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    Ddx39a DEAD box helicase 39a [ Mus musculus (house mouse) ]

    Gene ID: 68278, updated on 28-Oct-2024

    Summary

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    Official Symbol
    Ddx39aprovided by MGI
    Official Full Name
    DEAD box helicase 39aprovided by MGI
    Primary source
    MGI:MGI:1915528
    See related
    Ensembl:ENSMUSG00000005481 AllianceGenome:MGI:1915528
    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
    BAT1; DDXL; Ddx39; URH49; 2610307C23Rik
    Summary
    Predicted to enable several functions, including ATP hydrolysis activity; RNA helicase activity; and identical protein binding activity. Predicted to be involved in mRNA export from nucleus and mRNA splicing, via spliceosome. Predicted to be located in nuclear speck. Predicted to colocalize with cytoplasm. Is expressed in several structures, including genitourinary system; gut; hemolymphoid system; integumental system; and nervous system. Orthologous to human DDX39A (DExD-box helicase 39A). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in liver E14 (RPKM 54.2), liver E14.5 (RPKM 51.8) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Ddx39a in Genome Data Viewer
    Location:
    8 C2; 8 40.22 cM
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (84441806..84453533)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (83715177..83726904)

    Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E1372 Neighboring gene GIPC PDZ domain containing family, member 1 Neighboring gene STARR-positive B cell enhancer ABC_E11744 Neighboring gene prostaglandin E receptor 1 (subtype EP1) Neighboring gene protein kinase N1 Neighboring gene STARR-positive B cell enhancer ABC_E9319 Neighboring gene STARR-seq mESC enhancer starr_22095 Neighboring gene STARR-positive B cell enhancer ABC_E562 Neighboring gene microRNA 1668 Neighboring gene adhesion G protein-coupled receptor E5 Neighboring gene CapStarr-seq enhancer MGSCv37_chr8:86260655-86260859 Neighboring gene CapStarr-seq enhancer MGSCv37_chr8:86263836-86264037 Neighboring gene CapStarr-seq enhancer MGSCv37_chr8:86271935-86272044 Neighboring gene predicted gene, 46046 Neighboring gene STARR-positive B cell enhancer ABC_E10 Neighboring gene predicted gene, 42030

    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 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. Up-regulation of DDX39 in human pancreatic cancer cells with acquired gemcitabine resistance compared to gemcitabine-sensitive parental cells. Kuramitsu Y, et al. Anticancer Res, 2013 Aug. PMID 23898070
    2. Growth-regulated expression and G0-specific turnover of the mRNA that encodes URH49, a mammalian DExH/D box protein that is highly related to the mRNA export protein UAP56. Pryor A, et al. Nucleic Acids Res, 2004. PMID 15047853, Free PMC Article
    3. Interferon-induced antiviral protein MxA interacts with the cellular RNA helicases UAP56 and URH49. Wisskirchen C, et al. J Biol Chem, 2011 Oct 7. PMID 21859714, Free PMC Article
    4. HSF2BP Interacts with a Conserved Domain of BRCA2 and Is Required for Mouse Spermatogenesis. Brandsma I, et al. Cell Rep, 2019 Jun 25. PMID 31242413
    5. Differential expression of paralog RNA binding proteins establishes a dynamic splicing program required for normal cerebral cortex development. Cesari E, et al. Nucleic Acids Res, 2024 May 8. PMID 38324473, Free PMC Article

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The expression of DDX39 in gemcitabine-sensitive KLM1 and -resistant KLM1-R cells was compared.
      Title: Up-regulation of DDX39 in human pancreatic cancer cells with acquired gemcitabine resistance compared to gemcitabine-sensitive parental cells.
    2. Mx proteins exert their antiviral activity against IAV by interfering with the function of the RNA helicases UAP56 and URH49
      Title: Interferon-induced antiviral protein MxA interacts with the cellular RNA helicases UAP56 and URH49.
    3. Regulation of URH49 mRNA expression and comparison with the related UAP56 RNA helicase.
      Title: Growth-regulated expression and G0-specific turnover of the mRNA that encodes URH49, a mammalian DExH/D box protein that is highly related to the mRNA export protein UAP56.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (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 ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA helicase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA export from nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA export from nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA export from nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    colocalizes_with cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    ATP-dependent RNA helicase DDX39A
    Names
    ATP-dependent RNA helicase DDX39
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 39
    DEAD box protein 39
    DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 39
    UAP56-related helicase, 49 kDa
    NP_001350045.1
    NP_001350046.1
    NP_932099.2
    XP_017168441.1

    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_001363116.1 → NP_001350045.1  ATP-dependent RNA helicase DDX39A isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest protein-coding transcript and encodes isoform a. Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AC164432
      Consensus CDS
      CCDS22460.1
      UniProtKB/Swiss-Prot
      Q3UJV4, Q8C2C2, Q8VDW0
      UniProtKB/TrEMBL
      Q3T9L0, Q3TIE4, Q3TPL7, Q3U837, Q3UVN0
      Related
      ENSMUSP00000105435.2, ENSMUST00000109810.2
      Conserved Domains (2) summary
      cd18787
      Location:261 → 390
      SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases
      cd17950
      Location:43 → 250
      DEADc_DDX39; DEAD-box helicase domain of DEAD box protein 39

    2. NM_001363117.1 → NP_001350046.1  ATP-dependent RNA helicase DDX39A isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) has a shorter and distinct N-terminus compared to isoform a.
      Source sequence(s)
      AC164432, AK151395
      UniProtKB/TrEMBL
      Q3UAF1
      Conserved Domains (1) summary
      COG0513
      Location:1 → 221
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]

    3. NM_197982.3 → NP_932099.2  ATP-dependent RNA helicase DDX39A isoform a

      See identical proteins and their annotated locations for NP_932099.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AC164432, AK145927
      Consensus CDS
      CCDS22460.1
      UniProtKB/Swiss-Prot
      Q3UJV4, Q8C2C2, Q8VDW0
      UniProtKB/TrEMBL
      Q3T9L0, Q3TIE4, Q3TPL7, Q3U837, Q3UVN0
      Related
      ENSMUSP00000019576.9, ENSMUST00000019576.15
      Conserved Domains (2) summary
      cd18787
      Location:261 → 390
      SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases
      cd17950
      Location:43 → 250
      DEADc_DDX39; DEAD-box helicase domain of DEAD box protein 39

    RNA

    1. NR_156447.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' and 3' ends compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC164432, AK137114

    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_000074.7 Reference GRCm39 C57BL/6J

      Range
      84441806..84453533
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017312952.3 → XP_017168441.1  ATP-dependent RNA helicase DDX39A isoform X1

      UniProtKB/TrEMBL
      Q3UAF1
      Conserved Domains (1) summary
      COG0513
      Location:1 → 221
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8VDW0.1 GenPept UniProtKB/Swiss-Prot:Q8VDW0

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