Human immunodeficiency virus 1, complete genome.
type: Entry
definition: Human immunodeficiency virus 1, complete genome.
sequence version: NC_001802.1
sequence date: 2018-08-13
sequence: sequence
division: VRL
label: NC_001802.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA485481
keyword: RefSeq
source: Human immunodeficiency virus 1 (HIV-1)
organism: Human immunodeficiency virus 1
taxonomy: Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae; Lentivirus; Primate lentivirus group.
reference: 1
references: 9362478
reference: 2
reference: 3
reference: 4
reference: 5
comment: REVIEWED REFSEQ: This record has been curated by NCBI staff. The\nreference sequence was derived from AF033819.\nThe annotation of this sequence was corrected and updated with the\nkind help of Dr. Colombe Chappey (ViroLogic Inc., South San\nFrancisco, CA USA) and Roger Ptak (Southern Research Institute,\nFrederick, MD USA).\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000353
sequence length: 9181
topology: linear
so has quality: SO_0000987
location: 1..9181
location: region:1-9181:1
RO_0002162: 11676

NC_001802
type: RefSeq
SIO_000068: refseq

PRJNA485481
type: BioProject
SIO_000068: bioproject

1
title: Signal peptide fragments of preprolactin and HIV-1 p-gp160 interact with calmodulin
author: Martoglio, B.
author: Graf, R.
author: Dobberstein, B.
journal: EMBO J.
volume: 16
issue: 22
pages: 6636-6645
year: 1997
pubmed: 9362478

9362478
type: PubMed
SIO_000068: pubmed

2
title: Appendix 2: Retroviral taxonomy, protein structure, sequences, and genetic maps
author: Petropoulos, C.J.
journal: (in) Coffin,J.M. (Ed.); RETROVIRUSES: 757; Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, NY, USA (1997)

3
title: Direct Submission
journal: Submitted (07-AUG-2002) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA

4
title: Direct Submission
author: Chappey, C.
journal: Submitted (15-MAR-1999) NIH, NLM, Rockville Pike, Bethesda, MD 20894, USA
comments: Sequence update by submitter

5
title: Direct Submission
author: Chappey, C.
journal: Submitted (12-NOV-1997) NIH, NLM, Rockville Pike, Bethesda, MD 20894, USA

position:1:1
position: 1
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:9181:1
position: 9181
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-9181:1:source
so part of: sequence
organism: Human immunodeficiency virus 1
mol type: genomic RNA
note: strain for reference annotation

11676
type: Taxonomy
SIO_000068: taxonomy

misc_feature
type: Miscellaneous Feature
subclass of: SO_0000001
RO_0002162: 11676
note: repeat; positions of RNA transcription initialization and polyadenylation; Region: R
so part of: sequence
location: 1..96
location: region:1-96:1
so has part: feature:1-96:1:region

position:96:1
position: 96
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-96:1:region

regulatory
type: Feature
subclass of: SO_0000001
RO_0002162: 11676
regulatory class: polyA_signal_sequence
note: both 5' and 3' poly A signals are transcribed into RNA, but the 5' one is suppressed
so part of: sequence
location: 73..78
location: region:73-78:1
so has part: feature:73-78:1:region

position:73:1
position: 73
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:78:1
position: 78
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:73-78:1:region

5'UTR
type: Five Prime UTR
subclass of: SO_0000204
RO_0002162: 11676
so part of: sequence
location: 97..181
location: region:97-181:1
so has part: feature:97-181:1:region

position:97:1
position: 97
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:181:1
position: 181
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:97-181:1:region

primer_bind
type: Primer Binding Site
subclass of: SO_0005850
RO_0002162: 11676
so part of: sequence
location: 182..199
location: region:182-199:1
so has part: feature:182-199:1:region

position:182:1
position: 182
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:199:1
position: 199
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:182-199:1:region

HIV1gp1
type: Gene
subclass of: SO_0000704
RO_0002162: 11676
gene: gag-pol
locus tag: HIV1gp1
so part of: sequence
location: 336..4642
location: region:336-4642:1
so has part: feature:336-4642:1:exon
subclass of: SO_0000010

155348
type: Gene
SIO_000068: ncbigene

position:336:1
position: 336
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4642:1
position: 4642
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:336-4642:1:exon

HIV1gp1
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 11676
gene: gag-pol
locus tag: HIV1gp1
ribosomal slippage: true
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
translation: MGARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQPSLQTGSEELRSLYNTVATLYCVHQRIEIKDTKEALDKIEEEQNKSKKKAQQAAADTGHSNQVSQNYPIVQNIQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVLAEAMSQVTNSATIMMQRGNFRNQRKIVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQANFLREDLAFLQGKAREFSSEQTRANSPTRRELQVWGRDNNSPSEAGADRQGTVSFNFPQVTLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNFPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVLFLDGIDKAQDEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTIHTDNGSNFTGATVRAACWWAGIKQEFGIPYNPQSQGVVESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRVYYRDSRNPLWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED
SIO_010081: HIV1gp1
subclass of: SO_0000673
so part of: HIV1gp1
location: join(336..1637,1637..4642)
location: region:336-4642:1
so has part: feature:336-1637:1:exon
so has part: feature:1637-4642:1:exon

NP_057849.4
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:336-1637:1:exon

position:1637:1
position: 1637
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1637-4642:1:exon

HIV1gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11676
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*
SIO_010081: HIV1gp1
subclass of: SO_0000673
so part of: HIV1gp1
location: join(1632..1637,1637..1798)
location: region:1632-1798:1
so has part: feature:1632-1637:1:exon
so has part: feature:1637-1798:1:exon

NP_787043.1
type: Protein
SIO_000068: ncbiprotein

position:1632:1
position: 1632
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1798:1
position: 1798
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1632-1637:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1637-1798:1:exon

HIV1gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11676
gene: gag-pol
locus tag: HIV1gp1
product: Pol
note: unprocessed Pol polyprotein; includes part of the transframe peptide, protease, reverse transcriptase and integrase domains.
SIO_010081: HIV1gp1
subclass of: SO_0000673
so part of: HIV1gp1
location: 1655..4639
location: region:1655-4639:1
so has part: feature:1655-4639:1:exon

NP_789740.1
type: Protein
SIO_000068: ncbiprotein

position:1655:1
position: 1655
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4639:1
position: 4639
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1655-4639:1:exon

HIV1gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11676
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
SIO_010081: HIV1gp1
subclass of: SO_0000673
so part of: HIV1gp1
location: 1799..2095
location: region:1799-2095:1
so has part: feature:1799-2095:1:exon

NP_705926.1
type: Protein
SIO_000068: ncbiprotein

position:1799:1
position: 1799
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2095:1
position: 2095
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1799-2095:1:exon

HIV1gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11676
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
SIO_010081: HIV1gp1
subclass of: SO_0000673
so part of: HIV1gp1
location: 2096..3775
location: region:2096-3775:1
so has part: feature:2096-3775:1:exon

NP_705927.1
type: Protein
SIO_000068: ncbiprotein

position:2096:1
position: 2096
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3775:1
position: 3775
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2096-3775:1:exon

HIV1gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11676
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
SIO_010081: HIV1gp1
subclass of: SO_0000673
so part of: HIV1gp1
location: 2096..3415
location: region:2096-3415:1
so has part: feature:2096-3415:1:exon

NP_789739.1
type: Protein
SIO_000068: ncbiprotein

position:3415:1
position: 3415
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2096-3415:1:exon

HIV1gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11676
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
SIO_010081: HIV1gp1
subclass of: SO_0000673
so part of: HIV1gp1
location: 3776..4639
location: region:3776-4639:1
so has part: feature:3776-4639:1:exon

NP_705928.1
type: Protein
SIO_000068: ncbiprotein

position:3776:1
position: 3776
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3776-4639:1:exon

HIV1gp2
type: Gene
subclass of: SO_0000704
RO_0002162: 11676
gene: gag
locus tag: HIV1gp2
so part of: sequence
location: 336..1838
location: region:336-1838:1
so has part: feature:336-1838:1:exon
subclass of: SO_0000010

155030
type: Gene
SIO_000068: ncbigene

position:1838:1
position: 1838
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:336-1838:1:exon

HIV1gp2
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 11676
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)
translation: MGARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQPSLQTGSEELRSLYNTVATLYCVHQRIEIKDTKEALDKIEEEQNKSKKKAQQAAADTGHSNQVSQNYPIVQNIQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVLAEAMSQVTNSATIMMQRGNFRNQRKIVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWPSYKGRPGNFLQSRPEPTAPPEESFRSGVETTTPPQKQEPIDKELYPLTSLRSLFGNDPSSQ
SIO_010081: HIV1gp2
subclass of: SO_0000673
so part of: HIV1gp2
location: 336..1838
location: region:336-1838:1
so has part: feature:336-1838:1:exon

NP_057850.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:336-1838:1:exon

HIV1gp2
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11676
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
SIO_010081: HIV1gp2
subclass of: SO_0000673
so part of: HIV1gp2
location: 336..731
location: region:336-731:1
so has part: feature:336-731:1:exon

NP_579876.2
type: Protein
SIO_000068: ncbiprotein

position:731:1
position: 731
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:336-731:1:exon

HIV1gp2
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11676
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
SIO_010081: HIV1gp2
subclass of: SO_0000673
so part of: HIV1gp2
location: 732..1424
location: region:732-1424:1
so has part: feature:732-1424:1:exon

NP_579880.1
type: Protein
SIO_000068: ncbiprotein

position:732:1
position: 732
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1424:1
position: 1424
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:732-1424:1:exon

HIV1gp2
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11676
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.
SIO_010081: HIV1gp2
subclass of: SO_0000673
so part of: HIV1gp2
location: 1425..1466
location: region:1425-1466:1
so has part: feature:1425-1466:1:exon

NP_579882.1
type: Protein
SIO_000068: ncbiprotein

position:1425:1
position: 1425
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1466:1
position: 1466
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1425-1466:1:exon

HIV1gp2
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11676
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
SIO_010081: HIV1gp2
subclass of: SO_0000673
so part of: HIV1gp2
location: 1467..1631
location: region:1467-1631:1
so has part: feature:1467-1631:1:exon

NP_579881.1
type: Protein
SIO_000068: ncbiprotein

position:1467:1
position: 1467
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1631:1
position: 1631
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1467-1631:1:exon

HIV1gp2
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11676
gene: gag
locus tag: HIV1gp2
product: p1
note: important for virus infectivity, protein processing, and genomic RNA dimer stability
SIO_010081: HIV1gp2
subclass of: SO_0000673
so part of: HIV1gp2
location: 1632..1679
location: region:1632-1679:1
so has part: feature:1632-1679:1:exon

NP_787042.1
type: Protein
SIO_000068: ncbiprotein

position:1679:1
position: 1679
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1632-1679:1:exon

HIV1gp2
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11676
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
SIO_010081: HIV1gp2
subclass of: SO_0000673
so part of: HIV1gp2
location: 1680..1835
location: region:1680-1835:1
so has part: feature:1680-1835:1:exon

NP_579883.1
type: Protein
SIO_000068: ncbiprotein

position:1680:1
position: 1680
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1835:1
position: 1835
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1680-1835:1:exon

HIV1gp3
type: Gene
subclass of: SO_0000704
RO_0002162: 11676
gene: vif
locus tag: HIV1gp3
so part of: sequence
location: 4587..5165
location: region:4587-5165:1
so has part: feature:4587-5165:1:exon
subclass of: SO_0000010

155459
type: Gene
SIO_000068: ncbigene

position:4587:1
position: 4587
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5165:1
position: 5165
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4587-5165:1:exon

HIV1gp3
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 11676
gene: vif
locus tag: HIV1gp3
note: p23; viral infectivity factor; viral accessory protein important for virus replication in vivo
codon start: 1
product: Vif
translation: MENRWQVMIVWQVDRMRIRTWKSLVKHHMYVSGKARGWFYRHHYESPHPRISSEVHIPLGDARLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPELADQLIHLYYFDCFSDSAIRKALLGHIVSPRCEYQAGHNKVGSLQYLALAALITPKKIKPPLPSVTKLTEDRWNKPQKTKGHRGSHTMNGH
SIO_010081: HIV1gp3
subclass of: SO_0000673
so part of: HIV1gp3
location: 4587..5165
location: region:4587-5165:1
so has part: feature:4587-5165:1:exon

NP_057851.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4587-5165:1:exon

HIV1gp4
type: Gene
subclass of: SO_0000704
RO_0002162: 11676
gene: vpr
locus tag: HIV1gp4
so part of: sequence
location: 5105..5396
location: region:5105-5396:1
so has part: feature:5105-5396:1:exon
subclass of: SO_0000010

155807
type: Gene
SIO_000068: ncbigene

position:5105:1
position: 5105
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5396:1
position: 5396
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5105-5396:1:exon

HIV1gp4
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 11676
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
translation: MEQAPEDQGPQREPHNEWTLELLEELKNEAVRHFPRIWLHGLGQHIYETYGDTWAGVEAIIRILQQLLFIHFRIGCRHSRIGVTRQRRARNGASRS
SIO_010081: HIV1gp4
subclass of: SO_0000673
so part of: HIV1gp4
location: join(5105..5319,5321..5396)
location: region:5105-5396:1
so has part: feature:5105-5319:1:exon
so has part: feature:5321-5396:1:exon

NP_057852.2
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5105-5319:1:exon

position:5319:1
position: 5319
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:5321-5396:1:exon

position:5321:1
position: 5321
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

HIV1gp5
type: Gene
subclass of: SO_0000704
RO_0002162: 11676
gene: tat
locus tag: HIV1gp5
so part of: sequence
location: 5377..7970
location: region:5377-7970:1
so has part: feature:5377-7970:1:exon
subclass of: SO_0000010

155871
type: Gene
SIO_000068: ncbigene

position:5377:1
position: 5377
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7970:1
position: 7970
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5377-7970:1:exon

HIV1gp5
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 11676
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
translation: MEPVDPRLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKALGISYGRKKRRQRRRAHQNSQTHQASLSKQPTSQPRGDPTGPKE
SIO_010081: HIV1gp5
subclass of: SO_0000673
so part of: HIV1gp5
location: join(5377..5591,7925..7970)
location: region:5377-7970:1
so has part: feature:5377-5591:1:exon
so has part: feature:7925-7970:1:exon

NP_057853.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5377-5591:1:exon

position:5591:1
position: 5591
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:7925-7970:1:exon

position:7925:1
position: 7925
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

HIV1gp6
type: Gene
subclass of: SO_0000704
RO_0002162: 11676
gene: rev
locus tag: HIV1gp6
so part of: sequence
location: 5516..8199
location: region:5516-8199:1
so has part: feature:5516-8199:1:exon
subclass of: SO_0000010

155908
type: Gene
SIO_000068: ncbigene

position:5516:1
position: 5516
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8199:1
position: 8199
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5516-8199:1:exon

HIV1gp6
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 11676
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
translation: MAGRSGDSDEELIRTVRLIKLLYQSNPPPNPEGTRQARRNRRRRWRERQRQIHSISERILGTYLGRSAEPVPLQLPPLERLTLDCNEDCGTSGTQGVGSPQILVESPTVLESGTKE
SIO_010081: HIV1gp6
subclass of: SO_0000673
so part of: HIV1gp6
location: join(5516..5591,7925..8199)
location: region:5516-8199:1
so has part: feature:5516-5591:1:exon
so has part: feature:7925-8199:1:exon

NP_057854.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5516-5591:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:7925-8199:1:exon

HIV1gp7
type: Gene
subclass of: SO_0000704
RO_0002162: 11676
gene: vpu
locus tag: HIV1gp7
so part of: sequence
location: 5608..5856
location: region:5608-5856:1
so has part: feature:5608-5856:1:exon
subclass of: SO_0000010

155945
type: Gene
SIO_000068: ncbigene

position:5608:1
position: 5608
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5856:1
position: 5856
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5608-5856:1:exon

HIV1gp7
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 11676
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
translation: MQPIPIVAIVALVVAIIIAIVVWSIVIIEYRKILRQRKIDRLIDRLIERAEDSGNESEGEISALVEMGVEMGHHAPWDVDDL
SIO_010081: HIV1gp7
subclass of: SO_0000673
so part of: HIV1gp7
location: 5608..5856
location: region:5608-5856:1
so has part: feature:5608-5856:1:exon

NP_057855.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5608-5856:1:exon

HIV1gp8
type: Gene
subclass of: SO_0000704
RO_0002162: 11676
gene: env
locus tag: HIV1gp8
so part of: sequence
location: 5771..8341
location: region:5771-8341:1
so has part: feature:5771-8341:1:exon
subclass of: SO_0000010

155971
type: Gene
SIO_000068: ncbigene

position:5771:1
position: 5771
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8341:1
position: 8341
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5771-8341:1:exon

HIV1gp8
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 11676
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
translation: MRVKEKYQHLWRWGWRWGTMLLGMLMICSATEKLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLVNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVSLKCTDLKNDTNTNSSSGRMIMEKGEIKNCSFNISTSIRGKVQKEYAFFYKLDIIPIDNDTTSYKLTSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSVNFTDNAKTIIVQLNTSVEINCTRPNNNTRKRIRIQRGPGRAFVTIGKIGNMRQAHCNISRAKWNNTLKQIASKLREQFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCNSTQLFNSTWFNSTWSTEGSNNTEGSDTITLPCRIKQIINMWQKVGKAMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQREKRAVGIGALFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKDQQLLGIWGCSGKLICTTAVPWNASWSNKSLEQIWNHTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWFNITNWLWYIKLFIMIVGGLVGLRIVFAVLSIVNRVRQGYSPLSFQTHLPTPRGPDRPEGIEEEGGERDRDRSIRLVNGSLALIWDDLRSLCLFSYHRLRDLLLIVTRIVELLGRRGWEALKYWWNLLQYWSQELKNSAVSLLNATAIAVAEGTDRVIEVVQGACRAIRHIPRRIRQGLERILL
SIO_010081: HIV1gp8
subclass of: SO_0000673
so part of: HIV1gp8
location: 5771..8341
location: region:5771-8341:1
so has part: feature:5771-8341:1:exon

NP_057856.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5771-8341:1:exon

HIV1gp8
type: Signal Peptide
subclass of: SO_0000418
RO_0002162: 11676
gene: env
locus tag: HIV1gp8
product: hypothetical protein
SIO_010081: HIV1gp8
subclass of: SO_0000673
so part of: HIV1gp8
location: 5771..5854
location: region:5771-5854:1
so has part: feature:5771-5854:1:exon

NP_579893.2
type: Protein
SIO_000068: ncbiprotein

position:5854:1
position: 5854
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5771-5854:1:exon

HIV1gp8
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11676
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
SIO_010081: HIV1gp8
subclass of: SO_0000673
so part of: HIV1gp8
location: 5855..7303
location: region:5855-7303:1
so has part: feature:5855-7303:1:exon

NP_579894.2
type: Protein
SIO_000068: ncbiprotein

position:5855:1
position: 5855
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7303:1
position: 7303
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5855-7303:1:exon

HIV1gp8
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11676
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
SIO_010081: HIV1gp8
subclass of: SO_0000673
so part of: HIV1gp8
location: 7304..8338
location: region:7304-8338:1
so has part: feature:7304-8338:1:exon

NP_579895.1
type: Protein
SIO_000068: ncbiprotein

position:7304:1
position: 7304
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8338:1
position: 8338
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7304-8338:1:exon

HIV1gp10
type: Gene
subclass of: SO_0000704
RO_0002162: 11676
gene: asp
locus tag: HIV1gp10
so part of: sequence
location: complement(6919..7488)
location: region:6919-7488:-1
so has part: feature:6919-7488:-1:exon
subclass of: SO_0000010

19424028
type: Gene
SIO_000068: ncbigene

position:6919:-1
position: 6919
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:7488:-1
position: 7488
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6919-7488:-1:exon

HIV1gp10
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 11676
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
translation: MPQTVSCNRCCCASIALSKLFCCCTIPDNNCLACTVSVIEAAPIVLPAAPKNPRNKAPIPTALFSLCTTLLFALVGATPNGSIFTTLYLYNSLLQLSLISPPPGLKISDSLLLLPPSLVNSSPVIFDEHLICPLMGGAYIAFPTFCHMFIICFILHGRVIVSLPSVLFDPSVLQVLLNQVLLNSCVELQ
SIO_010081: HIV1gp10
subclass of: SO_0000673
so part of: HIV1gp10
location: complement(6919..7488)
location: region:6919-7488:-1
so has part: feature:6919-7488:-1:exon

YP_009028572.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6919-7488:-1:exon

HIV1gp9
type: Gene
subclass of: SO_0000704
RO_0002162: 11676
gene: nef
locus tag: HIV1gp9
so part of: sequence
location: 8343..8963
location: region:8343-8963:1
so has part: feature:8343-8963:1:exon
subclass of: SO_0000010

156110
type: Gene
SIO_000068: ncbigene

position:8343:1
position: 8343
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8963:1
position: 8963
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:8343-8963:1:exon

HIV1gp9
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 11676
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
translation: MGGKWSKSSVIGWPTVRERMRRAEPAADRVGAASRDLEKHGAITSSNTAATNAACAWLEAQEEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPDWQNYTPGPGVRYPLTFGWCYKLVPVEPDKIEEANKGENTSLLHPVSLHGMDDPEREVLEWRFDSRLAFHHVARELHPEYFKNC
SIO_010081: HIV1gp9
subclass of: SO_0000673
so part of: HIV1gp9
location: 8343..8963
location: region:8343-8963:1
so has part: feature:8343-8963:1:exon

NP_057857.2
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:8343-8963:1:exon

3'UTR
type: Three Prime UTR
subclass of: SO_0000205
RO_0002162: 11676
so part of: sequence
location: 8631..9085
location: region:8631-9085:1
so has part: feature:8631-9085:1:region

position:8631:1
position: 8631
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:9085:1
position: 9085
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:8631-9085:1:region

misc_feature
type: Miscellaneous Feature
subclass of: SO_0000001
RO_0002162: 11676
note: repeat; positions of RNA transcription initialization and polyadenylation; Region: R
so part of: sequence
location: 9086..9181
location: region:9086-9181:1
so has part: feature:9086-9181:1:region

position:9086:1
position: 9086
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:9086-9181:1:region

regulatory
type: Feature
subclass of: SO_0000001
RO_0002162: 11676
regulatory class: polyA_signal_sequence
note: both 5' and 3' poly A signals are transcribed into RNA, but the 5' one is suppressed
so part of: sequence
location: 9158..9163
location: region:9158-9163:1
so has part: feature:9158-9163:1:region

position:9158:1
position: 9158
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:9163:1
position: 9163
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:9158-9163:1:region