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

Summary

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

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_086023.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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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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

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_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

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

NM_001106645.1: Suppressed sequence

Description

NM_001106645.1: This RefSeq was removed because it is a nonsense-mediated mRNA decay (NMD) candidate.