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

Gene ID: 10212, updated on 2-Nov-2024

Summary

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Official Symbol
DDX39Aprovided by HGNC
Official Full Name
DExD-box helicase 39Aprovided by HGNC
Primary source
HGNC:HGNC:17821
See related
Ensembl:ENSG00000123136 MIM:619906; AllianceGenome:HGNC:17821
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
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Genomic context

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See DDX39A in Genome Data Viewer
Location:
19p13.12
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (14408798..14419383, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (14535472..14546052, complement)
RS_2024_09 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 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14444577-14445252 Neighboring gene MPRA-validated peak3382 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14449292-14449792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14449793-14450293 Neighboring gene long intergenic non-protein coding RNA 1842 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14459126-14460004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14460803-14461304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14461305-14461804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14162 Neighboring gene Sharpr-MPRA regulatory region 7322 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14163 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10244 Neighboring gene adhesion G protein-coupled receptor E5 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:14507248-14508447 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:14512346-14513545 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14515967-14516596 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14516597-14517226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14165 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10246 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10247 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14167 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14168 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14169 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14544012-14544585 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14544586-14545158 Neighboring gene Sharpr-MPRA regulatory region 2073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14170 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14171 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14555029-14555529 Neighboring gene Sharpr-MPRA regulatory region 3261 Neighboring gene protein kinase N1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14582511-14583159 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14586151-14586819 Neighboring gene prostaglandin E receptor 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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Related articles in PubMed

  1. DDX39 as a predictor of clinical prognosis and immune checkpoint therapy efficacy in patients with clear cell renal cell carcinoma. Bao Y, et al. Int J Biol Sci, 2021. PMID 34421357, Free PMC Article
  2. The Mammalian Ecdysoneless Protein Interacts with RNA Helicase DDX39A To Regulate Nuclear mRNA Export. Saleem I, et al. Mol Cell Biol, 2021 Jun 23. PMID 33941617, Free PMC Article
  3. URH49 exports mRNA by remodeling complex formation and mediating the NXF1-dependent pathway. Fujita KI, et al. Biochim Biophys Acta Gene Regul Mech, 2020 Feb. PMID 31917363
  4. DDX39 promotes hepatocellular carcinoma growth and metastasis through activating Wnt/β-catenin pathway. Zhang T, et al. Cell Death Dis, 2018 Jun 4. PMID 29867138, Free PMC Article
  5. Identification of DDX39A as a Potential Biomarker for Unfavorable Neuroblastoma Using a Proteomic Approach. Otake K, et al. Pediatr Blood Cancer, 2016 Feb. PMID 26469522

See all (169) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Intron Retention of DDX39A Driven by SNRPD2 is a Crucial Splicing Axis for Oncogenic MYC/Spliceosome Program in Hepatocellular Carcinoma.
    Title: Intron Retention of DDX39A Driven by SNRPD2 is a Crucial Splicing Axis for Oncogenic MYC/Spliceosome Program in Hepatocellular Carcinoma.
  2. Parsing the roles of DExD-box proteins DDX39A and DDX39B in alternative RNA splicing.
    Title: Parsing the roles of DExD-box proteins DDX39A and DDX39B in alternative RNA splicing.
  3. Terminal regions of UAP56 and URH49 are required for their distinct complex formation functioning to an essential role in mRNA processing and export.
    Title: Terminal regions of UAP56 and URH49 are required for their distinct complex formation functioning to an essential role in mRNA processing and export.
  4. Structural differences between the closely related RNA helicases, UAP56 and URH49, fashion distinct functional apo-complexes.
    Title: Structural differences between the closely related RNA helicases, UAP56 and URH49, fashion distinct functional apo-complexes.
  5. DDX39 as a predictor of clinical prognosis and immune checkpoint therapy efficacy in patients with clear cell renal cell carcinoma.
    Title: DDX39 as a predictor of clinical prognosis and immune checkpoint therapy efficacy in patients with clear cell renal cell carcinoma.
  6. The Mammalian Ecdysoneless Protein Interacts with RNA Helicase DDX39A To Regulate Nuclear mRNA Export.
    Title: The Mammalian Ecdysoneless Protein Interacts with RNA Helicase DDX39A To Regulate Nuclear mRNA Export.
  7. SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity.
    Title: SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity.
  8. UAP56- and URH49-dependent mRNA export pathways are integrated into NXF1 through the remodeling of each complex formation by ATP loading.
    Title: URH49 exports mRNA by remodeling complex formation and mediating the NXF1-dependent pathway.
  9. DDX39 regulates hepatocellular carcinoma progression by activating Wnt/beta-catenin pathway.
    Title: DDX39 promotes hepatocellular carcinoma growth and metastasis through activating Wnt/β-catenin pathway.
  10. DDX39B and its paralog DDX39A regulate androgen receptor splice variant AR-V7 generation
    Title: The RNA helicase DDX39B and its paralog DDX39A regulate androgen receptor splice variant AR-V7 generation.
Submit: New GeneRIF Correction See all GeneRIFs (23)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC8417, MGC18203, MGC29546

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP hydrolysis activity EXP
Inferred from Experiment
more info
 PubMed 
enables RNA binding HDA PubMed 
enables RNA helicase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in RNA export from nucleus TAS
Traceable Author Statement
more info
  
involved_in mRNA export from nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mRNA export from nucleus IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in 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 
located_in membrane HDA PubMed 
located_in nuclear speck IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
ATP-dependent RNA helicase DDX39A
Names
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_011525922.1
XP_054175470.1

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.

Genomic

  1. NG_029055.1 RefSeqGene

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

mRNA and Protein(s)

  1. NM_005804.4 → NP_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
    B1Q2N1, O00148, Q8N5M0, Q9BVP6, Q9H5W0
    UniProtKB/TrEMBL
    B4DX78
    Related
    ENSP00000242776.3, ENST00000242776.9
    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_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: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

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

mRNA and Protein(s)

  1. XM_011527620.2 → XP_011525922.1  ATP-dependent RNA helicase DDX39A isoform X1

    See identical proteins and their annotated locations for XP_011525922.1

    UniProtKB/Swiss-Prot
    B1Q2N1, O00148, Q8N5M0, Q9BVP6, Q9H5W0
    UniProtKB/TrEMBL
    B4DX78
    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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    14535472..14546052 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054319495.1 → XP_054175470.1  ATP-dependent RNA helicase DDX39A isoform X1

    UniProtKB/Swiss-Prot
    B1Q2N1, O00148, Q8N5M0, Q9BVP6, Q9H5W0

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.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O00148.2 GenPept UniProtKB/Swiss-Prot:O00148

Gene LinkOut

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