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DDX58 Gene

protein-coding   GIFtS: 63
GCID: GC09M032447

DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 58

  See DDX58-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 581 2     RLR-12 3
Retinoic Acid Inducible Gene I1 2     DEAD Box Protein 582 3
RNA Helicase RIG-I1 2     RIG-I-Like Receptor 12 3
Retinoic Acid-Inducible Gene 1 Protein2 3     RIGI2 5
Retinoic Acid-Inducible Gene I Protein2 3     DEAD/H (Asp-Glu-Ala-Asp/His) Box Polypeptide2
RIG-12 3     Probable ATP-Dependent RNA Helicase DDX582
RIG-I2 3     EC 3.6.4.133

External Ids:    HGNC: 191021   Entrez Gene: 235862   Ensembl: ENSG000001072017   OMIM: 6096315   UniProtKB: O957863   

Export aliases for DDX58 gene to outside databases

Previous GC identifer: GC09M032446


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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. GO annotations related to this gene include identical protein binding and ATP-dependent helicase activity. An important paralog of this gene is IFIH1.

UniProtKB/Swiss-Prot: DDX58_HUMAN, O95786
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 3'overhang at the 5'triphosphate end decreases and any 5'overhang 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


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000009.11  NC_018920.2  NT_008413.19  
Regulatory elements:
   Regulatory transcription factor binding sites in the DDX58 gene promoter:
         TBP   GR   AP-1   GR-beta   ATF-2   YY1   GATA-1   STAT3   c-Jun   GR-alpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidDDX58 promoter sequence
   Search Chromatin IP Primers for DDX58

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat DDX58


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 9p12   Ensembl cytogenetic band:  9p21.1   HGNC cytogenetic band: 9p12

DDX58 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DDX58 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M032447:  view genomic region     (about GC identifiers)

Start:
32,455,300 bp from pter      End:
32,526,322 bp from pter
Size:
71,023 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: DDX58_HUMAN, O95786 (See protein sequence)
Recommended Name: Probable ATP-dependent RNA helicase DDX58  
Size: 925 amino acids; 106600 Da
Cofactor: Zinc
Subunit: Monomer; maintained as a monomer in an autoinhibited state. Upon viral dsRNA binding and conformation
shift, homomultimerizes and interacts with MAVS/IPS1. 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
Selected PDB 3D structures from and Proteopedia for DDX58 (see all 15):
2LWD (3D)        2LWE (3D)        2QFB (3D)        2QFD (3D)        2RMJ (3D)        2YKG (3D)    
Secondary accessions: A2RU81 Q5HYE1 Q5VYT1 Q9NT04
Alternative splicing: 2 isoforms:  O95786-1   O95786-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for DDX58: NX_O95786

Explore proteomics data for DDX58 at MOPED

Post-translational modifications: 

  • 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
    activation1
  • ISGylated. Conjugated to ubiquitin-like protein ISG15 upon IFN-beta stimulation. ISGylation negatively regulates
    its function in antiviral signaling response1
  • Sumoylated, probably by MUL1; inhibiting its polyubiquitination1
  • 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 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 receptor1
  • Ubiquitination2 at Lys154, Lys164, Lys172
  • Modification sites at PhosphoSitePlus

  • See DDX58 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_055129.2  
    ENSEMBL proteins: 
     ENSP00000369197   ENSP00000369213   ENSP00000369212   ENSP00000442160   ENSP00000443055  
    Reactome Protein details: O95786

    DDX58 Human Recombinant Protein Products:

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    Novus Biologicals DDX58 Protein
    Novus Biologicals DDX58 Lysates
    Browse Sino Biological Recombinant Proteins
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    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

     
    Search eBioscience for Proteins for DDX58 

    DDX58 Antibody Products:

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    DDX58 Assay Products:

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    Search eBioscience for ELISAs for DDX58 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    DDX: DEAD-boxes

    Selected InterPro protein domains (see all 7):
     IPR011545 DNA/RNA_helicase_DEAD/DEAH_N
     IPR011029 DEATH-like_dom
     IPR027417 P-loop_NTPase
     IPR003593 AAA+_ATPase
     IPR021673 RIG-I_C-RD

    Graphical View of Domain Structure for InterPro Entry O95786

    ProtoNet protein and cluster: O95786

    1 Blocks protein domain: IPB001315 CARD interaction domain

    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
    Domain: The helicase domain is responsible for dsRNA recognition
    Domain: The 2 CARD domains are responsible for interaction with and signaling through MAVS/IPS1 and for
    association with the actin cytoskeleton
    Domain: The second CARD domain is the primary site for 'Lys-63'-linked ubiquitination
    Similarity: Belongs to the helicase family. RLR subfamily
    Similarity: Contains 2 CARD domains
    Similarity: Contains 1 helicase ATP-binding domain
    Similarity: Contains 1 helicase C-terminal domain


    Find genes that share domains with DDX58           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: DDX58_HUMAN, O95786
    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 3'overhang at the 5'triphosphate end decreases and any 5'overhang 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
    Catalytic activity: ATP + H(2)O = ADP + phosphate
    Induction: By bacterial lipopolysaccharides (LPS) in endothelial cells. By interferon (IFN)

         Enzyme Number (IUBMB): EC 3.6.4.131

         Gene Ontology (GO): Selected molecular function terms (see all 13):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding ----
    GO:0003677DNA binding ----
    GO:0003690double-stranded DNA binding IEA--
    GO:0003725double-stranded RNA binding TAS17079289
    GO:0003727single-stranded RNA binding IMP19211564
         
    Find genes that share ontologies with DDX58           About GenesLikeMe


    Phenotypes:
         9 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Ddx58):
     cellular  digestive/alimentary  growth/size/body  hematopoietic system  homeostasis/metabolism 
     immune system  liver/biliary system  mortality/aging  tumorigenesis 

    Find genes that share phenotypes with DDX58           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for DDX58: Ddx58tm1Zgwg Ddx58tm1Aki

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for DDX58
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for DDX58

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for DDX58
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for DDX58

    miRNA
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    Block miRNA regulation of human, mouse, rat DDX58 using miScript Target Protectors
    5 qRT-PCR Assays for microRNAs that regulate DDX58:
    hsa-miR-936 hsa-miR-362-5p hsa-miR-545 hsa-miR-548u hsa-miR-664
    SwitchGear 3'UTR luciferase reporter plasmidDDX58 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat DDX58

    Gene Editing
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    DDX58_HUMAN, O95786: 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: 

    CompartmentConfidence
    cytoskeleton5
    plasma membrane5
    cytosol4
    mitochondrion2
    nucleus2
    endoplasmic reticulum1
    endosome1
    extracellular1
    lysosome1
    vacuole1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IDA--
    GO:0005829cytosol TAS--
    GO:0005923tight junction IDA19122199
    GO:0015629actin cytoskeleton IDA19122199
    GO:0032587ruffle membrane IDA19122199

    Find genes that share ontologies with DDX58           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for DDX58 About   (see all 9)  
    See pathways by source

    SuperPathContained pathways About
    1RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways
    RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways0.47
    TRAF6 mediated IRF7 activation0.40
    RIG-I-like receptor signaling pathway0.47
    TRAF3-dependent IRF activation pathway0.00
    Negative regulators of RIG-I/MDA5 signaling0.42
    NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -100.00
    2Cytosolic sensors of pathogen-associated DNA
    TRAF6 mediated NF-kB activation0.55
    Cytosolic DNA-sensing pathway0.33
    3Interferon Signaling
    Interferon Signaling0.59
    ISG15 antiviral mechanism0.42
    Cytokine Signaling in Immune system0.59
    Antiviral mechanism by IFN-stimulated genes0.42
    4Influenza A
    Influenza A0.34
    Herpes simplex infection0.33
    Measles0.34
    5Toll-like receptor signaling pathway
    Hepatitis B0.31


    Find genes that share SuperPaths with DDX58           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Cell Signaling Technology (CST) Pathway for DDX58
        NF-kappaB Signaling

    Selected Reactome Pathways for DDX58 (see all 7)
        NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10
    TRAF3-dependent IRF activation pathway
    RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways
    Negative regulators of RIG-I/MDA5 signaling
    TRAF6 mediated IRF7 activation


    Selected Kegg Pathways  (Kegg details for DDX58) (see all 9):
        NF-kappa B signaling pathway
    RIG-I-like receptor signaling pathway
    Cytosolic DNA-sensing pathway
    Hepatitis C
    Hepatitis B

        Pathway & Disease-focused RT2 Profiler PCR Arrays including DDX58: 
              Innate & Adaptive Immune Responses in human mouse rat
              Antiviral Response in human mouse rat
              Type I Interferon Response in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for DDX58

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for DDX58 (O957861, 2, 3 ENSP000003692134) via UniProtKB, MINT, STRING, and/or I2D (see all 140)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CYLDQ9NQC71, 2, 3, ENSP000003089284EBI-995350,EBI-2117940 MINT-6804571 MINT-6804584 I2D: score=4 STRING: ENSP00000308928
    WRNIP1Q96S551, 3, ENSP000003701504EBI-995350,EBI-2513471 I2D: score=1 STRING: ENSP00000370150
    ZC3HAV1Q7Z2W41, 3, ENSP000002423514EBI-995350,EBI-922540 I2D: score=1 STRING: ENSP00000242351
    DDX3XO005711, 3EBI-995350,EBI-353779 I2D: score=1 
    ENSG00000183574Q999423I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 17):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0002230positive regulation of defense response to virus by host IMP19609254
    GO:0009597detection of virus IDA17079289
    GO:0009615response to virus TAS--
    GO:0016032viral process IEA--
    GO:0019048modulation by virus of host morphology or physiology ----

    Find genes that share ontologies with DDX58           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for DDX58

    5 Novoseek inferred chemical compound relationships for DDX58 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    polyinosinic-polycytidylic acid 84.4 9 16490936 (1), 18941247 (1), 19234166 (1), 19590242 (1) (see all 5)
    retinoic acid 65.8 28 17516545 (2), 15745153 (1), 17911629 (1), 19734229 (1) (see all 27)
    rantes 55.9 7 15612946 (3), 17395328 (2), 19837110 (1), 18632970 (1)
    poly(i-c) 53.7 2 15737993 (2)
    cycloheximide 11.5 5 15612946 (2), 17064399 (2), 15370293 (1)



    Find genes that share compounds with DDX58           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for DDX58 gene: 
    NM_014314.3  

    Unigene Cluster for DDX58:

    DEAD (Asp-Glu-Ala-Asp) box polypeptide 58
    Hs.190622  [show with all ESTs]
    Unigene Representative Sequence: NM_014314
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000379868 ENST00000379883(uc011lnr.1) ENST00000379882(uc010mji.3 uc003zra.3 uc010mjj.3 uc010mjk.1)
    ENST00000542096 ENST00000545044
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    SwitchGear 3'UTR luciferase reporter plasmidDDX58 3' UTR sequence
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    Additional mRNA sequence: 

    AF038963.1 AK023661.1 AK125989.1 AK301678.1 AK315040.1 AL137608.1 BC070029.1 BC107731.1 
    BC132786.1 BC136610.1 BX647917.1 

    13 DOTS entries:

    DT.409662  DT.92325140  DT.91650388  DT.121195814  DT.95330059  DT.100780569  DT.121195830  DT.121195882 
    DT.429628  DT.91769665  DT.91855115  DT.95181427  DT.91802214 

    Selected AceView cDNA sequences (see all 185):

    BM462986 AV645481 CB118537 BM825879 BM669635 AK125989 AW206733 AA251880 
    AI801182 AI873664 BX647917 AA679829 CD299987 AA885936 BM837370 AA626115 
    NM_014314 AA292388 AU280552 CB150537 AA126958 AI520921 AA174207 AI263384 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for DDX58    About this scheme

    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:              -           -                                                                                                         


    ECgene alternative splicing isoforms for DDX58

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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    DDX58 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GATCGCTTGT
    DDX58 Expression
    About this image


    DDX58 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 4) fully expand
     
     Blood (Cardiovascular System)    fully expand to see all 2 entries
             Granulocytes Peripheral Blood
     
     Testis (Reproductive System)
             XY Germ Cells Testis Cord
     
     Gonad
             XY Germ Cells Testis Cord
     
     Spleen (Hematopoietic System)
             Conventional Dendritic Cells II Spleen
    DDX58 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    DDX58 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.190622

    UniProtKB/Swiss-Prot: DDX58_HUMAN, O95786
    Tissue specificity: Present in vascular smooth cells (at protein level)

        Pathway & Disease-focused RT2 Profiler PCR Arrays including DDX58: 
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for DDX58 gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ddx581 , 5 DEAD (Asp-Glu-Ala-Asp) box polypeptide 581, 5 79.37(n)1
    77.16(a)1
      4 (20.24 cM)5
    2300731  NM_172689.31  NP_766277.31 
     402037735 
    lizard
    (Anolis carolinensis)
    Reptilia DDX586
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 58
    48(a)
    1 ↔ 1
    GL343463.1(19739-46391)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia ddx581 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 59.23(n)
    52.38(a)
      100495207  XM_002935671.2  XP_002935717.2 
    worm
    (Caenorhabditis elegans)
    Secernentea drh-11 drh-1 45.61(n)
    32.57(a)
      177425  NM_068617.7  NP_501018.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for DDX58 gene
    IFIH12  DHX582  DICER12  
    2 SIMAP similar genes for DDX58 using alignment to 6 protein entries:     DDX58_HUMAN (see all proteins):
    DHX58    MDA5

    Find genes that share paralogs with DDX58           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for DDX58 (see all 1551)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1507386191,2
    --32454901(+) CTCACA/GCCTGT 1 -- ds50010--------
    rs1401164731,2
    C--32454947(+) CACTTC/GAGGTC 1 -- ds50010--------
    rs1455698381,2
    --32455069(+) AGGCAG/TGAGAA 1 -- ds50010--------
    rs1477117131,2
    C--32455110(+) TGAGCC/TGAGAT 1 -- ds50010--------
    rs1909321861,2
    --32455251(+) CAATAC/GTGTAT 1 -- ds50010--------
    rs70450871,2
    C,F,A,H--32455262(+) tagtcT/Cgtttt 1 -- ds500118Minor allele frequency- C:0.29NS EA NA WA CSA 2215
    rs70290021,2
    C,F,A--32455320(+) agaggT/Cttaat 1 -- ut319Minor allele frequency- C:0.44NA WA CSA EA 369
    rs576693121,2
    C,F--32455396(+) AGGCAA/CGTCTT 1 -- ut312Minor allele frequency- C:0.12CSA WA 120
    rs1410328221,2
    C--32455458(+) ACTTAC/TAAAAC 1 -- ut310--------
    rs1498497281,2
    C--32455466(+) AACCAC/TCAGAT 1 -- ut310--------

    HapMap Linkage Disequilibrium report for DDX58 (32455300 - 32526322 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for DDX58:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv270911CNV Insertion20981092
    esv273272CNV Insertion20981092
    nsv519447CNV Loss19592680
    nsv831540CNV Gain17160897
    nsv893011CNV Gain21882294

    Human Gene Mutation Database (HGMD): DDX58
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing DDX58
    DNA2.0 Custom Variant and Variant Library Synthesis for DDX58

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 609631    OMIM disorders: --

    4 diseases for DDX58:    
    About MalaCards
    ebola hemorrhagic fever    parainfluenza virus type 3    west nile virus    influenza

    3 diseases from the University of Copenhagen DISEASES database for DDX58:
    Melanoma     Influenza     Ebola hemorrhagic fever

    Find genes that share disorders with DDX58           About GenesLikeMe

    9 Novoseek inferred disease relationships for DDX58 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    virus infection 71.9 26 17395328 (2), 18948594 (2), 17053203 (1), 17392790 (1) (see all 21)
    rna virus infections 66.8 4 17392790 (1), 17921696 (1), 19017631 (1)
    melanoma 60.3 36 19620789 (4), 17142768 (1), 19380577 (1), 17541283 (1) (see all 33)
    hepatitis c 46 4 16116171 (1), 16585524 (1), 20034464 (1), 17517627 (1)
    influenza 37.2 11 16797201 (2), 16537619 (2), 17942531 (2), 17053203 (1) (see all 5)
    necrosis 0 3 17182220 (1), 18617992 (1)
    shock 0 1 19234166 (1)
    inflammation 0 5 20167631 (1), 19126414 (1), 17942531 (1), 18505427 (1) (see all 5)
    tumors 0 20 17516545 (2), 18978796 (2), 19620789 (1), 18155685 (1) (see all 6)

    Genetic Association Database (GAD): DDX58
    Human Genome Epidemiology (HuGE) Navigator: DDX58 (5 documents)

    Export disorders for DDX58 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for DDX58 gene, integrated from 10 sources (see all 315):
    (articles sorted by number of sources associating them with DDX58)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Riplet/RNF135, a RING finger protein, ubiquitinates RIG-I to promote interferon-beta induction during the early phase of viral infection. (PubMed id 19017631)1, 2, 9 Oshiumi H.... Seya T. (J. Biol. Chem. 2009)
    2. TRIM25 RING-finger E3 ubiquitin ligase is essential for RIG-I- mediated antiviral activity. (PubMed id 17392790)1, 2, 9 Gack M.U.... Jung J.U. (Nature 2007)
    3. Regulation of signal transduction by enzymatically inactive antiviral RNA helicase proteins MDA5, RIG-I, and LGP2. (PubMed id 19211564)1, 2, 9 Bamming D. and Horvath C.M. (J. Biol. Chem. 2009)
    4. Nonself RNA-sensing mechanism of RIG-I helicase and activation of antiviral immune responses. (PubMed id 18242112)1, 2, 9 Takahasi K.... Fujita T. (Mol. Cell 2008)
    5. Retinoic acid-inducible gene-I is induced by interferon-gamma and regulates the expression of interferon-gamma stimulated gene 15 in MCF-7 cells. (PubMed id 15181474)1, 2, 9 Cui X.-F.... Satoh K. (Biochem. Cell Biol. 2004)
    6. Expression of retinoic acid-inducible gene-I in vascular smooth muscle cells stimulated with interferon-gamma. (PubMed id 15219805)1, 2, 9 Imaizumi T.... Satoh K. (Life Sci. 2004)
    7. RIG-I-dependent sensing of poly(dA:dT) through the induction of an RNA polymerase III-transcribed RNA intermediate. (PubMed id 19609254)1, 2, 9 Ablasser A....Hornung V. (Nat. Immunol. 2009)
    8. The tumour suppressor CYLD is a negative regulator of RIG-I-mediated antiviral response. (PubMed id 18636086)1, 2, 9 Friedman C.S.... Ting A.T. (EMBO Rep. 2008)
    9. Retinoic acid-inducible gene-I is induced in endothelial cells by LPS and regulates expression of COX-2. (PubMed id 11890704)1, 2, 9 Imaizumi T.... Satoh K. (Biochem. Biophys. Res. Commun. 2002)
    10. Rubella vaccine-induced cellular immunity: evidence of associations with polymorphisms in the Toll-like, vitamin A and D receptors, and innate immune response genes. (PubMed id 19902255)1, 4, 9 Ovsyannikova I.G....Poland G.A. (Hum. Genet. 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 23586 HGNC: 19102 AceView: TOPORSandDDX58 Ensembl:ENSG00000107201 euGenes: HUgn23586
    ECgene: DDX58 Kegg: 23586 H-InvDB: DDX58

    (According to HUGE)
    About This Section

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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for DDX58 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for DDX58 gene:
    Search GeneIP for patents involving DDX58

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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