Rodent pegivirus isolate CC61, complete genome.
type: Entry
definition: Rodent pegivirus isolate CC61, complete genome.
sequence version: NC_021154.1
sequence date: 2018-08-13
sequence: sequence
division: VRL
label: NC_021154.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA485481
keyword: RefSeq
source: Rodent pegivirus
organism: Rodent pegivirus
taxonomy: Viruses; Riboviria; Flaviviridae; Pegivirus; unclassified Pegivirus.
reference: 1
references: 23572554
reference: 2
reference: 3
comment: REVIEWED REFSEQ: This record has been curated by NCBI staff. The\nreference sequence was derived from KC815311.\nThe putative mature peptides added based on PMID 23572554.\n\n##Assembly-Data-START##\nAssembly Method :: Seqeuncher v. 5.0\nCoverage :: 4X\nSequencing Technology :: Sanger dideoxy sequencing\n##Assembly-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000353
sequence length: 11279
topology: linear
so has quality: SO_0000987
location: 1..11279
location: region:1-11279:1
RO_0002162: 1321391

NC_021154
type: RefSeq
SIO_000068: refseq

PRJNA485481
type: BioProject
SIO_000068: bioproject

1
title: Identification of rodent homologs of hepatitis C virus and pegiviruses
author: Kapoor, A.
author: Simmonds, P.
author: Scheel, T.K.
author: Hjelle, B.
author: Cullen, J.M.
author: Burbelo, P.D.
author: Chauhan, L.V.
author: Duraisamy, R.
author: Sanchez Leon, M.
author: Jain, K.
author: Vandegrift, K.J.
author: Calisher, C.H.
author: Rice, C.M.
author: Lipkin, W.I.
journal: MBio 4 (2), e00216-13 (2013)
pubmed: 23572554
comments: Publication Status: Online-Only

23572554
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
journal: Submitted (24-APR-2013) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA

3
title: Direct Submission
author: Kapoor, A.
journal: Submitted (22-MAR-2013) Columbia University, 722 west, 168 street, New York, NY 10032, USA

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

position:11279:1
position: 11279
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-11279:1:source
so part of: sequence
organism: Rodent pegivirus
mol type: genomic RNA
isolate: CC61
host: Neotoma lepida
country: USA
collection date: 2008

1321391
type: Taxonomy
SIO_000068: taxonomy

5'UTR
type: Five Prime UTR
subclass of: SO_0000204
RO_0002162: 1321391
so part of: sequence
location: 1..349
location: region:1-349:1
so has part: feature:1-349:1:region

position:349:1
position: 349
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-349:1:region

L105_gp1
type: Gene
subclass of: SO_0000704
RO_0002162: 1321391
locus tag: L105_gp1
old locus tag: RPgV_gp1
so part of: sequence
location: 350..10804
location: region:350-10804:1
so has part: feature:350-10804:1:exon
subclass of: SO_0000010

15382983
type: Gene
SIO_000068: ncbigene

position:350:1
position: 350
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:10804:1
position: 10804
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:350-10804:1:exon

L105_gp1
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1321391
locus tag: L105_gp1
old locus tag: RPgV_gp1
codon start: 1
product: polyprotein
translation: MAVYNSLVVRATVAAPVALWCLWSGIGFVCGASTTPTTVTPSPTPCSGFWDCIHRGFHGFGVALRDNLQYGGRLGLGIANPTLSPDLDWGKRPFDASGERLHGQFSGFAERVAELGRNISTTLRAGWKRTMLRAGAGFMKAAGVDFGSEVARQAAASMARRRRSLIASAPSVAPQPSTSFPLFTVCVLGFVALLLGVATGMGCRLRLLALLLLCSCAVPAESLPTSSRACWVPEHRALAFSNCCNETDIFWCTPWLCWTLPGCAVCTAEHGCWTMVGSGVSIVPSSKVGQVRRSSMDFFGVLGWVGVMAEGTGLGEYYSAAIVAGAFLMGHTAPSDIICNVSCSQAGTTWWYQAAPTVSAIIELLYSLPHAIFSLIESMPWVFGSLLLFHLGCGRWVQVVLLVFAVPGVLADCPHSNETFTNEEGQVDSWPFRSCTDKDFASNGTTCDCPFGVIIRHFNNDTDPYLDIPAICPESFPYTNFSWLCGWGSWWWVAHGVERPYSHPYMPPSPFSAICYILTNRTVLYNATIYPNTYAGVGRYPNYTASVLGPAPVTSCMLDRRPAMCGDCFGGCFYRDGSHSRPFGVCGGGVRDGPWHFAPLAVIYGNPNAPWWVPTRGTAELFATKYLHGYGCGLVNGLLNCWSCELGFSSDHRYNLTTGVWWPLPGEPTEVCINPQYRRSRLPPGPSWLELIQHTVDKVVGRTKCNPRKGWYPVCRDSAWYPPDGGLVVLVGDTQLTDSSPLLLKHFLGLYVALVVFMATAGARVVPTLLVLFGLFWFGYADCYPPCEWAYCSQYVCATSGGCFVGVGEGLCAGAGHLAPCGSGSSLPGSAVDALPVAYLAHYIGALFGVPSGSWLWFLVQAFSVQDWYYPADFICGNFTLVGAELEYDTNWLGFIAAFVVRPTALALVAIVIAGCAGLPLRTHFPYRAFAVAFHLASVSLIESGVVFGLAWWAADWFARAGADAALSRAVLASPVVGWAIRLPSWPEVILGVVCVALYMRVVGQARLAALVAYKLSRGLAGAALVVLLVCRGPERGALGYQLCLPEWDASIDLDDVWWYAAAFFTFCCISISLLTRRGVVFKLRVYARWCRLYCWLQLVVGHTPAGDYFRWRGASSLLWLAAGVLWPAEVAVVSMIIVCFAAVLDVFDALLERLLTASPSLRPLVNLANTLHSCLSDPELAAFLRARWHRGELLYDHAGQVAASLRERVVALDGCLEPLTLTGEALQEVYDDTFALTCGRWCGGNPVVARCGRSVLVGSAASVASLPPGYTLTAPLMVLRREMGFWKTLRISLTGRGDFPDSGQVVLLGTALSSSMACGVGGVLYATFHGTRGRALSTPHGPRNPYWTSPSEDVACYPLIPPLTSLTACDCASTSRWVITKHGTLVHGLASGEDRVRLDCPTRVSDLKGASGSPVLCDKGHAVGMLVGVLAKSGLAETARFVKPWTHSPGDAAKLTAPEFPSVPASGYKEVPYFAPTGSGKSTKFPAKLAQDGHNVLVLNPSVVTTKAMGPYMKKLVGKTPNIFAGTGASAMQIKTGSKITYCTYGRFLVNPQGFLDQKAVVVCDECHATDGTSILGIGVARALAEKAGVRLLVFATATPPGTQFTPHASITEETLDGDGDIPFYGVSLKASTYLKGRHVIFCHSKAECVRVAESLAGAGVKAVTYWRGTRHDVLTDDADLTVVATDAISTGYTGNFATCTDCCSVVEETVDVDLNPTFTINLITKAADAALRMQRRGRCGRGAPGTYYAVQKGAPPSGVCSTATAWAAAEAGFMWYGMPAADISRYLQTFQDCPYTSRLAGSPGDAVRVMECLKPLMHCAEVTQEALRETTWPMLTGIQKHVCYEADAAPPSDDIRWQGVNGTHATPLLYRLGQVDNAVTSHPLALKMAAALGDTSYHDTTIGPLLLAGAAVAAAAAIADSTGCLVVTAVWEVGSGGSPLWPGSKTADERGDVQGGEAPPGAQPPKVTPGEVKAAKDTAEVISEVATSLDYSFLSTLW…
SIO_010081: L105_gp1
subclass of: SO_0000673
so part of: L105_gp1
location: 350..10804
location: region:350-10804:1
so has part: feature:350-10804:1:exon

YP_007905734.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:350-10804:1:exon

L105_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 1321391
locus tag: L105_gp1
old locus tag: RPgV_gp1
product: putative signal peptide
inference: non-experimental evidence, no additional details recorded
SIO_010081: L105_gp1
subclass of: SO_0000673
so part of: L105_gp1
location: 350..442
location: region:350-442:1
so has part: feature:350-442:1:exon

YP_007905973.1
type: Protein
SIO_000068: ncbiprotein

position:442:1
position: 442
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:350-442:1:exon

L105_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 1321391
locus tag: L105_gp1
old locus tag: RPgV_gp1
product: putative Y protein
inference: non-experimental evidence, no additional details recorded
SIO_010081: L105_gp1
subclass of: SO_0000673
so part of: L105_gp1
location: 443..1015
location: region:443-1015:1
so has part: feature:443-1015:1:exon

YP_007905974.1
type: Protein
SIO_000068: ncbiprotein

position:443:1
position: 443
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1015:1
position: 1015
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:443-1015:1:exon

L105_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 1321391
locus tag: L105_gp1
old locus tag: RPgV_gp1
product: putative E1 protein
inference: non-experimental evidence, no additional details recorded
SIO_010081: L105_gp1
subclass of: SO_0000673
so part of: L105_gp1
location: 1016..1585
location: region:1016-1585:1
so has part: feature:1016-1585:1:exon

YP_007905975.1
type: Protein
SIO_000068: ncbiprotein

position:1016:1
position: 1016
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1585:1
position: 1585
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1016-1585:1:exon

L105_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 1321391
locus tag: L105_gp1
old locus tag: RPgV_gp1
product: putative E2 protein
inference: non-experimental evidence, no additional details recorded
SIO_010081: L105_gp1
subclass of: SO_0000673
so part of: L105_gp1
location: 1586..2698
location: region:1586-2698:1
so has part: feature:1586-2698:1:exon

YP_007905976.1
type: Protein
SIO_000068: ncbiprotein

position:1586:1
position: 1586
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2698:1
position: 2698
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1586-2698:1:exon

L105_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 1321391
locus tag: L105_gp1
old locus tag: RPgV_gp1
product: putative X protein
inference: non-experimental evidence, no additional details recorded
SIO_010081: L105_gp1
subclass of: SO_0000673
so part of: L105_gp1
location: 2699..3445
location: region:2699-3445:1
so has part: feature:2699-3445:1:exon

YP_007905977.1
type: Protein
SIO_000068: ncbiprotein

position:2699:1
position: 2699
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3445:1
position: 3445
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2699-3445:1:exon

L105_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 1321391
locus tag: L105_gp1
old locus tag: RPgV_gp1
product: putative NS2 protein
inference: non-experimental evidence, no additional details recorded
SIO_010081: L105_gp1
subclass of: SO_0000673
so part of: L105_gp1
location: 3446..4168
location: region:3446-4168:1
so has part: feature:3446-4168:1:exon

YP_007905978.1
type: Protein
SIO_000068: ncbiprotein

position:3446:1
position: 3446
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4168:1
position: 4168
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3446-4168:1:exon

L105_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 1321391
locus tag: L105_gp1
old locus tag: RPgV_gp1
product: putative NS3 protein
inference: non-experimental evidence, no additional details recorded
SIO_010081: L105_gp1
subclass of: SO_0000673
so part of: L105_gp1
location: 4169..5986
location: region:4169-5986:1
so has part: feature:4169-5986:1:exon

YP_007905979.1
type: Protein
SIO_000068: ncbiprotein

position:4169:1
position: 4169
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5986:1
position: 5986
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4169-5986:1:exon

L105_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 1321391
locus tag: L105_gp1
old locus tag: RPgV_gp1
product: putative NS4A protein
inference: non-experimental evidence, no additional details recorded
SIO_010081: L105_gp1
subclass of: SO_0000673
so part of: L105_gp1
location: 5987..6322
location: region:5987-6322:1
so has part: feature:5987-6322:1:exon

YP_007905980.1
type: Protein
SIO_000068: ncbiprotein

position:5987:1
position: 5987
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6322:1
position: 6322
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5987-6322:1:exon

L105_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 1321391
locus tag: L105_gp1
old locus tag: RPgV_gp1
product: putative NS4B protein
inference: non-experimental evidence, no additional details recorded
SIO_010081: L105_gp1
subclass of: SO_0000673
so part of: L105_gp1
location: 6323..7102
location: region:6323-7102:1
so has part: feature:6323-7102:1:exon

YP_007905981.1
type: Protein
SIO_000068: ncbiprotein

position:6323:1
position: 6323
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7102:1
position: 7102
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6323-7102:1:exon

L105_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 1321391
locus tag: L105_gp1
old locus tag: RPgV_gp1
product: putative NS5A protein
inference: non-experimental evidence, no additional details recorded
SIO_010081: L105_gp1
subclass of: SO_0000673
so part of: L105_gp1
location: 7103..9100
location: region:7103-9100:1
so has part: feature:7103-9100:1:exon

YP_007905982.1
type: Protein
SIO_000068: ncbiprotein

position:7103:1
position: 7103
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:9100:1
position: 9100
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7103-9100:1:exon

L105_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 1321391
locus tag: L105_gp1
old locus tag: RPgV_gp1
product: putative NS5B protein
experiment: experimental evidence, no additional details recorded
SIO_010081: L105_gp1
subclass of: SO_0000673
so part of: L105_gp1
location: 9101..10801
location: region:9101-10801:1
so has part: feature:9101-10801:1:exon

YP_007905983.1
type: Protein
SIO_000068: ncbiprotein

position:9101:1
position: 9101
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:10801:1
position: 10801
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:9101-10801:1:exon

3'UTR
type: Three Prime UTR
subclass of: SO_0000205
RO_0002162: 1321391
so part of: sequence
location: 10805..11279
location: region:10805-11279:1
so has part: feature:10805-11279:1:region

position:10805:1
position: 10805
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10805-11279:1:region