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    DDX58 DExD/H-box helicase 58 [ Homo sapiens (human) ]

    Gene ID: 23586, updated on 20-Apr-2017
    Official Symbol
    DDX58provided by HGNC
    Official Full Name
    DExD/H-box helicase 58provided by HGNC
    Primary source
    HGNC:HGNC:19102
    See related
    Ensembl:ENSG00000107201 MIM:609631; Vega:OTTHUMG00000019746
    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
    RIGI; 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 immune response. [provided by RefSeq, Jul 2008]
    Orthologs
    Location:
    9p21.1
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 9 NC_000009.12 (32455302..32526324, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (32455300..32526322, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene aconitase 1 Neighboring gene uncharacterized LOC105376014 Neighboring gene TOP1 binding arginine/serine rich protein Neighboring gene small integral membrane protein 27 Neighboring gene NADH:ubiquinone oxidoreductase subunit B6 Neighboring gene DNA fragmentation factor subunit beta pseudogene 1

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    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

    Go to the HIV-1, Human Interaction Database

    • Antiviral mechanism by IFN-stimulated genes, organism-specific biosystem (from REACTOME)
      Antiviral mechanism by IFN-stimulated genes, organism-specific biosystemThe ISG proteins generated by IFN pathways plays key roles in the induction of innate and adaptive immune responses.
    • Cytokine Signaling in Immune system, organism-specific biosystem (from REACTOME)
      Cytokine Signaling in Immune system, organism-specific biosystemCytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concen...
    • Cytosolic DNA-sensing pathway, organism-specific biosystem (from KEGG)
      Cytosolic DNA-sensing pathway, organism-specific biosystemSpecific families of pattern recognition receptors are responsible for detecting foreign DNA from invading microbes or host cells and generating innate immune responses. DAI is the first identified s...
    • Cytosolic DNA-sensing pathway, conserved biosystem (from KEGG)
      Cytosolic DNA-sensing pathway, conserved biosystemSpecific families of pattern recognition receptors are responsible for detecting foreign DNA from invading microbes or host cells and generating innate immune responses. DAI is the first identified s...
    • Deubiquitination, organism-specific biosystem (from REACTOME)
      Deubiquitination, organism-specific biosystemUbiquitination, the modification of proteins by the covalent attachment of ubiquitin (Ub), is a key regulatory mechanism for many many cellular processes, including protein degradation by the 26S pro...
    • Epstein-Barr virus infection, organism-specific biosystem (from KEGG)
      Epstein-Barr virus infection, organism-specific biosystemEpstein-Barr virus (EBV) is a ubiquitous human herpesvirus that is associated with oncogenesis. EBV infection to primary human B lymphocytes leads to induction of EBV-specific HLA-restricted cytotoxi...
    • Epstein-Barr virus infection, conserved biosystem (from KEGG)
      Epstein-Barr virus infection, conserved biosystemEpstein-Barr virus (EBV) is a ubiquitous human herpesvirus that is associated with oncogenesis. EBV infection to primary human B lymphocytes leads to induction of EBV-specific HLA-restricted cytotoxi...
    • Hepatitis B, organism-specific biosystem (from KEGG)
      Hepatitis B, organism-specific biosystemHepatitis B virus (HBV) is an enveloped virus and contains a partially double-stranded relaxed circular DNA (RC-DNA) genome. After entry into hepatocytes, HBV RC-DNA is transported to the nucleus and...
    • Hepatitis C, organism-specific biosystem (from KEGG)
      Hepatitis C, organism-specific biosystemHepatitis C virus (HCV) is a major cause of chronic liver disease. The HCV employ several strategies to perturb host cell immunity. After invasion, HCV RNA genome functions directly as an mRNA in the...
    • Hepatitis C, conserved biosystem (from KEGG)
      Hepatitis C, conserved biosystemHepatitis C virus (HCV) is a major cause of chronic liver disease. The HCV employ several strategies to perturb host cell immunity. After invasion, HCV RNA genome functions directly as an mRNA in the...
    • Herpes simplex infection, organism-specific biosystem (from KEGG)
      Herpes simplex infection, organism-specific biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...
    • Herpes simplex infection, conserved biosystem (from KEGG)
      Herpes simplex infection, conserved biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...
    • ISG15 antiviral mechanism, organism-specific biosystem (from REACTOME)
      ISG15 antiviral mechanism, organism-specific biosystemInterferon-stimulated gene 15 (ISG15) is a member of the ubiquitin-like (Ubl) family. It is strongly induced upon exposure to type I Interferons (IFNs), viruses, bacterial LPS, and other stresses. On...
    • Immune System, organism-specific biosystem (from REACTOME)
      Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
    • Influenza A, organism-specific biosystem (from KEGG)
      Influenza A, organism-specific biosystemInfluenza is a contagious respiratory disease caused by influenza virus infection. Influenza A virus is responsible for both annual seasonal epidemics and periodic worldwide pandemics. Novel strains ...
    • Influenza A, conserved biosystem (from KEGG)
      Influenza A, conserved biosystemInfluenza is a contagious respiratory disease caused by influenza virus infection. Influenza A virus is responsible for both annual seasonal epidemics and periodic worldwide pandemics. Novel strains ...
    • Innate Immune System, organism-specific biosystem (from REACTOME)
      Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
    • Interferon Signaling, organism-specific biosystem (from REACTOME)
      Interferon Signaling, organism-specific biosystemInterferons (IFNs) are cytokines that play a central role in initiating immune responses, especially antiviral and antitumor effects. There are three types of IFNs:Type I (IFN-alpha, -beta and others...
    • Measles, organism-specific biosystem (from KEGG)
      Measles, organism-specific biosystemMeasles virus (MV) is highly contagious virus that leads infant death worldwide. Humans are the unique natural reservoir for this virus. It causes severe immunosuppression favouring secondary bacteri...
    • Measles, conserved biosystem (from KEGG)
      Measles, conserved biosystemMeasles virus (MV) is highly contagious virus that leads infant death worldwide. Humans are the unique natural reservoir for this virus. It causes severe immunosuppression favouring secondary bacteri...
    • Metabolism of proteins, organism-specific biosystem (from REACTOME)
      Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
    • NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10, organism-specific biosystem (from REACTOME)
      NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10, organism-specific biosystemFas-AssociatedDeathDomain (FADD) and receptor interacting protein 1 (RIP1) are death domain containing molecules that interact with the C-terminal portion of IPS-1 and induce NF-kB through interactio...
    • NF-kappa B signaling pathway, organism-specific biosystem (from KEGG)
      NF-kappa B signaling pathway, organism-specific biosystemNuclear factor-kappa B (NF-kappa B) is the generic name of a family of transcription factors that function as dimers and regulate genes involved in immunity, inflammation and cell survival. There are...
    • NF-kappa B signaling pathway, conserved biosystem (from KEGG)
      NF-kappa B signaling pathway, conserved biosystemNuclear factor-kappa B (NF-kappa B) is the generic name of a family of transcription factors that function as dimers and regulate genes involved in immunity, inflammation and cell survival. There are...
    • Negative regulators of RIG-I/MDA5 signaling, organism-specific biosystem (from REACTOME)
      Negative regulators of RIG-I/MDA5 signaling, organism-specific biosystemAs with other cytokine systems, production of type I IFN is a transient process, and can be hazardous to the host if unregulated, resulting in chronic cellular toxicity or inflammatory and autoimmune...
    • Ovarian tumor domain proteases, organism-specific biosystem (from REACTOME)
      Ovarian tumor domain proteases, organism-specific biosystemHumans have 16 Overian tumour domain (OTU) family DUBs that can be evolutionally divided into three classes, the OTUs, the Otubains (OTUBs), and the A20-like OTUs (Komander et al. 2009). OTU family ...
    • Post-translational protein modification, organism-specific biosystem (from REACTOME)
      Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
    • RIG-I-like Receptor Signaling, organism-specific biosystem (from WikiPathways)
      RIG-I-like Receptor Signaling, organism-specific biosystemViral pathogen RNA are recognized by host helicases called RIG-I-like receptors (RLRs) that include DDX58 (RIG-I), DHX58 (LGP2), IFIH1 (MDA5), SNW1, and DDX17. These RLR proteins then go on to initia...
    • RIG-I-like receptor signaling pathway, organism-specific biosystem (from KEGG)
      RIG-I-like receptor signaling pathway, organism-specific biosystemSpecific families of pattern recognition receptors are responsible for detecting viral pathogens and generating innate immune responses. Non-self RNA appearing in a cell as a result of intracellular ...
    • RIG-I-like receptor signaling pathway, conserved biosystem (from KEGG)
      RIG-I-like receptor signaling pathway, conserved biosystemSpecific families of pattern recognition receptors are responsible for detecting viral pathogens and generating innate immune responses. Non-self RNA appearing in a cell as a result of intracellular ...
    • RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways, organism-specific biosystem (from REACTOME)
      RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways, organism-specific biosystemRIG-I-like helicases (RLHs) the retinoic acid inducible gene-I (RIG-I) and melanoma differentiation associated gene 5 (MDA5) are RNA helicases that recognize viral RNA present within the cytoplasm. F...
    • TRAF3-dependent IRF activation pathway, organism-specific biosystem (from REACTOME)
      TRAF3-dependent IRF activation pathway, organism-specific biosystemIPS-1/MAVS/Cardif/VISA with its TRAF-interaction motif (TIM) directly interacts with TRAF3 and recruits TRAF3 to the RIG-I/MDA5 signaling complex. TRAF3 acts as a scaffold for the assembly of a signa...
    • TRAF6 mediated IRF7 activation, organism-specific biosystem (from REACTOME)
      TRAF6 mediated IRF7 activation, organism-specific biosystemTRAF6 is crucial for both RIG-I- and MDA5-mediated antiviral responses. The absence of TRAF6 resulted in enhanced viral replication and a significant reduction in the production of type I IFNs and IL...
    • TRAF6 mediated NF-kB activation, organism-specific biosystem (from REACTOME)
      TRAF6 mediated NF-kB activation, organism-specific biosystemThe TRAF6/TAK1 signal activates a canonical IKK complex, resulting in the activation of NF-kB as well as MAPK cascades leading to the activation of AP-1. Although TRAF6/TAK1 has been implicated in To...
    • Ub-specific processing proteases, organism-specific biosystem (from REACTOME)
      Ub-specific processing proteases, organism-specific biosystemUb-specific processing proteases (USPs) are the largest of the DUB families with more than 50 members in humans. The USP catalytic domain varies considerably in size and consists of six conserved mo...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Potential readthrough

    Included gene: TOPORS

    Homology

    Clone Names

    • FLJ13599, DKFZp434J1111, DKFZp686N19181

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    double-stranded DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    double-stranded RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    double-stranded RNA binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    double-stranded RNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    helicase activity IEA
    Inferred from Electronic Annotation
    more info
     
    identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    single-stranded RNA binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    ubiquitin protein ligase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    zinc ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    RIG-I signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cytoplasmic pattern recognition receptor signaling pathway in response to virus TAS
    Traceable Author Statement
    more info
    PubMed 
    detection of virus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    innate immune response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    innate immune response TAS
    Traceable Author Statement
    more info
     
    negative regulation of type I interferon production TAS
    Traceable Author Statement
    more info
     
    positive regulation of defense response to virus by host IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of granulocyte macrophage colony-stimulating factor production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of interferon-alpha production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of interferon-alpha production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of interferon-beta production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of interferon-beta production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of interleukin-6 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of interleukin-8 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of sequence-specific DNA binding transcription factor activity IC
    Inferred by Curator
    more info
    PubMed 
    positive regulation of transcription factor import into nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription from RNA polymerase II promoter IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein deubiquitination TAS
    Traceable Author Statement
    more info
     
    regulation of cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of type III interferon production TAS
    Traceable Author Statement
    more info
    PubMed 
    response to exogenous dsRNA IEA
    Inferred from Electronic Annotation
    more info
     
    response to virus TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    actin cytoskeleton IDA
    Inferred from Direct Assay
    more info
    PubMed 
    bicellular tight junction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    cytosol TAS
    Traceable Author Statement
    more info
     
    ruffle membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    probable ATP-dependent RNA helicase DDX58
    Names
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 58
    DEAD box protein 58
    DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide
    RNA helicase RIG-I
    retinoic acid-inducible gene 1 protein
    retinoic acid-inducible gene I protein
    NP_055129.2

    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

    1. NG_046918.1 RefSeqGene

      Range
      5001..76023
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_014314.3NP_055129.2  probable ATP-dependent RNA helicase DDX58

      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
      O95786
      Related
      ENSP00000369213.2, OTTHUMP00000021185, ENST00000379883.2, OTTHUMT00000052011
      Conserved Domains (7) summary
      COG1111
      Location:243771
      MPH1; ERCC4-related helicase [Replication, recombination and repair]
      cd00046
      Location:258410
      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.
      cd08817
      Location:100189
      CARD_RIG-I_r2; Caspase activation and recruitment domain found in RIG-I, second repeat
      cd12090
      Location:469604
      MDA5_ID; Insert domain of MDA5
      pfam00271
      Location:617733
      Helicase_C; Helicase conserved C-terminal domain
      pfam11648
      Location:807922
      RIG-I_C-RD; C-terminal domain of RIG-I
      cl14633
      Location:292
      DD; Death Domain Superfamily of protein-protein interaction domains

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p7 Primary Assembly

      Range
      32455302..32526324 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018920.2 Alternate CHM1_1.1

      Range
      32455159..32526318 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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