Rigi RNA sensor RIG-I [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Rigiprovided by MGI
Official Full Name: RNA sensor RIG-Iprovided by MGI
Primary source: MGI:MGI:2442858
See related: Ensembl:ENSMUSG00000040296 AllianceGenome:MGI:2442858
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Ddx58; RIG-I; RLR-1; C330021E21; 6430573D20Rik
Summary: Enables double-stranded DNA binding activity; double-stranded RNA binding activity; and single-stranded RNA binding activity. Involved in several processes, including innate immune response; positive regulation of cytokine production; and response to virus. Acts upstream of or within response to exogenous dsRNA. Predicted to be located in actin cytoskeleton; bicellular tight junction; and ruffle membrane. Predicted to be part of ribonucleoprotein complex. Predicted to be active in cytoplasm. Is expressed in several structures, including foregut; olfactory epithelium; ovary; renal calyx; and submandibular gland primordium. Orthologous to human RIGI (RNA sensor RIG-I). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in placenta adult (RPKM 6.5), spleen adult (RPKM 6.4) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 4 A5; 4 20.24 cM

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	4	NC_000070.7 (40203775..40239843, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	4	NC_000070.6 (40203777..40239825, complement)

Chromosome 4 - NC_000070.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

DDX58 variant triggers IFN-beta-induced autophagy in trabecular meshwork and influences intraocular pressure.
Title: DDX58 variant triggers IFN-β-induced autophagy in trabecular meshwork and influences intraocular pressure.
DUSP4 modulates RIG-I- and STING-mediated IRF3-type I IFN response.
Title: DUSP4 modulates RIG-I- and STING-mediated IRF3-type I IFN response.
NR4A1 depletion inhibits colorectal cancer progression by promoting necroptosis via the RIG-I-like receptor pathway.
Title: NR4A1 depletion inhibits colorectal cancer progression by promoting necroptosis via the RIG-I-like receptor pathway.
CD97 negatively regulates the innate immune response against RNA viruses by promoting RNF125-mediated RIG-I degradation.
Title: CD97 negatively regulates the innate immune response against RNA viruses by promoting RNF125-mediated RIG-I degradation.
MAVS-loaded unanchored Lys63-linked polyubiquitin chains activate the RIG-I-MAVS signaling cascade.
Title: MAVS-loaded unanchored Lys63-linked polyubiquitin chains activate the RIG-I-MAVS signaling cascade.
Negative Regulation of RIG-I by Tim-3 Promotes H1N1 Infection.
Title: Negative Regulation of RIG-I by Tim-3 Promotes H1N1 Infection.
JMJD4-demethylated RIG-I prevents hepatic steatosis and carcinogenesis.
Title: JMJD4-demethylated RIG-I prevents hepatic steatosis and carcinogenesis.
RIG-I acts as a tumor suppressor in melanoma via regulating the activation of the MKK/p38MAPK signaling pathway.
Title: RIG-I acts as a tumor suppressor in melanoma via regulating the activation of the MKK/p38MAPK signaling pathway.
Involvement of RIG-I Pathway in Neurotropic Virus-Induced Acute Flaccid Paralysis and Subsequent Spinal Motor Neuron Death.
Title: Involvement of RIG-I Pathway in Neurotropic Virus-Induced Acute Flaccid Paralysis and Subsequent Spinal Motor Neuron Death.
Riok3 inhibits the antiviral immune response by facilitating TRIM40-mediated RIG-I and MDA5 degradation.
Title: Riok3 inhibits the antiviral immune response by facilitating TRIM40-mediated RIG-I and MDA5 degradation.

Submit: New GeneRIF Correction See all GeneRIFs (112)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (8)
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D10Mit157.2 (e-PCR), detects polymorphism
- UniSTS:126061

Gene Ontology Provided by MGI

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 ATP hydrolysis activity	ISS Inferred from Sequence or Structural Similarity more info
enables ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
enables GTP binding	IEA Inferred from Electronic Annotation more info
enables GTP binding	ISO Inferred from Sequence Orthology more info
enables RNA helicase activity	ISO Inferred from Sequence Orthology more info
enables RNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
enables double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables double-stranded RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables double-stranded RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables double-stranded RNA binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables pattern recognition receptor activity	IEA Inferred from Electronic Annotation more info
enables pattern recognition receptor activity	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables single-stranded RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables single-stranded RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables single-stranded RNA binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase binding	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in RIG-I signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in RIG-I signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in antiviral innate immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in antiviral innate immune response	ISO Inferred from Sequence Orthology more info
involved_in antiviral innate immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to exogenous dsRNA	ISO Inferred from Sequence Orthology more info
involved_in cellular response to exogenous dsRNA	ISS Inferred from Sequence or Structural Similarity more info
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in cytoplasmic pattern recognition receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in cytoplasmic pattern recognition receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in defense response to virus	ISO Inferred from Sequence Orthology more info
involved_in detection of virus	IEA Inferred from Electronic Annotation more info
involved_in detection of virus	ISO Inferred from Sequence Orthology more info
involved_in gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in innate immune response	IMP Inferred from Mutant Phenotype more info	PubMed
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 defense response to virus by host	ISS Inferred from Sequence or Structural Similarity 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	IEA Inferred from Electronic Annotation 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-alpha production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of interferon-beta production	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of interferon-beta production	ISO Inferred from Sequence Orthology more info	PubMed
involved_in positive regulation of interferon-beta production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interferon-beta production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of interleukin-6 production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interleukin-6 production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of interleukin-8 production	IEA Inferred from Electronic Annotation 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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of response to cytokine stimulus	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of response to cytokine stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation 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 positive regulation of tumor necrosis factor production	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cell migration	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell migration	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within response to exogenous dsRNA	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to virus	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in actin cytoskeleton	ISO Inferred from Sequence Orthology more info
located_in actin cytoskeleton	ISS Inferred from Sequence or Structural Similarity more info
located_in bicellular tight junction	ISO Inferred from Sequence Orthology more info
located_in bicellular tight junction	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	TAS Traceable Author Statement more info
part_of ribonucleoprotein complex	ISO Inferred from Sequence Orthology more info
part_of ribonucleoprotein complex	ISS Inferred from Sequence or Structural Similarity more info
located_in ruffle membrane	ISO Inferred from Sequence Orthology more info
located_in ruffle membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: antiviral innate immune response receptor RIG-I

Names: ATP-dependent RNA helicase DDX58; DEAD (Asp-Glu-Ala-Asp) box polypeptide 58; DEAD box protein 58; DEAD/H box helicase 58; DEAD/H box polypeptide RIG-I; RIG-1; RIG-I-like receptor 1; probable ATP-dependent RNA helicase DDX58; retinoic acid-inducible gene 1 protein; retinoic acid-inducible gene I protein; retinoic acid-inducible gene-I

NP_766277.3

EC 3.6.4.13

XP_036019879.1

EC 3.6.4.13

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)

NM_172689.3 → NP_766277.3 antiviral innate immune response receptor RIG-I

See identical proteins and their annotated locations for NP_766277.3

Status: VALIDATED

Source sequence(s)

AK049305, AK087261, BC127163

Consensus CDS

CCDS18043.1

UniProtKB/Swiss-Prot

A2AP28, Q6Q899, Q8C320, Q8C5I3, Q8C7T2

UniProtKB/TrEMBL

A7YY79

Related

ENSMUSP00000042433.6, ENSMUST00000037907.13

Conserved Domains (7) summary

COG1111
Location:242 → 807

MPH1; ERCC4-related helicase [Replication, recombination and repair]

cd00046
Location:259 → 411

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.

cd08816
Location:2 → 92

CARD_RIG-I_r1; Caspase activation and recruitment domain found in RIG-I, first repeat

cd08817
Location:100 → 188

CARD_RIG-I_r2; Caspase activation and recruitment domain found in RIG-I, second repeat

cd12090
Location:470 → 605

MDA5_ID; Insert domain of MDA5

pfam00271
Location:614 → 734

Helicase_C; Helicase conserved C-terminal domain

pfam11648
Location:808 → 923

RIG-I_C-RD; C-terminal domain of RIG-I

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000070.7 Reference GRCm39 C57BL/6J

Range

40203775..40239843 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036163986.1 → XP_036019879.1 antiviral innate immune response receptor RIG-I isoform X1

Conserved Domains (4) summary

cd15805
Location:437 → 550

RIG-I_C; C-terminal domain of Retinoic acid-inducible gene (RIG)-I protein, a cytoplasmic viral RNA receptor

cd12090
Location:101 → 236

MDA5_ID; Insert domain of MDA5

cl38915
Location:241 → 374

DEAD-like_helicase_C; C-terminal helicase domain of the DEAD-like helicases

cl28899
Location:1 → 74

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily