LOCUS       NC_001722              10359 bp ss-RNA     linear   VRL 22-APR-2009
DEFINITION  Human immunodeficiency virus 2, complete genome.
ACCESSION   NC_001722
VERSION     NC_001722.1  GI:9628880
DBLINK      BioProject: PRJNA14991
KEYWORDS    RefSeq.
SOURCE      Human immunodeficiency virus 2 (HIV-2)
  ORGANISM  Human immunodeficiency virus 2
            Viruses; Retro-transcribing viruses; Retroviridae;
            Orthoretrovirinae; Lentivirus; Primate lentivirus group.
REFERENCE   1  (sites)
  AUTHORS   Kirchhoff,F., Jentsch,K.D., Bachmann,B., Stuke,A., Laloux,C.,
            Luke,W., Stahl-Hennig,C., Schneider,J., Nieselt,K., Eigen,M. et al.
  TITLE     A novel proviral clone of HIV-2: biological and phylogenetic
            relationship to other primate immunodeficiency viruses
  JOURNAL   Virology 177 (1), 305-311 (1990)
   PUBMED   2353457
REFERENCE   2  (bases 1 to 10359)
  AUTHORS   Kirchhoff,F., Jentsch,K., Bachmann,B., Stuke,A., Laloux,C.,
            Lueke,W., Stahl-Henning,C., Schneider,J., Nieselt,K., Eigen,M. and
            Hunsmann,G.
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 10359)
  CONSRTM   NCBI Genome Project
  TITLE     Direct Submission
  JOURNAL   Submitted (09-SEP-2004) National Center for Biotechnology
            Information, NIH, Bethesda, MD 20894, USA
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from M30502.
            Kindly submitted prior to publication by Dr. F. Kirchhoff, DPZ,
            Gottingen, 0551/3851-0. HIV2BEN was isolated from a German AIDS
            patient(with predominantly neurological complications) who was
            probably infected in Mali (Klemm et al., J Neuro 235,304,1988). The
            sequence was determined from two clones: bases 1903 to 5057 and
            7293 to 9131 were from MK2 and bases 1 to 1902, 5058 to 7292 and
            9132 to 10359 were from MK6.
            [2]  sites; for [1].
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..10359
                     /organism="Human immunodeficiency virus 2"
                     /proviral
                     /mol_type="genomic RNA"
                     /isolate="BEN"
                     /db_xref="taxon:11709"
                     /clone="MK[2,6]."
     LTR             1..855
                     /note="5' LTR"
     primer_bind     859..875
                     /note="primer (Lys-tRNA) binding site"
     gene            1103..5754
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /db_xref="GeneID:1490001"
     CDS             join(1103..2398,2398..5754)
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /ribosomal_slippage
                     /note="translated by ribosomal slip at 'TTTTTTA'"
                     /codon_start=1
                     /product="gag-pol fusion polyprotein"
                     /protein_id="NP_663784.1"
                     /db_xref="GI:21898538"
                     /db_xref="GeneID:1490001"
                     /translation="MGARNSVLRGKKADELEKVRLRPGGKKKYRLKHIVWAANELDKF
                     GLAESLLESKEGCQKILRVLDPLVPTGSENLKSLFNTVCVIWCLHAEEKVKDTEEAKK
                     LAQRHLVAETGTAEKMPNTSRPTAPPSGKRGNYPVQQAGGNYVHVPLSPRTLNAWVKL
                     VEEKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIREIINEEAADWDSQH
                     PIPGPLPAGQLRDPRGSDIAGTTSTVDEQIQWMYRPQNPVPVGNIYRRWIQIGLQKCV
                     RKYNPTNILDIKQGPKEPFQSYVDRFYKSLRAEQTDPAVKNWMTQTLLIQNANPDCKL
                     VLKGLGMNPTLEEMLTACQGVGGPGQKARLMAEALKEAMGPSPIPFAAAQQRKAIRYW
                     NCGKEGHSARQCRAPRRQGCWKCGKPGHIMANCPERQAGFFRVGPTGKEASQLPRDPS
                     PSGADTNSTSGRSSSGTVGEIYAAREKAEGAEGETIQRGDGGLAAPRAERDTSQRGDR
                     GLAAPQFSLWKRPVVTAYIEDQPVEVLLDTGADDSIVAGIELGDNYTPKIVGGIGGFI
                     NTKEYKNVEIKVLNKRVRATIMTGDTPINIFGRNILTALGMSLNLPVAKIEPIKVTLK
                     PGKDGPRLKQWPLTKEKIEALKEICEKMEKEGQLEEAPPTNPYNTPTFAIKKKDKNKW
                     RMLIDFRELNKVTQDFTEIQLGIPHPAGLAKKKRISILDVGDAYFSIPLHEDFRQYTA
                     FTLPAVNNMEPGKRYIYKVLPQGWKGSPAIFQYTMRQVLEPFRKANPDVILIQYMDDI
                     LIASDRTGLEHDKVVLQLKELLNGLGFSTPDEKFQKDPPFQWMGCELWPTKWKLQKLQ
                     LPQKDIWTVNDIQKLVGVLNWAAQIYSGIKTKHLCRLIRGKMTLTEEVQWTELAEAEL
                     EENKIILSQEQEGYYYQEEKELEATIQKSQGHQWTYKIHQEEKILKVGKYAKIKNTHT
                     NGVRLLAQVVQKIGKEALVIWGRIPKFHLPVERETWEQWWDNYWQVTWIPEWDFVSTP
                     PLVRLTFNLVGDPIPGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKVLEQTTNQQAE
                     LEVFRMALADSGPKVNIIVDSQYVMGIVAGQPTESENRIVNQIIEEMIKKEAVYVAWV
                     PAHKGIGGNQEVDHLVSQGIRQVLFLEKIEPAQEEHEKYHSIIKELTHKFGIPLLVAR
                     QIVNSCAQCQQKGEAIHGQVNAEIGVWQMDYTHLEGKIIIVAVHVASGFIEAEVIPQE
                     SGRQTALFLLKLASRWPITHLHTDNGPNFTSQEVKMVAWWVGIEQSFGVPYNPQSQGV
                     VEAMNHHLKNQISRIREQANTIETIVLMAVHCMNFKRRGGIGDMTPAERLINMITTEQ
                     EIQFLQRKNSNFKNFQVYYREGRDQLWKGPGELLWKGEGAVIVKVGTDIKVVPRRKAK
                     IIRDYGGRQELDSSPHLEGAREDGEMACPCQVPEIQNKRPRGGALCSPPQGGMGMVDL
                     QQGNIPTTRKKSSRNTGILEPNTRKRMALLSCSKINLVYRKVLDRCYPRLCRHPNT"
     misc_feature    1106..1507
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="gag gene protein p17 (matrix protein); Region:
                     Gag_p17; pfam00540"
                     /db_xref="CDD:109591"
     misc_feature    1553..2197
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="gag gene protein p24 (core nucleocapsid protein);
                     Region: Gag_p24; pfam00607"
                     /db_xref="CDD:201337"
     misc_feature    join(2150..2398,2398..>2466)
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="universal minicircle sequence binding protein
                     (UMSBP); Provisional; Region: PTZ00368"
                     /db_xref="CDD:173561"
     misc_feature    2330..2383
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="Zinc knuckle; Region: zf-CCHC; pfam00098"
                     /db_xref="CDD:189387"
     misc_feature    2668..2910
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="Retropepsins, pepsin-like aspartate proteases;
                     Region: HIV_retropepsin_like; cd05482"
                     /db_xref="CDD:133149"
     misc_feature    order(2710..2712,2716..2718,2722..2724,2773..2781,
                     2887..2889)
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="inhibitor binding site; inhibition site"
                     /db_xref="CDD:133149"
     misc_feature    2710..2718
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="catalytic motif [active]"
                     /db_xref="CDD:133149"
     misc_feature    2710..2712
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="Catalytic residue [active]"
                     /db_xref="CDD:133149"
     misc_feature    order(2773..2787,2791..2805)
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="Active site flap [active]"
                     /db_xref="CDD:133149"
     misc_feature    2986..3633
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="RT_like: Reverse transcriptase (RT, RNA-dependent
                     DNA polymerase)_like family. An RT gene is usually
                     indicative of a mobile element such as a retrotransposon
                     or retrovirus. RTs occur in a variety of mobile elements,
                     including retrotransposons; Region: RT_like; cl02808"
                     /db_xref="CDD:207741"
     misc_feature    3121..3633
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="Reverse transcriptase (RNA-dependent DNA
                     polymerase); Region: RVT_1; pfam00078"
                     /db_xref="CDD:200982"
     misc_feature    order(3262..3279,3385..3390,3481..3483,3487..3492,
                     3622..3627)
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="active site"
                     /db_xref="CDD:73150"
     misc_feature    order(3262..3279,3385..3387,3487..3489)
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="NTP binding site [chemical binding]; other site"
                     /db_xref="CDD:73150"
     misc_feature    3388..3390
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="nucleic acid binding site [nucleotide binding];
                     other site"
                     /db_xref="CDD:73150"
     misc_feature    3682..3855
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="Reverse transcriptase thumb domain; Region:
                     RVT_thumb; pfam06817"
                     /db_xref="CDD:115473"
     misc_feature    3913..4188
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="Reverse transcriptase connection domain; Region:
                     RVT_connect; pfam06815"
                     /db_xref="CDD:203523"
     misc_feature    4234..4602
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="RNase H; Region: RNase_H; pfam00075"
                     /db_xref="CDD:200979"
     misc_feature    order(4258..4269,4351..4356,4363..4365,4423..4425,
                     4534..4536,4588..4590)
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="RNA/DNA hybrid binding site [nucleotide binding];
                     other site"
                     /db_xref="CDD:187690"
     misc_feature    order(4258..4260,4423..4425)
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="active site"
                     /db_xref="CDD:187690"
     misc_feature    4633..4752
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="Integrase Zinc binding domain; Region:
                     Integrase_Zn; pfam02022"
                     /db_xref="CDD:202092"
     misc_feature    4786..5097
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="Integrase core domain; Region: rve; pfam00665"
                     /db_xref="CDD:201381"
     misc_feature    5269..5421
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="Integrase DNA binding domain; Region: IN_DBD_C;
                     pfam00552"
                     /db_xref="CDD:144223"
     CDS             1103..2668
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /codon_start=1
                     /product="gag polyprotein"
                     /protein_id="NP_056837.1"
                     /db_xref="GI:9628881"
                     /db_xref="GeneID:1490001"
                     /translation="MGARNSVLRGKKADELEKVRLRPGGKKKYRLKHIVWAANELDKF
                     GLAESLLESKEGCQKILRVLDPLVPTGSENLKSLFNTVCVIWCLHAEEKVKDTEEAKK
                     LAQRHLVAETGTAEKMPNTSRPTAPPSGKRGNYPVQQAGGNYVHVPLSPRTLNAWVKL
                     VEEKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIREIINEEAADWDSQH
                     PIPGPLPAGQLRDPRGSDIAGTTSTVDEQIQWMYRPQNPVPVGNIYRRWIQIGLQKCV
                     RKYNPTNILDIKQGPKEPFQSYVDRFYKSLRAEQTDPAVKNWMTQTLLIQNANPDCKL
                     VLKGLGMNPTLEEMLTACQGVGGPGQKARLMAEALKEAMGPSPIPFAAAQQRKAIRYW
                     NCGKEGHSARQCRAPRRQGCWKCGKPGHIMANCPERQAGFLGLGPRGKKPRNFPVTQA
                     PQGLIPTAPPADPAAELLERYMQQGRKQREQRERPYKEVTEDLLHLEQRETPHREETE
                     DLLHLNSLFGKDQ"
     misc_feature    1106..1507
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="gag gene protein p17 (matrix protein); Region:
                     Gag_p17; pfam00540"
                     /db_xref="CDD:109591"
     misc_feature    1553..2197
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="gag gene protein p24 (core nucleocapsid protein);
                     Region: Gag_p24; pfam00607"
                     /db_xref="CDD:201337"
     misc_feature    2276..2320
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="Zinc knuckle; Region: zf-CCHC; pfam00098"
                     /db_xref="CDD:189387"
     misc_feature    2330..2383
                     /gene="gag-pol"
                     /locus_tag="HIV2gp1"
                     /note="Zinc knuckle; Region: zf-CCHC; pfam00098"
                     /db_xref="CDD:189387"
     gene            5423..6070
                     /locus_tag="HIV2gp2"
                     /db_xref="GeneID:1724712"
     CDS             5423..6070
                     /locus_tag="HIV2gp2"
                     /codon_start=1
                     /product="vif protein"
                     /protein_id="NP_056839.1"
                     /db_xref="GI:9628883"
                     /db_xref="GeneID:1724712"
                     /translation="MEEDRNWIVVPTWRVPGRMEKWHALVKYLKYRTKDLEEVRYVPH
                     HKVGWAWWTCSRVIFPLQGKSHLEIQAYWNLTPEKGWLSSHAVRLTWYTEKFWTDVTP
                     DCADILIHSTYFSCFTAGEVRRAIRGEKLLSCCNYPQAHKAQVPSLQYLALVVVQQND
                     RPQRKGTARKQWRRDHWRGLRVAREDHRSLKQGGSEPSAPRAHFPGVAKVLEILA"
     misc_feature    5429..6007
                     /locus_tag="HIV2gp2"
                     /note="Retroviral Vif (Viral infectivity) protein; Region:
                     Vif; pfam00559"
                     /db_xref="CDD:109609"
     gene            5898..6239
                     /locus_tag="HIV2gp3"
                     /db_xref="GeneID:1724714"
     CDS             5898..6239
                     /locus_tag="HIV2gp3"
                     /codon_start=1
                     /product="vpx protein"
                     /protein_id="NP_056840.1"
                     /db_xref="GI:9628884"
                     /db_xref="GeneID:1724714"
                     /translation="MTDPRERVPPGNSGEETIGEAFEWLERTIEALNREAVNHLPREL
                     IFQVWQRSWRYWHDEQGMSASYTKYRYLCLMQKAIFTHFKRGCTCWGEDMGREGLEDQ
                     GPPPPPPPGLV"
     misc_feature    5910..6191
                     /locus_tag="HIV2gp3"
                     /note="VPR/VPX protein; Region: VPR; pfam00522"
                     /db_xref="CDD:109573"
     gene            6239..6502
                     /locus_tag="HIV2gp4"
                     /db_xref="GeneID:1724718"
     CDS             6239..6502
                     /locus_tag="HIV2gp4"
                     /codon_start=1
                     /product="vpr protein"
                     /protein_id="NP_056841.1"
                     /db_xref="GI:9628885"
                     /db_xref="GeneID:1724718"
                     /translation="MTEAPTEFPPEDGTPRRDLGSDWVIETLREIKEEALRHFDPRLL
                     IALGYYIHNRHGDTLEGARELIKTLQRALFVHFRAGCNRSRIG"
     misc_feature    6254..6499
                     /locus_tag="HIV2gp4"
                     /note="VPR/VPX protein; Region: VPR; pfam00522"
                     /db_xref="CDD:109573"
     gene            6402..8957
                     /locus_tag="HIV2gp5"
                     /db_xref="GeneID:1724713"
     CDS             join(6402..6697,8861..8957)
                     /locus_tag="HIV2gp5"
                     /codon_start=1
                     /product="tat protein"
                     /protein_id="NP_056842.1"
                     /db_xref="GI:9628886"
                     /db_xref="GeneID:1724713"
                     /translation="METPLKAPESSLKPYNEPSSCTSERDVTAQELAKQGEELLAQLH
                     RPLEPCTNKCYCKRCSFHCQLCFSKKGLGISYERKGRRRRTPRKTKTPSPSAPDKSIS
                     TRTGDSQPTKEQKKTSEATVVTTCGLGQ"
     misc_feature    6471..>6632
                     /locus_tag="HIV2gp5"
                     /note="Transactivating regulatory protein (Tat); Region:
                     Tat; pfam00539"
                     /db_xref="CDD:201292"
     exon            <6402..6697
                     /locus_tag="HIV2gp5"
                     /note="tat protein,  (first expressed exon)"
                     /number=2
     gene            6628..9102
                     /locus_tag="HIV2gp6"
                     /db_xref="GeneID:1724716"
     CDS             join(6628..6697,8861..9102)
                     /locus_tag="HIV2gp6"
                     /codon_start=1
                     /product="rev protein"
                     /protein_id="NP_056843.1"
                     /db_xref="GI:9628887"
                     /db_xref="GeneID:1724716"
                     /translation="MSERADEEGLQGKLRLLRLLHQTNPYPQGPGTASQRRNRRRRRR
                     RQWLRLVALANKLCAVPDPPTDSPLDRAIQHLQRLTIQELPDPPTDLPESNSNQGLAE
                     T"
     misc_feature    join(6631..6697,8861..9060)
                     /locus_tag="HIV2gp6"
                     /note="REV protein (anti-repression trans-activator
                     protein); Region: REV; pfam00424"
                     /db_xref="CDD:189539"
     exon            <6628..6697
                     /locus_tag="HIV2gp6"
                     /note="rev protein,  (first expressed exon)"
                     /number=2
     gene            6704..9286
                     /locus_tag="HIV2gp7"
                     /db_xref="GeneID:1724717"
     CDS             6704..9286
                     /locus_tag="HIV2gp7"
                     /codon_start=1
                     /product="env polyprotein"
                     /protein_id="NP_056844.1"
                     /db_xref="GI:9628888"
                     /db_xref="GeneID:1724717"
                     /translation="MEPGRNQLFVVILLTSACLVYCSQYVTVFYGIPAWKNASIPLFC
                     ATKNRDTWGTIQCLPDNDDYQEIILNVTEAFDAWNNTVTEQAVEDVWHLFETSIKPCV
                     KLTPLCVAMNCSRVQGNTTTPNPRTSSSTTSRPPTSAASIINETSNCIENNTCAGLGY
                     EEMMQCEFNMKGLEQDKKRRYKDTWYLEDVVCDNTTAGTCYMRHCNTSIIKESCDKHY
                     WDAMRFRYCAPPGFALLRCNDTNYSGFEPKCTKVVAASCTRMMETQTSTWFGFNGTRA
                     ENRTYIYWHGRDNRTIISLNKYYNLTMRCKRPGNKTVLPITLMSGLVFHSQPINTRPR
                     QAWCRFGGRWREAMQEVKQTLVQHPRYKGINDTGKINFTKPGAGSDPEVAFMWTNCRG
                     EFLYCNMTWFLNWVEDKNQTRRNYCHIKQIINTWHKVGKNVYLPPREGELACESTVTS
                     IIANIDIDKNRTHTNITFSAEVAELYRLELGDYKLIEITPIGFAPTDQRRYSSTPVRN
                     KRGVFVLGFLGFLATAGSAMGARSLTLSAQSRTLLAGIVQQQQQLLDVVKRQQEMLRL
                     TVWGTKNLQARVTAIEKYLKHQAQLNSWGCAFRQVCHTTVPWVNDSLSPDWKNMTWQE
                     WEKQVRYLEANISQSLEEAQIQQEKNMYELQKLNSWDILGNWFDLTSWVKYIQYGVHI
                     VVGIIALRIAIYVVQLLSRFRKGYRPVFSSPPGYLQQIHIHKDRGQPANEGTEEDVGG
                     DSGYDLWPWPINYVQFLIHLLTRLLIGLYNICRDLLSKNSPTRRLISQSLTAIRDWLR
                     LKAAQLQYGCEWIQEAFQAFARTTRETLAGAWGWLWEAARRIGRGILAVPRRIRQGAE
                     LALL"
     misc_feature    6773..8233
                     /locus_tag="HIV2gp7"
                     /note="Envelope glycoprotein GP120; Region: GP120;
                     pfam00516"
                     /db_xref="CDD:109567"
     misc_feature    8387..8680
                     /locus_tag="HIV2gp7"
                     /note="heptad repeat 1-heptad repeat 2 region (ectodomain)
                     of the gp41 subunit of human immunodeficiency virus
                     (HIV-1), and related domains; Region: HIV-1-like_HR1-HR2;
                     cd09909"
                     /db_xref="CDD:197369"
     misc_feature    order(8387..8395,8399..8416,8420..8428,8432..8437,
                     8441..8446,8453..8458,8462..8470,8474..8503,8513..8515,
                     8519..8521,8525..8527,8552..8557,8564..8569,8576..8578,
                     8585..8590,8597..8602,8606..8611,8618..8623,8627..8632,
                     8639..8644,8660..8665,8672..8674)
                     /locus_tag="HIV2gp7"
                     /note="homotrimer interface [polypeptide binding]; other
                     site"
                     /db_xref="CDD:197369"
     misc_feature    8387..8476
                     /locus_tag="HIV2gp7"
                     /note="HR1; other site"
                     /db_xref="CDD:197369"
     misc_feature    order(8552..8611,8615..8650,8654..8680)
                     /locus_tag="HIV2gp7"
                     /note="HR2; other site"
                     /db_xref="CDD:197369"
     exon            8861..>9102
                     /locus_tag="HIV2gp6"
                     /note="rev protein"
                     /number=3
     exon            8861..>8957
                     /locus_tag="HIV2gp6"
                     /note="tat protein,  (AA at 8862)"
                     /number=3
     gene            9120..9893
                     /locus_tag="HIV2gp8"
                     /db_xref="GeneID:1724715"
     CDS             9120..9893
                     /locus_tag="HIV2gp8"
                     /codon_start=1
                     /product="nef protein"
                     /protein_id="NP_056845.1"
                     /db_xref="GI:9628889"
                     /db_xref="GeneID:1724715"
                     /translation="MGASGSKKLSKHSRGLRERLLRARGDGYGKQRDASGGEYSQFQE
                     ESGREQNSPSCEGQQYQQGEYMNSPWRNPATERQKDLYRQQNMDDVDSDDDDLIGVPV
                     TPRVPRREMTYKLAIDMSHFIKEKGGLQGMFYSRRRHRILDIYLEKEEGIIPDWQNYT
                     HGPGVRYPMYFGWLWKLVSVELSQEAEEDEANCLVHPAQTSRHDDEHGETLVWQFDSM
                     LAYNYKAFTLYPEEFGHKSGLPEKEWKAKLKARGIPYSE"
     misc_feature    9123..9824
                     /locus_tag="HIV2gp8"
                     /note="Negative factor, (F-Protein) or Nef; Region:
                     F-protein; pfam00469"
                     /db_xref="CDD:109523"
     LTR             9505..10359
                     /note="3' LTR"
     polyA_signal    10211..10216
ORIGIN      
        1 tgcaagggat gttttacagt aggaggagac atagaatcct agacatatac ctagaaaaag
       61 aggaagggat aataccagat tggcagaatt atactcatgg gccaggagta aggtacccaa
      121 tgtacttcgg gtggctgtgg aagctagtat cagtagaact ctcacaagag gcagaggaag
      181 atgaggccaa ctgcttagta cacccagcac aaacaagcag acatgatgat gagcatgggg
      241 agacattagt gtggcagttt gactccatgc tggcctataa ctacaaggcc ttcactctgt
      301 acccagaaga gtttgggcac aagtcaggat tgccagagaa agaatggaag gcaaaactga
      361 aagcaagagg gataccatat agtgaataac aggaacaacc atacttggtc aaggcaggaa
      421 gtagctacta agaaacagct gaggctgcag ggactttcca gaaggggctg taaccaaggg
      481 agggacatgg gaggagctgg tggggaacgc cctcatactt actgtataaa tgtacccgct
      541 tcttgcattg tattcagtcg ctctgcggag aggctggcag atcgagccct gagaggttct
      601 ctccagcact agcaggtaga gcctgggtgt tccctgctgg actctcacca gtacttggcc
      661 ggtactgggc agacggctcc acgcttgctt gcttaaagac ctcttcaata aagctgccag
      721 ttagaagcaa gttaagtgtg tgttcccatc tctcctagtc gccgcctggt cattcggtgt
      781 tcatctgagt aacaagaccc tggtctgtta ggacccttct cgctttggga atccaaggca
      841 ggaaaatccc tagcaggttg gcgcccgaac agggacttga agaggactga gaagccctgg
      901 aactcggctg agtgaaggca gtaagggcgg caggaacaaa ccacgacgga gtgctcctag
      961 aaaggcgcgg gccgaggtac caaaggcggc gtgtggagcg ggagtgaaag aggcctccgg
     1021 gtgaaggtaa gtacctacac caaaaactgt agccagaaaa ggcttgttat cctaccttta
     1081 gacaggtaga agattgtggg agatgggcgc gagaaactcc gtcttgagag ggaaaaaagc
     1141 agacgaatta gaaaaagtta ggttacggcc cggcggaaag aaaaagtaca ggttaaaaca
     1201 tattgtgtgg gcagcgaatg aattggataa attcggattg gcagagagcc tgttggagtc
     1261 aaaagaaggt tgccaaaaga ttctcagagt tttagatcca ttagtaccaa cagggtcaga
     1321 aaatttaaaa agccttttta ataccgtctg cgtcatttgg tgcttgcacg cagaagagaa
     1381 agtgaaagat actgaggaag caaagaaact agcacagaga catctagtgg cagaaactgg
     1441 aactgcagag aaaatgccaa atacaagtag accaacagca ccacctagtg ggaaaagagg
     1501 aaactacccc gtgcaacaag cgggtggcaa ctatgtccat gtgccactga gcccccgaac
     1561 tctaaatgca tgggtaaaat tagtggagga aaagaagttc ggggcagaag tagtgccagg
     1621 atttcaggca ctctcagaag gctgcacgcc ctatgatatt aatcaaatgc ttaattgtgt
     1681 gggcgatcac caagcagcta tgcaaataat cagagagatt attaatgaag aagcagcaga
     1741 ctgggattcg cagcacccaa taccaggccc cttaccagca ggacagctca gagacccaag
     1801 agggtctgac atagcaggaa caacaagcac agtagatgaa cagatccagt ggatgtatag
     1861 gccacaaaat cccgtaccgg tagggaacat ctacagaaga tggatccaaa tagggctgca
     1921 aaagtgtgtc agaaagtaca acccaactaa catcttagac ataaaacagg gaccaaaaga
     1981 accgttccaa agctatgtag acaggttcta caaaagcttg agggcagaac aaacagaccc
     2041 agcagtaaaa aattggatga cccaaacgct gctaatacag aatgccaacc cagactgcaa
     2101 gttagtacta aaaggactgg ggatgaatcc caccctagaa gagatgctaa ccgcctgcca
     2161 gggggtaggc ggaccaggcc agaaagccag gctaatggct gaagccctaa aagaggctat
     2221 gggaccaagc cctatcccat ttgcagcagc ccaacaaaga aaggcaatta ggtattggaa
     2281 ctgtggaaag gagggacact cggcaagaca gtgccgagca cctagaagac agggctgctg
     2341 gaagtgtggc aagccaggac acatcatggc aaactgcccg gaaagacagg caggtttttt
     2401 agggttgggc ccacggggaa agaagcctcg caacttcccc gtgacccaag cccctcaggg
     2461 gctgatacca acagcacctc cggcagatcc agcagcggaa ctgttggaga gatatatgca
     2521 gcaagggaga aagcagaggg agcagaggga gagaccatac aaagaggtga cggaggactt
     2581 gctgcacctc gagcagagag agacacctca cagagaggag acagaggact tgctgcacct
     2641 caattctctc tttggaaaag accagtagtc acagcgtaca tcgaggatca gccggtagaa
     2701 gtcttactag acacaggggc tgatgactca atagtagcag gaatagaatt aggggacaat
     2761 tacactccaa aaatagtagg gggaataggg ggatttataa acaccaaaga atacaaaaat
     2821 gtagaaataa aagtactaaa taaaagagta agagccacca taatgacagg agatacccca
     2881 atcaacatct ttggcagaaa tattctgaca gccttaggca tgtcattaaa tttaccagtt
     2941 gccaagatag agccaataaa agtaacattg aagccaggga aagatggacc aaggctgaaa
     3001 caatggcccc taacaaaaga gaaaatagaa gcactaaaag agatctgtga aaaaatggaa
     3061 aaagagggcc agctagaaga ggcacctcca actaatcctt ataatacccc cacatttgca
     3121 attaagaaaa aggacaagaa caaatggagg atgctgatag attttagaga actaaataag
     3181 gtgactcaag atttcacaga aattcagcta ggaattccac acccggcagg actagccaaa
     3241 aagaaaagga tctctatatt agatgtaggg gatgcctatt tttccatacc actacatgaa
     3301 gattttaggc agtatactgc atttacccta ccagcagtaa acaatatgga accaggaaaa
     3361 agatatatat ataaagtctt gccacaagga tggaagggat caccagcaat ttttcaatac
     3421 acaatgaggc aagtcttaga acctttcaga aaagcaaacc cagatgtcat tctcatccag
     3481 tacatggatg atatcttaat agctagtgac aggacaggtt tagagcatga caaagtggtc
     3541 ctgcagctaa aagaacttct aaatggccta gggttttcta ctccagatga gaagttccaa
     3601 aaagaccctc catttcaatg gatgggctgt gaactatggc caactaaatg gaagctgcag
     3661 aaactacaac tgccccagaa agacatatgg acagtcaatg acatccaaaa gctagtggga
     3721 gtcttaaatt gggcggcaca aatctattca ggaataaaaa ccaaacactt atgtagacta
     3781 attagaggaa aaatgacact cacagaagaa gtgcagtgga cagaactagc agaagcagag
     3841 ctagaagaaa acaaaattat cttgagccag gaacaagaag gatattatta ccaagaagaa
     3901 aaagaattag aggcaacaat ccaaaaaagc caaggacatc aatggacata caaaatacac
     3961 caggaagaga aaatcctaaa agtaggaaag tatgcaaaga taaaaaatac ccataccaat
     4021 ggggtcagat tactagcaca ggtagttcag aaaataggaa aagaggcact agtcatttgg
     4081 ggacggatac caaaatttca cctgccagtg gagagagaga cctgggagca gtggtgggat
     4141 aactactggc aagtgacatg gatcccagag tgggactttg tatctacccc accactggtc
     4201 aggttaacat ttaacctagt aggagatcct ataccaggcg cagagacctt ctacacagat
     4261 ggatcatgca atagacagtc aaaagaggga aaagcaggat atgtaacaga tagaggaaaa
     4321 gacaaagtaa aagtattaga acaaactacc aatcagcagg cagaattaga agtctttcgg
     4381 atggcactgg cagactcagg cccaaaggtt aatatcatag tagattcaca gtatgtaatg
     4441 gggatagtag caggccagcc aacagagtca gaaaatagaa tagtgaacca gatcatagaa
     4501 gaaatgataa agaaggaagc agtctatgtt gcatgggtcc cagcccataa aggcatagga
     4561 ggaaaccagg aagtagacca tttagtaagt caaggcatca gacaagtatt attcctggaa
     4621 aagatagagc ccgctcaaga ggaacatgaa aaatatcata gcattataaa agaactaacc
     4681 cataaatttg gaatacccct tctagtagca agacagatag taaactcatg tgcccaatgc
     4741 caacagaaag gagaagccat acatgggcaa gtaaatgcag aaataggcgt ttggcaaatg
     4801 gactacacac acttagaagg aaaaatcatt atagtagcag tacatgttgc aagtggattc
     4861 atagaagcag aagtcatccc acaggaatca ggaaggcaga cagcactctt cctattaaaa
     4921 ctggccagta ggtggccaat aacgcacttg cacacagaca atggccccaa cttcacttca
     4981 caggaagtga agatggtggc atggtgggta ggtatagaac aatcctttgg agtaccttac
     5041 aacccacaaa gccagggagt agtagaagca atgaatcacc acctaaagaa tcagataagt
     5101 agaattagag aacaggcaaa tacaatagaa acaatagtac tgatggcagt tcattgcatg
     5161 aattttaaaa gaaggggagg aataggggat atgaccccag cagaaagact aatcaacatg
     5221 attaccacag aacaagaaat acaattcctc caaagaaaaa attcaaattt taaaaatttc
     5281 caggtctatt acagagaagg cagagatcag ctgtggaaag gacctggtga actactgtgg
     5341 aagggagaag gagcagtcat agtcaaggta gggacagaca taaaagtagt accaagaagg
     5401 aaggccaaga ttatcaggga ctatggagga agacaggaac tggatagtag tccccacctg
     5461 gagggtgcca gggaggatgg agaaatggca tgcccttgtc aagtacctga aatacagaac
     5521 aaaagaccta gaggaggtgc gctatgttcc ccaccacaag gtgggatggg catggtggac
     5581 ttgcagcagg gtaatattcc cactacaagg aaaaagtcat ctagaaatac aggcatattg
     5641 gaacctaaca ccagaaaaag gatggctctc ctctcatgca gtaagattaa cctggtatac
     5701 agaaaagttc tggacagatg ttaccccaga ctgtgcagac atcctaatac atagcactta
     5761 tttctcttgc tttacggcag gtgaagtaag aagagccatc agaggggaaa agttattgtc
     5821 ctgctgcaac tatccccaag ctcataaagc acaggtacca tcacttcaat acctagccct
     5881 agtagtagta caacaaaatg acagacccca gagaaagggt accgccagga aacagtggag
     5941 aagagaccat tggagaggcc ttcgagtggc tagagaggac catagaagcc ttaaacaggg
     6001 aggcagtgaa ccatctgccc cgagagctca ttttccaggt gtggcaaagg tcctggagat
     6061 attggcatga tgaacaaggg atgtcagcaa gctacacaaa gtatagatat ttgtgcctaa
     6121 tgcaaaaagc tatatttaca catttcaaga gagggtgcac ttgctggggg gaggacatgg
     6181 gccgggaagg attggaagac caaggacctc cccctcctcc ccctccaggt ctagtctaat
     6241 gactgaagca ccaacagagt ttcccccaga agatgggacc ccacggaggg acttagggag
     6301 tgactgggta atagaaactc tgagggaaat aaaggaagaa gccttaagac attttgatcc
     6361 ccgcttgcta attgctcttg gctactatat ccataataga catggagaca cccttgaagg
     6421 cgccagagag ctcattaaaa ccctacaacg agccctcttc gtgcacttca gagcgggatg
     6481 taaccgctca agaattggct aaacaaggag aagaactcct tgcccagctg caccgacccc
     6541 tagagccatg cactaacaaa tgctattgta agcgatgcag tttccattgc cagctgtgtt
     6601 tctcgaaaaa ggggctcgga atatcatatg agcgaaaggg cagacgaaga aggactccaa
     6661 ggaaaactaa gactccttcg ccttctgcac cagacaagtg agtatggagc ctggtaggaa
     6721 tcagctgttt gttgtcattt tactaacaag tgcttgctta gtatattgta gccagtatgt
     6781 gactgttttc tatggcatac ccgcgtggaa aaatgcatct attcccttat tttgtgcaac
     6841 taaaaataga gacacttggg ggaccataca gtgcttgcca gacaatgatg attatcagga
     6901 aataatttta aatgtgacag aggcttttga tgcatggaat aatacagtga cagaacaagc
     6961 agtagaagat gtctggcatc tatttgagac atcaataaaa ccatgtgtca agctaacacc
     7021 tctatgtgtg gcaatgaatt gtagcagggt tcaagggaat accacgaccc cgaatcccag
     7081 gacctcgagt tccacaacct cgagaccacc cacatccgca gcctccataa taaatgaaac
     7141 ttctaactgc atagaaaaca acacatgcgc aggattaggg tatgaggaga tgatgcaatg
     7201 tgagttcaat atgaaggggt tagaacaaga taagaaaagg aggtataagg acacatggta
     7261 tttagaagat gtggtttgtg acaacacaac agctggcaca tgttacatga gacattgcaa
     7321 cacatcaatc atcaaagagt catgtgataa gcactattgg gatgctatga ggtttagata
     7381 ctgtgcacca ccgggctttg ccctattaag atgtaatgat accaactatt caggctttga
     7441 acctaagtgc actaaagtag tagctgcttc atgcacaagg atgatggaaa cgcaaacttc
     7501 tacttggttt ggctttaatg gcactagagc agaaaataga acatatatct attggcatgg
     7561 cagagataat aggactatca ttagcttaaa caagtattat aatctcacaa tgcgttgtaa
     7621 gagaccagga aataagacag ttttaccaat aacacttatg tcaggattag tgtttcactc
     7681 tcagccaatc aacacaaggc ctaggcaggc atggtgccgg tttggaggca gatggaggga
     7741 agccatgcag gaggtgaagc aaacccttgt acaacatccc agatacaaag gaatcaatga
     7801 tacagggaaa attaacttta cgaaaccggg agcaggctca gacccggaag tggcatttat
     7861 gtggactaac tgcagaggag aatttctcta ctgtaacatg acttggttcc tcaattgggt
     7921 agaagacaag aaccaaacac ggcgcaacta ttgccatata aagcagataa ttaatacctg
     7981 gcataaagta gggaaaaatg tatatttgcc tcctagggaa ggggagttgg cctgtgaatc
     8041 aacagtaacc agcataattg ctaacattga catagataaa aatcggactc ataccaacat
     8101 tacctttagt gcagaagtgg cagaactgta ccgattagaa ctgggagact acaaattaat
     8161 agaaataaca ccaattggct tcgcacctac agatcagaga aggtactcct caactccagt
     8221 gaggaacaaa agaggtgtgt tcgtgctagg gttcttgggt tttctcgcga cagcaggttc
     8281 tgcaatgggc gcgcggtccc tgacgctgtc agcccagtcc cggactttac tggccgggat
     8341 agtgcagcaa cagcaacagc tgttggacgt agtcaagaga caacaagaaa tgttgcgact
     8401 gaccgtctgg ggaacgaaaa acctccaggc aagagtcact gctatcgaga agtacctaaa
     8461 gcatcaggca cagctaaatt catggggatg tgcgtttaga caggtctgcc acactactgt
     8521 accgtgggta aatgactctt tatcgcctga ctggaaaaat atgacatggc aggagtggga
     8581 gaaacaagtc cgctacctag aggcaaatat cagtcaaagt ttagaagaag cccaaattca
     8641 acaagaaaag aatatgtatg aattacaaaa attaaatagc tgggatattc ttggcaactg
     8701 gtttgactta acctcctggg tcaagtatat tcaatatgga gtgcatatag tagtgggaat
     8761 aatagcttta agaatagcaa tctatgtagt gcaattgtta agtagattta gaaagggcta
     8821 taggcctgtt ttctcttccc cccccggtta tctccaacag atccatatcc acaaggaccg
     8881 gggacagcca gccaacgaag gaacagaaga agacgtcgga ggcgacagtg gttacgactt
     8941 gtggccttgg ccaataaact atgtgcagtt cctgatccac ctactgactc gcctcttgat
     9001 cgggctatac aacatctgca gagacttact atccaagaac tccccgaccc gccgactgat
     9061 ctcccagagt ctaacagcaa tcagggactg gctgagactt aaggcggccc aactgcaata
     9121 tgggtgcgag tggatccaag aagctttcca agcattcgcg aggactacga gagagactct
     9181 tgcgggcgcg tggggatggt tatgggaagc agcgcgacgc atcgggaggg gaatactcgc
     9241 agttccaaga agaatcaggc agggagcaga actcgccctc ctgtgaggga cagcagtatc
     9301 agcagggaga gtacatgaac agcccatgga gaaacccagc aacagaaaga cagaaagatt
     9361 tgtataggca gcaaaatatg gatgatgtag attctgatga tgatgaccta ataggagttc
     9421 ctgttacacc aagagtacca cggagagaaa tgacctataa attggcaata gatatgtcac
     9481 attttataaa agaaaaaggg ggactgcaag ggatgtttta cagtaggagg agacatagaa
     9541 tcctagacat atacctagaa aaagaggaag ggataatacc agattggcag aattatactc
     9601 atgggccagg agtaaggtac ccaatgtact tcgggtggct gtggaagcta gtatcagtag
     9661 aactctcaca agaggcagag gaagatgagg ccaactgctt agtacaccca gcacaaacaa
     9721 gcagacatga tgatgagcat ggggagacat tagtgtggca gtttgactcc atgctggcct
     9781 ataactacaa ggccttcact ctgtacccag aagagtttgg gcacaagtca ggattgccag
     9841 agaaagaatg gaaggcaaaa ctgaaagcaa gagggatacc atatagtgaa taacaggaac
     9901 aaccatactt ggtcaaggca ggaagtagct actaagaaac agctgaggct gcagggactt
     9961 tccagaaggg gctgtaacca agggagggac atgggaggag ctggtgggga acgccctcat
    10021 acttactgta taaatgtacc cgcttcttgc attgtattca gtcgctctgc ggagaggctg
    10081 gcagatcgag ccctgagagg ttctctccag cactagcagg tagagcctgg gtgttccctg
    10141 ctggactctc accagtactt ggccggtact gggcagacgg ctccacgctt gcttgcttaa
    10201 agacctcttc aataaagctg ccagttagaa gcaagttaag tgtgtgttcc catctctcct
    10261 agtcgccgcc tggtcattcg gtgttcatct gagtaacaag accctggtct gttaggaccc
    10321 ttctcgcttt gggaatccaa ggcaggaaaa tccctagca
//
