Simian immunodeficiency virus, complete genome.
type: Entry
definition: Simian immunodeficiency virus, complete genome.
sequence version: NC_001549.1
sequence date: 2018-08-13
sequence: sequence
division: VRL
label: NC_001549.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA485481
keyword: RefSeq
source: Simian immunodeficiency virus (SIV)
organism: Simian immunodeficiency virus
taxonomy: Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae; Lentivirus; Primate lentivirus group.
reference: 1
references: 2024476
reference: 2
comment: REVIEWED REFSEQ: This record has been curated by NCBI staff. The\nreference sequence was derived from M58410.\nOn Feb 10, 2013 this sequence version replaced NC_001870.1.\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000353
sequence length: 9623
topology: linear
so has quality: SO_0000987
location: 1..9623
location: region:1-9623:1
RO_0002162: 11723

NC_001549
type: RefSeq
SIO_000068: refseq

PRJNA485481
type: BioProject
SIO_000068: bioproject

1
title: A highly divergent proviral DNA clone of SIV from a distinct species of African green monkey
author: Fomsgaard, A.
author: Hirsch, V.M.
author: Allan, J.S.
author: Johnson, P.R.
journal: Virology
volume: 182
issue: 1
pages: 397-402
year: 1991
pubmed: 2024476

2024476
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
journal: Submitted (09-SEP-2004) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA

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

position:9623:1
position: 9623
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-9623:1:source
so part of: sequence
organism: Simian immunodeficiency virus
mol type: genomic RNA
isolate: 677
host: Cercopithecus aethiops (African green monkey)
clone: gri-1

11723
type: Taxonomy
SIO_000068: taxonomy

repeat_region
type: Repeat Region
subclass of: SO_0000657
RO_0002162: 11723
note: 5' LTR
rpt type: long_terminal_repeat
so part of: sequence
location: 1..688
location: region:1-688:1
so has part: feature:1-688:1:region

position:688:1
position: 688
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-688:1:region

repeat_region
type: Repeat Region
subclass of: SO_0000657
RO_0002162: 11723
note: R repeat 5' copy
so part of: sequence
location: 461..588
location: region:461-588:1
so has part: feature:461-588:1:region

position:461:1
position: 461
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:588:1
position: 588
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:461-588:1:region

SIVgp1
type: Gene
subclass of: SO_0000704
RO_0002162: 11723
gene: gag-pol
locus tag: SIVgp1
so part of: sequence
location: 897..5314
location: region:897-5314:1
so has part: feature:897-5314:1:exon
subclass of: SO_0000010

1490009
type: Gene
SIO_000068: ncbigene

position:897:1
position: 897
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5314:1
position: 5314
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:897-5314:1:exon

SIVgp1
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 11723
gene: gag-pol
locus tag: SIVgp1
ribosomal slippage: true
codon start: 1
product: Gag-Pol
translation: MGGGHSALSGRSLDTFEKIRLRPNGKKKYQIKHLIWAGKEMERFGLHEKLLETKEGCQKIIEVLTPLEPTGSEGLKALFNLCCVIWCIHAEQKVKDTEEAVVTVKQHYHLVDKNEKAAKKKNETTAPPGGESRNYPVVNQNNAWVHQPLSPRTLNAWVKCVEEKRWGAEVVPMFQALSEGCLSYDVNQMLNVIGDHQGALQILKEVINEEAAEWDRTHRPPAGPLPAGQLRDPTGSDIAGTTSSIQEQIEWTFNANPRIDVGAQYRKWVILGLQKVVQMYNPQKVLDIRQGPKEPFQDYVDRFYKALRAEQAPQDVKNWMTQTLLIQNANPDCKLILKGLGMNPTLEEMLIACQGVGGPQHKAKLMVEMMSNGQNMVQVGPQKKGPRGPLKCFNCGKFGHMQRECKAPRQIKCFKCGKIGHMAKDCKNGQANFFRVWPLGRSETKKFCAIQRRHSWSGTNSPPNGNSLRSSKEAPPAVCREGTAPERGERTDKETEGERSGGCFLELPLWRRPMKRVIIEGTPVQALLDTGADDTIIQEKDLHFPPHKPWRSKVVGGIGGGIHVKEYQGVQVQLEDKIITGSILIGSTPINIIGRNILAQAGMKLVMGVLSSQIEETKVQLKEGKDGPKLKQWPLSREKIEALTEICKQMEEEGKLSRIGGENPYNTPVFAIKKKDKTQWRMLVDFRELNKATQDFFEVQLGIPHPAGLQKKKQITVIDIGDAYYSIPLCKEFRKYTAFTIPSVNNTGPGIRYQFNCLPQGWKGSPTIFQNTAANILEEIKRHTPGLEIVQYMDDLWLASDHDETRHNQQVDIVRKMLLEKGLETPDKKVQREPPWEWMGYKLHPNKWTINKIELPPLEGEWTVNKIQKVVGVLNWASQIYPGIKTKHTCAMLRGKKNLLEEIVWTEEAEAEYKNNQGIVQETQEGTYYDPLKELIATVQKQGEGQWTYQFTQEGAVLKVGRYAKQRETHTNDLRTLAHLVQKICKEALTIWGRLPRVQLPVDKKTWDMWWQDYWQVSWIPEWEFVSTPLLVKLWYSLVKEPIKGEDVYYVDGAASKVTKLGKAGYLSERGKSRIRELENTTNQQAELTAVKMALEDSGENVNIVTDSQYVMNILTACPQESNSPLVEQIIQALMKKRQVYLQWVPAHKGIGGNTEIDKLVSKGIRQILFLDRIEEAQDDHAKYHNNWRSMVQEFGLPNIVAKEIVAACPKCQIRGEPKHGQVDASIETWQMDCTHLEGKVIIVAVHVASGFIEAEVIPRETGKETAHFLLKLLARWPVKHLHTDNGPNFTSQNVAAVCWWGNIEHTTGIPYNPQSQGSVESMNRQLKEIISQIRDDCERLETAVQMATHIHNFKRKGGIGGISSAERLVNMLTTQLELNTLQNQIQKILNFKVYYREGRDPVWKGPARLIWKGEGAVVIKEGEDIKVVPRRKAKIIKDYGERKTMDSEGSMEGVREANKQMEGDSDLQDQE
SIO_010081: SIVgp1
subclass of: SO_0000673
so part of: SIVgp1
location: join(897..2197,2197..5314)
location: region:897-5314:1
so has part: feature:897-2197:1:exon
so has part: feature:2197-5314:1:exon

NP_687035.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:897-2197:1:exon

position:2197:1
position: 2197
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:2197-5314:1:exon

SIVgp1
type: Miscellaneous Feature
subclass of: SO_0000001
RO_0002162: 11723
gene: gag-pol
locus tag: SIVgp1
note: pol protein
SIO_010081: SIVgp1
subclass of: SO_0000673
so part of: SIVgp1
location: 897..5314
location: region:897-5314:1
so has part: feature:897-5314:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:897-5314:1:exon

SIVgp1
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 11723
gene: gag-pol
locus tag: SIVgp1
codon start: 1
product: gag protein
translation: MGGGHSALSGRSLDTFEKIRLRPNGKKKYQIKHLIWAGKEMERFGLHEKLLETKEGCQKIIEVLTPLEPTGSEGLKALFNLCCVIWCIHAEQKVKDTEEAVVTVKQHYHLVDKNEKAAKKKNETTAPPGGESRNYPVVNQNNAWVHQPLSPRTLNAWVKCVEEKRWGAEVVPMFQALSEGCLSYDVNQMLNVIGDHQGALQILKEVINEEAAEWDRTHRPPAGPLPAGQLRDPTGSDIAGTTSSIQEQIEWTFNANPRIDVGAQYRKWVILGLQKVVQMYNPQKVLDIRQGPKEPFQDYVDRFYKALRAEQAPQDVKNWMTQTLLIQNANPDCKLILKGLGMNPTLEEMLIACQGVGGPQHKAKLMVEMMSNGQNMVQVGPQKKGPRGPLKCFNCGKFGHMQRECKAPRQIKCFKCGKIGHMAKDCKNGQANFLGYGHWGGAKPRNFVQYRGDTVGLEPTAPPMETAYDPAKKLLQQYAEKGQRLREEREQTRKQKEKEVEDVSLSSLFGGDQ
SIO_010081: SIVgp1
subclass of: SO_0000673
so part of: SIVgp1
location: 897..2438
location: region:897-2438:1
so has part: feature:897-2438:1:exon

NP_054369.1
type: Protein
SIO_000068: ncbiprotein

position:2438:1
position: 2438
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:897-2438:1:exon

SIVgp2
type: Gene
subclass of: SO_0000704
RO_0002162: 11723
gene: vif
locus tag: SIVgp2
so part of: sequence
location: 5214..5873
location: region:5214-5873:1
so has part: feature:5214-5873:1:exon
subclass of: SO_0000010

1490005
type: Gene
SIO_000068: ncbigene

position:5214:1
position: 5214
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5873:1
position: 5873
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5214-5873:1:exon

SIVgp2
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 11723
gene: vif
locus tag: SIVgp2
codon start: 1
product: vif protein
translation: MEREKQWIVRVVWRVSERQISRWRGIVTYKIRNKQLPWEYRHHWQVQWQFWTYSQFIIPLSKDDYIEVNIYHNLTPERGWLSSHGVGLSYYHQKGYKTEVDPGTADRMIHLYYFNCFTDRAIQQAIRGEKYTWCTFKEGHKGQVQSLQLLALVAYTNGIRKRSKRTFTRMAGNLGSRQGAMGRMATRHAQGSKRRSQKALWNEHANPSMELLCRGGKET
SIO_010081: SIVgp2
subclass of: SO_0000673
so part of: SIVgp2
location: 5214..5873
location: region:5214-5873:1
so has part: feature:5214-5873:1:exon

NP_054370.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5214-5873:1:exon

SIVgp3
type: Gene
subclass of: SO_0000704
RO_0002162: 11723
gene: vpx
locus tag: SIVgp3
so part of: sequence
location: 5683..6039
location: region:5683-6039:1
so has part: feature:5683-6039:1:exon
subclass of: SO_0000010

1490006
type: Gene
SIO_000068: ncbigene

position:5683:1
position: 5683
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6039:1
position: 6039
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5683-6039:1:exon

SIVgp3
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 11723
gene: vpx
locus tag: SIVgp3
codon start: 1
product: vpx protein
translation: MASGRDPREPLPGWLEIWDLDREPWDEWLQDMLRDLNEEARRHFGMNMLIRVWNYCVEEGRRHNTPWNEIGYKYYRIVQKSMFVHFRCGCRRRGPFSPYEERRNGQGGGAPPPPPGLA
SIO_010081: SIVgp3
subclass of: SO_0000673
so part of: SIVgp3
location: 5683..6039
location: region:5683-6039:1
so has part: feature:5683-6039:1:exon

NP_054371.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5683-6039:1:exon

SIVgp4
type: Gene
subclass of: SO_0000704
RO_0002162: 11723
gene: tat
locus tag: SIVgp4
pseudo: true
so part of: sequence
location: 5993..8449
location: region:5993-8449:1
so has part: feature:5993-8449:1:exon

1490004
type: Gene
SIO_000068: ncbigene

position:5993:1
position: 5993
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8449:1
position: 8449
reference: sequence
type: ForwardStrandPosition
type: ExactPosition
type: FuzzyPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5993-8449:1:exon

SIVgp4
type: Miscellaneous Feature
subclass of: SO_0000001
RO_0002162: 11723
gene: tat
locus tag: SIVgp4
note: tat protein
pseudo: true
SIO_010081: SIVgp4
subclass of: SO_0000673
so part of: SIVgp4
location: 5993..8449
location: region:5993-8449:1
so has part: feature:5993-8449:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:5993-8449:1:exon

SIVgp5
type: Gene
subclass of: SO_0000704
RO_0002162: 11723
gene: rev1
locus tag: SIVgp5
pseudo: true
so part of: sequence
location: 6135..8750
location: region:6135-8750:1
so has part: feature:6135-8750:1:exon

1490003
type: Gene
SIO_000068: ncbigene

position:6135:1
position: 6135
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8750:1
position: 8750
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6135-8750:1:exon

SIVgp5
type: Miscellaneous Feature
subclass of: SO_0000001
RO_0002162: 11723
gene: rev1
locus tag: SIVgp5
note: rev protein
pseudo: true
SIO_010081: SIVgp5
subclass of: SO_0000673
so part of: SIVgp5
location: 6135..8750
location: region:6135-8750:1
so has part: feature:6135-8750:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:6135-8750:1:exon

SIVgp6
type: Gene
subclass of: SO_0000704
RO_0002162: 11723
gene: env
locus tag: SIVgp6
so part of: sequence
location: 6202..8766
location: region:6202-8766:1
so has part: feature:6202-8766:1:exon
subclass of: SO_0000010

1490007
type: Gene
SIO_000068: ncbigene

position:6202:1
position: 6202
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8766:1
position: 8766
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6202-8766:1:exon

SIVgp6
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 11723
gene: env
locus tag: SIVgp6
codon start: 1
product: envelope protein
translation: MGRLLIKILIIAIGISIGIGNLYVTVFYGIPVWKNSTVQAFCMTPNTNMWATTNCIPDDHDNTEVPLNITEAFEAWDNPLVKQAESNIHLLFEQTMRPCVKLSPICIKMSCVELNGTATTKATTTATTTMTTPCQNCSTEQIEGEMAEEPASNCTFAIAGYQRDVKKNYSMTWYDQELVCNNKTGSEKGSKDCYMIHCNDSVIKEACDKTYWDTLRVRYCAPAGYALLKCNDKDYRGFAPKCKNVSVVHCTRLINTTITTGIGLNGSRSENRTEIWQKGGNDNDTVIIKLNKFYNLTVRCRRPGNKTVLPVTIMAGLVFHSQKYNTRLKQAWCHFQGDWKGAWKEVREEVKKVKNLTEVSIENIHLRRIWGDPESANFWFNCQGEFFYCKMDWFINYLNNRTEDAEGTNRTCDKGKPGPGPCVQRTYVACHIRQVVNDWYTVSKKVYAPPREGHLECNSSVTALYVAIDYNNKSGPINVTLSPQVRSIWAYELGDYKLVEITPIGFAPTDVRRYTGPTREKRVPFVLGFLGFLGAAGTAMGAAATTLTVQSRHLLAGILQQQKNLLAAVEQQQQLLKLTIWGVKNLNARVTALEKYLEDQARLNSWGCAWKQVCHTTVPWKYNNTPKWDNMTWLEWERQINALEGNITQLLEEAQNQESKNLDLYQKLDDWSGFWSWFSLSTWLGYVKIGFLVIVIILGLRFAWVLWGCIRNIRQGYNPLPQIHIHSSAERPDNGGGQDRGGESSSSKLIRLQEESSTPSRINNWWLNFKSCSLRIRTWCYNICLTLLIFIRTAVGYLQYGLQQLQEAATGLAQALARAAREAWGRLGAIVRSAYRAVINSPRRVRQGLEKVLG
SIO_010081: SIVgp6
subclass of: SO_0000673
so part of: SIVgp6
location: 6202..8766
location: region:6202-8766:1
so has part: feature:6202-8766:1:exon

NP_054372.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6202-8766:1:exon

SIVgp4
type: Exon
subclass of: SO_0000147
RO_0002162: 11723
gene: tat
locus tag: SIVgp4
product: tat protein
pseudo: true
SIO_010081: SIVgp4
subclass of: SO_0000673
so part of: SIVgp4
location: 8368..>8449
location: region:8368-8449:1
so has part: feature:8368-8449:1:exon

position:8368:1
position: 8368
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:8368-8449:1:exon

SIVgp7
type: Gene
subclass of: SO_0000704
RO_0002162: 11723
gene: nef
locus tag: SIVgp7
so part of: sequence
location: 8600..9271
location: region:8600-9271:1
so has part: feature:8600-9271:1:exon
subclass of: SO_0000010

1490008
type: Gene
SIO_000068: ncbigene

position:8600:1
position: 8600
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:9271:1
position: 9271
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:8600-9271:1:exon

SIVgp7
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 11723
gene: nef
locus tag: SIVgp7
codon start: 1
product: nef protein
translation: MGSSNSKRQQQGLLKLWRGLRGKPGADWVLLSDPLIGQSSTVQEECGKALKKSWGKGKMTPDGRRLQEGDTFDEWDDDEEEVGFPVQPRVPLRQMTYKLAVDFSHFLKSKGGLDGIYYSERREKILNLYALNEWGIIDDWQAYSPGPGIRYPRVFGFCFKLVPVDLHEEARNCERHCLMHPAQMGEDPDGIDHGEVLVWKFDPKLAVEYRPDMFKDMHEHAKR
SIO_010081: SIVgp7
subclass of: SO_0000673
so part of: SIVgp7
location: 8600..9271
location: region:8600-9271:1
so has part: feature:8600-9271:1:exon

NP_054373.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:8600-9271:1:exon

repeat_region
type: Repeat Region
subclass of: SO_0000657
RO_0002162: 11723
note: 3' LTR
rpt type: long_terminal_repeat
so part of: sequence
location: 8937..9623
location: region:8937-9623:1
so has part: feature:8937-9623:1:region

position:8937:1
position: 8937
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:8937-9623:1:region

repeat_region
type: Repeat Region
subclass of: SO_0000657
RO_0002162: 11723
note: R repeat 3' copy
so part of: sequence
location: 9407..9524
location: region:9407-9524:1
so has part: feature:9407-9524:1:region

position:9407:1
position: 9407
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:9524:1
position: 9524
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:9407-9524:1:region

regulatory
type: Feature
subclass of: SO_0000001
RO_0002162: 11723
regulatory class: polyA_signal_sequence
so part of: sequence
location: 9506..9511
location: region:9506-9511:1
so has part: feature:9506-9511:1:region

position:9506:1
position: 9506
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:9511:1
position: 9511
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:9506-9511:1:region