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    Ddx39 DEAD (Asp-Glu-Ala-Asp) box polypeptide 39 [ Mus musculus (house mouse) ]

    Gene ID: 68278, updated on 31-Jan-2019

    Summary

    Official Symbol
    Ddx39provided by MGI
    Official Full Name
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 39provided by MGI
    Primary source
    MGI:MGI:1915528
    See related
    Ensembl:ENSMUSG00000005481
    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; URH49; Ddx39a; 2610307C23Rik
    Expression
    Ubiquitous expression in liver E14 (RPKM 54.2), liver E14.5 (RPKM 51.8) and 28 other tissues See more
    Orthologs

    Genomic context

    See Ddx39 in Genome Data Viewer
    Location:
    8; 8 C2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 8 NC_000074.6 (83715177..83723351)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 8 NC_000074.5 (86239098..86247247)

    Chromosome 8 - NC_000074.6Genomic Context describing neighboring genes Neighboring gene GIPC PDZ domain containing family, member 1 Neighboring gene prostaglandin E receptor 1 (subtype EP1) Neighboring gene protein kinase N1 Neighboring gene microRNA 1668 Neighboring gene adhesion G protein-coupled receptor E5 Neighboring gene predicted gene, 46046

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (2) 

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    ATPase activity ISO
    Inferred from Sequence Orthology
    more info
     
    helicase activity IEA
    Inferred from Electronic Annotation
    more info
     
    hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
     
    identical protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
     
    nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    RNA splicing IEA
    Inferred from Electronic Annotation
    more info
     
    mRNA export from nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    mRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    colocalizes_with cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    nuclear speck ISO
    Inferred from Sequence Orthology
    more info
     
    nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    ATP-dependent RNA helicase DDX39A
    Names
    ATP-dependent RNA helicase DDX39
    DEAD box protein 39
    DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 39
    UAP56-related helicase, 49 kDa
    NP_932099.2
    XP_006531395.1
    XP_017168438.1
    XP_017168439.1
    XP_017168440.1
    XP_017168441.1

    NCBI Reference Sequences (RefSeq)

    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_001363116.1NP_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
      Conserved Domains (1) summary
      COG0513
      Location:30421
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
    2. NM_001363117.1NP_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
      Conserved Domains (1) summary
      COG0513
      Location:1221
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
    3. NM_197982.3NP_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
      Q8VDW0
      Related
      ENSMUSP00000019576.8, ENSMUST00000019576.14
      Conserved Domains (1) summary
      COG0513
      Location:30421
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]

    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: Mus musculus Annotation Release 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000074.6 Reference GRCm38.p4 C57BL/6J

      Range
      83715177..83723351
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017312949.1XP_017168438.1  ATP-dependent RNA helicase DDX39A isoform X1

    2. XM_017312951.1XP_017168440.1  ATP-dependent RNA helicase DDX39A isoform X3

    3. XM_017312950.1XP_017168439.1  ATP-dependent RNA helicase DDX39A isoform X1

    4. XM_006531332.3XP_006531395.1  ATP-dependent RNA helicase DDX39A isoform X2

      UniProtKB/Swiss-Prot
      Q8VDW0
      Related
      ENSMUSP00000105435.1, ENSMUST00000109810.1
      Conserved Domains (1) summary
      COG0513
      Location:30421
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
    5. XM_017312952.1XP_017168441.1  ATP-dependent RNA helicase DDX39A isoform X4

      UniProtKB/TrEMBL
      Q3UAF1
      Conserved Domains (1) summary
      COG0513
      Location:1221
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
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