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    Ddx41 DEAD box helicase 41 [ Mus musculus (house mouse) ]

    Gene ID: 72935, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Ddx41provided by MGI
    Official Full Name
    DEAD box helicase 41provided by MGI
    Primary source
    MGI:MGI:1920185
    See related
    Ensembl:ENSMUSG00000021494 AllianceGenome:MGI:1920185
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    ABS; 2900024F02Rik
    Summary
    Enables DNA binding activity. Acts upstream of or within cellular response to interferon-beta; defense response to virus; and positive regulation of transcription by RNA polymerase II. Located in endoplasmic reticulum and nucleus. Is expressed in hippocampus; pancreas; and testis. Orthologous to human DDX41 (DEAD-box helicase 41). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in ovary adult (RPKM 33.6), spleen adult (RPKM 30.7) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Ddx41 in Genome Data Viewer
    Location:
    13 B1; 13 30.06 cM
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 13 NC_000079.7 (55678223..55684471, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 13 NC_000079.6 (55530410..55536658, complement)

    Chromosome 13 - NC_000079.7Genomic Context describing neighboring genes Neighboring gene PDZ and LIM domain 7 Neighboring gene microRNA 6945 Neighboring gene STARR-positive B cell enhancer ABC_E10796 Neighboring gene docking protein 3 Neighboring gene CapStarr-seq enhancer MGSCv37_chr13:55637802-55638169 Neighboring gene predicted gene, 46416 Neighboring gene family with sequence similarity 193, member B Neighboring gene predicted gene, 31364

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Germline DDX41 mutations cause ineffective hematopoiesis and myelodysplasia. Chlon TM, et al. Cell Stem Cell, 2021 Nov 4. PMID 34473945, Free PMC Article
    2. Bruton's tyrosine kinase phosphorylates DDX41 and activates its binding of dsDNA and STING to initiate type 1 interferon response. Lee KG, et al. Cell Rep, 2015 Feb 24. PMID 25704810
    3. The E3 ubiquitin ligase TRIM21 negatively regulates the innate immune response to intracellular double-stranded DNA. Zhang Z, et al. Nat Immunol, 2013 Feb. PMID 23222971, Free PMC Article
    4. DDX41 is needed for pre- and postnatal hematopoietic stem cell differentiation in mice. Ma J, et al. Stem Cell Reports, 2022 Apr 12. PMID 35303436, Free PMC Article
    5. The helicase DDX41 recognizes the bacterial secondary messengers cyclic di-GMP and cyclic di-AMP to activate a type I interferon immune response. Parvatiyar K, et al. Nat Immunol, 2012 Dec. PMID 23142775, Free PMC Article

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. DDX41 is needed for pre- and postnatal hematopoietic stem cell differentiation in mice.
      Title: DDX41 is needed for pre- and postnatal hematopoietic stem cell differentiation in mice.
    2. Both DDX41 and cGAS are needed for the antiretroviral innate immune response to murine leukemia virus (MLV) and HIV in primary mouse macrophages and dendritic cells.
      Title: DDX41 Recognizes RNA/DNA Retroviral Reverse Transcripts and Is Critical for In Vivo Control of Murine Leukemia Virus Infection.
    3. Tyr364 and Tyr414 of DDX41 are critical for its recognition of AT-rich DNA and binding to STING, and tandem mass spectrometry identifies Tyr414 as the BTK phosphorylation site.
      Title: Bruton's tyrosine kinase phosphorylates DDX41 and activates its binding of dsDNA and STING to initiate type 1 interferon response.
    4. TRIM21 is an interferon-inducible E3 ligase that induces the Lys48-linked ubiquitination and degradation of DDX41 and negatively regulates the innate immune response to intracellular double-stranded DNA.
      Title: The E3 ubiquitin ligase TRIM21 negatively regulates the innate immune response to intracellular double-stranded DNA.
    5. DDX41 is an additional DNA sensor that depends on STING to sense pathogenic DNA.
      Title: The helicase DDX41 senses intracellular DNA mediated by the adaptor STING in dendritic cells.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (6)  1 citation
    • Endonuclease-mediated (2) 

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA helicase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cellular response to interferon-beta IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within defense response to virus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of catalytic step 2 spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of spliceosomal complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    probable ATP-dependent RNA helicase DDX41
    Names
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 41
    DEAD box protein 41
    DEAD-box protein abstrakt
    NP_598820.2
    XP_030103292.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_134059.2 → NP_598820.2  probable ATP-dependent RNA helicase DDX41

      See identical proteins and their annotated locations for NP_598820.2

      Status: VALIDATED

      Source sequence(s)
      AK013586, AK151427, BE864921, CJ303880, CX231996
      Consensus CDS
      CCDS26549.1
      UniProtKB/Swiss-Prot
      Q3U0E0, Q91VN6
      UniProtKB/TrEMBL
      Q3TI21
      Related
      ENSMUSP00000021956.9, ENSMUST00000021956.9
      Conserved Domains (3) summary
      smart00487
      Location:196 → 409
      DEXDc; DEAD-like helicases superfamily
      cd00268
      Location:183 → 397
      DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...
      pfam00271
      Location:418 → 527
      Helicase_C; Helicase conserved C-terminal domain

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000079.7 Reference GRCm39 C57BL/6J

      Range
      55678223..55684471 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030247432.2 → XP_030103292.1  probable ATP-dependent RNA helicase DDX41 isoform X1

      Conserved Domains (2) summary
      COG0513
      Location:20 → 433
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
      cd17951
      Location:59 → 264
      DEADc_DDX41; DEAD-box helicase domain of DEAD box protein 41

    RNA

    1. XR_003950486.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q91VN6.2 GenPept UniProtKB/Swiss-Prot:Q91VN6

    Gene LinkOut

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