacatat agtatgggca 
     901 agcagggagc tagaacgatt cgcagttaat cctggcctgt tagaaacatc agaaggctgt 
     961 agacaaatac tgggacagct acaaccatcc cttcagacag gatcagaaga acttagatca 
    1021 ttatataata cagtagcaac cctctattgt gtgcatcaaa ggatagagat aaaagacacc 
    1081 aaggaagctt tagacaagat agaggaagag caaaacaaaa gtaagaaaaa agcacagcaa 
    1141 gcagcagctg acacaggaca cagcaatcag gtcagccaaa attaccctat agtgcagaac 
    1201 atccaggggc aaatggtaca tcaggccata tcacctagaa ctttaaatgc atgggtaaaa 
    1261 gtagtagaag agaaggcttt cagcccagaa gtgataccca tgttttcagc attatcagaa 
    1321 ggagccaccc cacaagattt aaacaccatg ctaaacacag tggggggaca tcaagcagcc 
    1381 atgcaaatgt taaaagagac catcaatgag gaagctgcag aatgggatag agtgcatcca 
    1441 gtgcatgcag ggcctattgc accaggccag atgagagaac caaggggaag tgacatagca 
    1501 ggaactacta gtacccttca ggaacaaata ggatggatga caaataatcc acctatccca 
    1561 gtaggagaaa tttataaaag atggataatc ctgggattaa ataaaatagt aagaatgtat 
    1621 agccctacca gcattctgga cataagacaa ggaccaaagg aaccctttag agactatgta 
    1681 gaccggttct ataaaactct aagagccgag caagcttcac aggaggtaaa aaattggatg 
    1741 acagaaacct tgttggtcca aaatgcgaac ccagattgta agactatttt aaaagcattg 
    1801 ggaccagcgg ctacactaga agaaatgatg acagcatgtc agggagtagg aggacccggc 
    1861 cataaggcaa gagttttggc tgaagcaatg agccaagtaa caaattcagc taccataatg 
    1921 atgcagagag gcaattttag gaaccaaaga aagattgtta agtgtttcaa ttgtggcaaa 
    1981 gaagggcaca cagccagaaa ttgcagggcc cctaggaaaa agggctgttg gaaatgtgga 
    2041 aaggaaggac accaaatgaa agattgtact gagagacagg ctaatttttt agggaagatc 
    2101 tggccttcct acaagggaag gccagggaat tttcttcaga gcagaccaga gccaacagcc 
    2161 ccaccagaag agagcttcag gtctggggta gagacaacaa ctccccctca gaagcaggag 
    2221 ccgatagaca aggaactgta tcctttaact tccctcaggt cactctttgg caacgacccc 
    2281 tcgtcacaat aaagataggg gggcaactaa aggaagctct attagataca ggagcagatg 
    2341 atacagtatt agaagaaatg agtttgccag gaagatggaa accaaaaatg atagggggaa 
    2401 ttggaggttt tatcaaagta agacagtatg atcagatact catagaaatc tgtggacata 
    2461 aagctatagg tacagtatta gtaggaccta cacctgtcaa cataattgga agaaatctgt 
    2521 tgactcagat tggttgcact ttaaattttc ccattagccc tattgagact gtaccagtaa 
    2581 aattaaagcc aggaatggat ggcccaaaag ttaaacaatg gccattgaca gaagaaaaaa 
    2641 taaaagcatt agtagaaatt tgtacagaga tggaaaagga agggaaaatt tcaaaaattg 
    2701 ggcctgaaaa tccatacaat actccagtat ttgccataaa gaaaaaagac agtactaaat 
    2761 ggagaaaatt agtagatttc agagaactta ataagagaac tcaagacttc tgggaagttc 
    2821 aattaggaat accacatccc gcagggttaa aaaagaaaaa atcagtaaca gtactggatg 
    2881 tgggtgatgc atatttttca gttcccttag atgaagactt caggaagtat actgcattta 
    2941 ccatacctag tataaacaat gagacaccag ggattagata tcagtacaat gtgcttccac 
    3001 agggatggaa aggatcacca gcaatattcc aaagtagcat gacaaaaatc ttagagcctt 
    3061 ttagaaaaca aaatccagac atagttatct atcaatacat ggatgatttg tatgtaggat 
    3121 ctgacttaga aatagggcag catagaacaa aaatagagga gctgagacaa catctgttga 
    3181 ggtggggact taccacacca gacaaaaaac atcagaaaga acctccattc ctttggatgg 
    3241 gttatgaact ccatcctgat aaatggacag tacagcctat agtgctgcca gaaaaagaca 
    3301 gctggactgt caatgacata cagaagttag tggggaaatt gaattgggca agtcagattt 
    3361 acccagggat taaagtaagg caattatgta aactccttag aggaaccaaa gcactaacag 
    3421 aagtaatacc actaacagaa gaagcagagc tagaactggc agaaaacaga gagattctaa 
    3481 aagaaccagt acatggagtg tattatgacc catcaaaaga cttaatagca gaaatacaga 
    3541 agcaggggca aggccaatgg acatatcaaa tttatcaaga gccatttaaa aatctgaaaa 
    3601 caggaaaata tgcaagaatg aggggtgccc acactaatga tgtaaaacaa ttaacagagg 
    3661 cagtgcaaaa aataaccaca gaaagcatag taatatgggg aaagactcct aaatttaaac 
    3721 tgcccataca aaaggaaaca tgggaaacat ggtggacaga gtattggcaa gccacctgga 
    3781 ttcctgagtg ggagtttgtt aatacccctc ccttagtgaa attatggtac cagttagaga 
    3841 aagaacccat agtaggagca gaaaccttct atgtagatgg ggcagctaac agggagacta 
    3901 aattaggaaa agcaggatat gttactaata gaggaagaca aaaagttgtc accctaactg 
    3961 acacaacaaa tcagaagact gagttacaag caatttatct agctttgcag gattcgggat 
    4021 tagaagtaaa catagtaaca gactcacaat atgcattagg aatcattcaa gcacaaccag 
    4081 atcaaagtga atcagagtta gtcaatcaaa taatagagca gttaataaaa aaggaaaagg 
    4141 tctatctggc atgggtacca gcacacaaag gaattggagg aaatgaacaa gtagataaat 
    4201 tagtcagtgc tggaatcagg aaagtactat ttttagatgg aatagataag gcccaagatg 
    4261 aacatgagaa atatcacagt aattggagag caatggctag tgattttaac ctgccacctg 
    4321 tagtagcaaa agaaatagta gccagctgtg ataaatgtca gctaaaagga gaagccatgc 
    4381 atggacaagt agactgtagt ccaggaatat ggcaactaga ttgtacacat ttagaaggaa 
    4441 aagttatcct ggtagcagtt catgtagcca gtggatatat agaagcagaa gttattccag 
    4501 cagaaacagg gcaggaaaca gcatattttc ttttaaaatt agcaggaaga tggccagtaa 
    4561 aaacaataca tactgacaat ggcagcaatt tcaccggtgc tacggttagg gccgcctgtt 
    4621 ggtgggcggg aatcaagcag gaatttggaa ttccctacaa tccccaaagt caaggagtag 
    4681 tagaatctat gaataaagaa ttaaagaaaa ttataggaca ggtaagagat caggctgaac 
    4741 atcttaagac agcagtacaa atggcagtat tcatccacaa ttttaaaaga aaagggggga 
    4801 ttggggggta cagtgcaggg gaaagaatag tagacataat agcaacagac atacaaacta 
    4861 aagaattaca aaaacaaatt acaaaaattc aaaattttcg ggtttattac agggacagca 
    4921 gaaatccact ttggaaagga ccagcaaagc tcctctggaa aggtgaaggg gcagtagtaa 
    4981 tacaagataa tagtgacata aaagtagtgc caagaagaaa agcaaagatc attagggatt 
    5041 atggaaaaca gatggcaggt gatgattgtg tggcaagtag acaggatgag gattagaaca 
    5101 tggaaaagtt tagtaaaaca ccatatgtat gtttcaggga aagctagggg atggttttat 
    5161 agacatcact atgaaagccc tcatccaaga ataagttcag aagtacacat cccactaggg 
    5221 gatgctagat tggtaataac aacatattgg ggtctgcata caggagaaag agactggcat 
    5281 ttgggtcagg gagtctccat agaatggagg aaaaagagat atagcacaca agtagaccct 
    5341 gaactagcag accaactaat tcatctgtat tactttgact gtttttcaga ctctgctata 
    5401 agaaaggcct tattaggaca catagttagc cctaggtgtg aatatcaagc aggacataac 
    5461 aaggtaggat ctctacaata cttggcacta gcagcattaa taacaccaaa aaagataaag 
    5521 ccacctttgc ctagtgttac gaaactgaca gaggatagat ggaacaagcc ccagaagacc 
    5581 aagggccaca gagggagcca cacaatgaat ggacactaga gcttttagag gagcttaaga 
    5641 atgaagctgt tagacatttt cctaggattt ggctccatgg cttagggcaa catatctatg 
    5701 aaacttatgg ggatacttgg gcaggagtgg aagccataat aagaattctg caacaactgc 
    5761 tgtttatcca ttttcagaat tgggtgtcga catagcagaa taggcgttac tcgacagagg 
    5821 agagcaagaa atggagccag tagatcctag actagagccc tggaagcatc caggaagtca 
    5881 gcctaaaact gcttgtacca attgctattg taaaaagtgt tgctttcatt gccaagtttg 
    5941 tttcataaca aaagccttag gcatctccta tggcaggaag aagcggagac agcgacgaag 
    6001 agctcatcag aacagtcaga ctcatcaagc ttctctatca aagcagtaag tagtacatgt 
    6061 aacgcaacct ataccaatag tagcaatagt agcattagta gtagcaataa taatagcaat 
    6121 agttgtgtgg tccatagtaa tcatagaata taggaaaata ttaagacaaa gaaaaataga 
    6181 caggttaatt gatagactaa tagaaagagc agaagacagt ggcaatgaga gtgaaggaga 
    6241 aatatcagca cttgtggaga tgggggtgga gatggggcac catgctcctt gggatgttga 
    6301 tgatctgtag tgctacagaa aaattgtggg tcacagtcta ttatggggta cctgtgtgga 
    6361 aggaagcaac caccactcta ttttgtgcat cagatgctaa agcatatgat acagaggtac 
    6421 ataatgtttg ggccacacat gcctgtgtac ccacagaccc caacccacaa gaagtagtat 
    6481 tggtaaatgt gacagaaaat tttaacatgt ggaaaaatga catggtagaa cagatgcatg 
    6541 aggatataat cagtttatgg gatcaaagcc taaagccatg tgtaaaatta accccactct 
    6601 gtgttagttt aaagtgcact gatttgaaga atgatactaa taccaatagt agtagcggga 
    6661 gaatgataat ggagaaagga gagataaaaa actgctcttt caatatcagc acaagcataa 
    6721 gaggtaaggt gcagaaagaa tatgcatttt tttataaact tgatataata ccaatagata 
    6781 atgatactac cagctataag ttgacaagtt gtaacacctc agtcattaca caggcctgtc 
    6841 caaaggtatc ctttgagcca attcccatac attattgtgc cccggctggt tttgcgattc 
    6901 taaaatgtaa taataagacg ttcaatggaa caggaccatg tacaaatgtc agcacagtac 
    6961 aatgtacaca tggaattagg ccagtagtat caactcaact gctgttaaat ggcagtctag 
    7021 cagaagaaga ggtagtaatt agatctgtca atttcacgga caatgctaaa accataatag 
    7081 tacagctgaa cacatctgta gaaattaatt gtacaagacc caacaacaat acaagaaaaa 
    7141 gaatccgtat ccagagagga ccagggagag catttgttac aataggaaaa ataggaaata 
    7201 tgagacaagc acattgtaac attagtagag caaaatggaa taacacttta aaacagatag 
    7261 ctagcaaatt aagagaacaa tttggaaata ataaaacaat aatctttaag caatcctcag 
    7321 gaggggaccc agaaattgta acgcacagtt ttaattgtgg aggggaattt ttctactgta 
    7381 attcaacaca actgtttaat agtacttggt ttaatagtac ttggagtact gaagggtcaa 
    7441 ataacactga aggaagtgac acaatcaccc tcccatgcag aataaaacaa attataaaca 
    7501 tgtggcagaa agtaggaaaa gcaatgtatg cccctcccat cagtggacaa attagatgtt 
    7561 catcaaatat tacagggctg ctattaacaa gagatggtgg taatagcaac aatgagtccg 
    7621 agatcttcag acctggagga ggagatatga gggacaattg gagaagtgaa ttatataaat 
    7681 ataaagtagt aaaaattgaa ccattaggag tagcacccac caaggcaaag agaagagtgg 
    7741 tgcagagaga aaaaagagca gtgggaatag gagctttgtt ccttgggttc ttgggagcag 
    7801 caggaagcac tatgggcgca gcctcaatga cgctgacggt acaggccaga caattattgt 
    7861 ctggtatagt gcagcagcag aacaatttgc tgagggctat tgaggcgcaa cagcatctgt 
    7921 tgcaactcac agtctggggc atcaagcagc tccaggcaag aatcctggct gtggaaagat 
    7981 acctaaagga tcaacagctc ctggggattt ggggttgctc tggaaaactc atttgcacca 
    8041 ctgctgtgcc ttggaatgct agttggagta ataaatctct ggaacagatt tggaatcaca 
    8101 cgacctggat ggagtgggac agagaaatta acaattacac aagcttaata cactccttaa 
    8161 ttgaagaatc gcaaaaccag caagaaaaga atgaacaaga attattggaa ttagataaat 
    8221 gggcaagttt gtggaattgg tttaacataa caaattggct gtggtatata aaattattca 
    8281 taatgatagt aggaggcttg gtaggtttaa gaatagtttt tgctgtactt tctatagtga 
    8341 atagagttag gcagggatat tcaccattat cgtttcagac ccacctccca accccgaggg 
    8401 gacccgacag gcccgaagga atagaagaag aaggtggaga gagagacaga gacagatcca 
    8461 ttcgattagt gaacggatcc ttggcactta tctgggacga tctgcggagc ctgtgcctct 
    8521 tcagctacca ccgcttgaga gacttactct tgattgtaac gaggattgtg gaacttctgg 
    8581 gacgcagggg gtgggaagcc ctcaaatatt ggtggaatct cctacagtat tggagtcagg 
    8641 aactaaagaa tagtgctgtt agcttgctca atgccacagc catagcagta gctgagggga 
    8701 cagatagggt tatagaagta gtacaaggag cttgtagagc tattcgccac atacctagaa 
    8761 gaataagaca gggcttggaa aggattttgc tataagatgg gtggcaagtg gtcaaaaagt 
    8821 agtgtgattg gatggcctac tgtaagggaa agaatgagac gagctgagcc agcagcagat 
    8881 agggtgggag cagcatctcg agacctggaa aaacatggag caatcacaag tagcaataca 
    8941 gcagctacca atgctgcttg tgcctggcta gaagcacaag aggaggagga ggtgggtttt 
    9001 ccagtcacac ctcaggtacc tttaagacca atgacttaca aggcagctgt agatcttagc 
    9061 cactttttaa aagaaaaggg gggactggaa gggctaattc actcccaaag aagacaagat 
    9121 atccttgatc tgtggatcta ccacacacaa ggctacttcc ctgattagca gaactacaca 
    9181 ccagggccag gggtcagata tccactgacc tttggatggt gctacaagct agtaccagtt 
    9241 gagccagata agatagaaga ggccaataaa ggagagaaca ccagcttgtt acaccctgtg 
    9301 agcctgcatg ggatggatga cccggagaga gaagtgttag agtggaggtt tgacagccgc 
    9361 ctagcatttc atcacgtggc ccgagagctg catccggagt acttcaagaa ctgctgacat 
    9421 cgagcttgct acaagggact ttccgctggg gactttccag ggaggcgtgg cctgggcggg 
    9481 actggggagt ggcgagccct cagatcctgc atataagcag ctgctttttg cctgtactgg 
    9541 gtctctctgg ttagaccaga tctgagcctg ggagctctct ggctaactag ggaacccact 
    9601 gcttaagcct caataaagct tgccttgagt gcttcaagta gtgtgtgccc gtctgttgtg 
    9661 tgactctggt aactagagat ccctcagacc cttttagtca gtgtggaaaa tctctagca
//
last modified: Tue May 31 10:56 2022


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