Hepatitis C virus genotype 1, complete genome.
type: Entry
definition: Hepatitis C virus genotype 1, complete genome.
sequence version: NC_004102.1
sequence date: 2019-07-11
sequence: sequence
division: VRL
label: NC_004102.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA485481
keyword: RefSeq
source: Hepatitis C virus genotype 1
organism: Hepatitis C virus genotype 1
taxonomy: Viruses; Riboviria; Flaviviridae; Hepacivirus.
reference: 1
references: 12588970
reference: 2
references: 11907211
reference: 3
references: 9228008
reference: 4
reference: 5
comment: REVIEWED REFSEQ: This record has been curated by NCBI staff. The\nreference sequence was derived from AF009606.\nThe mature peptides have been annotated by the NCBI staff using the\ndata from current literature as well as other annotations available\nfor this virus.\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000353
sequence length: 9646
topology: linear
so has quality: SO_0000987
location: 1..9646
location: region:1-9646:1
RO_0002162: 41856

NC_004102
type: RefSeq
SIO_000068: refseq

PRJNA485481
type: BioProject
SIO_000068: bioproject

1
title: Triple decoding of hepatitis C virus RNA by programmed translational frameshifting
author: Choi, J.
author: Xu, Z.
author: Ou, J.H.
journal: Mol. Cell. Biol.
volume: 23
issue: 5
pages: 1489-1497
year: 2003
pubmed: 12588970

12588970
type: PubMed
SIO_000068: pubmed

2
title: Subcellular localization and topology of the p7 polypeptide of hepatitis C virus
author: Carrere-Kremer, S.
author: Montpellier-Pala, C.
author: Cocquerel, L.
author: Wychowski, C.
author: Penin, F.
author: Dubuisson, J.
journal: J. Virol.
volume: 76
issue: 8
pages: 3720-3730
year: 2002
pubmed: 11907211

11907211
type: PubMed
SIO_000068: pubmed

3
title: Transmission of hepatitis C by intrahepatic inoculation with transcribed RNA
author: Kolykhalov, A.A.
author: Agapov, E.V.
author: Blight, K.J.
author: Mihalik, K.
author: Feinstone, S.M.
author: Rice, C.M.
journal: Science
volume: 277
issue: 5325
pages: 570-574
year: 1997
pubmed: 9228008

9228008
type: PubMed
SIO_000068: pubmed

4
title: Direct Submission
journal: Submitted (07-AUG-2002) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA

5
title: Direct Submission
author: Kolykhalov, A.A.
author: Rice, C.M.
journal: Submitted (19-JUN-1997) Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Ave., St. Louis, MO 63110-1093, USA

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

position:9646:1
position: 9646
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-9646:1:source
so part of: sequence
organism: Hepatitis C virus genotype 1
mol type: genomic RNA
serotype: 1a
isolate: H77
note: assembled from cDNA library representing a population of Hepatitis C virus genomes; viable virus can be reconstituted from this sequence

41856
type: Taxonomy
SIO_000068: taxonomy

5'UTR
type: Five Prime UTR
subclass of: SO_0000204
RO_0002162: 41856
so part of: sequence
location: 1..341
location: region:1-341:1
so has part: feature:1-341:1:region

position:341:1
position: 341
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-341:1:region

HCVgp1
type: Gene
subclass of: SO_0000704
RO_0002162: 41856
gene: POLY
locus tag: HCVgp1
so part of: sequence
location: 342..9377
location: region:342-9377:1
so has part: feature:342-9377:1:exon
subclass of: SO_0000010

951475
type: Gene
SIO_000068: ncbigene

position:342:1
position: 342
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:9377:1
position: 9377
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:342-9377:1:exon

HCVgp1
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 41856
gene: POLY
locus tag: HCVgp1
codon start: 1
product: polyprotein
translation: MSTNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEGRTWAQPGYPWPLYGNEGCGWAGWLLSPRGSRPSWGPTDPRRRSRNLGKVIDTLTCGFADLMGYIPLVGAPLGGAARALAHGVRVLEDGVNYATGNLPGCSFSIFLLALLSCLTVPASAYQVRNSSGLYHVTNDCPNSSIVYEAADAILHTPGCVPCVREGNASRCWVAVTPTVATRDGKLPTTQLRRHIDLLVGSATLCSALYVGDLCGSVFLVGQLFTFSPRRHWTTQDCNCSIYPGHITGHRMAWDMMMNWSPTAALVVAQLLRIPQAIMDMIAGAHWGVLAGIAYFSMVGNWAKVLVVLLLFAGVDAETHVTGGSAGRTTAGLVGLLTPGAKQNIQLINTNGSWHINSTALNCNESLNTGWLAGLFYQHKFNSSGCPERLASCRRLTDFAQGWGPISYANGSGLDERPYCWHYPPRPCGIVPAKSVCGPVYCFTPSPVVVGTTDRSGAPTYSWGANDTDVFVLNNTRPPLGNWFGCTWMNSTGFTKVCGAPPCVIGGVGNNTLLCPTDCFRKHPEATYSRCGSGPWITPRCMVDYPYRLWHYPCTINYTIFKVRMYVGGVEHRLEAACNWTRGERCDLEDRDRSELSPLLLSTTQWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGVGSSIASWAIKWEYVVLLFLLLADARVCSCLWMMLLISQAEAALENLVILNAASLAGTHGLVSFLVFFCFAWYLKGRWVPGAVYAFYGMWPLLLLLLALPQRAYALDTEVAASCGGVVLVGLMALTLSPYYKRYISWCMWWLQYFLTRVEAQLHVWVPPLNVRGGRDAVILLMCVVHPTLVFDITKLLLAIFGPLWILQASLLKVPYFVRVQGLLRICALARKIAGGHYVQMAIIKLGALTGTYVYNHLTPLRDWAHNGLRDLAVAVEPVVFSRMETKLITWGADTAACGDIINGLPVSARRGQEILLGPADGMVSKGWRLLAPITAYAQQTRGLLGCIITSLTGRDKNQVEGEVQIVSTATQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSVAATLGFGAYMSKAHGVDPNIRTGVRTITTGSPITYSTYGKFLADGGCSGGAYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLATATPPGSVTVSHPNIEEVALSTTGEIPFYGKAIPLEVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVSTDALMTGFTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGRGKPGIYRFVAPGERPSGMFDSSVLCECYDAGCAWYELTPAETTVRLRAYMNTPGLPVCQDHLEFWEGVFTGLTHIDAHFLSQTKQSGENFPYLVAYQATVCARAQAPPPSWDQMWKCLIRLKPTLHGPTPLLYRLGAVQNEVTLTHPITKYIMTCMSADLEVVTSTWVLVGGVLAALAAYCLSTGCVVIVGRIVLSGKPAIIPDREVLYQEFDEMEECSQHLPYIEQGMMLAEQFKQKALGLLQTASRQAEVITPAVQTNWQKLEVFWAKHMWNFISGIQYLAGLSTLPGNPAIASLMAFTAAVTSPLTTGQTLLFNILGGWVAAQLAAPGAATAFVGAGLAGAAIGSVGLGKVLVDILAGYGAGVAGALVAFKIMSGEVPSTEDLVNLLPAILSPGALVVGVVCAAILRRHVGPGEGAVQWMNRLIAFASRGNHVSPTHYVPESDAAARVTAILSSLTVTQLLRRLHQWISSECTTPCSGSWLRDIWDWICEVLSDFKTWLKAKLM…
SIO_010081: HCVgp1
subclass of: SO_0000673
so part of: HCVgp1
location: 342..9377
location: region:342-9377:1
so has part: feature:342-9377:1:exon

NP_671491.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:342-9377:1:exon

HCVgp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 41856
gene: POLY
locus tag: HCVgp1
product: core protein
note: cleaved from polyprotein by signal peptidase; further processed to loose the C-terminal signal peptide and thereby to be released (as a smaller protein, p19c) from the endoplasmic reticulum membrane; viral capsid protein; reportedly involved in diverse processes, e.g. viral morphogenesis or regulation of host gene expression; p21c
SIO_010081: HCVgp1
subclass of: SO_0000673
so part of: HCVgp1
location: 342..914
location: region:342-914:1
so has part: feature:342-914:1:exon

NP_751919.1
type: Protein
SIO_000068: ncbiprotein

position:914:1
position: 914
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:342-914:1:exon

HCVgp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 41856
gene: POLY
locus tag: HCVgp1
product: envelope protein E1
note: viral envelope protein; product of cellular signal peptidase; forms a heterodimer with the E2 protein
SIO_010081: HCVgp1
subclass of: SO_0000673
so part of: HCVgp1
location: 915..1490
location: region:915-1490:1
so has part: feature:915-1490:1:exon

NP_751920.1
type: Protein
SIO_000068: ncbiprotein

position:915:1
position: 915
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1490:1
position: 1490
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:915-1490:1:exon

HCVgp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 41856
gene: POLY
locus tag: HCVgp1
product: envelope protein E2
note: viral envelope protein; product of cellular signal peptidase; forms a heterodimer with the E1 protein
SIO_010081: HCVgp1
subclass of: SO_0000673
so part of: HCVgp1
location: 1491..2579
location: region:1491-2579:1
so has part: feature:1491-2579:1:exon

NP_751921.1
type: Protein
SIO_000068: ncbiprotein

position:1491:1
position: 1491
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2579:1
position: 2579
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1491-2579:1:exon

HCVgp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 41856
gene: POLY
locus tag: HCVgp1
product: protein p7
note: product of cellular signal peptidase; integral membrane polypeptide; has a double membrane-spanning topology, with both its N and C termini oriented toward the extracellular environment
SIO_010081: HCVgp1
subclass of: SO_0000673
so part of: HCVgp1
location: 2580..2768
location: region:2580-2768:1
so has part: feature:2580-2768:1:exon

NP_751922.1
type: Protein
SIO_000068: ncbiprotein

position:2580:1
position: 2580
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2768:1
position: 2768
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2580-2768:1:exon

HCVgp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 41856
gene: POLY
locus tag: HCVgp1
product: nonstructural protein NS2
note: N-terminus is cleaved by a cellular signal peptidase; C-terminus is produced by the only known cleavage event mediated by the NS2-NS3 metal-dependent proteinase; membrane protein with 2 internal signal sequences; suggested type III membrane topology protein; inhibitor of CIDE-B-induced apoptosis
SIO_010081: HCVgp1
subclass of: SO_0000673
so part of: HCVgp1
location: 2769..3419
location: region:2769-3419:1
so has part: feature:2769-3419:1:exon

NP_751923.1
type: Protein
SIO_000068: ncbiprotein

position:2769:1
position: 2769
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3419:1
position: 3419
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2769-3419:1:exon

HCVgp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 41856
gene: POLY
locus tag: HCVgp1
product: protease/helicase protein NS3
note: N-terminus is produced by the only cleavage in HCV polyprotein mediated by the NS2-NS3 metal-dependent proteinase; cleaves itself at the C-terminus; with the help of NS4A, mediates processing of all the other HCV non-structural proteins; physically and functionally interacts with the NS5B RNA polymerase; susceptible to inhibition by the N-terminal cleavage products of substrate peptides
SIO_010081: HCVgp1
subclass of: SO_0000673
so part of: HCVgp1
location: 3420..5312
location: region:3420-5312:1
so has part: feature:3420-5312:1:exon

NP_803144.1
type: Protein
SIO_000068: ncbiprotein

position:3420:1
position: 3420
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5312:1
position: 5312
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3420-5312:1:exon

HCVgp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 41856
gene: POLY
locus tag: HCVgp1
product: nonstructural protein NS4A
note: cofactor for the NS3 protease
SIO_010081: HCVgp1
subclass of: SO_0000673
so part of: HCVgp1
location: 5313..5474
location: region:5313-5474:1
so has part: feature:5313-5474:1:exon

NP_751925.1
type: Protein
SIO_000068: ncbiprotein

position:5313:1
position: 5313
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5474:1
position: 5474
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5313-5474:1:exon

HCVgp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 41856
gene: POLY
locus tag: HCVgp1
product: nonstructural protein NS4B
note: membrane protein; negative regulator of the NS3-NS5B replication complex
SIO_010081: HCVgp1
subclass of: SO_0000673
so part of: HCVgp1
location: 5475..6257
location: region:5475-6257:1
so has part: feature:5475-6257:1:exon

NP_751926.1
type: Protein
SIO_000068: ncbiprotein

position:5475:1
position: 5475
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6257:1
position: 6257
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5475-6257:1:exon

HCVgp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 41856
gene: POLY
locus tag: HCVgp1
product: nonstructural protein NS5A
note: phosphorylated; associated with interferon sensitivity
SIO_010081: HCVgp1
subclass of: SO_0000673
so part of: HCVgp1
location: 6258..7601
location: region:6258-7601:1
so has part: feature:6258-7601:1:exon

NP_751927.1
type: Protein
SIO_000068: ncbiprotein

position:6258:1
position: 6258
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7601:1
position: 7601
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6258-7601:1:exon

HCVgp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 41856
gene: POLY
locus tag: HCVgp1
product: RNA-dependent RNA polymerase NS5B
note: RdRp
SIO_010081: HCVgp1
subclass of: SO_0000673
so part of: HCVgp1
location: 7602..9374
location: region:7602-9374:1
so has part: feature:7602-9374:1:exon

NP_751928.1
type: Protein
SIO_000068: ncbiprotein

position:7602:1
position: 7602
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:9374:1
position: 9374
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7602-9374:1:exon

HCVgp1
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 41856
gene: POLY
locus tag: HCVgp1
ribosomal slippage: true
note: 17-kDa frameshift protein F; some of the functions that were earlier attributed to the core protein may actually be mediated by F; similarly to HCV core and NS5A proteins, F is associated with the endoplasmic reticulum and, therefore, may play a role in HCV morphogenesis or replication; -2/+1 frameshift; although the exact location of the frameshift is unknown, it was mapped to codons 9 to 11 of the core protein coding sequence.
codon start: 1
product: protein F
translation: MSTNPKPQRKPNVTPTVAHRTSSSRVAVRSLVEFTCCRAGALDWVCARRGRLPSGRNLEVDVSLSPRHVGPRAGPGLSPGTLGPSMAMRVAGGRDGSCLPVALGLAGAPQTPGVGRAIWVRSSIPLRAASPTSWGTYRSSAPLLEALPGPWRMASGFWKTA
SIO_010081: HCVgp1
subclass of: SO_0000673
so part of: HCVgp1
location: join(342..369,371..828)
location: region:342-828:1
so has part: feature:342-369:1:exon
so has part: feature:371-828:1:exon

NP_803170.1
type: Protein
SIO_000068: ncbiprotein

position:828:1
position: 828
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:342-369:1:exon

position:369:1
position: 369
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:371-828:1:exon

position:371:1
position: 371
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

3'UTR
type: Three Prime UTR
subclass of: SO_0000205
RO_0002162: 41856
so part of: sequence
location: 9378..9646
location: region:9378-9646:1
so has part: feature:9378-9646:1:region

position:9378:1
position: 9378
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:9378-9646:1:region