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    Rig1 RNA sensor RIG-1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 297989, updated on 30-Mar-2024

    Summary

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    Official Symbol
    Rig1provided by RGD
    Official Full Name
    RNA sensor RIG-1provided by RGD
    Primary source
    RGD:1309460
    See related
    Ensembl:ENSRNOG00000006384 AllianceGenome:RGD:1309460
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Ddx58
    Summary
    Predicted to enable several functions, including nucleic acid binding activity; ubiquitin protein ligase binding activity; and zinc ion binding activity. Predicted to be involved in several processes, including positive regulation of cytokine production; regulation of transcription, DNA-templated; and response to virus. Predicted to act upstream of or within response to exogenous dsRNA. Predicted to be located in several cellular components, including actin cytoskeleton; bicellular tight junction; and ruffle membrane. Predicted to be part of ribonucleoprotein complex. Predicted to be active in cytoplasm. Orthologous to human DDX58 (DExD/H-box helicase 58). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Liver (RPKM 140.6), Kidney (RPKM 102.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    5q22
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (60117398..60165995, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (55321351..55369947, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (56486584..56536898, complement)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene RNA, U7 small nuclear 97 Neighboring gene aconitase 1 Neighboring gene uncharacterized LOC120102855 Neighboring gene TOP1 binding arginine/serine rich protein, E3 ubiquitin ligase Neighboring gene small integral membrane protein 27 Neighboring gene NADH:ubiquinone oxidoreductase subunit B6

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. RIG-I helicase-independent pathway in sendai virus-activated dendritic cells is critical for preventing lung metastasis of AT6.3 prostate cancer. Kato T, et al. Neoplasia, 2010 Nov. PMID 21076616, Free PMC Article
    2. Structural basis for ubiquitin-mediated antiviral signal activation by RIG-I. Peisley A, et al. Nature, 2014 May 1. PMID 24590070, Free PMC Article
    3. Structural and functional insights into 5'-ppp RNA pattern recognition by the innate immune receptor RIG-I. Wang Y, et al. Nat Struct Mol Biol, 2010 Jul. PMID 20581823, Free PMC Article
    4. Recognition of 5' triphosphate by RIG-I helicase requires short blunt double-stranded RNA as contained in panhandle of negative-strand virus. Schlee M, et al. Immunity, 2009 Jul 17. PMID 19576794, Free PMC Article
    5. Retinoic acid-induced gene-1 (RIG-I) associates with the actin cytoskeleton via caspase activation and recruitment domain-dependent interactions. Mukherjee A, et al. J Biol Chem, 2009 Mar 6. PMID 19122199, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Results indicate the essential role of RIG-I-independent signaling on antimetastatic effect induced by rSeV-activated DCs and may provide important insights to DC-based immunotherapy for advanced malignancies.
      Title: RIG-I helicase-independent pathway in sendai virus-activated dendritic cells is critical for preventing lung metastasis of AT6.3 prostate cancer.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables GTP binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA helicase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables double-stranded RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables pattern recognition receptor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables single-stranded RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ubiquitin protein ligase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in RIG-I signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in antiviral innate immune response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cellular response to exogenous dsRNA ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cytoplasmic pattern recognition receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in detection of virus ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in innate immune response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of defense response to virus by host ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of granulocyte macrophage colony-stimulating factor production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of interferon-alpha production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of interferon-beta production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of interleukin-6 production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of interleukin-8 production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of myeloid dendritic cell cytokine production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of response to cytokine stimulus ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of tumor necrosis factor production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of cell migration ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within response to exogenous dsRNA ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in response to virus ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in actin cytoskeleton ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in bicellular tight junction ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of ribonucleoprotein complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in ruffle membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    antiviral innate immune response receptor RIG-I
    Names
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 58
    DEXD/H-box helicase 58
    probable ATP-dependent RNA helicase DDX58
    NP_001382000.1

    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_001395071.1 → NP_001382000.1  antiviral innate immune response receptor RIG-I

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000005
      UniProtKB/TrEMBL
      A0A8I6AN81, D4ADT5
      Related
      ENSRNOP00000057492.5, ENSRNOT00000060765.5
      Conserved Domains (5) summary
      COG1111
      Location:242 → 784
      MPH1; ERCC4-related helicase [Replication, recombination and repair]
      cd08816
      Location:2 → 92
      CARD_RIG-I_r1; Caspase activation and recruitment domain found in RIG-I, first repeat
      cd08817
      Location:100 → 186
      CARD_RIG-I_r2; Caspase activation and recruitment domain found in RIG-I, second repeat
      cd15805
      Location:806 → 919
      RIG-I_C; C-terminal domain of Retinoic acid-inducible gene (RIG)-I protein, a cytoplasmic viral RNA receptor
      cd18073
      Location:242 → 443
      DEXHc_RIG-I_DDX58; DEXH-box helicase domain of RIG-I

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086023.1 Reference GRCr8

      Range
      60117398..60165995 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001106645.1: Suppressed sequence

      Description
      NM_001106645.1: This RefSeq was removed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein Strain
    Heading Accession and Version

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