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Aliases for DDX58 Gene

Aliases for DDX58 Gene

  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 58 2 3
  • Retinoic Acid-Inducible Gene 1 Protein 3 4
  • Retinoic Acid-Inducible Gene I Protein 3 4
  • DEAD Box Protein 58 3 4
  • RNA Helicase RIG-I 2 3
  • RIG-I 3 4
  • RLR-1 3 4
  • RIGI 3 6
  • DEAD/H (Asp-Glu-Ala-Asp/His) Box Polypeptide 3
  • Probable ATP-Dependent RNA Helicase DDX58 3
  • Retinoic Acid Inducible Gene I 2
  • RIG-I-Like Receptor 1 4
  • EC 3.6.4.13 4
  • SGMRT2 3
  • RIG-1 4

External Ids for DDX58 Gene

Previous GeneCards Identifiers for DDX58 Gene

  • GC09M032446

Summaries for DDX58 Gene

Entrez Gene Summary for DDX58 Gene

  • 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 immune response. [provided by RefSeq, Jul 2008]

GeneCards Summary for DDX58 Gene

DDX58 (DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 58) is a Protein Coding gene. Diseases associated with DDX58 include ebola hemorrhagic fever and parainfluenza virus type 3. Among its related pathways are Epstein-Barr virus infection and Interferon Signaling. GO annotations related to this gene include identical protein binding and ATP-dependent helicase activity. An important paralog of this gene is DICER1.

UniProtKB/Swiss-Prot for DDX58 Gene

  • Innate immune receptor which acts as a cytoplasmic sensor of viral nucleic acids and plays a major role in sensing viral infection and in the activation of a cascade of antiviral responses including the induction of type I interferons and proinflammatory cytokines. Its ligands include: 5-triphosphorylated ssRNA and dsRNA and short dsRNA (<1 kb in length). In addition to the 5-triphosphate moiety, blunt-end base pairing at the 5-end of the RNA is very essential. Overhangs at the non-triphosphorylated end of the dsRNA RNA have no major impact on its activity. A 3overhang at the 5triphosphate end decreases and any 5overhang at the 5 triphosphate end abolishes its activity. Upon ligand binding it associates with mitochondria antiviral signaling protein (MAVS/IPS1) which activates the IKK-related kinases: TBK1 and IKBKE which phosphorylate interferon regulatory factors: IRF3 and IRF7 which in turn activate transcription of antiviral immunological genes, including interferons (IFNs); IFN-alpha and IFN-beta. Detects both positive and negative strand RNA viruses including members of the families Paramyxoviridae: Human respiratory syncytial virus and measles virus (MeV), Rhabdoviridae: vesicular stomatitis virus (VSV), Orthomyxoviridae: influenza A and B virus, Flaviviridae: Japanese encephalitis virus (JEV), hepatitis C virus (HCV), dengue virus (DENV) and west Nile virus (WNV). It also detects rotavirus and reovirus. Also involved in antiviral signaling in response to viruses containing a dsDNA genome such as Epstein-Barr virus (EBV). Detects dsRNA produced from non-self dsDNA by RNA polymerase III, such as Epstein-Barr virus-encoded RNAs (EBERs). May play important roles in granulocyte production and differentiation, bacterial phagocytosis and in the regulation of cell migration.

Gene Wiki entry for DDX58 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DDX58 Gene

Genomics for DDX58 Gene

Regulatory Elements for DDX58 Gene

Genomic Location for DDX58 Gene

Start:
32,455,302 bp from pter
End:
32,526,324 bp from pter
Size:
71,023 bases
Orientation:
Minus strand

Genomic View for DDX58 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for DDX58 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DDX58 Gene

Proteins for DDX58 Gene

  • Protein details for DDX58 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95786-DDX58_HUMAN
    Recommended name:
    Probable ATP-dependent RNA helicase DDX58
    Protein Accession:
    O95786
    Secondary Accessions:
    • A2RU81
    • Q5HYE1
    • Q5VYT1
    • Q9NT04

    Protein attributes for DDX58 Gene

    Size:
    925 amino acids
    Molecular mass:
    106600 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    • Monomer; maintained as a monomer in an autoinhibited state. Upon viral dsRNA binding and conformation shift, homomultimerizes and interacts (via tandem CARD domain) with MAVS/IPS1 promoting its filamentation. Interacts with DHX58/LGP2, IKBKE, TBK1 and TMEM173/STING. Interacts (via CARD domain) with TRIM25 (via SPRY domain). Interacts with RNF135. Interacts with CYLD. Interacts with NLRC5; blocks the interaction of MAVS/IPS1 to DDX58. Interacts with SRC. Interacts with protein Z of Guanarito virus, Machupo virus, Junin arenavirus and Sabia virus. This interaction disrupts its interaction with MAVS/IPS1, impeding downstream IRF3 and NF-kappa-B activation and resulting in decreased IFN-beta induction. Interacts (via CARD domain) with Human respiratory syncytial virus A non-structural protein 2 (NS2) and this interaction disrupts its interaction with MAVS/IPS1, impeding downstream IRF3 activation. Interacts with Rotavirus A non-structural protein 1 (NSP1) and this interaction induces down-regulation of DDX58/RIG-I. Interacts with DDX60. Interacts with isoform 2 of ZC3HAV1 (via zinc-fingers) in an RNA-dependent manner. Interacts with herpes simplex virus 1 protein US11; this interaction prevents the interaction of MAVS/IPS1 to DDX58.

    Three dimensional structures from OCA and Proteopedia for DDX58 Gene

    Alternative splice isoforms for DDX58 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DDX58 Gene

Proteomics data for DDX58 Gene at MOPED

Post-translational modifications for DDX58 Gene

  • ISGylated. Conjugated to ubiquitin-like protein ISG15 upon IFN-beta stimulation. ISGylation negatively regulates its function in antiviral signaling response.
  • Phosphorylated in resting cells and dephosphorylated in RNA virus-infected cells. Phosphorylation at Thr-770, Ser-854 and Ser-855 results in inhibition of its activity while dephosphorylation at these sites results in its activation.
  • Sumoylated, probably by MUL1; inhibiting its polyubiquitination.
  • Ubiquitinated. Undergoes Lys-48- and Lys-63-linked ubiquitination. Lys-172 is the critical site for TRIM25-mediated ubiquitination, for MAVS/IPS1 binding and to induce anti-viral signal transduction. Lys-154, Lys-164 and Lys-172 are critical sites for RNF135-mediated and TRIM4-mediated ubiquitination. Deubiquitinated by CYLD, a protease that selectively cleaves Lys-63-linked ubiquitin chains. Also probably deubiquitinated by USP17L2/USP17 that cleaves Lys-48-and Lys-63-linked ubiquitin chains and positively regulates the receptor.
  • Ubiquitination at Lys154, Lys164, and Lys172
  • Modification sites at PhosphoSitePlus

Other Protein References for DDX58 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for DDX58 (DDX58)

No data available for DME Specific Peptides for DDX58 Gene

Domains for DDX58 Gene

Gene Families for DDX58 Gene

HGNC:
  • DDX :DEAD-boxes

Graphical View of Domain Structure for InterPro Entry

O95786

UniProtKB/Swiss-Prot:

DDX58_HUMAN :
  • O95786
Domain:
  • The repressor domain controls homomultimerization and interaction with MAVS/IPS1. In the absence of viral infection, the protein is maintained as a monomer in an autoinhibited state with the CARD domains masked through intramolecular interactions mediated by the repressor domain. Upon binding to viral RNA in the presence of ATP, the repressor domain induces a conformational change exposing the CARD domain and promotes dimerization and CARD interactions with the adapter protein MAVS/IPS1 leading to the induction of downstream signaling
  • The helicase domain is responsible for dsRNA recognition
  • The 2 CARD domains are responsible for interaction with and signaling through MAVS/IPS1 and for association with the actin cytoskeleton
  • The second CARD domain is the primary site for Lys-63-linked ubiquitination
  • Contains 2 CARD domains.
  • Contains 1 helicase ATP-binding domain.
  • Contains 1 helicase C-terminal domain.
Family:
  • Belongs to the helicase family. RLR subfamily.
genes like me logo Genes that share domains with DDX58: view

Function for DDX58 Gene

Molecular function for DDX58 Gene

UniProtKB/Swiss-Prot CatalyticActivity: ATP + H(2)O = ADP + phosphate
UniProtKB/Swiss-Prot Function: Innate immune receptor which acts as a cytoplasmic sensor of viral nucleic acids and plays a major role in sensing viral infection and in the activation of a cascade of antiviral responses including the induction of type I interferons and proinflammatory cytokines. Its ligands include: 5-triphosphorylated ssRNA and dsRNA and short dsRNA (<1 kb in length). In addition to the 5-triphosphate moiety, blunt-end base pairing at the 5-end of the RNA is very essential. Overhangs at the non-triphosphorylated end of the dsRNA RNA have no major impact on its activity. A 3overhang at the 5triphosphate end decreases and any 5overhang at the 5 triphosphate end abolishes its activity. Upon ligand binding it associates with mitochondria antiviral signaling protein (MAVS/IPS1) which activates the IKK-related kinases: TBK1 and IKBKE which phosphorylate interferon regulatory factors: IRF3 and IRF7 which in turn activate transcription of antiviral immunological genes, including interferons (IFNs); IFN-alpha and IFN-beta. Detects both positive and negative strand RNA viruses including members of the families Paramyxoviridae: Human respiratory syncytial virus and measles virus (MeV), Rhabdoviridae: vesicular stomatitis virus (VSV), Orthomyxoviridae: influenza A and B virus, Flaviviridae: Japanese encephalitis virus (JEV), hepatitis C virus (HCV), dengue virus (DENV) and west Nile virus (WNV). It also detects rotavirus and reovirus. Also involved in antiviral signaling in response to viruses containing a dsDNA genome such as Epstein-Barr virus (EBV). Detects dsRNA produced from non-self dsDNA by RNA polymerase III, such as Epstein-Barr virus-encoded RNAs (EBERs). May play important roles in granulocyte production and differentiation, bacterial phagocytosis and in the regulation of cell migration.
UniProtKB/Swiss-Prot Induction: By bacterial lipopolysaccharides (LPS) in endothelial cells. By interferon (IFN).

Enzyme Numbers (IUBMB) for DDX58 Gene

Gene Ontology (GO) - Molecular Function for DDX58 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding --
GO:0003677 DNA binding --
GO:0003690 double-stranded DNA binding IEA --
GO:0003725 double-stranded RNA binding TAS 17079289
GO:0003727 single-stranded RNA binding IMP 19211564
genes like me logo Genes that share ontologies with DDX58: view
genes like me logo Genes that share phenotypes with DDX58: view

Animal Models for DDX58 Gene

MGI Knock Outs for DDX58:

Animal Model Products

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for DDX58

In Situ Assay Products

Flow Cytometry Products

No data available for miRNA , Transcription Factor Targeting and HOMER Transcription for DDX58 Gene

Localization for DDX58 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DDX58 Gene

Cytoplasm. Cell projection, ruffle membrane. Cytoplasm, cytoskeleton. Cell junction, tight junction. Note=Colocalized with TRIM25 at cytoplasmic perinuclear bodies. Associated with the actin cytoskeleton at membrane ruffles.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for DDX58 Gene COMPARTMENTS Subcellular localization image for DDX58 gene
Compartment Confidence
cytoskeleton 5
plasma membrane 5
cytosol 4
mitochondrion 2
nucleus 2
endoplasmic reticulum 1
endosome 1
extracellular 1
lysosome 1
vacuole 1

Gene Ontology (GO) - Cellular Components for DDX58 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA --
GO:0005829 cytosol TAS --
GO:0005923 bicellular tight junction IDA 19122199
GO:0015629 actin cytoskeleton IDA 19122199
GO:0032587 ruffle membrane IDA 19122199
genes like me logo Genes that share ontologies with DDX58: view

Pathways for DDX58 Gene

genes like me logo Genes that share pathways with DDX58: view

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for DDX58 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002230 positive regulation of defense response to virus by host IMP 19609254
GO:0008152 metabolic process IEA --
GO:0009597 detection of virus IDA 17079289
GO:0009615 response to virus TAS 21616437
GO:0010628 positive regulation of gene expression IDA 24409285
genes like me logo Genes that share ontologies with DDX58: view

Compounds for DDX58 Gene

(5) Novoseek inferred chemical compound relationships for DDX58 Gene

Compound -log(P) Hits PubMed IDs
polyinosinic-polycytidylic acid 84.4 5
retinoic acid 65.8 28
rantes 55.9 7
poly(i-c) 53.7 2
cycloheximide 11.5 5
genes like me logo Genes that share compounds with DDX58: view

Transcripts for DDX58 Gene

mRNA/cDNA for DDX58 Gene

Unigene Clusters for DDX58 Gene

DEAD (Asp-Glu-Ala-Asp) box polypeptide 58:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for DDX58

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for DDX58

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for DDX58 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20
SP1: -
SP2: - - -
SP3: - -

Relevant External Links for DDX58 Gene

GeneLoc Exon Structure for
DDX58
ECgene alternative splicing isoforms for
DDX58

Expression for DDX58 Gene

mRNA expression in normal human tissues for DDX58 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for DDX58 Gene

SOURCE GeneReport for Unigene cluster for DDX58 Gene Hs.190622

mRNA Expression by UniProt/SwissProt for DDX58 Gene

O95786-DDX58_HUMAN
Tissue specificity: Present in vascular smooth cells (at protein level).
genes like me logo Genes that share expressions with DDX58: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues for DDX58 Gene

Orthologs for DDX58 Gene

This gene was present in the common ancestor of animals.

Orthologs for DDX58 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia DDX58 35
  • 99.68 (n)
  • 100 (a)
DDX58 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia DDX58 35
  • 86.32 (n)
  • 81.11 (a)
DDX58 36
  • 79 (a)
OneToOne
dog
(Canis familiaris)
Mammalia DDX58 35
  • 87.46 (n)
  • 82.61 (a)
DDX58 36
  • 82 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ddx58 35
  • 79.37 (n)
  • 77.16 (a)
Ddx58 16
Ddx58 36
  • 77 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia DDX58 36
  • 62 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia DDX58 36
  • 48 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ddx58 35
  • 59.23 (n)
  • 52.38 (a)
worm
(Caenorhabditis elegans)
Secernentea drh-1 35
  • 45.61 (n)
  • 32.57 (a)
drh-1 36
  • 22 (a)
ManyToMany
drh-3 36
  • 18 (a)
ManyToMany
Species with no ortholog for DDX58:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • zebrafish (Danio rerio)

Evolution for DDX58 Gene

ENSEMBL:
Gene Tree for DDX58 (if available)
TreeFam:
Gene Tree for DDX58 (if available)

Paralogs for DDX58 Gene

Paralogs for DDX58 Gene

Selected SIMAP similar genes for DDX58 Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with DDX58: view

Variants for DDX58 Gene

Sequence variations from dbSNP and Humsavar for DDX58 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type MAF
rs3609 -- 32,526,822(+) ACATT(C/T)GCATG upstream-variant-2KB
rs10363 -- 32,455,544(+) CTCCC(A/G)TCAGG utr-variant-3-prime
rs581493 -- 32,508,354(+) agaga(C/T)caaca intron-variant
rs582509 -- 32,508,588(+) tcccc(C/G)caagt intron-variant
rs582647 -- 32,501,549(+) TACTT(C/T)CATGG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for DDX58 Gene

Variant ID Type Subtype PubMed ID
nsv893011 CNV Gain 21882294
nsv519447 CNV Loss 19592680
esv273272 CNV Insertion 20981092
esv270911 CNV Insertion 20981092
nsv831540 CNV Gain 17160897

Relevant External Links for DDX58 Gene

HapMap Linkage Disequilibrium report
DDX58
Human Gene Mutation Database (HGMD)
DDX58

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DDX58 Gene

Disorders for DDX58 Gene

MalaCards: The human disease database

MalaCards: The human disease database. (4) Diseases for DDX58 Gene including...

Search for DDX58 Gene in MalaCards »

(3) University of Copenhagen DISEASES for DDX58 Gene

(9) Novoseek inferred disease relationships for DDX58 Gene

Disease -log(P) Hits PubMed IDs
virus infection 71.9 23
rna virus infections 66.8 3
melanoma 60.3 36
hepatitis c 46 4
influenza 37.2 8

Relevant External Links for DDX58

Genetic Association Database (GAD)
DDX58
Human Genome Epidemiology (HuGE) Navigator
DDX58
genes like me logo Genes that share disorders with DDX58: view

No data available for UniProtKB/Swiss-Prot for DDX58 Gene

Publications for DDX58 Gene

  1. Retinoic acid-inducible gene-I is induced by interferon-gamma and regulates the expression of interferon-gamma stimulated gene 15 in MCF-7 cells. (PMID: 15181474) Cui X.-F. … Satoh K. (Biochem. Cell Biol. 2004) 3 4 23
  2. The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses. (PMID: 15208624) Yoneyama M. … Fujita T. (Nat. Immunol. 2004) 3 4 23
  3. Expression of retinoic acid-inducible gene-I in vascular smooth muscle cells stimulated with interferon-gamma. (PMID: 15219805) Imaizumi T. … Satoh K. (Life Sci. 2004) 3 4 23
  4. Retinoic acid-inducible gene-I is induced in endothelial cells by LPS and regulates expression of COX-2. (PMID: 11890704) Imaizumi T. … Satoh K. (Biochem. Biophys. Res. Commun. 2002) 3 4 23
  5. Human ISG15 conjugation targets both IFN-induced and constitutively expressed proteins functioning in diverse cellular pathways. (PMID: 16009940) Zhao C. … Krug R.M. (Proc. Natl. Acad. Sci. U.S.A. 2005) 3 4 23

Products for DDX58 Gene

  • Addgene plasmids for DDX58

Sources for DDX58 Gene

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