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

Gene ID: 89827, updated on 2-May-2024

Summary

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Official Symbol
Ddx39aprovided by RGD
Official Full Name
DExD-box helicase 39Aprovided by RGD
Primary source
RGD:619920
See related
Ensembl: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 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 be located in nuclear speck. Predicted to colocalize with cytoplasm. Orthologous to human DDX39A (DExD-box helicase 39A). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Thymus (RPKM 370.9), Spleen (RPKM 223.1) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Genomic sequence and expression profile of murine Bat1a and Nfkbil1. Allcock R, et al. DNA Seq, 2006 Aug. PMID 17312949
  2. SOCS3 suppresses the expression of IL-4 cytokine by inhibiting the phosphorylation of c-Jun through the ERK signaling pathway in rat mast cell line RBL-2H3. Kim D, et al. Mol Immunol, 2011 Feb. PMID 21168220
  3. 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
  4. The BAT1 gene in the MHC encodes an evolutionarily conserved putative nuclear RNA helicase of the DEAD family. Peelman LJ, et al. Genomics, 1995 Mar 20. PMID 7601445
  5. ATP is required for interactions between UAP56 and two conserved mRNA export proteins, Aly and CIP29, to assemble the TREX complex. Dufu K, et al. Genes Dev, 2010 Sep 15. PMID 20844015, Free PMC Article

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Overexpression of SOCS3 was found to reduce the level of calcium ionophore-induced phosphorylation of ERK1/2 and c-Jun transcription factor
    Title: SOCS3 suppresses the expression of IL-4 cytokine by inhibiting the phosphorylation of c-Jun through the ERK signaling pathway in rat mast cell line RBL-2H3.
Submit: New GeneRIF Correction

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 RNA helicase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA 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 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
  
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
  
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 (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_053563.2 → NP_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
    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

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_039098047.2 → XP_038953975.1  ATP-dependent RNA helicase DDX39A isoform X1

    UniProtKB/TrEMBL
    A0A8L2QK42
    Related
    ENSRNOP00000040666.3
    Conserved Domains (1) summary
    COG0513
    Location:27 → 247
    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
Q5U216.1 GenPept UniProtKB/Swiss-Prot:Q5U216

Gene LinkOut

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