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

Gene ID: 10212, updated on 3-Dec-2024

Summary

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

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

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

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 ATP-dependent H2AZ histone chaperone activity IEA
Inferred from Electronic Annotation
more info
 
enables ATP-dependent H3-H4 histone complex chaperone activity IEA
Inferred from Electronic Annotation
more info
 
enables DNA clamp loader activity IEA
Inferred from Electronic Annotation
more info
 
enables RNA binding HDA PubMed 
enables RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables RNA helicase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables chromatin extrusion motor activity IEA
Inferred from Electronic Annotation
more info
 
enables cohesin loader activity IEA
Inferred from Electronic Annotation
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 chromatin looping IEA
Inferred from Electronic Annotation
more info
 
involved_in chromatin remodeling 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 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 
involved_in negative regulation of RNA export from nucleus IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of innate immune response IDA
Inferred from Direct Assay
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
 
is_active_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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)

NEW Try the new Transcript table

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
    B1Q2N1, O00148, Q8N5M0, Q9BVP6, Q9H5W0
    UniProtKB/TrEMBL
    B4DX78
    Related
    ENSP00000242776.3, ENST00000242776.9
    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_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_011527620.2XP_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: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

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_054319495.1XP_054175470.1  ATP-dependent RNA helicase DDX39A isoform X1

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

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.