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    Ddx39b DExD-box helicase 39B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 114612, updated on 9-Dec-2024

    Summary

    Official Symbol
    Ddx39bprovided by RGD
    Official Full Name
    DExD-box helicase 39Bprovided by RGD
    Primary source
    RGD:70923
    See related
    EnsemblRapid:ENSRNOG00000000841 AllianceGenome:RGD:70923
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    p47; Bat1; Bat1a
    Summary
    Predicted to enable several functions, including ATP hydrolysis activity; ATP-dependent protein binding activity; and RNA binding activity. Involved in several processes, including positive regulation of cell growth involved in cardiac muscle cell development; positive regulation of macromolecule biosynthetic process; and positive regulation of vascular associated smooth muscle cell proliferation. Located in nuclear matrix. Part of protein-containing complex. Human ortholog(s) of this gene implicated in type 1 diabetes mellitus. Orthologous to human DDX39B (DExD-box helicase 39B). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 912.2), Spleen (RPKM 608.4) and 9 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See Ddx39b in Genome Data Viewer
    Location:
    20p12
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (3577200..3589651, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (3547702..3585064, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (4806103..4818600, complement)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene VPS52 subunit of GARP complex, pseudogene 3 Neighboring gene RT1 class I, locus1 Neighboring gene Small nucleolar RNA SNORD83 Neighboring gene small nucleolar RNA SNORD83 Neighboring gene ATPase H+ transporting V1 subunit G2 Neighboring gene NFKB inhibitor like 1 Neighboring gene lymphotoxin alpha

    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

    Bibliography

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 ATP-dependent activity, acting on RNA ISO
    Inferred from Sequence Orthology
    more info
     
    enables ATP-dependent protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP-dependent protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA clamp loader activity IEA
    Inferred from Electronic Annotation
    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 RNA helicase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables U4 snRNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables U4 snRNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables U6 snRNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables U6 snRNA binding ISO
    Inferred from Sequence Orthology
    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 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
     
    enables protein-containing complex binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in RNA secondary structure unwinding IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in RNA secondary structure unwinding ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in RNA splicing ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in chromatin looping IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in liver development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    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 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
     
    involved_in mRNA transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cell growth involved in cardiac muscle cell development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of translation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of vascular associated smooth muscle cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in spliceosomal complex assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in spliceosomal complex assembly ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    part_of U4 snRNP IEA
    Inferred from Electronic Annotation
    more info
     
    part_of U4 snRNP ISO
    Inferred from Sequence Orthology
    more info
     
    part_of U6 snRNP IEA
    Inferred from Electronic Annotation
    more info
     
    part_of U6 snRNP ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nuclear matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
     
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
     
    part_of spliceosomal complex ISO
    Inferred from Sequence Orthology
    more info
     
    part_of transcription export complex IEA
    Inferred from Electronic Annotation
    more info
     
    part_of transcription export complex ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    spliceosome RNA helicase Ddx39b
    Names
    56 kDa U2AF65-associated protein
    ATP-dependent RNA helicase p47
    D17H6S81E-1
    D20H6S81e
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B
    DEAD box protein UAP56
    DEAD-box helicase 39B
    HLA-B associated transcript 1
    HLA-B-associated transcript 1A
    Nuclear RNA helicase
    spliceosome RNA helicase Bat1
    NP_579834.2
    XP_063134999.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_133300.3NP_579834.2  spliceosome RNA helicase Ddx39b

      See identical proteins and their annotated locations for NP_579834.2

      Status: VALIDATED

      Source sequence(s)
      BC080243, DY309526
      UniProtKB/Swiss-Prot
      Q63413, Q811A6, Q8R2G9
      UniProtKB/TrEMBL
      A0A8I6A103, A6KTX4
      Related
      ENSRNOP00000001115.4, ENSRNOT00000001115.8
      Conserved Domains (2) summary
      cd18787
      Location:262391
      SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases
      cd17950
      Location:44251
      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_086038.1 Reference GRCr8

      Range
      3577200..3589651 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063278929.1XP_063134999.1  spliceosome RNA helicase Ddx39b isoform X1

      UniProtKB/Swiss-Prot
      Q63413, Q811A6, Q8R2G9
      UniProtKB/TrEMBL
      A0A8I6A103, A6KTX4