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

Gene ID: 68278, updated on 26-Sep-2022

Summary

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
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Genomic context

See Ddx39a in Genome Data Viewer
Location:
8; 8 C2
Exon count:
14
Annotation release Status Assembly Chr Location
109 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 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 Neighboring gene predicted gene, 42030

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 Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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 binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables RNA helicase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 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
PubMed 
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
PubMed 
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

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_001363116.1NP_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
    Consensus CDS
    CCDS22460.1
    UniProtKB/Swiss-Prot
    Q8C2C2
    UniProtKB/TrEMBL
    A0A6P7RHM1, A0A8C6H0C5
    Related
    ENSMUSP00000105435.2, ENSMUST00000109810.2
    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
  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
    UniProtKB/TrEMBL
    A0A6P7RHA7, Q3UAF1
    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
    Q8C2C2, Q8VDW0
    UniProtKB/TrEMBL
    A0A6P7RHM1, A0A8C6H0C5
    Related
    ENSMUSP00000019576.9, ENSMUST00000019576.15
    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

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 109 details...Open this link in a new tab

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_017312952.3XP_017168441.1  ATP-dependent RNA helicase DDX39A isoform X1

    UniProtKB/TrEMBL
    A0A6P7RHA7, Q3UAF1
    Conserved Domains (1) summary
    COG0513
    Location:1221
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]