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

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: mouse all
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Genomic context

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_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Novel role for Ddx39 in differentiation and telomere length regulation of embryonic stem cells.
Title: Novel role for Ddx39 in differentiation and telomere length regulation of embryonic stem cells.
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.
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.
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.
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.
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.
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.
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.
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.
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.

Submit: New GeneRIF Correction See all GeneRIFs (24)

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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH12356 (e-PCR)
- UniSTS:63566

STS-X84700 (e-PCR)
- UniSTS:9558

RH79172 (e-PCR)
- UniSTS:74960

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 more info	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 more info	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

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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

EC 3.6.4.13

XP_011525922.1

EC 3.6.4.13

XP_054175470.1

EC 3.6.4.13

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

NG_029055.1 RefSeqGene

Range

5043..15586

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

14408798..14419383 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_060943.1 Alternate T2T-CHM13v2.0

Range

14535472..14546052 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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.
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.
NR_038336.1: Suppressed sequence

Description

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