RIGI RNA sensor RIG-I [Homo sapiens (human)] - Gene

Summary

Official Symbol: RIGIprovided by HGNC
Official Full Name: RNA sensor RIG-Iprovided by HGNC
Primary source: HGNC:HGNC:19102
See related: Ensembl:ENSG00000107201 MIM:609631; AllianceGenome:HGNC:19102
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: RIG1; DDX58; RIG-I; RLR-1; SGMRT2
Summary: DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases which are implicated in a number of cellular processes involving RNA binding and alteration of RNA secondary structure. This gene encodes a protein containing RNA helicase-DEAD box protein motifs and a caspase recruitment domain (CARD). It is involved in viral double-stranded (ds) RNA recognition and the regulation of the antiviral innate immune response. Mutations in this gene are associated with Singleton-Merten syndrome 2. [provided by RefSeq, Aug 2020]
Annotation information: Note: RARRES3 (Gene ID: 5920) and DDX58 (Gene ID: 23586) share the RIG1/RIG-1 alias in common. RIG1 is a widely used alternative name for DExD/H-box helicase 58 (DDX58), which can be confused with the retinoic acid receptor responder 3 (RARRES3) gene, since they share the same alias. [22 Jan 2019]; Note: This gene has been reviewed for its involvement in coronavirus biology, and is involved in immune response or antiviral activity.
Expression: Ubiquitous expression in appendix (RPKM 7.8), spleen (RPKM 7.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9p21.1

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (32455302..32526196, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (32471227..32542369, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (32455300..32526194, complement)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Proofreading mechanisms of the innate immune receptor RIG-I: distinguishing self and viral RNA.
Title: Proofreading mechanisms of the innate immune receptor RIG-I: distinguishing self and viral RNA.
The RNA helicase DHX35 functions as a co-sensor for RIG-I-mediated innate immunity.
Title: The RNA helicase DHX35 functions as a co-sensor for RIG-I-mediated innate immunity.
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.
Mammalian reovirus micro1 protein attenuates RIG-I and MDA5-mediated signaling transduction by blocking IRF3 phosphorylation and nuclear translocation.
Title: Mammalian reovirus µ1 protein attenuates RIG-I and MDA5-mediated signaling transduction by blocking IRF3 phosphorylation and nuclear translocation.
Activation of the RIG-I/MAVS Signaling Pathway during Human Adenovirus Type 3 Infection Impairs the Pro-Inflammatory Response Induced by Secondary Infection with Staphylococcus aureus.
Title: Activation of the RIG-I/MAVS Signaling Pathway during Human Adenovirus Type 3 Infection Impairs the Pro-Inflammatory Response Induced by Secondary Infection with Staphylococcus aureus.
IFI16 Positively Regulates RIG-I-Mediated Type I Interferon Production in a STING-Independent Manner.
Title: IFI16 Positively Regulates RIG-I-Mediated Type I Interferon Production in a STING-Independent Manner.
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.
Functional comparisons of the virus sensor RIG-I from humans, the microbat Myotis daubentonii, and the megabat Rousettus aegyptiacus, and their response to SARS-CoV-2 infection.
Title: Functional comparisons of the virus sensor RIG-I from humans, the microbat Myotis daubentonii, and the megabat Rousettus aegyptiacus, and their response to SARS-CoV-2 infection.
Coxsackievirus A6 2C protein antagonizes IFN-beta production through MDA5 and RIG-I depletion.
Title: Coxsackievirus A6 2C protein antagonizes IFN-β production through MDA5 and RIG-I depletion.
A conserved isoleucine in the binding pocket of RIG-I controls immune tolerance to mitochondrial RNA.
Title: A conserved isoleucine in the binding pocket of RIG-I controls immune tolerance to mitochondrial RNA.

Submit: New GeneRIF Correction See all GeneRIFs (466)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Singleton-Merten syndrome 2 MedGen: C4225380 OMIM: 616298 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Vpr	vpr	HIV-1 Vpr upregulates the gene expression of DDX58 in human monocyte-derived dendritic cells	PubMed
	vpr	HIV-1 Vpr upregulates the gene expression of DDX58 in human monocyte-derived macrophages	PubMed
retropepsin	gag-pol	HIV-1 PR targets and relocalizes RIG-I to an insoluble membrane fraction followed by lysosome-mediated degradation	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH47960 (e-PCR)
- UniSTS:54559

SHGC-147173 (e-PCR)
- UniSTS:175657

SHGC-57118 (e-PCR)
- UniSTS:32560

RH78416 (e-PCR)
- UniSTS:89149

RH69451 (e-PCR)
- UniSTS:73331

SHGC-56591 (e-PCR)
- UniSTS:55175

SHGC-57421 (e-PCR)
- UniSTS:72344

G59518 (e-PCR)
- UniSTS:136681

G43514 (e-PCR)
- UniSTS:94971

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IMP Inferred from Mutant Phenotype more info	PubMed
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	IMP Inferred from Mutant Phenotype more info	PubMed
enables RNA helicase activity	IMP Inferred from Mutant Phenotype more info	PubMed
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	IEA Inferred from Electronic Annotation more info
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	IMP Inferred from Mutant Phenotype more info	PubMed
enables double-stranded RNA binding	TAS Traceable Author Statement more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables pattern recognition receptor activity	IDA Inferred from Direct Assay more info	PubMed
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	IMP Inferred from Mutant Phenotype more info	PubMed
enables ubiquitin protein ligase binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in RIG-I signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in RIG-I signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in antiviral innate immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in antiviral innate immune response	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to exogenous dsRNA	IMP Inferred from Mutant Phenotype more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
involved_in cytoplasmic pattern recognition receptor signaling pathway	TAS Traceable Author Statement more info	PubMed
involved_in defense response to virus	IDA Inferred from Direct Assay more info	PubMed
involved_in detection of virus	IDA Inferred from Direct Assay more info	PubMed
involved_in gene expression	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of defense response to virus by host	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of granulocyte macrophage colony-stimulating factor production	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of interferon-alpha production	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of interferon-alpha production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of interferon-beta production	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of interferon-beta production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of interleukin-6 production	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of interleukin-6 production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of interleukin-8 production	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of myeloid dendritic cell cytokine production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of response to cytokine stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of tumor necrosis factor production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of type III interferon production	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within response to exogenous dsRNA	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to virus	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in actin cytoskeleton	IDA Inferred from Direct Assay more info	PubMed
located_in bicellular tight junction	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
part_of ribonucleoprotein complex	IDA Inferred from Direct Assay more info	PubMed
located_in ruffle membrane	IDA Inferred from Direct Assay more info	PubMed

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 (Asp-Glu-Ala-Asp/His) box polypeptide; DExD/H-box helicase 58; RNA helicase RIG-I; probable ATP-dependent RNA helicase DDX58; retinoic acid-inducible gene 1 protein; retinoic acid-inducible gene I protein

NP_001372836.1

EC 3.6.4.13

NP_001372838.1

EC 3.6.4.13

NP_001372839.1

EC 3.6.4.13

NP_001372841.1

EC 3.6.4.13

NP_001372842.1

EC 3.6.4.13

NP_001372843.1

EC 3.6.4.13

NP_055129.2

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.

Genomic

NG_046918.1 RefSeqGene

Range

5129..76023

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001385907.1 → NP_001372836.1 antiviral innate immune response receptor RIG-I isoform 2

Status: REVIEWED

Source sequence(s)

AL161783, AL353671

UniProtKB/TrEMBL

A0AAQ5BIF4, A0AAQ5BIG4

Related

ENSP00000520439.1, ENST00000715270.1

Conserved Domains (5) summary

COG1111
Location:243 → 769

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

cd08817
Location:100 → 189

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

cd15805
Location:803 → 916

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

cd18073
Location:241 → 440

DEXHc_RIG-I_DDX58; DEXH-box helicase domain of RIG-I

cl14633
Location:2 → 92

DD; Death Domain Superfamily of protein-protein interaction domains
NM_001385909.1 → NP_001372838.1 antiviral innate immune response receptor RIG-I isoform 3

Status: REVIEWED

Source sequence(s)

AL161783, AL353671

UniProtKB/TrEMBL

A0AAQ5BIF4

Conserved Domains (6) summary

cd08817
Location:100 → 189

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

cd15805
Location:748 → 861

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

cd12090
Location:469 → 604

MDA5_ID; Insert domain of MDA5

cd18073
Location:241 → 442

DEXHc_RIG-I_DDX58; DEXH-box helicase domain of RIG-I

cl38915
Location:609 → 671

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

cl14633
Location:2 → 92

DD; Death Domain Superfamily of protein-protein interaction domains
NM_001385910.1 → NP_001372839.1 antiviral innate immune response receptor RIG-I isoform 4

Status: REVIEWED

Source sequence(s)

AL161783, AL353671

UniProtKB/TrEMBL

B3KWW1

Conserved Domains (4) summary

COG1111
Location:96 → 624

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

cd15805
Location:658 → 771

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

cd18073
Location:94 → 295

DEXHc_RIG-I_DDX58; DEXH-box helicase domain of RIG-I

cl14633
Location:1 → 42

DD; Death Domain Superfamily of protein-protein interaction domains
NM_001385912.1 → NP_001372841.1 antiviral innate immune response receptor RIG-I isoform 5

Status: REVIEWED

Source sequence(s)

AL161783, AL353671

UniProtKB/TrEMBL

A2A376, B3KWW1

Conserved Domains (3) summary

COG1111
Location:40 → 568

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

cd15805
Location:602 → 715

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

cd18073
Location:38 → 239

DEXHc_RIG-I_DDX58; DEXH-box helicase domain of RIG-I
NM_001385913.1 → NP_001372842.1 antiviral innate immune response receptor RIG-I isoform 6

Status: REVIEWED

Source sequence(s)

AL161783, AL353671

UniProtKB/TrEMBL

A0AAQ5BIF4

Conserved Domains (5) summary

COG1111
Location:238 → 766

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

cd08817
Location:100 → 184

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

cd15805
Location:800 → 913

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

cd18073
Location:236 → 437

DEXHc_RIG-I_DDX58; DEXH-box helicase domain of RIG-I

cl14633
Location:2 → 92

DD; Death Domain Superfamily of protein-protein interaction domains
NM_001385914.1 → NP_001372843.1 antiviral innate immune response receptor RIG-I isoform 7

Status: REVIEWED

Source sequence(s)

AL161783, AL353671

UniProtKB/TrEMBL

B3KWW1

Conserved Domains (4) summary

COG1111
Location:95 → 623

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

cd15805
Location:657 → 770

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

cd18073
Location:93 → 294

DEXHc_RIG-I_DDX58; DEXH-box helicase domain of RIG-I

cl14633
Location:1 → 42

DD; Death Domain Superfamily of protein-protein interaction domains
NM_014314.4 → NP_055129.2 antiviral innate immune response receptor RIG-I isoform 1

See identical proteins and their annotated locations for NP_055129.2

Status: REVIEWED

Source sequence(s)

AA862613, AF038963, AL161783, BC070029, DN998145

Consensus CDS

CCDS6526.1

UniProtKB/Swiss-Prot

A2RU81, O95786, Q5HYE1, Q5VYT1, Q9NT04

UniProtKB/TrEMBL

A0AAQ5BIF4

Related

ENSP00000369213.2, ENST00000379883.3

Conserved Domains (4) summary

cd08817
Location:100 → 189

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

cd15805
Location:805 → 918

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

cl14633
Location:2 → 92

DD; Death Domain Superfamily of protein-protein interaction domains

cl17041
Location:243 → 771

helicase_insert_domain; helicase_insert_domain