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    Ddx39a DExD-box helicase 39A [ Rattus norvegicus (Norway rat) ]

    Gene ID: 89827, updated on 27-Nov-2024

    Summary

    Official Symbol
    Ddx39aprovided by RGD
    Official Full Name
    DExD-box helicase 39Aprovided by RGD
    Primary source
    RGD:619920
    See related
    EnsemblRapid:ENSRNOG00000004373 AllianceGenome:RGD:619920
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Ddxl; Ddx39
    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 cytoplasm and nuclear speck. Orthologous to human DDX39A (DExD-box helicase 39A). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 370.9), Spleen (RPKM 223.1) and 9 other tissues See more
    Orthologs
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    Genomic context

    See Ddx39a in Genome Data Viewer
    Location:
    19q11
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 19 NC_086037.1 (41323465..41331413, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 19 NC_051354.1 (24418743..24427422, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 19 NC_005118.4 (24846530..24854886)

    Chromosome 19 - NC_086037.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134483332 Neighboring gene adhesion G protein-coupled receptor E5 Neighboring gene transfer RNA alanine (anticodon AGC) 20 Neighboring gene U6 spliceosomal RNA Neighboring gene uncharacterized LOC120098561 Neighboring gene protein kinase N1

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC105369

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP hydrolysis activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables ATP-dependent H2AZ histone chaperone activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP-dependent H3-H4 histone complex chaperone activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA clamp loader activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA binding 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 chromatin extrusion motor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables cohesin loader activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables helicase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables hydrolase 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 chromatin looping IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
     
    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
     
    involved_in negative regulation of RNA export from nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of innate immune response ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in 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
     
    is_active_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in 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 (Asp-Glu-Ala-Asp) box polypeptide 39
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 39A
    DEAD box protein 39
    DEAD-box helicase 39A
    nuclear RNA helicase, DECD variant of DEAD box family
    NP_446015.2
    XP_038953975.1

    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_053563.2NP_446015.2  ATP-dependent RNA helicase DDX39A

      See identical proteins and their annotated locations for NP_446015.2

      Status: PROVISIONAL

      Source sequence(s)
      BC086328
      UniProtKB/Swiss-Prot
      O70498, Q5U216
      UniProtKB/TrEMBL
      A0A8I6A2E4, A6IYD0
      Related
      ENSRNOP00000068949.1, ENSRNOT00000090312.3
      Conserved Domains (2) summary
      cd18787
      Location:261390
      SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases
      cd17950
      Location:43250
      DEADc_DDX39; DEAD-box helicase domain of DEAD box protein 39

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086037.1 Reference GRCr8

      Range
      41323465..41331413 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039098047.2XP_038953975.1  ATP-dependent RNA helicase DDX39A isoform X1

      UniProtKB/TrEMBL
      A0A8L2QK42
      Related
      ENSRNOP00000110804.1, ENSRNOT00000149968.1
      Conserved Domains (1) summary
      COG0513
      Location:27247
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]