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Entry version 143 (05 Jun 2019)
Sequence version 2 (27 Jul 2011)
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Protein

Probable ATP-dependent RNA helicase DDX58

Gene

Ddx58

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

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: newcastle disease virus (NDV) and Sendai virus (SeV), 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 orthoreovirus. 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.6 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi811ZincPROSITE-ProRule annotation1
Metal bindingi814ZincPROSITE-ProRule annotation1
Metal bindingi865ZincPROSITE-ProRule annotation1
Metal bindingi870ZincPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi265 – 272ATPPROSITE-ProRule annotation8

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionHelicase, Hydrolase, RNA-binding
Biological processAntiviral defense, Immunity, Innate immunity
LigandATP-binding, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-MMU-1169408 ISG15 antiviral mechanism
R-MMU-5689880 Ub-specific processing proteases
R-MMU-8983711 OAS antiviral response
R-MMU-936440 Negative regulators of DDX58/IFIH1 signaling

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Probable ATP-dependent RNA helicase DDX58 (EC:3.6.4.13)
Alternative name(s):
DEAD box protein 58
RIG-I-like receptor 1
Short name:
RLR-1
Retinoic acid-inducible gene 1 protein
Short name:
RIG-1
Retinoic acid-inducible gene I protein
Short name:
RIG-I
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:Ddx58
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiMus musculus (Mouse)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri10090 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000589 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 4

Organism-specific databases

Mouse genome database (MGD) from Mouse Genome Informatics (MGI)

More...
MGIi
MGI:2442858 Ddx58

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

Cell junction, Cell membrane, Cell projection, Cytoplasm, Cytoskeleton, Membrane, Tight junction

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the ‘Pathology and Biotech’ section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Death between E12.5 and E14 due to liver apoptosis. Those who are born alive show growth retardation and die within 3 weeks.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi813K → R: Greatly decreases 'K-48'-linked ubiquitination. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001440941 – 926Probable ATP-dependent RNA helicase DDX58Add BLAST926

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section describes <strong>covalent linkages</strong> of various types formed <strong>between two proteins (interchain cross-links)</strong> or <strong>between two parts of the same protein (intrachain cross-links)</strong>, except the disulfide bonds that are annotated in the <a href="http://www.uniprot.org/manual/disulfid">'Disulfide bond'</a> subsection.<p><a href='/help/crosslnk' target='_top'>More...</a></p>Cross-linki154Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki164Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki181Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei771Phosphothreonine; by CK2By similarity1
Cross-linki813Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Modified residuei859N6-acetyllysineBy similarity1

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Phosphorylated in resting cells and dephosphorylated in RNA virus-infected cells. Phosphorylation at Thr-771 results in inhibition of its activity while dephosphorylation at these sites results in its activation.By similarity
ISGylated. Conjugated to ubiquitin-like protein ISG15 upon IFN-beta stimulation. ISGylation negatively regulates its function in antiviral signaling response.By similarity
Sumoylated, probably by MUL1; inhibiting its polyubiquitination.By similarity
Ubiquitinated. Undergoes 'Lys-48'- and 'Lys-63'-linked ubiquitination. Lys-154 and Lys-164 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. Ubiquitinated at Lys-181 by RNF125, leading to its degradation: ubiquitination takes place upon viral infection and is enhanced 'Lys-63'-linked ubiquitination of the CARD domains, which promote interaction with VCP/p97 and subsequent recruitment of RNF125 (By similarity). Ubiquitinated at Lys-813 by CBL, leading to its degradation: ubiquitination takes place upon viral infection and involves 'Lys-48'-linked ubiquitination (PubMed:23374343).By similarity1 Publication

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

Encyclopedia of Proteome Dynamics

More...
EPDi
Q6Q899

PaxDb, a database of protein abundance averages across all three domains of life

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PaxDbi
Q6Q899

PeptideAtlas

More...
PeptideAtlasi
Q6Q899

PRoteomics IDEntifications database

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PRIDEi
Q6Q899

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

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iPTMneti
Q6Q899

Comprehensive resource for the study of protein post-translational modifications (PTMs) in human, mouse and rat.

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PhosphoSitePlusi
Q6Q899

SwissPalm database of S-palmitoylation events

More...
SwissPalmi
Q6Q899

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the ‘Expression’ section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

By interferon (IFN).

Gene expression databases

Bgee dataBase for Gene Expression Evolution

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Bgeei
ENSMUSG00000040296 Expressed in 163 organ(s), highest expression level in mesenteric lymph node

ExpressionAtlas, Differential and Baseline Expression

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ExpressionAtlasi
Q6Q899 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
Q6Q899 MM

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Monomer; maintained as a monomer in an autoinhibited state (By similarity). Upon viral dsRNA binding and conformation shift, homomultimerizes and interacts (via tandem CARD domain) with MAVS/IPS1 promoting its filamentation (By similarity). Interacts with DHX58/LGP2, IKBKE, TBK1 and TMEM173/STING (By similarity). Interacts (via CARD domain) with TRIM25 (via SPRY domain) (By similarity). Interacts with RNF135 (By similarity). Interacts with CYLD (By similarity). Interacts with NLRC5; blocks the interaction of MAVS/IPS1 to DDX58 (By similarity). Interacts with SRC (By similarity). Interacts with DDX60 (By similarity). Interacts with isoform 2 of ZC3HAV1 (via zinc-fingers) in an RNA-dependent manner (By similarity). Interacts (via tandem CARD domain) with SEC14L1; the interaction is direct and impairs the interaction of DDX58 with MAVS/IPS1 (By similarity). Interacts with VCP/p97; interaction is direct and leads to recruit RNF125 and subsequent ubiquitination and degradation (By similarity). Interacts with NOP53; may regulate DDX58 through USP15-mediated 'Lys-63'-linked deubiquitination (By similarity). Interacts with SIGLEC10, CBL and PTPN11; these interactions are involved in 'Lys-48'-linked deubiquitination and degradation following infection with RNA viruses (PubMed:23374343). Interacts with LRRC25 (By similarity). Interacts with ZCCHC3; leading to activate DDX58/RIG-I (By similarity).By similarity1 Publication

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction_section%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
230926, 7 interactors

Database of interacting proteins

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DIPi
DIP-61741N

Protein interaction database and analysis system

More...
IntActi
Q6Q899, 4 interactors

STRING: functional protein association networks

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STRINGi
10090.ENSMUSP00000042433

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1926
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
Q6Q899

Database of comparative protein structure models

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ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

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MobiDBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
Q6Q899

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini1 – 87CARD 1Add BLAST87
Domaini92 – 172CARD 2Add BLAST81
Domaini252 – 431Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST180
Domaini611 – 777Helicase C-terminalPROSITE-ProRule annotationAdd BLAST167
Domaini791 – 926RLR CTRPROSITE-ProRule annotationAdd BLAST136

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni219 – 926Interaction with ZC3HAV1By similarityAdd BLAST708

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a short (usually not more than 20 amino acids) conserved sequence motif of biological significance.<p><a href='/help/motif' target='_top'>More...</a></p>Motifi373 – 376DECH box4

<p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

The helicase domain is responsible for dsRNA recognition. Interacts with IFIT3 (via N-terminus).By similarity
The 2 CARD domains are responsible for interaction with and signaling through MAVS/IPS1 and for association with the actin cytoskeleton.By similarity
The RLR CTR 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 RLR CTR domain. Upon binding to viral RNA in the presence of ATP, the RLR CTR 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 second CARD domain is the primary site for 'Lys-63'-linked ubiquitination.By similarity

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the helicase family. RLR subfamily.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

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eggNOGi
KOG0354 Eukaryota
COG1111 LUCA

Ensembl GeneTree

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GeneTreei
ENSGT00940000153173

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

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HOGENOMi
HOG000230911

InParanoid: Eukaryotic Ortholog Groups

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InParanoidi
Q6Q899

KEGG Orthology (KO)

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KOi
K12646

Database of Orthologous Groups

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OrthoDBi
1337630at2759

TreeFam database of animal gene trees

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TreeFami
TF330258

Family and domain databases

Conserved Domains Database

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CDDi
cd08817 CARD_RIG-I_r2, 1 hit
cd00079 HELICc, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

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Gene3Di
2.170.150.30, 1 hit

Integrated resource of protein families, domains and functional sites

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InterProi
View protein in InterPro
IPR031964 CARD_dom
IPR042145 CARD_RIG-I_r2
IPR006935 Helicase/UvrB_N
IPR014001 Helicase_ATP-bd
IPR001650 Helicase_C
IPR027417 P-loop_NTPase
IPR041204 RIG-I_C
IPR038557 RLR_C_sf
IPR021673 RLR_CTR

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF16739 CARD_2, 2 hits
PF00271 Helicase_C, 1 hit
PF04851 ResIII, 1 hit
PF18119 RIG-I_C, 1 hit
PF11648 RIG-I_C-RD, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00487 DEXDc, 1 hit
SM00490 HELICc, 1 hit

Superfamily database of structural and functional annotation

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SUPFAMi
SSF52540 SSF52540, 2 hits

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51192 HELICASE_ATP_BIND_1, 1 hit
PS51194 HELICASE_CTER, 1 hit
PS51789 RLR_CTR, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequences (4+)i

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

This entry describes 4 <p>This subsection of the ‘Sequence’ section lists the alternative protein sequences (isoforms) that can be generated from the same gene by a single or by the combination of up to four biological events (alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting). Additionally, this section gives relevant information on each alternative protein isoform.<p><a href='/help/alternative_products' target='_top'>More...</a></p> isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 4 described isoforms and 1 potential isoform that is computationally mapped.Show allAlign All

Isoform 1 (identifier: Q6Q899-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MTAEQRQNLQ AFRDYIKKIL DPTYILSYMS SWLEDEEVQY IQAEKNNKGP
60 70 80 90 100
MEAASLFLQY LLKLQSEGWF QAFLDALYHA GYCGLCEAIE SWDFQKIEKL
110 120 130 140 150
EEHRLLLRRL EPEFKATVDP NDILSELSEC LINQECEEIR QIRDTKGRMA
160 170 180 190 200
GAEKMAECLI RSDKENWPKV LQLALEKDNS KFSELWIVDK GFKRAESKAD
210 220 230 240 250
EDDGAEASSI QIFIQEEPEC QNLSQNPGPP SEASSNNLHS PLKPRNYQLE
260 270 280 290 300
LALPAKKGKN TIICAPTGCG KTFVSLLICE HHLKKFPCGQ KGKVVFFANQ
310 320 330 340 350
IPVYEQQATV FSRYFERLGY NIASISGATS DSVSVQHIIE DNDIIILTPQ
360 370 380 390 400
ILVNNLNNGA IPSLSVFTLM IFDECHNTSK NHPYNQIMFR YLDHKLGESR
410 420 430 440 450
DPLPQVVGLT ASVGVGDAKT AEEAMQHICK LCAALDASVI ATVRDNVAEL
460 470 480 490 500
EQVVYKPQKI SRKVASRTSN TFKCIISQLM KETEKLAKDV SEELGKLFQI
510 520 530 540 550
QNREFGTQKY EQWIVGVHKA CSVFQMADKE EESRVCKALF LYTSHLRKYN
560 570 580 590 600
DALIISEDAQ MTDALNYLKA FFHDVREAAF DETERELTRR FEEKLEELEK
610 620 630 640 650
VSRDPSNENP KLRDLYLVLQ EEYHLKPETK TILFVKTRAL VDALKKWIEE
660 670 680 690 700
NPALSFLKPG ILTGRGRTNR ATGMTLPAQK CVLEAFRASG DNNILIATSV
710 720 730 740 750
ADEGIDIAEC NLVILYEYVG NVIKMIQTRG RGRARDSKCF LLTSSADVIE
760 770 780 790 800
KEKANMIKEK IMNESILRLQ TWDEMKFGKT VHRIQVNEKL LRDSQHKPQP
810 820 830 840 850
VPDKENKKLL CGKCKNFACY TADIRVVETS HYTVLGDAFK ERFVCKPHPK
860 870 880 890 900
PKIYDNFEKK AKIFCAKQNC SHDWGIFVRY KTFEIPVIKI ESFVVEDIVS
910 920
GVQNRHSKWK DFHFERIQFD PAEMSV
Length:926
Mass (Da):105,975
Last modified:July 27, 2011 - v2
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i119FC0F88BC56957
GO
Isoform 2 (identifier: Q6Q899-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-454: Missing.
     455-460: YKPQKI → MPLTPV

Note: No experimental confirmation available.
Show »
Length:472
Mass (Da):54,658
Checksum:iD4614CA1A8BAC4EF
GO
Isoform 3 (identifier: Q6Q899-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     407-410: VGLT → FPIF
     411-926: Missing.

Note: No experimental confirmation available.
Show »
Length:410
Mass (Da):46,841
Checksum:iECC9E3D2D2BC5FE0
GO
Isoform 4 (identifier: Q6Q899-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     192-227: FKRAESKADEDDGAEASSIQIFIQEEPECQNLSQNP → GVLQERTLDPAALLPVLPTLLSIRGAVHFRYQRLYP
     228-926: Missing.

Note: No experimental confirmation available.
Show »
Length:227
Mass (Da):26,479
Checksum:i4FCBEE047EFB9AD0
GO

<p>In eukaryotic reference proteomes, unreviewed entries that are likely to belong to the same gene are computationally mapped, based on gene identifiers from Ensembl, EnsemblGenomes and model organism databases.<p><a href='/help/gene_centric_isoform_mapping' target='_top'>More...</a></p>Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A2AP29A2AP29_MOUSE
Probable ATP-dependent RNA helicase...
Ddx58
707Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti4E → A in AAS59532 (Ref. 1) Curated1
Sequence conflicti282H → R in AAS59532 (Ref. 1) Curated1
Sequence conflicti604D → G in AAS59532 (Ref. 1) Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section describes the sequence of naturally occurring alternative protein isoform(s). The changes in the amino acid sequence may be due to alternative splicing, alternative promoter usage, alternative initiation, or ribosomal frameshifting.<p><a href='/help/var_seq' target='_top'>More...</a></p>Alternative sequenceiVSP_0160551 – 454Missing in isoform 2. 1 PublicationAdd BLAST454
Alternative sequenceiVSP_016056192 – 227FKRAE…LSQNP → GVLQERTLDPAALLPVLPTL LSIRGAVHFRYQRLYP in isoform 4. 1 PublicationAdd BLAST36
Alternative sequenceiVSP_016057228 – 926Missing in isoform 4. 1 PublicationAdd BLAST699
Alternative sequenceiVSP_016058407 – 410VGLT → FPIF in isoform 3. 1 Publication4
Alternative sequenceiVSP_016059411 – 926Missing in isoform 3. 1 PublicationAdd BLAST516
Alternative sequenceiVSP_016060455 – 460YKPQKI → MPLTPV in isoform 2. 1 Publication6

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AY553221 mRNA Translation: AAS59532.1
AL831793 Genomic DNA No translation available.
CH466538 Genomic DNA Translation: EDL05445.1
AK049305 mRNA Translation: BAC33670.1
AK078287 mRNA Translation: BAC37205.1
AK087261 mRNA Translation: BAC39830.1

The Consensus CDS (CCDS) project

More...
CCDSi
CCDS18043.1 [Q6Q899-1]

NCBI Reference Sequences

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RefSeqi
NP_766277.3, NM_172689.3 [Q6Q899-1]

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...
Ensembli
ENSMUST00000037907; ENSMUSP00000042433; ENSMUSG00000040296 [Q6Q899-1]

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
230073

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
mmu:230073

UCSC genome browser

More...
UCSCi
uc008she.1 mouse [Q6Q899-2]
uc008shf.1 mouse [Q6Q899-1]
uc008shg.1 mouse [Q6Q899-3]
uc008shh.1 mouse [Q6Q899-4]

Keywords - Coding sequence diversityi

Alternative splicing

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY553221 mRNA Translation: AAS59532.1
AL831793 Genomic DNA No translation available.
CH466538 Genomic DNA Translation: EDL05445.1
AK049305 mRNA Translation: BAC33670.1
AK078287 mRNA Translation: BAC37205.1
AK087261 mRNA Translation: BAC39830.1
CCDSiCCDS18043.1 [Q6Q899-1]
RefSeqiNP_766277.3, NM_172689.3 [Q6Q899-1]

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3TBKX-ray2.14A240-794[»]
6BZHX-ray2.50A/B/C/D/E2-189[»]
SMRiQ6Q899
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi230926, 7 interactors
DIPiDIP-61741N
IntActiQ6Q899, 4 interactors
STRINGi10090.ENSMUSP00000042433

PTM databases

iPTMnetiQ6Q899
PhosphoSitePlusiQ6Q899
SwissPalmiQ6Q899

Proteomic databases

EPDiQ6Q899
PaxDbiQ6Q899
PeptideAtlasiQ6Q899
PRIDEiQ6Q899

Protocols and materials databases

The DNASU plasmid repository

More...
DNASUi
230073
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000037907; ENSMUSP00000042433; ENSMUSG00000040296 [Q6Q899-1]
GeneIDi230073
KEGGimmu:230073
UCSCiuc008she.1 mouse [Q6Q899-2]
uc008shf.1 mouse [Q6Q899-1]
uc008shg.1 mouse [Q6Q899-3]
uc008shh.1 mouse [Q6Q899-4]

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
23586
MGIiMGI:2442858 Ddx58

Phylogenomic databases

eggNOGiKOG0354 Eukaryota
COG1111 LUCA
GeneTreeiENSGT00940000153173
HOGENOMiHOG000230911
InParanoidiQ6Q899
KOiK12646
OrthoDBi1337630at2759
TreeFamiTF330258

Enzyme and pathway databases

ReactomeiR-MMU-1169408 ISG15 antiviral mechanism
R-MMU-5689880 Ub-specific processing proteases
R-MMU-8983711 OAS antiviral response
R-MMU-936440 Negative regulators of DDX58/IFIH1 signaling

Miscellaneous databases

EvolutionaryTraceiQ6Q899

Protein Ontology

More...
PROi
PR:Q6Q899

The Stanford Online Universal Resource for Clones and ESTs

More...
SOURCEi
Search...

Gene expression databases

BgeeiENSMUSG00000040296 Expressed in 163 organ(s), highest expression level in mesenteric lymph node
ExpressionAtlasiQ6Q899 baseline and differential
GenevisibleiQ6Q899 MM

Family and domain databases

CDDicd08817 CARD_RIG-I_r2, 1 hit
cd00079 HELICc, 1 hit
Gene3Di2.170.150.30, 1 hit
InterProiView protein in InterPro
IPR031964 CARD_dom
IPR042145 CARD_RIG-I_r2
IPR006935 Helicase/UvrB_N
IPR014001 Helicase_ATP-bd
IPR001650 Helicase_C
IPR027417 P-loop_NTPase
IPR041204 RIG-I_C
IPR038557 RLR_C_sf
IPR021673 RLR_CTR
PfamiView protein in Pfam
PF16739 CARD_2, 2 hits
PF00271 Helicase_C, 1 hit
PF04851 ResIII, 1 hit
PF18119 RIG-I_C, 1 hit
PF11648 RIG-I_C-RD, 1 hit
SMARTiView protein in SMART
SM00487 DEXDc, 1 hit
SM00490 HELICc, 1 hit
SUPFAMiSSF52540 SSF52540, 2 hits
PROSITEiView protein in PROSITE
PS51192 HELICASE_ATP_BIND_1, 1 hit
PS51194 HELICASE_CTER, 1 hit
PS51789 RLR_CTR, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiDDX58_MOUSE
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q6Q899
Secondary accession number(s): A2AP28
, Q8C320, Q8C5I3, Q8C7T2
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 8, 2005
Last sequence update: July 27, 2011
Last modified: June 5, 2019
This is version 143 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
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