LOCUS NC_001802 9181 bp ss-RNA linear VRL 13-AUG-2018
DEFINITION Human immunodeficiency virus 1, complete genome.
ACCESSION NC_001802
VERSION NC_001802.1
DBLINK BioProject: PRJNA485481
KEYWORDS RefSeq.
SOURCE Human immunodeficiency virus 1 (HIV-1)
ORGANISM Human immunodeficiency virus 1
Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes;
Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus.
REFERENCE 1 (bases 1 to 9181)
AUTHORS Martoglio,B., Graf,R. and Dobberstein,B.
TITLE Signal peptide fragments of preprolactin and HIV-1 p-gp160 interact
with calmodulin
JOURNAL EMBO J. 16 (22), 6636-6645 (1997)
PUBMED 9362478
REFERENCE 2 (bases 1 to 9181)
AUTHORS Petropoulos,C.J.
TITLE Appendix 2: Retroviral taxonomy, protein structure, sequences, and
genetic maps
JOURNAL (in) Coffin,J.M. (Ed.);
RETROVIRUSES: 757;
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York,
NY, USA (1997)
REFERENCE 3 (bases 1 to 9181)
CONSRTM NCBI Genome Project
TITLE Direct Submission
JOURNAL Submitted (07-AUG-2002) National Center for Biotechnology
Information, NIH, Bethesda, MD 20894, USA
REFERENCE 4 (bases 1 to 9181)
AUTHORS Chappey,C.
TITLE Direct Submission
JOURNAL Submitted (15-MAR-1999) NIH, NLM, Rockville Pike, Bethesda, MD
20894, USA
REMARK Sequence update by submitter
REFERENCE 5 (bases 1 to 9181)
AUTHORS Chappey,C.
TITLE Direct Submission
JOURNAL Submitted (12-NOV-1997) NIH, NLM, Rockville Pike, Bethesda, MD
20894, USA
COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The
reference sequence was derived from AF033819.
The annotation of this sequence was corrected and updated with the
kind help of Dr. Colombe Chappey (ViroLogic Inc., South San
Francisco, CA USA) and Roger Ptak (Southern Research Institute,
Frederick, MD USA).
COMPLETENESS: full length.
FEATURES Location/Qualifiers
source 1..9181
/organism="Human immunodeficiency virus 1"
/mol_type="genomic RNA"
/db_xref="taxon:11676"
/note="strain for reference annotation"
misc_feature 1..96
/note="repeat; positions of RNA transcription
initialization and polyadenylation; Region: R"
regulatory 73..78
/regulatory_class="polyA_signal_sequence"
/note="both 5' and 3' poly A signals are transcribed into
RNA, but the 5' one is suppressed"
5'UTR 97..181
primer_bind 182..199
gene 336..4642
/gene="gag-pol"
/locus_tag="HIV1gp1"
/db_xref="GeneID:155348"
CDS join(336..1637,1637..4642)
/gene="gag-pol"
/locus_tag="HIV1gp1"
/ribosomal_slippage
/note="fusion protein consisting of the viral structural
proteins and enzymes; cleaved by the viral protease into
individual mature proteins; The processing products of the
Gag and Gag-Pol polyproteins were annotated with the help
of Pettit et al., 2003 and references therein; Pr160"
/codon_start=1
/product="Gag-Pol"
/protein_id="NP_057849.4"
/db_xref="GeneID:155348"
/translation="MGARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERF
AVNPGLLETSEGCRQILGQLQPSLQTGSEELRSLYNTVATLYCVHQRIEIKDTKEALD
KIEEEQNKSKKKAQQAAADTGHSNQVSQNYPIVQNIQGQMVHQAISPRTLNAWVKVVE
EKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPV
HAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRM
YSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTIL
KALGPAATLEEMMTACQGVGGPGHKARVLAEAMSQVTNSATIMMQRGNFRNQRKIVKC
FNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQANFLREDLAFLQGKAREFSS
EQTRANSPTRRELQVWGRDNNSPSEAGADRQGTVSFNFPQVTLWQRPLVTIKIGGQLK
EALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVG
PTPVNIIGRNLLTQIGCTLNFPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEI
CTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIP
HPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGW
KGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLR
WGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQ
IYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIA
EIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGK
TPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVD
GAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQY
ALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKV
LFLDGIDKAQDEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCS
PGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTIHT
DNGSNFTGATVRAACWWAGIKQEFGIPYNPQSQGVVESMNKELKKIIGQVRDQAEHLK
TAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRVYYRDSR
NPLWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED"
misc_feature 339..731
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="gag gene protein p17 (matrix protein); Region:
Gag_p17; pfam00540"
/db_xref="CDD:249943"
misc_feature 780..1424
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="gag gene protein p24 (core nucleocapsid protein);
Region: Gag_p24; pfam00607"
/db_xref="CDD:279002"
misc_feature 1506..1553
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="zinc finger; Region: ZnF_C2HC; smart00343"
/db_xref="CDD:197667"
misc_feature 1569..1619
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="zinc finger; Region: ZnF_C2HC; smart00343"
/db_xref="CDD:197667"
mat_peptide join(1632..1637,1637..1798)
/gene="gag-pol"
/locus_tag="HIV1gp1"
/product="Gag-Pol Transframe peptide"
/experiment="DESCRIPTION:[PMID:15527852]"
/note="the Glu-Asp-Leu tripeptide (positions 4-6) is a
specific inhibitor of the HIV-1 protease. Involved in
regulation of the protease-mediated polyprotein
processing; alternative p6 protein; p6*"
/protein_id="NP_787043.1"
mat_peptide 1655..4639
/gene="gag-pol"
/locus_tag="HIV1gp1"
/product="Pol"
/note="unprocessed Pol polyprotein; includes part of the
transframe peptide, protease, reverse transcriptase and
integrase domains."
/protein_id="NP_789740.1"
mat_peptide 1799..2095
/gene="gag-pol"
/locus_tag="HIV1gp1"
/product="aspartic peptidase"
/experiment="DESCRIPTION:[PMID:2537531]"
/experiment="DESCRIPTION:[PMID:2548279]"
/experiment="DESCRIPTION:[PMID:3290901]"
/note="The proteinase domain of Gag-Pol (in the form of
homodimer) mediates all the cleavages in the polyprotein.
Cleaves itself from the polyprotein late in particle
assembly; protease"
/protein_id="NP_705926.1"
misc_feature 1817..2092
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="Retroviral aspartyl protease; Region: RVP;
pfam00077"
/db_xref="CDD:278505"
misc_feature order(1871..1873,1877..1879,1883..1885,1934..1942,
2048..2050)
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="inhibitor binding site; inhibition site"
/db_xref="CDD:133149"
misc_feature 1871..1879
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="catalytic motif [active]"
/db_xref="CDD:133149"
misc_feature 1871..1873
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="Catalytic residue [active]"
/db_xref="CDD:133149"
misc_feature order(1934..1948,1952..1966)
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="Active site flap [active]"
/db_xref="CDD:133149"
mat_peptide 2096..3775
/gene="gag-pol"
/locus_tag="HIV1gp1"
/product="p66 subunit"
/experiment="DESCRIPTION:[PMID:1374166]"
/experiment="EXISTENCE:[PMID:4316300]"
/note="transcribes single stranded viral RNA genome into
double stranded proviral DNA; HIV-1 reverse transcriptase
is composed of the p66 subunit (this protein) and the p51
subunit that lacks the RNAse H domain of the larger
subunit"
/protein_id="NP_705927.1"
mat_peptide 2096..3415
/gene="gag-pol"
/locus_tag="HIV1gp1"
/product="reverse transcriptase p51 subunit"
/note="HIV-1 reverse transcriptase is composed of the p66
subunit and the p51 subunit (this protein) that lacks the
RNAse H domain of the larger subunit"
/protein_id="NP_789739.1"
misc_feature 2147..2797
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="RT_Rtv: Reverse transcriptases (RTs) from
retroviruses (Rtvs). RTs catalyze the conversion of
single-stranded RNA into double-stranded viral DNA for
integration into host chromosomes. Proteins in this
subfamily contain long terminal repeats (LTRs) and...;
Region: RT_Rtv; cd01645"
/db_xref="CDD:238823"
misc_feature order(2165..2170,2276..2278,2288..2290,2309..2311,
2315..2323,2327..2329,2336..2338,2360..2362,2366..2371,
2375..2377,2423..2440,2546..2551,2555..2557,2564..2566,
2642..2644,2648..2653,2783..2788)
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="active site"
/db_xref="CDD:238823"
misc_feature order(2165..2170,2315..2323,2327..2329,2336..2338,
2360..2362,2366..2371,2375..2377,2549..2551,2555..2557,
2564..2566,2642..2644,2783..2788)
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="DNA binding site [nucleotide binding]"
/db_xref="CDD:238823"
misc_feature 2282..2797
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="Reverse transcriptase (RNA-dependent DNA
polymerase); Region: RVT_1; pfam00078"
/db_xref="CDD:278506"
misc_feature order(2288..2290,2309..2311,2423..2440,2546..2548,
2648..2650)
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="dNTP binding site [chemical binding]; other site"
/db_xref="CDD:238823"
misc_feature order(2393..2404,2630..2632,2636..2638,2657..2659,
2663..2665,2774..2776)
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="NNRTI binding site; other site"
/db_xref="CDD:238823"
misc_feature 2822..2983
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="Reverse transcriptase thumb domain; Region:
RVT_thumb; pfam06817"
/db_xref="CDD:284283"
misc_feature 3047..3352
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="Reverse transcriptase connection domain; Region:
RVT_connect; pfam06815"
/db_xref="CDD:284281"
misc_feature 3404..3766
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="RNase H; Region: RNase_H; pfam00075"
/db_xref="CDD:278503"
misc_feature order(3422..3433,3527..3529,3587..3589,3698..3700,
3752..3754)
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="RNA/DNA hybrid binding site [nucleotide binding];
other site"
/db_xref="CDD:259998"
misc_feature order(3422..3424,3587..3589)
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="active site"
/db_xref="CDD:259998"
mat_peptide 3776..4639
/gene="gag-pol"
/locus_tag="HIV1gp1"
/product="integrase"
/experiment="DESCRIPTION:[PMID:7983732]"
/experiment="DESCRIPTION:[PMID:8035478]"
/note="mediates integration of the viral DNA into the
infected cell chromosome"
/protein_id="NP_705928.1"
misc_feature 3797..3910
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="Integrase Zinc binding domain; Region:
Integrase_Zn; pfam02022"
/db_xref="CDD:280240"
misc_feature 3947..4252
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="Integrase core domain; Region: rve; pfam00665"
/db_xref="CDD:279057"
misc_feature 4436..4579
/gene="gag-pol"
/locus_tag="HIV1gp1"
/note="Integrase DNA binding domain; Region: IN_DBD_C;
pfam00552"
/db_xref="CDD:278951"
gene 336..1838
/gene="gag"
/locus_tag="HIV1gp2"
/db_xref="GeneID:155030"
CDS 336..1838
/gene="gag"
/locus_tag="HIV1gp2"
/note="The processing products of the Gag and Gag-Pol
polyproteins were annotated with the help of Pettit et
al., 2003 and references therein"
/codon_start=1
/product="Pr55(Gag)"
/protein_id="NP_057850.1"
/db_xref="GeneID:155030"
/translation="MGARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERF
AVNPGLLETSEGCRQILGQLQPSLQTGSEELRSLYNTVATLYCVHQRIEIKDTKEALD
KIEEEQNKSKKKAQQAAADTGHSNQVSQNYPIVQNIQGQMVHQAISPRTLNAWVKVVE
EKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPV
HAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRM
YSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTIL
KALGPAATLEEMMTACQGVGGPGHKARVLAEAMSQVTNSATIMMQRGNFRNQRKIVKC
FNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWPSYKGRPGNFLQ
SRPEPTAPPEESFRSGVETTTPPQKQEPIDKELYPLTSLRSLFGNDPSSQ"
mat_peptide 336..731
/gene="gag"
/locus_tag="HIV1gp2"
/product="matrix"
/experiment="DESCRIPTION:[PMID:12032547]"
/experiment="DESCRIPTION:[PMID:1710290]"
/experiment="DESCRIPTION:[PMID:8610175]"
/note="viral structural protein; forms the outer
structural shell of HIV-1 virions; involved in the nuclear
import of the HIV-1 preintegration complex; p17"
/protein_id="NP_579876.2"
misc_feature 339..731
/gene="gag"
/locus_tag="HIV1gp2"
/note="gag gene protein p17 (matrix protein); Region:
Gag_p17; pfam00540"
/db_xref="CDD:249943"
mat_peptide 732..1424
/gene="gag"
/locus_tag="HIV1gp2"
/product="capsid"
/experiment="DESCRIPTION:[PMID:15208690]"
/experiment="DESCRIPTION:[PMID:16041386]"
/experiment="DESCRIPTION:[PMID:21248851]"
/note="viral structural protein; forms the core of HIV-1
virions; p24"
/protein_id="NP_579880.1"
misc_feature 780..1424
/gene="gag"
/locus_tag="HIV1gp2"
/note="gag gene protein p24 (core nucleocapsid protein);
Region: Gag_p24; pfam00607"
/db_xref="CDD:279002"
misc_feature <1380..1622
/gene="gag"
/locus_tag="HIV1gp2"
/note="Arginine methyltransferase-interacting protein,
contains RING Zn-finger [Posttranslational modification,
protein turnover, chaperones / Intracellular trafficking
and secretion]; Region: AIR1; cl26705"
/db_xref="CDD:331526"
mat_peptide 1425..1466
/gene="gag"
/locus_tag="HIV1gp2"
/product="p2"
/note="Processing of Gag-Pol by the protease domain dimer
starts with cleavage between the p2 and nucleocapsid
proteins."
/protein_id="NP_579882.1"
mat_peptide 1467..1631
/gene="gag"
/locus_tag="HIV1gp2"
/product="nucleocapsid"
/experiment="DESCRIPTION:[PMID:1639074]"
/experiment="DESCRIPTION:[PMID:7666546]"
/note="viral structural protein; coats the genomic RNA
inside the virion core; binds and delivers full-length
viral RNAs into assembling HIV-1 virions; p7"
/protein_id="NP_579881.1"
mat_peptide 1632..1679
/gene="gag"
/locus_tag="HIV1gp2"
/product="p1"
/note="important for virus infectivity, protein
processing, and genomic RNA dimer stability"
/protein_id="NP_787042.1"
mat_peptide 1680..1835
/gene="gag"
/locus_tag="HIV1gp2"
/product="p6"
/experiment="DESCRIPTION:[PMID:10085158]"
/experiment="DESCRIPTION:[PMID:15527852]"
/note="important for incorporation of Vpr into assembling
HIV-1 virions; helps mediate efficient virus particle
release from infected cells"
/protein_id="NP_579883.1"
misc_feature 1680..1793
/gene="gag"
/locus_tag="HIV1gp2"
/note="Gag protein p6; Region: Gag_p6; pfam08705"
/db_xref="CDD:312289"
gene 4587..5165
/gene="vif"
/locus_tag="HIV1gp3"
/db_xref="GeneID:155459"
CDS 4587..5165
/gene="vif"
/locus_tag="HIV1gp3"
/note="p23; viral infectivity factor; viral accessory
protein important for virus replication in vivo"
/codon_start=1
/product="Vif"
/protein_id="NP_057851.1"
/db_xref="GeneID:155459"
/translation="MENRWQVMIVWQVDRMRIRTWKSLVKHHMYVSGKARGWFYRHHY
ESPHPRISSEVHIPLGDARLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPEL
ADQLIHLYYFDCFSDSAIRKALLGHIVSPRCEYQAGHNKVGSLQYLALAALITPKKIK
PPLPSVTKLTEDRWNKPQKTKGHRGSHTMNGH"
misc_feature 4587..5162
/gene="vif"
/locus_tag="HIV1gp3"
/note="Retroviral Vif (Viral infectivity) protein; Region:
Vif; pfam00559"
/db_xref="CDD:278957"
gene 5105..5396
/gene="vpr"
/locus_tag="HIV1gp4"
/db_xref="GeneID:155807"
CDS join(5105..5319,5321..5396)
/gene="vpr"
/locus_tag="HIV1gp4"
/exception="artificial frameshift"
/note="p15; viral protein R; viral accessory protein
important for virus replication in vivo; involved in the
nuclear import of the HIV-1 preintegration complex;
induces G2 cell cycle arrest; influences mutation rates
during viral DNA synthesis; An artificial frameshift
eliminating the orf-disrupting nucleotide at position 5320
is introduced to obtain the typical HIV-1 Vpr protein
sequence. For this particular HIV-1 strain, HXB2, only a
short (78 amino acid long) variant of the Vpr sequence can
be obtained by translation of nucleotides 5105 through
5341 without the frameshift"
/codon_start=1
/product="Vpr"
/protein_id="NP_057852.2"
/db_xref="GeneID:155807"
/translation="MEQAPEDQGPQREPHNEWTLELLEELKNEAVRHFPRIWLHGLGQ
HIYETYGDTWAGVEAIIRILQQLLFIHFRIGCRHSRIGVTRQRRARNGASRS"
misc_feature join(5105..5319,5321..5351)
/gene="vpr"
/locus_tag="HIV1gp4"
/note="VPR/VPX protein; Region: VPR; pfam00522"
/db_xref="CDD:278923"
gene 5377..7970
/gene="tat"
/locus_tag="HIV1gp5"
/db_xref="GeneID:155871"
CDS join(5377..5591,7925..7970)
/gene="tat"
/locus_tag="HIV1gp5"
/note="p14; transcriptional activator; viral regulatory
protein required for virus replication; transactivates the
viral LTR promoter through interactions with cellular
transcription factors; associated with pathogenic effects
of the virus; the length of Tat varies depending on virus
strain or clade"
/codon_start=1
/product="Tat"
/protein_id="NP_057853.1"
/db_xref="GeneID:155871"
/translation="MEPVDPRLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKALG
ISYGRKKRRQRRRAHQNSQTHQASLSKQPTSQPRGDPTGPKE"
misc_feature 5383..5568
/gene="tat"
/locus_tag="HIV1gp5"
/note="Transactivating regulatory protein (Tat); Region:
Tat; pfam00539"
/db_xref="CDD:278940"
gene 5516..8199
/gene="rev"
/locus_tag="HIV1gp6"
/db_xref="GeneID:155908"
CDS join(5516..5591,7925..8199)
/gene="rev"
/locus_tag="HIV1gp6"
/note="p19; regulator of expression of virion proteins;
prevents splicing of viral RNA; shuttles unspliced viral
RNA to the cytoplasm for expression of viral proteins and
incorporation of full length viral genomic RNA into
virions"
/codon_start=1
/product="Rev"
/protein_id="NP_057854.1"
/db_xref="GeneID:155908"
/translation="MAGRSGDSDEELIRTVRLIKLLYQSNPPPNPEGTRQARRNRRRR
WRERQRQIHSISERILGTYLGRSAEPVPLQLPPLERLTLDCNEDCGTSGTQGVGSPQI
LVESPTVLESGTKE"
misc_feature join(5519..5591,7925..8121)
/gene="rev"
/locus_tag="HIV1gp6"
/note="REV protein (anti-repression trans-activator
protein); Region: REV; pfam00424"
/db_xref="CDD:278833"
gene 5608..5856
/gene="vpu"
/locus_tag="HIV1gp7"
/db_xref="GeneID:155945"
CDS 5608..5856
/gene="vpu"
/locus_tag="HIV1gp7"
/note="p16; viral protein U; viral accessory protein
important for virus replication in vivo; promotes
degradation of CD4 and down-regulates cell surface
expression of MHC class I proteins; helps mediate
efficient virus particle release from infected cells;
reported to induce apoptosis by suppressing the nuclear
factor kappaB-dependent expression of antiapoptotic
factors; may attenuate the level of Env precursor(gp160)
biosynthesis; Vpu and gp160 are translated from different
reading frames of the same bicistronic mRNA"
/codon_start=1
/product="Vpu"
/protein_id="NP_057855.1"
/db_xref="GeneID:155945"
/translation="MQPIPIVAIVALVVAIIIAIVVWSIVIIEYRKILRQRKIDRLID
RLIERAEDSGNESEGEISALVEMGVEMGHHAPWDVDDL"
misc_feature <5674..5844
/gene="vpu"
/locus_tag="HIV1gp7"
/note="Vpu protein; Region: Vpu; pfam00558"
/db_xref="CDD:109608"
gene 5771..8341
/gene="env"
/locus_tag="HIV1gp8"
/db_xref="GeneID:155971"
CDS 5771..8341
/gene="env"
/locus_tag="HIV1gp8"
/note="gp160; envelope glycoprotein; envelope polyprotein;
cleaved by cellular proteases into mature proteins gp120
and gp41"
/codon_start=1
/product="Envelope surface glycoprotein gp160, precursor"
/protein_id="NP_057856.1"
/db_xref="GeneID:155971"
/translation="MRVKEKYQHLWRWGWRWGTMLLGMLMICSATEKLWVTVYYGVPV
WKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLVNVTENFNMWKNDMVE
QMHEDIISLWDQSLKPCVKLTPLCVSLKCTDLKNDTNTNSSSGRMIMEKGEIKNCSFN
ISTSIRGKVQKEYAFFYKLDIIPIDNDTTSYKLTSCNTSVITQACPKVSFEPIPIHYC
APAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSVN
FTDNAKTIIVQLNTSVEINCTRPNNNTRKRIRIQRGPGRAFVTIGKIGNMRQAHCNIS
RAKWNNTLKQIASKLREQFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCNSTQLFN
STWFNSTWSTEGSNNTEGSDTITLPCRIKQIINMWQKVGKAMYAPPISGQIRCSSNIT
GLLLTRDGGNSNNESEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQR
EKRAVGIGALFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQNNLLRAIEAQQHLL
QLTVWGIKQLQARILAVERYLKDQQLLGIWGCSGKLICTTAVPWNASWSNKSLEQIWN
HTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWFNITNWLWYI
KLFIMIVGGLVGLRIVFAVLSIVNRVRQGYSPLSFQTHLPTPRGPDRPEGIEEEGGER
DRDRSIRLVNGSLALIWDDLRSLCLFSYHRLRDLLLIVTRIVELLGRRGWEALKYWWN
LLQYWSQELKNSAVSLLNATAIAVAEGTDRVIEVVQGACRAIRHIPRRIRQGLERILL
"
sig_peptide 5771..5854
/gene="env"
/locus_tag="HIV1gp8"
/product="hypothetical protein"
/protein_id="NP_579893.2"
mat_peptide 5855..7303
/gene="env"
/locus_tag="HIV1gp8"
/product="Envelope surface glycoprotein gp120"
/experiment="DESCRIPTION:[PMID:24179160]"
/note="mediates binding of HIV-1 to CD4 and cellular
co-receptors; cooperates with gp41 to mediate fusion of
viral membrane with cellular membrane during virus entry
into cells; Envelope surface unit; SU"
/protein_id="NP_579894.2"
misc_feature 5870..7303
/gene="env"
/locus_tag="HIV1gp8"
/note="Envelope glycoprotein GP120; Region: GP120;
pfam00516"
/db_xref="CDD:278917"
mat_peptide 7304..8338
/gene="env"
/locus_tag="HIV1gp8"
/product="Envelope transmembrane domain"
/note="cooperates with gp120 to mediate fusion of viral
membrane with cellular membrane during virus entry into
cells; Envelope transmembrane glycoprotein gp41; TM"
/protein_id="NP_579895.1"
misc_feature 7358..7948
/gene="env"
/locus_tag="HIV1gp8"
/note="Retroviral envelope protein; Region: GP41;
pfam00517"
/db_xref="CDD:306906"
misc_feature order(7385..7444,7451..7549)
/gene="env"
/locus_tag="HIV1gp8"
/note="HR1; other site"
/db_xref="CDD:197369"
misc_feature order(7391..7393,7397..7405,7409..7426,7430..7444,
7451..7468,7472..7489,7493..7501,7505..7510,7514..7519,
7526..7531,7535..7543,7547..7576,7586..7588,7592..7594,
7598..7609,7637..7642,7649..7654,7661..7663,7670..7675,
7682..7687,7691..7696,7703..7708,7712..7717,7724..7729,
7745..7750,7757..7759)
/gene="env"
/locus_tag="HIV1gp8"
/note="homotrimer interface [polypeptide binding]; other
site"
/db_xref="CDD:197369"
misc_feature order(7637..7696,7700..7735,7739..7765)
/gene="env"
/locus_tag="HIV1gp8"
/note="HR2; other site"
/db_xref="CDD:197369"
gene complement(6919..7488)
/gene="asp"
/locus_tag="HIV1gp10"
/db_xref="GeneID:19424028"
CDS complement(6919..7488)
/gene="asp"
/locus_tag="HIV1gp10"
/note="minus-strand-encoded antisense protein of unknown
function; region is highly conserved and likely analogous
to the HTLV-1 encoded, HBZ, a nuclear basic region leucine
zipper (b-ZIP) protein"
/codon_start=1
/product="Asp"
/protein_id="YP_009028572.1"
/db_xref="GeneID:19424028"
/translation="MPQTVSCNRCCCASIALSKLFCCCTIPDNNCLACTVSVIEAAPI
VLPAAPKNPRNKAPIPTALFSLCTTLLFALVGATPNGSIFTTLYLYNSLLQLSLISPP
PGLKISDSLLLLPPSLVNSSPVIFDEHLICPLMGGAYIAFPTFCHMFIICFILHGRVI
VSLPSVLFDPSVLQVLLNQVLLNSCVELQ"
gene 8343..8963
/gene="nef"
/locus_tag="HIV1gp9"
/db_xref="GeneID:156110"
CDS 8343..8963
/gene="nef"
/locus_tag="HIV1gp9"
/note="p27; negative factor; viral accessory protein;
important for virus replication in vivo; determinant of
HIV-1 pathogenesis; down-regulates cell surface CD4 and
MHC class I molecules; enhances virus infectivity through;
interactions with multiple cellular signaling proteins;
This particular nucleotide sequence has a premature stop
codon in place of a well-conserved tryptophan codon at
position 8712-8714 that truncates the HIV1 Nef protein
sequence to a 123 amino acids-long N-terminal portion (not
shown)"
/codon_start=1
/transl_except=(pos:8712..8714,aa:Trp)
/product="Nef"
/protein_id="NP_057857.2"
/db_xref="GeneID:156110"
/translation="MGGKWSKSSVIGWPTVRERMRRAEPAADRVGAASRDLEKHGAIT
SSNTAATNAACAWLEAQEEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIH
SQRRQDILDLWIYHTQGYFPDWQNYTPGPGVRYPLTFGWCYKLVPVEPDKIEEANKGE
NTSLLHPVSLHGMDDPEREVLEWRFDSRLAFHHVARELHPEYFKNC"
misc_feature 8346..8957
/gene="nef"
/locus_tag="HIV1gp9"
/note="Negative factor, (F-Protein) or Nef; Region:
F-protein; pfam00469"
/db_xref="CDD:249884"
3'UTR 8631..9085
misc_feature 9086..9181
/note="repeat; positions of RNA transcription
initialization and polyadenylation; Region: R"
regulatory 9158..9163
/regulatory_class="polyA_signal_sequence"
/note="both 5' and 3' poly A signals are transcribed into
RNA, but the 5' one is suppressed"
ORIGIN
1 ggtctctctg gttagaccag atctgagcct gggagctctc tggctaacta gggaacccac
61 tgcttaagcc tcaataaagc ttgccttgag tgcttcaagt agtgtgtgcc cgtctgttgt
121 gtgactctgg taactagaga tccctcagac ccttttagtc agtgtggaaa atctctagca
181 gtggcgcccg aacagggacc tgaaagcgaa agggaaacca gaggagctct ctcgacgcag
241 gactcggctt gctgaagcgc gcacggcaag aggcgagggg cggcgactgg tgagtacgcc
301 aaaaattttg actagcggag gctagaagga gagagatggg tgcgagagcg tcagtattaa
361 gcgggggaga attagatcga tgggaaaaaa ttcggttaag gccaggggga aagaaaaaat
421 ataaattaaa acatatagta tgggcaagca gggagctaga acgattcgca gttaatcctg
481 gcctgttaga aacatcagaa ggctgtagac aaatactggg acagctacaa ccatcccttc
541 agacaggatc agaagaactt agatcattat ataatacagt agcaaccctc tattgtgtgc
601 atcaaaggat agagataaaa gacaccaagg aagctttaga caagatagag gaagagcaaa
661 acaaaagtaa gaaaaaagca cagcaagcag cagctgacac aggacacagc aatcaggtca
721 gccaaaatta ccctatagtg cagaacatcc aggggcaaat ggtacatcag gccatatcac
781 ctagaacttt aaatgcatgg gtaaaagtag tagaagagaa ggctttcagc ccagaagtga
841 tacccatgtt ttcagcatta tcagaaggag ccaccccaca agatttaaac accatgctaa
901 acacagtggg gggacatcaa gcagccatgc aaatgttaaa agagaccatc aatgaggaag
961 ctgcagaatg ggatagagtg catccagtgc atgcagggcc tattgcacca ggccagatga
1021 gagaaccaag gggaagtgac atagcaggaa ctactagtac ccttcaggaa caaataggat
1081 ggatgacaaa taatccacct atcccagtag gagaaattta taaaagatgg ataatcctgg
1141 gattaaataa aatagtaaga atgtatagcc ctaccagcat tctggacata agacaaggac
1201 caaaggaacc ctttagagac tatgtagacc ggttctataa aactctaaga gccgagcaag
1261 cttcacagga ggtaaaaaat tggatgacag aaaccttgtt ggtccaaaat gcgaacccag
1321 attgtaagac tattttaaaa gcattgggac cagcggctac actagaagaa atgatgacag
1381 catgtcaggg agtaggagga cccggccata aggcaagagt tttggctgaa gcaatgagcc
1441 aagtaacaaa ttcagctacc ataatgatgc agagaggcaa ttttaggaac caaagaaaga
1501 ttgttaagtg tttcaattgt ggcaaagaag ggcacacagc cagaaattgc agggccccta
1561 ggaaaaaggg ctgttggaaa tgtggaaagg aaggacacca aatgaaagat tgtactgaga
1621 gacaggctaa ttttttaggg aagatctggc cttcctacaa gggaaggcca gggaattttc
1681 ttcagagcag accagagcca acagccccac cagaagagag cttcaggtct ggggtagaga
1741 caacaactcc ccctcagaag caggagccga tagacaagga actgtatcct ttaacttccc
1801 tcaggtcact ctttggcaac gacccctcgt cacaataaag ataggggggc aactaaagga
1861 agctctatta gatacaggag cagatgatac agtattagaa gaaatgagtt tgccaggaag
1921 atggaaacca aaaatgatag ggggaattgg aggttttatc aaagtaagac agtatgatca
1981 gatactcata gaaatctgtg gacataaagc tataggtaca gtattagtag gacctacacc
2041 tgtcaacata attggaagaa atctgttgac tcagattggt tgcactttaa attttcccat
2101 tagccctatt gagactgtac cagtaaaatt aaagccagga atggatggcc caaaagttaa
2161 acaatggcca ttgacagaag aaaaaataaa agcattagta gaaatttgta cagagatgga
2221 aaaggaaggg aaaatttcaa aaattgggcc tgaaaatcca tacaatactc cagtatttgc
2281 cataaagaaa aaagacagta ctaaatggag aaaattagta gatttcagag aacttaataa
2341 gagaactcaa gacttctggg aagttcaatt aggaatacca catcccgcag ggttaaaaaa
2401 gaaaaaatca gtaacagtac tggatgtggg tgatgcatat ttttcagttc ccttagatga
2461 agacttcagg aagtatactg catttaccat acctagtata aacaatgaga caccagggat
2521 tagatatcag tacaatgtgc ttccacaggg atggaaagga tcaccagcaa tattccaaag
2581 tagcatgaca aaaatcttag agccttttag aaaacaaaat ccagacatag ttatctatca
2641 atacatggat gatttgtatg taggatctga cttagaaata gggcagcata gaacaaaaat
2701 agaggagctg agacaacatc tgttgaggtg gggacttacc acaccagaca aaaaacatca
2761 gaaagaacct ccattccttt ggatgggtta tgaactccat cctgataaat ggacagtaca
2821 gcctatagtg ctgccagaaa aagacagctg gactgtcaat gacatacaga agttagtggg
2881 gaaattgaat tgggcaagtc agatttaccc agggattaaa gtaaggcaat tatgtaaact
2941 ccttagagga accaaagcac taacagaagt aataccacta acagaagaag cagagctaga
3001 actggcagaa aacagagaga ttctaaaaga accagtacat ggagtgtatt atgacccatc
3061 aaaagactta atagcagaaa tacagaagca ggggcaaggc caatggacat atcaaattta
3121 tcaagagcca tttaaaaatc tgaaaacagg aaaatatgca agaatgaggg gtgcccacac
3181 taatgatgta aaacaattaa cagaggcagt gcaaaaaata accacagaaa gcatagtaat
3241 atggggaaag actcctaaat ttaaactgcc catacaaaag gaaacatggg aaacatggtg
3301 gacagagtat tggcaagcca cctggattcc tgagtgggag tttgttaata cccctccctt
3361 agtgaaatta tggtaccagt tagagaaaga acccatagta ggagcagaaa ccttctatgt
3421 agatggggca gctaacaggg agactaaatt aggaaaagca ggatatgtta ctaatagagg
3481 aagacaaaaa gttgtcaccc taactgacac aacaaatcag aagactgagt tacaagcaat
3541 ttatctagct ttgcaggatt cgggattaga agtaaacata gtaacagact cacaatatgc
3601 attaggaatc attcaagcac aaccagatca aagtgaatca gagttagtca atcaaataat
3661 agagcagtta ataaaaaagg aaaaggtcta tctggcatgg gtaccagcac acaaaggaat
3721 tggaggaaat gaacaagtag ataaattagt cagtgctgga atcaggaaag tactattttt
3781 agatggaata gataaggccc aagatgaaca tgagaaatat cacagtaatt ggagagcaat
3841 ggctagtgat tttaacctgc cacctgtagt agcaaaagaa atagtagcca gctgtgataa
3901 atgtcagcta aaaggagaag ccatgcatgg acaagtagac tgtagtccag gaatatggca
3961 actagattgt acacatttag aaggaaaagt tatcctggta gcagttcatg tagccagtgg
4021 atatatagaa gcagaagtta ttccagcaga aacagggcag gaaacagcat attttctttt
4081 aaaattagca ggaagatggc cagtaaaaac aatacatact gacaatggca gcaatttcac
4141 cggtgctacg gttagggccg cctgttggtg ggcgggaatc aagcaggaat ttggaattcc
4201 ctacaatccc caaagtcaag gagtagtaga atctatgaat aaagaattaa agaaaattat
4261 aggacaggta agagatcagg ctgaacatct taagacagca gtacaaatgg cagtattcat
4321 ccacaatttt aaaagaaaag gggggattgg ggggtacagt gcaggggaaa gaatagtaga
4381 cataatagca acagacatac aaactaaaga attacaaaaa caaattacaa aaattcaaaa
4441 ttttcgggtt tattacaggg acagcagaaa tccactttgg aaaggaccag caaagctcct
4501 ctggaaaggt gaaggggcag tagtaataca agataatagt gacataaaag tagtgccaag
4561 aagaaaagca aagatcatta gggattatgg aaaacagatg gcaggtgatg attgtgtggc
4621 aagtagacag gatgaggatt agaacatgga aaagtttagt aaaacaccat atgtatgttt
4681 cagggaaagc taggggatgg ttttatagac atcactatga aagccctcat ccaagaataa
4741 gttcagaagt acacatccca ctaggggatg ctagattggt aataacaaca tattggggtc
4801 tgcatacagg agaaagagac tggcatttgg gtcagggagt ctccatagaa tggaggaaaa
4861 agagatatag cacacaagta gaccctgaac tagcagacca actaattcat ctgtattact
4921 ttgactgttt ttcagactct gctataagaa aggccttatt aggacacata gttagcccta
4981 ggtgtgaata tcaagcagga cataacaagg taggatctct acaatacttg gcactagcag
5041 cattaataac accaaaaaag ataaagccac ctttgcctag tgttacgaaa ctgacagagg
5101 atagatggaa caagccccag aagaccaagg gccacagagg gagccacaca atgaatggac
5161 actagagctt ttagaggagc ttaagaatga agctgttaga cattttccta ggatttggct
5221 ccatggctta gggcaacata tctatgaaac ttatggggat acttgggcag gagtggaagc
5281 cataataaga attctgcaac aactgctgtt tatccatttt cagaattggg tgtcgacata
5341 gcagaatagg cgttactcga cagaggagag caagaaatgg agccagtaga tcctagacta
5401 gagccctgga agcatccagg aagtcagcct aaaactgctt gtaccaattg ctattgtaaa
5461 aagtgttgct ttcattgcca agtttgtttc ataacaaaag ccttaggcat ctcctatggc
5521 aggaagaagc ggagacagcg acgaagagct catcagaaca gtcagactca tcaagcttct
5581 ctatcaaagc agtaagtagt acatgtaatg caacctatac caatagtagc aatagtagca
5641 ttagtagtag caataataat agcaatagtt gtgtggtcca tagtaatcat agaatatagg
5701 aaaatattaa gacaaagaaa aatagacagg ttaattgata gactaataga aagagcagaa
5761 gacagtggca atgagagtga aggagaaata tcagcacttg tggagatggg ggtggagatg
5821 gggcaccatg ctccttggga tgttgatgat ctgtagtgct acagaaaaat tgtgggtcac
5881 agtctattat ggggtacctg tgtggaagga agcaaccacc actctatttt gtgcatcaga
5941 tgctaaagca tatgatacag aggtacataa tgtttgggcc acacatgcct gtgtacccac
6001 agaccccaac ccacaagaag tagtattggt aaatgtgaca gaaaatttta acatgtggaa
6061 aaatgacatg gtagaacaga tgcatgagga tataatcagt ttatgggatc aaagcctaaa
6121 gccatgtgta aaattaaccc cactctgtgt tagtttaaag tgcactgatt tgaagaatga
6181 tactaatacc aatagtagta gcgggagaat gataatggag aaaggagaga taaaaaactg
6241 ctctttcaat atcagcacaa gcataagagg taaggtgcag aaagaatatg cattttttta
6301 taaacttgat ataataccaa tagataatga tactaccagc tataagttga caagttgtaa
6361 cacctcagtc attacacagg cctgtccaaa ggtatccttt gagccaattc ccatacatta
6421 ttgtgccccg gctggttttg cgattctaaa atgtaataat aagacgttca atggaacagg
6481 accatgtaca aatgtcagca cagtacaatg tacacatgga attaggccag tagtatcaac
6541 tcaactgctg ttaaatggca gtctagcaga agaagaggta gtaattagat ctgtcaattt
6601 cacggacaat gctaaaacca taatagtaca gctgaacaca tctgtagaaa ttaattgtac
6661 aagacccaac aacaatacaa gaaaaagaat ccgtatccag agaggaccag ggagagcatt
6721 tgttacaata ggaaaaatag gaaatatgag acaagcacat tgtaacatta gtagagcaaa
6781 atggaataac actttaaaac agatagctag caaattaaga gaacaatttg gaaataataa
6841 aacaataatc tttaagcaat cctcaggagg ggacccagaa attgtaacgc acagttttaa
6901 ttgtggaggg gaatttttct actgtaattc aacacaactg tttaatagta cttggtttaa
6961 tagtacttgg agtactgaag ggtcaaataa cactgaagga agtgacacaa tcaccctccc
7021 atgcagaata aaacaaatta taaacatgtg gcagaaagta ggaaaagcaa tgtatgcccc
7081 tcccatcagt ggacaaatta gatgttcatc aaatattaca gggctgctat taacaagaga
7141 tggtggtaat agcaacaatg agtccgagat cttcagacct ggaggaggag atatgaggga
7201 caattggaga agtgaattat ataaatataa agtagtaaaa attgaaccat taggagtagc
7261 acccaccaag gcaaagagaa gagtggtgca gagagaaaaa agagcagtgg gaataggagc
7321 tttgttcctt gggttcttgg gagcagcagg aagcactatg ggcgcagcct caatgacgct
7381 gacggtacag gccagacaat tattgtctgg tatagtgcag cagcagaaca atttgctgag
7441 ggctattgag gcgcaacagc atctgttgca actcacagtc tggggcatca agcagctcca
7501 ggcaagaatc ctggctgtgg aaagatacct aaaggatcaa cagctcctgg ggatttgggg
7561 ttgctctgga aaactcattt gcaccactgc tgtgccttgg aatgctagtt ggagtaataa
7621 atctctggaa cagatttgga atcacacgac ctggatggag tgggacagag aaattaacaa
7681 ttacacaagc ttaatacact ccttaattga agaatcgcaa aaccagcaag aaaagaatga
7741 acaagaatta ttggaattag ataaatgggc aagtttgtgg aattggttta acataacaaa
7801 ttggctgtgg tatataaaat tattcataat gatagtagga ggcttggtag gtttaagaat
7861 agtttttgct gtactttcta tagtgaatag agttaggcag ggatattcac cattatcgtt
7921 tcagacccac ctcccaaccc cgaggggacc cgacaggccc gaaggaatag aagaagaagg
7981 tggagagaga gacagagaca gatccattcg attagtgaac ggatccttgg cacttatctg
8041 ggacgatctg cggagcctgt gcctcttcag ctaccaccgc ttgagagact tactcttgat
8101 tgtaacgagg attgtggaac ttctgggacg cagggggtgg gaagccctca aatattggtg
8161 gaatctccta cagtattgga gtcaggaact aaagaatagt gctgttagct tgctcaatgc
8221 cacagccata gcagtagctg aggggacaga tagggttata gaagtagtac aaggagcttg
8281 tagagctatt cgccacatac ctagaagaat aagacagggc ttggaaagga ttttgctata
8341 agatgggtgg caagtggtca aaaagtagtg tgattggatg gcctactgta agggaaagaa
8401 tgagacgagc tgagccagca gcagataggg tgggagcagc atctcgagac ctggaaaaac
8461 atggagcaat cacaagtagc aatacagcag ctaccaatgc tgcttgtgcc tggctagaag
8521 cacaagagga ggaggaggtg ggttttccag tcacacctca ggtaccttta agaccaatga
8581 cttacaaggc agctgtagat cttagccact ttttaaaaga aaagggggga ctggaagggc
8641 taattcactc ccaaagaaga caagatatcc ttgatctgtg gatctaccac acacaaggct
8701 acttccctga ttagcagaac tacacaccag ggccaggggt cagatatcca ctgacctttg
8761 gatggtgcta caagctagta ccagttgagc cagataagat agaagaggcc aataaaggag
8821 agaacaccag cttgttacac cctgtgagcc tgcatgggat ggatgacccg gagagagaag
8881 tgttagagtg gaggtttgac agccgcctag catttcatca cgtggcccga gagctgcatc
8941 cggagtactt caagaactgc tgacatcgag cttgctacaa gggactttcc gctggggact
9001 ttccagggag gcgtggcctg ggcgggactg gggagtggcg agccctcaga tcctgcatat
9061 aagcagctgc tttttgcctg tactgggtct ctctggttag accagatctg agcctgggag
9121 ctctctggct aactagggaa cccactgctt aagcctcaat aaagcttgcc ttgagtgctt
9181 c
//
