Rice yellow mottle virus complete genome, isolate CI4.
type: Entry
definition: Rice yellow mottle virus complete genome, isolate CI4.
sequence version: NC_001575.2
sequence date: 2018-08-13
sequence: sequence
division: VRL
label: NC_001575.2
type: RefSeq
SIO_000068: refseq
dblink: PRJNA485481
keyword: RefSeq
keyword: coat protein
keyword: complete genome
keyword: ORF1
keyword: ORF2a
keyword: ORF2b
keyword: ORF4
keyword: P1
keyword: protease
keyword: RNA-dependent RNA polymerase
keyword: VPg
source: Rice yellow mottle virus
organism: Rice yellow mottle virus
taxonomy: Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage; Sobemovirus.
reference: 1
references: 23830075
reference: 2
references: 21068217
reference: 3
references: 19748532
reference: 4
references: 15843686
reference: 5
references: 15016846
reference: 6
references: 10848968
reference: 7
references: 7886961
reference: 8
reference: 9
comment: REVIEWED REFSEQ: This record has been curated by NCBI staff. The\nreference sequence is identical to AJ608206.\nOn Feb 11, 2013 this sequence version replaced NC_001575.1.\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000353
sequence length: 4449
topology: linear
so has quality: SO_0000987
location: 1..4449
location: region:1-4449:1
RO_0002162: 31744

NC_001575
type: RefSeq
SIO_000068: refseq

PRJNA485481
type: BioProject
SIO_000068: bioproject

1
title: An essential fifth coding ORF in the sobemoviruses
author: Ling, R.
author: Pate, A.E.
author: Carr, J.P.
author: Firth, A.E.
journal: Virology 446 (1-2), 397-408 (2013)
pubmed: 23830075

23830075
type: PubMed
SIO_000068: pubmed

2
title: Protein-RNA linkage and post-translational modifications of two sobemovirus VPgs
author: Olspert, A.
author: Peil, L.
author: Hebrard, E.
author: Fargette, D.
author: Truve, E.
journal: J. Gen. Virol. 92 (PT 2), 445-452 (2011)
pubmed: 21068217

21068217
type: PubMed
SIO_000068: pubmed

3
title: Stem-loop structure of Cocksfoot mottle virus RNA is indispensable for programmed -1 ribosomal frameshifting
author: Tamm, T.
author: Suurvali, J.
author: Lucchesi, J.
author: Olspert, A.
author: Truve, E.
journal: Virus Res. 146 (1-2), 73-80 (2009)
pubmed: 19748532

19748532
type: PubMed
SIO_000068: pubmed

4
title: Factors affecting translation at the programmed -1 ribosomal frameshifting site of Cocksfoot mottle virus RNA in vivo
author: Makelainen, K.
author: Makinen, K.
journal: Nucleic Acids Res.
volume: 33
issue: 7
pages: 2239-2247
year: 2005
pubmed: 15843686

15843686
type: PubMed
SIO_000068: pubmed

5
title: Inferring the evolutionary history of rice yellow mottle virus from genomic, phylogenetic, and phylogeographic studies
author: Fargette, D.
author: Pinel, A.
author: Abubakar, Z.
author: Traore, O.
author: Brugidou, C.
author: Fatogoma, S.
author: Hebrard, E.
author: Choisy, M.
author: Sere, Y.
author: Fauquet, C.
author: Konate, G.
journal: J. Virol.
volume: 78
issue: 7
pages: 3252-3261
year: 2004
pubmed: 15016846

15016846
type: PubMed
SIO_000068: pubmed

6
title: Regulation of -1 ribosomal frameshifting directed by cocksfoot mottle sobemovirus genome
author: Lucchesi, J.
author: Makelainen, K.
author: Merits, A.
author: Tamm, T.
author: Makinen, K.
journal: Eur. J. Biochem.
volume: 267
issue: 12
pages: 3523-3529
year: 2000
pubmed: 10848968

10848968
type: PubMed
SIO_000068: pubmed

7
title: The putative replicase of the cocksfoot mottle sobemovirus is translated as a part of the polyprotein by -1 ribosomal frameshift
author: Makinen, K.
author: Naess, V.
author: Tamm, T.
author: Truve, E.
author: Aaspollu, A.
author: Saarma, M.
journal: Virology
volume: 207
issue: 2
pages: 566-571
year: 1995
pubmed: 7886961

7886961
type: PubMed
SIO_000068: pubmed

8
title: Direct Submission
journal: Submitted (08-FEB-2013) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA

9
title: Direct Submission
author: Fargette, D.
journal: Submitted (18-NOV-2003) Fargette D., Dgpc, Ird, BP 64501, 34394 Montpellier cedex 5, FRANCE

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

position:4449:1
position: 4449
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4449:1:source
so part of: sequence
organism: Rice yellow mottle virus
mol type: genomic RNA
isolate: CI4
country: Cote d'Ivoire

31744
type: Taxonomy
SIO_000068: taxonomy

RYMVgp1
type: Gene
subclass of: SO_0000704
RO_0002162: 31744
locus tag: RYMVgp1
so part of: sequence
location: 81..554
location: region:81-554:1
so has part: feature:81-554:1:exon
subclass of: SO_0000010

1496989
type: Gene
SIO_000068: ncbigene

position:81:1
position: 81
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:554:1
position: 554
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:81-554:1:exon

RYMVgp1
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 31744
locus tag: RYMVgp1
function: possible roles in suppression of post-transcriptional gene silencing and viral movement
note: ORF1
codon start: 1
product: P1
translation: MTRLEVLIRPTQQTVAKAIAVGYTHALTWVWHSQTWDVDAVSDPVLSADFNPEKVGWVSVSFACTRCTAHYYTSEQVKYFVNIPPVHYDVVCADCERSVQQDDEIDREHDERNAEISACNARALSEGRPASLVYLSRDACDIPEHSGTCRFDKYLNF
SIO_010081: RYMVgp1
subclass of: SO_0000673
so part of: RYMVgp1
location: 81..554
location: region:81-554:1
so has part: feature:81-554:1:exon

YP_007438860.1
type: Protein
SIO_000068: ncbiprotein

IPR021971
type: InterPro
SIO_000068: interpro

Q709L6
type: UniProt
SIO_000068: uniprot

urn:…
SIO_000300: 1
SIO_000628: feature:81-554:1:exon

RYMVgp6
type: Gene
subclass of: SO_0000704
RO_0002162: 31744
gene: ORFx
locus tag: RYMVgp6
so part of: sequence
location: 566..820
location: region:566-820:1
so has part: feature:566-820:1:exon
subclass of: SO_0000010

17778958
type: Gene
SIO_000068: ncbigene

position:566:1
position: 566
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:820:1
position: 820
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:566-820:1:exon

RYMVgp6
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 31744
gene: ORFx
locus tag: RYMVgp6
inference: non-experimental evidence, no additional details recorded
note: non-AUG initiation; exact initiation site not experimentally determined; inferred from homology to Px protein in Turnip rosette virus
codon start: 1
transl except: (pos:566..568,aa:Met)
product: Px
translation: MPTSKERSWFRLTRDGLFCCWSLSHSHQGNDEGGLPPPHRLGWVDSGRDSLRAPARDGVIVGNPLSYHSKLDRAVSSRELQPVR
SIO_010081: RYMVgp6
subclass of: SO_0000673
so part of: RYMVgp6
location: 566..820
location: region:566-820:1
so has part: feature:566-820:1:exon

YP_008873118.2
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:566-820:1:exon

RYMVgp5
type: Gene
subclass of: SO_0000704
RO_0002162: 31744
locus tag: RYMVgp5
so part of: sequence
location: 609..3607
location: region:609-3607:1
so has part: feature:609-3607:1:exon
subclass of: SO_0000010

14669062
type: Gene
SIO_000068: ncbigene

position:609:1
position: 609
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3607:1
position: 3607
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:609-3607:1:exon

RYMVgp5
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 31744
locus tag: RYMVgp5
note: encodes membrane anchor, protease, VPg, RdRp; Predicted from homology with Cocksfoot mottle sobemovirus
codon start: 1
product: polyprotein P2ab
translation: MGSSVVGRFLTRTKETTRVDSHLLIVLAGLIAAAIVSERLPVTASLWAIPSAIIANWIVLSAHESFSRFVEGVEIEPMSTLRYGKVQSAPRFDPSRGYVVDVSYNGHVIPVILDFTTTTALSVPQRVNPGVSMEASRGGLPPTSVKLEDVPPSVVVLYHDSVRLGLGTRVRTPTGRDLLMTNHHIAALEPNGIAYKGHLKKVALDAPVIACDHPHIDCAFYEVPPKIWSLLGVKSASLKPLVKQTAVSLFGGSSSTDFSSCVGIAQIGDNPFLIRHQSTTCSGWSGSPLYHKGCVVGLHIGAADGYNVASNVAWYFHTFKKEVIVESPFEIYGKFREANSEEYDESLRHGVQYAEYDFSGDTIRASSNTWVRERERYHAEERRKSGQPSWADRFGDDSGEDVDIETSHPVAPSIPRTRRKRSKRVEQFVDAVSECSFSFESAREGIVPETSAYDHVPLNLPGGGLEPSGESALGRLIQLGEYRWDSLGDSLPSDGMPFSYVGKSGVIFGEHAGKSVCAAVKDAISVFPDLEGFGWPERGSKAELDSLILQAGRFNRTVCPSGLAQAVQSLQERYPKVPPRRCLRDEWRFDDIFDEVERILCETGEVNSASSPGVPLAGLANSNGEVRGLARDLVCLAVVERLNALASVDPRQHNWTPRELVEKGLCDPVRLFVKNEPHPRRKLLERRFRLISSVSLVDQLVERMLFGPQNNTEISTWWQWPSKPGMGLLTPEQIRLVWDDVFQKHQAHPAAEADISGFDWSVQDWELWSDLAIRINRGNFQGNLRRAAISRYYCFMNSVFQLSDGTLIQQELPGLMKSGSYCTSSTNSRIRCLMAELIGSPWCIAMGDDSVEGWIEGAQSKYAALGHTCKEYYPCKTRGRELLEFNFCSHLIRRGHAELTSWPKACFRFLSSKHEDFEDLWVELHTCGVRSRIERYLRGIGRVSHKDGQEGQENQLQPGAARKEEGPTPTWTVGGAPASTGSSGSGLPDIWDGSWSTIF
SIO_010081: RYMVgp5
subclass of: SO_0000673
so part of: RYMVgp5
location: join(609..1985,1985..3607)
location: region:609-3607:1
so has part: feature:609-1985:1:exon
so has part: feature:1985-3607:1:exon

YP_007500964.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:609-1985:1:exon

position:1985:1
position: 1985
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1985-3607:1:exon

RYMVgp5
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 31744
locus tag: RYMVgp5
product: VPg protein
experiment: EXISTENCE: mass spectrometry[ 21068217]
note: Viral genome-linked protein (VPg) attached to the 5' end of viral RNA. Viral RNA linked to serine at position 1.VPg acts as a primer for replication by interacting with viral RdRp and also regulates translation by interacting with initiation factor.
SIO_010081: RYMVgp5
subclass of: SO_0000673
so part of: RYMVgp5
location: 1584..1823
location: region:1584-1823:1
so has part: feature:1584-1823:1:exon

YP_007518453.1
type: Protein
SIO_000068: ncbiprotein

position:1584:1
position: 1584
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1823:1
position: 1823
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1584-1823:1:exon

RYMVgp2
type: Gene
subclass of: SO_0000704
RO_0002162: 31744
locus tag: RYMVgp2
so part of: sequence
location: 609..2426
location: region:609-2426:1
so has part: feature:609-2426:1:exon
subclass of: SO_0000010

1496992
type: Gene
SIO_000068: ncbigene

position:2426:1
position: 2426
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:609-2426:1:exon

RYMVgp2
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 31744
locus tag: RYMVgp2
note: encodes membrane anchor, protease, VPg, P10, P8
codon start: 1
product: polyprotein P2a
translation: MGSSVVGRFLTRTKETTRVDSHLLIVLAGLIAAAIVSERLPVTASLWAIPSAIIANWIVLSAHESFSRFVEGVEIEPMSTLRYGKVQSAPRFDPSRGYVVDVSYNGHVIPVILDFTTTTALSVPQRVNPGVSMEASRGGLPPTSVKLEDVPPSVVVLYHDSVRLGLGTRVRTPTGRDLLMTNHHIAALEPNGIAYKGHLKKVALDAPVIACDHPHIDCAFYEVPPKIWSLLGVKSASLKPLVKQTAVSLFGGSSSTDFSSCVGIAQIGDNPFLIRHQSTTCSGWSGSPLYHKGCVVGLHIGAADGYNVASNVAWYFHTFKKEVIVESPFEIYGKFREANSEEYDESLRHGVQYAEYDFSGDTIRASSNTWVRERERYHAEERRKSGQPSWADRFGDDSGEDVDIETSHPVAPSIPRTRRKRSKRVEQFVDAVSECSFSFESAREGIVPETSAYDHVPLNCQGAGSSLRASPPLDGLSNSENTAGTPSVIPSLPTECPSATLENRVSSLENMLGKVSAQLSKTQSQYSQILKDLAGLRGEVKQSLTPSSSKPAGSTERYVPPGSRKQSNHSKKGTQKSPPGDASGTSGGSTTSSMKSKESSAKPAK
SIO_010081: RYMVgp2
subclass of: SO_0000673
so part of: RYMVgp2
location: 609..2426
location: region:609-2426:1
so has part: feature:609-2426:1:exon

YP_007438861.1
type: Protein
SIO_000068: ncbiprotein

Q709L5
type: GOA
SIO_000068: goa

IPR009003
type: InterPro
SIO_000068: interpro

Q709L5
type: UniProt
SIO_000068: uniprot

urn:…
SIO_000300: 1
SIO_000628: feature:609-2426:1:exon

RYMVgp2
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 31744
locus tag: RYMVgp2
product: VPg protein
note: Viral genome-linked protein (VPg) attached to the 5' end of viral RNA. Viral RNA linked to serine at position 1. VPg acts as a primer for replication by interacting with viral RdRp and also regulates translation by interacting with initiation factor.
SIO_010081: RYMVgp2
subclass of: SO_0000673
so part of: RYMVgp2
location: 1584..1835
location: region:1584-1835:1
so has part: feature:1584-1835:1:exon

YP_007518452.1
type: Protein
SIO_000068: ncbiprotein

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

urn:…
SIO_000300: 1
SIO_000628: feature:1584-1835:1:exon

RYMVgp4
type: Gene
subclass of: SO_0000704
RO_0002162: 31744
locus tag: RYMVgp4
so part of: sequence
location: 3447..4166
location: region:3447-4166:1
so has part: feature:3447-4166:1:exon
subclass of: SO_0000010

1496991
type: Gene
SIO_000068: ncbigene

position:3447:1
position: 3447
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4166:1
position: 4166
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3447-4166:1:exon

RYMVgp4
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 31744
locus tag: RYMVgp4
codon start: 1
product: capsid protein
translation: MARKGKKTNSNQGQQGKRKGRRPRGRSAEPQLQRAPVAQASRISGTVPGPLSSNTWPLHSVEFLADFKRSSTSADATTYDCVPFNLPRVWSLARCYSMWKPTRWDVVYLPEVSATVAGSIEMCFLYDYADTIPSDTGKMSRTAGFVTSSVWYGAEGCHLLSGGSARNAVVASMDCSRVGWKRVTSSIPSSVDPNVVNTILPARLAVRSSIKPTVSDTPGKLYVIASMVLRDPVDPTLNT
SIO_010081: RYMVgp4
subclass of: SO_0000673
so part of: RYMVgp4
location: 3447..4166
location: region:3447-4166:1
so has part: feature:3447-4166:1:exon

YP_007438863.1
type: Protein
SIO_000068: ncbiprotein

Q9DH71
type: GOA
SIO_000068: goa

IPR000937
type: InterPro
SIO_000068: interpro

Q9DH71
type: UniProt
SIO_000068: uniprot

urn:…
SIO_000300: 1
SIO_000628: feature:3447-4166:1:exon