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DDX39A DExD-box helicase 39A [ Homo sapiens (human) ]

Gene ID: 10212, updated on 12-Oct-2019

Summary

Official Symbol
DDX39Aprovided by HGNC
Official Full Name
DExD-box helicase 39Aprovided by HGNC
Primary source
HGNC:HGNC:17821
See related
Ensembl:ENSG00000123136
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BAT1; DDXL; BAT1L; DDX39; URH49
Summary
This gene encodes a member of the DEAD box protein family. These proteins are characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD) and are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure, such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of the DEAD box protein family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene is thought to play a role in the prognosis of patients with gastrointestinal stromal tumors. A pseudogene of this gene is present on chromosome 13. Alternate splicing results in multiple transcript variants. Additional alternatively spliced transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Sep 2013]
Expression
Broad expression in testis (RPKM 59.3), bone marrow (RPKM 58.2) and 24 other tissues See more
Orthologs

Genomic context

See DDX39A in Genome Data Viewer
Location:
19p13.12
Exon count:
13
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (14408798..14419383, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (14519610..14530195, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1841 Neighboring gene long intergenic non-protein coding RNA 1842 Neighboring gene adhesion G protein-coupled receptor E5 Neighboring gene Sharpr-MPRA regulatory region 3261 Neighboring gene protein kinase N1 Neighboring gene prostaglandin E receptor 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02).
NHGRI GWA Catalog

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC8417, MGC18203, MGC29546

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
ATPase activity EXP
Inferred from Experiment
more info
PubMed 
RNA binding HDA PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA helicase activity IEA
Inferred from Electronic Annotation
more info
 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA export from nucleus TAS
Traceable Author Statement
more info
 
mRNA 3'-end processing TAS
Traceable Author Statement
more info
 
mRNA export from nucleus IGI
Inferred from Genetic Interaction
more info
PubMed 
mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA splicing, via spliceosome IGI
Inferred from Genetic Interaction
more info
PubMed 
Component Evidence Code Pubs
colocalizes_with cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
membrane HDA PubMed 
nuclear speck IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
transcription export complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
ATP-dependent RNA helicase DDX39A
Names
DEAD (Asp-Glu-Ala-Asp) box polypeptide 39
DEAD (Asp-Glu-Ala-Asp) box polypeptide 39A
DEAD box protein 39
DEAD-box helicase 39A
DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 39
UAP56-related helicase, 49 kDa
nuclear RNA helicase URH49
nuclear RNA helicase, DECD variant of DEAD box family
NP_005795.2
XP_006722669.1
XP_011525922.1
XP_011525923.1
XP_024307078.1
XP_024307079.1
XP_024307080.1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_029055.1 RefSeqGene

    Range
    5043..15586
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_005804.4NP_005795.2  ATP-dependent RNA helicase DDX39A

    See identical proteins and their annotated locations for NP_005795.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript.
    Source sequence(s)
    BC001009, BM792110, DA432925
    Consensus CDS
    CCDS12308.1
    UniProtKB/Swiss-Prot
    O00148
    Related
    ENSP00000242776.3, ENST00000242776.9
    Conserved Domains (1) summary
    COG0513
    Location:30421
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]

RNA

  1. NR_046366.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 3' region compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BC032128, BM792110, DA432925
    Related
    ENST00000324340.13

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

    Range
    14408798..14419383 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006722606.4XP_006722669.1  ATP-dependent RNA helicase DDX39A isoform X3

    See identical proteins and their annotated locations for XP_006722669.1

    Conserved Domains (1) summary
    COG0513
    Location:1216
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
  2. XM_024451311.1XP_024307079.1  ATP-dependent RNA helicase DDX39A isoform X3

    Conserved Domains (1) summary
    COG0513
    Location:1216
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
  3. XM_024451312.1XP_024307080.1  ATP-dependent RNA helicase DDX39A isoform X3

    Conserved Domains (1) summary
    COG0513
    Location:1216
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
  4. XM_024451310.1XP_024307078.1  ATP-dependent RNA helicase DDX39A isoform X2

    Conserved Domains (1) summary
    COG0513
    Location:41256
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
  5. XM_011527620.1XP_011525922.1  ATP-dependent RNA helicase DDX39A isoform X1

    See identical proteins and their annotated locations for XP_011525922.1

    UniProtKB/Swiss-Prot
    O00148
    Conserved Domains (1) summary
    COG0513
    Location:30421
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
  6. XM_011527621.3XP_011525923.1  ATP-dependent RNA helicase DDX39A isoform X3

    See identical proteins and their annotated locations for XP_011525923.1

    Conserved Domains (1) summary
    COG0513
    Location:1216
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001204057.1: Suppressed sequence

    Description
    NM_001204057.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript (with non-consensus splice site) and the protein.
  2. NM_138998.1: Suppressed sequence

    Description
    NM_138998.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
  3. NR_038336.1: Suppressed sequence

    Description
    NR_038336.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.
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