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Aliases for DDX39A Gene

Aliases for DDX39A Gene

  • DExD-Box Helicase 39A 2 3 5
  • DEAD/H (Asp-Glu-Ala-Asp/His) Box Polypeptide 39 2 3
  • UAP56-Related Helicase, 49 KDa 2 3
  • Nuclear RNA Helicase URH49 3 4
  • DEAD-Box Helicase 39A 2 3
  • DEAD Box Protein 39 3 4
  • DDX39 3 4
  • Nuclear RNA Helicase, DECD Variant Of DEAD Box Family 3
  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 39A 3
  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 39 3
  • ATP-Dependent RNA Helicase DDX39A 3
  • EC 3.6.4.13 4
  • BAT1L 3
  • URH49 3
  • BAT1 3
  • DDXL 3

External Ids for DDX39A Gene

Previous HGNC Symbols for DDX39A Gene

  • DDX39

Previous GeneCards Identifiers for DDX39A Gene

  • GC19M014521

Summaries for DDX39A Gene

Entrez Gene Summary for DDX39A Gene

  • 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]

GeneCards Summary for DDX39A Gene

DDX39A (DExD-Box Helicase 39A) is a Protein Coding gene. Diseases associated with DDX39A include Gastrointestinal Stromal Tumor and Inflammatory Bowel Disease 6. Among its related pathways are RNA Polymerase II Transcription Termination and Gene Expression. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and hydrolase activity. An important paralog of this gene is DDX39B.

UniProtKB/Swiss-Prot for DDX39A Gene

  • Isoform 1: Involved in pre-mRNA splicing. Required for the export of mRNA out of the nucleus.

Gene Wiki entry for DDX39A Gene

Additional gene information for DDX39A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DDX39A Gene

Genomics for DDX39A Gene

GeneHancer (GH) Regulatory Elements for DDX39A Gene

Promoters and enhancers for DDX39A Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19I014415 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 579.1 +1.5 1461 5.2 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A ZNF2 YY1 SLC30A9 POLR2B DDX39A AKAP8 BRD4 DCAF15 RFX1 CCDC130 GIPC1 ADGRE2 ZNF333 DNAJB1
GH19I014000 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 38.3 +415.3 415283 7 ZFP64 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 ZNF263 SP3 NFYC RFX1 CCDC130 TRMT1 DDX39A DCAF15 ZNF333 MRI1 LOC284454 TECR PKN1
GH19I014378 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 35.9 +36.8 36807 7.7 HDGF PKNOX1 CLOCK SMAD1 ARNT SIN3A FEZF1 YBX1 ZNF2 IRF4 ADGRE5 CCDC130 AKAP8 MRI1 ZNF333 BRD4 DDX39A DCAF15 RFX1 LOC284454
GH19I014135 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 37.8 +281.3 281299 5.5 CLOCK DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC ZNF610 GLIS1 ASF1B LOC100507373 DDX39A DCAF15 RFX1 CCDC130 PRKACA ZNF333 PALM3 PIR43598
GH19I013747 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 26.4 +671.2 671164 2.2 HDGF PKNOX1 SMAD1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 CCDC130 TRMT1 DDX39A MRI1 DCAF15 RFX1 LOC284454 ZNF333 ADGRL1 RNASEH2A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around DDX39A on UCSC Golden Path with GeneCards custom track

Genomic Locations for DDX39A Gene

Genomic Locations for DDX39A Gene
chr19:14,408,798-14,419,383
(GRCh38/hg38)
Size:
10,586 bases
Orientation:
Minus strand
chr19:14,519,610-14,530,195
(GRCh37/hg19)

Genomic View for DDX39A Gene

Genes around DDX39A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DDX39A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DDX39A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DDX39A Gene

Proteins for DDX39A Gene

  • Protein details for DDX39A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O00148-DX39A_HUMAN
    Recommended name:
    ATP-dependent RNA helicase DDX39A
    Protein Accession:
    O00148
    Secondary Accessions:
    • B1Q2N1
    • Q8N5M0
    • Q9BVP6
    • Q9H5W0

    Protein attributes for DDX39A Gene

    Size:
    427 amino acids
    Molecular mass:
    49130 Da
    Quaternary structure:
    • Binds ALYREF/THOC4 and DDX39B/BAT1. Interacts with SARNP. Interacts with human cytomegalovirus/HHV-5 protein UL69. Interacts with MX1.
    SequenceCaution:
    • Sequence=BAB15509.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for DDX39A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DDX39A Gene

Post-translational modifications for DDX39A Gene

  • Ubiquitination at Lys35 and posLast=221221

No data available for DME Specific Peptides for DDX39A Gene

Domains & Families for DDX39A Gene

Gene Families for DDX39A Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for DDX39A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O00148

UniProtKB/Swiss-Prot:

DX39A_HUMAN :
  • Belongs to the DEAD box helicase family. DECD subfamily.
Family:
  • Belongs to the DEAD box helicase family. DECD subfamily.
genes like me logo Genes that share domains with DDX39A: view

Function for DDX39A Gene

Molecular function for DDX39A Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.
UniProtKB/Swiss-Prot Function:
Isoform 1: Involved in pre-mRNA splicing. Required for the export of mRNA out of the nucleus.
UniProtKB/Swiss-Prot Induction:
Up-regulated in proliferating cells. Present at low levels in quiescent cells.

Enzyme Numbers (IUBMB) for DDX39A Gene

Phenotypes From GWAS Catalog for DDX39A Gene

Gene Ontology (GO) - Molecular Function for DDX39A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA,HDA 22658674
GO:0004004 ATP-dependent RNA helicase activity IBA --
GO:0004386 helicase activity IEA --
GO:0005515 protein binding IPI 14667819
genes like me logo Genes that share ontologies with DDX39A: view
genes like me logo Genes that share phenotypes with DDX39A: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for DDX39A Gene

Localization for DDX39A Gene

Subcellular locations from UniProtKB/Swiss-Prot for DDX39A Gene

Nucleus. Cytoplasm. Note=Can translocate to the cytoplasm in the presence of MX1.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for DDX39A gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for DDX39A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS,IDA 21859714
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IBA --
GO:0005730 nucleolus IBA --
GO:0005737 colocalizes_with cytoplasm IDA,IEA 21859714
genes like me logo Genes that share ontologies with DDX39A: view

Pathways & Interactions for DDX39A Gene

genes like me logo Genes that share pathways with DDX39A: view

Gene Ontology (GO) - Biological Process for DDX39A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome IGI 15047853
GO:0006369 termination of RNA polymerase II transcription TAS --
GO:0006397 mRNA processing IEA --
GO:0006405 RNA export from nucleus TAS --
GO:0006406 mRNA export from nucleus IGI 15047853
genes like me logo Genes that share ontologies with DDX39A: view

No data available for SIGNOR curated interactions for DDX39A Gene

Drugs & Compounds for DDX39A Gene

(3) Drugs for DDX39A Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
ATP Investigational Nutra Agonist 0

(1) Additional Compounds for DDX39A Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
genes like me logo Genes that share compounds with DDX39A: view

Transcripts for DDX39A Gene

Unigene Clusters for DDX39A Gene

DEAD (Asp-Glu-Ala-Asp) box polypeptide 39A:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for DDX39A Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3a · 3b · 3c ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b · 8c · 8d · 8e · 8f ^ 9a · 9b · 9c · 9d ^ 10 ^
SP1: - - - - - - - - - - - - - - -
SP2: - - - - - - - - - - - - - - -
SP3: - - - - - - - - - - - - - - -
SP4: - - - - - - - - - - - - - - -
SP5: - - - - - - - - - - - - - -
SP6: - -
SP7: - - - - - - - - - - - - - - -
SP8: - - - - - - - - -
SP9: - - - - - -
SP10:
SP11: - - - - - - - - - - - - -
SP12: - - - - - - -
SP13: - - - - - - - - - -
SP14: - - - -
SP15: - - - - - - - - -
SP16: - - - - - - - - - - - -
SP17: - - - - - -
SP18: - - - -
SP19: - -
SP20:
SP21:
SP22:
SP23: - - - - - - - - -
SP24: -

ExUns: 11a · 11b · 11c · 11d ^ 12a · 12b · 12c ^ 13a · 13b · 13c ^ 14a · 14b · 14c ^ 15 ^ 16 ^ 17 ^ 18
SP1: - - - - - -
SP2: - - - - - - -
SP3: - - - -
SP4: - -
SP5: - - - -
SP6: - - - -
SP7: -
SP8:
SP9: - - - - -
SP10: - - - -
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19:
SP20: - -
SP21:
SP22: -
SP23:
SP24:

Relevant External Links for DDX39A Gene

GeneLoc Exon Structure for
DDX39A
ECgene alternative splicing isoforms for
DDX39A

Expression for DDX39A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for DDX39A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for DDX39A Gene

This gene is overexpressed in Testis (x4.5).

Protein differential expression in normal tissues from HIPED for DDX39A Gene

This gene is overexpressed in Liver (24.8), Nasal epithelium (11.6), Peripheral blood mononuclear cells (6.6), and Tlymphocyte (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for DDX39A Gene



Protein tissue co-expression partners for DDX39A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of DDX39A Gene:

DDX39A

SOURCE GeneReport for Unigene cluster for DDX39A Gene:

Hs.311609

mRNA Expression by UniProt/SwissProt for DDX39A Gene:

O00148-DX39A_HUMAN
Tissue specificity: Detected in testis, and at lower levels in brain, kidney, lung, thymus, spleen and salivary gland.

Evidence on tissue expression from TISSUES for DDX39A Gene

  • Lung(4.8)
  • Nervous system(4)
  • Bone marrow(2.1)
genes like me logo Genes that share expression patterns with DDX39A: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for DDX39A Gene

Orthologs for DDX39A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for DDX39A Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia DDX39 34
  • 96 (a)
OneToOne
DDX39A 33
  • 89.85 (n)
dog
(Canis familiaris)
Mammalia DDX39A 33 34
  • 91.1 (n)
chimpanzee
(Pan troglodytes)
Mammalia DDX39A 34
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ddx39 33 16 34
  • 88.91 (n)
rat
(Rattus norvegicus)
Mammalia Ddx39a 33
  • 88.29 (n)
oppossum
(Monodelphis domestica)
Mammalia DDX39A 34
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia DDX39A 34
  • 75 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia DDX39A 34
  • 93 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ddx39a 33
  • 79.16 (n)
African clawed frog
(Xenopus laevis)
Amphibia ddx39-prov 33
zebrafish
(Danio rerio)
Actinopterygii ddx39ab 34
  • 92 (a)
OneToMany
ddx39aa 34
  • 91 (a)
OneToMany
ddx39b 33
  • 80.56 (n)
Dr.1108 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9011 33
fruit fly
(Drosophila melanogaster)
Insecta Hel25E 34
  • 83 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea hel-1 33 34
  • 67.78 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SUB2 34
  • 60 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G11200 33
  • 65.99 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10395 34
  • 81 (a)
OneToMany
Species where no ortholog for DDX39A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for DDX39A Gene

ENSEMBL:
Gene Tree for DDX39A (if available)
TreeFam:
Gene Tree for DDX39A (if available)

Paralogs for DDX39A Gene

Paralogs for DDX39A Gene

Pseudogenes.org Pseudogenes for DDX39A Gene

genes like me logo Genes that share paralogs with DDX39A: view

Variants for DDX39A Gene

Sequence variations from dbSNP and Humsavar for DDX39A Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs786205516 likely-pathogenic, not provided 14,410,271(-) A/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1000048124 -- 14,408,622(-) G/A downstream_transcript_variant
rs1000183340 -- 14,419,929(-) G/A upstream_transcript_variant
rs1000244471 -- 14,418,488(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000411332 -- 14,419,659(-) C/G upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for DDX39A Gene

Variant ID Type Subtype PubMed ID
nsv833764 CNV loss 17160897
nsv1160590 CNV deletion 26073780

Variation tolerance for DDX39A Gene

Residual Variation Intolerance Score: 22.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.42; 42.78% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DDX39A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
DDX39A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DDX39A Gene

Disorders for DDX39A Gene

MalaCards: The human disease database

(2) MalaCards diseases for DDX39A Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
gastrointestinal stromal tumor
  • gist
inflammatory bowel disease 6
  • ibd6
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for DDX39A

genes like me logo Genes that share disorders with DDX39A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for DDX39A Gene

Publications for DDX39A Gene

  1. Intracellular characterization of DDX39, a novel growth-associated RNA helicase. (PMID: 17196963) Sugiura T … Nagano Y (Experimental cell research 2007) 3 4 22 58
  2. 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. (PMID: 15047853) Pryor A … Johnson LF (Nucleic acids research 2004) 3 4 22 58
  3. Interferon-induced antiviral protein MxA interacts with the cellular RNA helicases UAP56 and URH49. (PMID: 21859714) Wisskirchen C … Pavlovic J (The Journal of biological chemistry 2011) 3 4 58
  4. DDX39, upregulated in lung squamous cell cancer, displays RNA helicase activities and promotes cancer cell growth. (PMID: 17548965) Sugiura T … Noguchi Y (Cancer biology & therapy 2007) 3 4 58
  5. Nuclear localization of poly(A)+ mRNA following siRNA reduction of expression of the mammalian RNA helicases UAP56 and URH49. (PMID: 16949217) Kapadia F … Johnson LF (Gene 2006) 3 22 58

Products for DDX39A Gene

Sources for DDX39A Gene

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