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RIGI RNA sensor RIG-I [ Sus scrofa (pig) ]

Gene ID: 396723, updated on 17-Aug-2024

Summary

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Official Symbol
RIGIprovided by VGNC
Official Full Name
RNA sensor RIG-Iprovided by VGNC
Primary source
VGNC:VGNC:95905
See related
Ensembl:ENSSSCG00000030408
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Sus scrofa
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Suina; Suidae; Sus
Also known as
DDX58; RIG-1; RIG-I; RLR-1; RHIV-1
Expression
Ubiquitous expression in liver (RPKM 18.0), lung (RPKM 17.9) and 8 other tissues See more
Orthologs
human mouse all
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Genomic context

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See RIGI in Genome Data Viewer
Location:
chromosome: 10
Exon count:
24
Annotation release Status Assembly Chr Location
106 current Sscrofa11.1 (GCF_000003025.6) 10 NC_010452.4 (33891720..33976151)
105 previous assembly Sscrofa10.2 (GCF_000003025.5) 10 NC_010452.3 (38145289..38189016)

Chromosome 10 - NC_010452.4Genomic Context describing neighboring genes Neighboring gene NADH:ubiquinone oxidoreductase subunit B6 Neighboring gene TOP1 binding arginine/serine rich protein, E3 ubiquitin ligase Neighboring gene aconitase 1 Neighboring gene translation initiation factor IF-2-like Neighboring gene peroxisomal biogenesis factor 19 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Transcriptome data used for gene annotation Transcriptome data used for gene annotation
  • Description: Nine kinds of tissues and a mixture of multiple tissues were sequenced for genome annotation
  • BioProject: PRJNA311523
  • Publication: PMID 27646534
  • Analysis date: Thu Dec 14 17:10:49 2017

Bibliography

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Related articles in PubMed

  1. RIG-I is responsible for activation of type I interferon pathway in Seneca Valley virus-infected porcine cells to suppress viral replication. Li P, et al. Virol J, 2018 Oct 23. PMID 30352599, Free PMC Article
  2. An RNA helicase, RHIV -1, induced by porcine reproductive and respiratory syndrome virus (PRRSV) is mapped on porcine chromosome 10q13. Zhang X, et al. Microb Pathog, 2000 May. PMID 10799277
  3. Identification of the RNA Pseudoknot within the 3' End of the Porcine Reproductive and Respiratory Syndrome Virus Genome as a Pathogen-Associated Molecular Pattern To Activate Antiviral Signaling via RIG-I and Toll-Like Receptor 3. Xie S, et al. J Virol, 2018 Jun 15. PMID 29618647, Free PMC Article
  4. Classical swine fever virus triggers RIG-I and MDA5-dependent signaling pathway to IRF-3 and NF-κB activation to promote secretion of interferon and inflammatory cytokines in porcine alveolar macrophages. Dong XY, et al. Virol J, 2013 Sep 13. PMID 24034559, Free PMC Article
  5. Porcine circovirus 2 infection induces IFNβ expression through increased expression of genes involved in RIG-I and IRF7 signaling pathways. Dvorak CMT, et al. Virus Res, 2018 Jul 15. PMID 29864504

See all (13) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. These results indicate for the first time that TRIM25 inhibits Porcine reproductive and respiratory virus replication and that the N protein antagonizes the antiviral activity by interfering with TRIM25-mediated RIG-I ubiquitination.
    Title: Nucleocapsid protein of porcine reproductive and respiratory syndrome virus antagonizes the antiviral activity of TRIM25 by interfering with TRIM25-mediated RIG-I ubiquitination.
  2. This study indicated that RIG-I showed an antiviral role against Seneca valley virus and was essential for activation of type I IFN signaling during SVV infection.
    Title: RIG-I is responsible for activation of type I interferon pathway in Seneca Valley virus-infected porcine cells to suppress viral replication.
  3. Key regulators involved in Porcine circovirus 2 infection were identified as IFNbeta, DDX58 (RIG-I), and IRF7.
    Title: Porcine circovirus 2 infection induces IFNβ expression through increased expression of genes involved in RIG-I and IRF7 signaling pathways.
  4. RIG-I and TLR3 interact with the pseudoknot of Porcine Reproductive and Respiratory Syndrome Virus 3' untranslated regions. Both RIG-I and TLR3 are required for the pseudoknot to induce interferon response.
    Title: Identification of the RNA Pseudoknot within the 3' End of the Porcine Reproductive and Respiratory Syndrome Virus Genome as a Pathogen-Associated Molecular Pattern To Activate Antiviral Signaling via RIG-I and Toll-Like Receptor 3.
  5. Viral RNA polymerase components PB2, PB1, and PA directly target RIG-I.
    Title: Interactions between the influenza A virus RNA polymerase components and retinoic acid-inducible gene I.
  6. These data indicate that classical swine fever virus can be recognized by both RIG-I and MDA5 to initiate the RIG-I signaling pathway to trigger innate defenses against infection.
    Title: Classical swine fever virus triggers RIG-I and MDA5-dependent signaling pathway to IRF-3 and NF-κB activation to promote secretion of interferon and inflammatory cytokines in porcine alveolar macrophages.
  7. DDX58 had two nonsynonymous SNPs in the helicase domain.
    Title: Differences in distribution of single nucleotide polymorphisms among intracellular pattern recognition receptors in pigs.
Submit: New GeneRIF Correction

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Gene Ontology Provided by RefSeq

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables double-stranded RNA binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables single-stranded RNA binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 PubMed 

General protein information

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Preferred Names
antiviral innate immune response receptor RIG-I; probable ATP-dependent RNA helicase DDX58
Names
ATP-dependent RNA helicase DDX58
DEAD (Asp-Glu-Ala-Asp) box polypeptide 58
DEAD box protein 58
DExD/H-box helicase 58
RIG-I-like receptor 1
RNA helicase induced by virus
retinoic acid inducible protein I
retinoic acid-inducible gene 1 protein
NP_998969.2
XP_020919713.1
XP_020919714.1
XP_020919715.1
XP_020919716.1
XP_020919717.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_213804.2 → NP_998969.2  antiviral innate immune response receptor RIG-I

    See identical proteins and their annotated locations for NP_998969.2

    Status: PROVISIONAL

    Source sequence(s)
    AB426546
    UniProtKB/TrEMBL
    A0A8D1J1I8, A8CYB8, B9WZD6
    Conserved Domains (7) summary
    COG1111
    Location:240 → 796
    MPH1; ERCC4-related helicase [Replication, recombination and repair]
    cd00046
    Location:257 → 409
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd08817
    Location:100 → 186
    CARD_RIG-I_r2; Caspase activation and recruitment domain found in RIG-I, second repeat
    cd12090
    Location:468 → 608
    MDA5_ID; Insert domain of MDA5
    pfam00271
    Location:621 → 737
    Helicase_C; Helicase conserved C-terminal domain
    pfam11648
    Location:818 → 926
    RIG-I_C-RD; C-terminal domain of RIG-I
    cl14633
    Location:2 → 92
    DD; Death Domain Superfamily of protein-protein interaction domains

RefSeqs of Annotated Genomes: Sus scrofa Annotation Release 106 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference Sscrofa11.1 Primary Assembly

Genomic

  1. NC_010452.4 Reference Sscrofa11.1 Primary Assembly

    Range
    33891720..33976151
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021064058.1 → XP_020919717.1  probable ATP-dependent RNA helicase DDX58 isoform X2

    UniProtKB/TrEMBL
    A0A8D0I1A7, A0A8D1WI72
    Conserved Domains (3) summary
    cd08817
    Location:100 → 186
    CARD_RIG-I_r2; Caspase activation and recruitment domain found in RIG-I, second repeat
    cl14633
    Location:2 → 92
    DD; Death Domain Superfamily of protein-protein interaction domains
    cl17041
    Location:240 → 796
    helicase_insert_domain

  2. XM_021064056.1 → XP_020919715.1  probable ATP-dependent RNA helicase DDX58 isoform X2

    UniProtKB/TrEMBL
    A0A8D0I1A7, A0A8D1WI72
    Related
    ENSSSCP00000023307.3, ENSSSCT00000026775.3
    Conserved Domains (3) summary
    cd08817
    Location:100 → 186
    CARD_RIG-I_r2; Caspase activation and recruitment domain found in RIG-I, second repeat
    cl14633
    Location:2 → 92
    DD; Death Domain Superfamily of protein-protein interaction domains
    cl17041
    Location:240 → 796
    helicase_insert_domain

  3. XM_021064055.1 → XP_020919714.1  probable ATP-dependent RNA helicase DDX58 isoform X2

    UniProtKB/TrEMBL
    A0A8D0I1A7, A0A8D1WI72
    Conserved Domains (3) summary
    cd08817
    Location:100 → 186
    CARD_RIG-I_r2; Caspase activation and recruitment domain found in RIG-I, second repeat
    cl14633
    Location:2 → 92
    DD; Death Domain Superfamily of protein-protein interaction domains
    cl17041
    Location:240 → 796
    helicase_insert_domain

  4. XM_021064057.1 → XP_020919716.1  probable ATP-dependent RNA helicase DDX58 isoform X2

    UniProtKB/TrEMBL
    A0A8D0I1A7, A0A8D1WI72
    Conserved Domains (3) summary
    cd08817
    Location:100 → 186
    CARD_RIG-I_r2; Caspase activation and recruitment domain found in RIG-I, second repeat
    cl14633
    Location:2 → 92
    DD; Death Domain Superfamily of protein-protein interaction domains
    cl17041
    Location:240 → 796
    helicase_insert_domain

  5. XM_021064054.1 → XP_020919713.1  probable ATP-dependent RNA helicase DDX58 isoform X1

    UniProtKB/TrEMBL
    A0A287AMJ0, A0A8D0I3K7
    Related
    ENSSSCP00000045260.2, ENSSSCT00000058360.3
    Conserved Domains (4) summary
    cd08817
    Location:100 → 186
    CARD_RIG-I_r2; Caspase activation and recruitment domain found in RIG-I, second repeat
    pfam11648
    Location:817 → 925
    RIG-I_C-RD; C-terminal domain of RIG-I
    cl14633
    Location:2 → 92
    DD; Death Domain Superfamily of protein-protein interaction domains
    cl17041
    Location:239 → 795
    helicase_insert_domain

RNA

  1. XR_002336113.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9GLV6.1 GenPept UniProtKB/Swiss-Prot:Q9GLV6

Gene LinkOut

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