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

Gene ID: 68278, updated on 11-Apr-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 RNA binding 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 act upstream of or within RNA splicing and mRNA processing. Predicted to be located in nuclear speck. Predicted to colocalize with cytoplasm. Is expressed in several structures, including brain; cardiovascular system; genitourinary system; gut; and hemolymphoid system gland. Orthologous to human DDX39A (DExD-box helicase 39A). [provided by Alliance of Genome Resources, Apr 2022]
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
  • 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. Beads-free protein immunoprecipitation for a mass spectrometry-based interactome and posttranslational modifications analysis. Mikula M, et al. Proteome Sci, 2015. PMID 26336360, Free PMC Article

See all (31) 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 ISO
Inferred from Sequence Orthology
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 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 nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within RNA splicing 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 ISO
Inferred from Sequence Orthology
more info
  
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
  
Component Evidence Code Pubs
colocalizes_with cytoplasm ISO
Inferred from Sequence Orthology
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

Gene LinkOut

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