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Aliases for DDX4 Gene

Aliases for DDX4 Gene

  • DEAD-Box Helicase 4 2 3 5
  • DEAD/H (Asp-Glu-Ala-Asp/His) Box Polypeptide 4 2 3
  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 4 2 3
  • DEAD Box Protein 4 3 4
  • Vasa Homolog 3 4
  • VASA 3 4
  • Probable ATP-Dependent RNA Helicase DDX4 3
  • EC 3.6.4.13 4

External Ids for DDX4 Gene

Previous GeneCards Identifiers for DDX4 Gene

  • GC05P055195
  • GC05P056462
  • GC05P055004
  • GC05P055049
  • GC05P055050
  • GC05P055069
  • GC05P052007

Summaries for DDX4 Gene

Entrez Gene Summary for DDX4 Gene

  • DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), 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 this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, which is a homolog of VASA proteins in Drosophila and several other species. The gene is specifically expressed in the germ cell lineage in both sexes and functions in germ cell development. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009]

GeneCards Summary for DDX4 Gene

DDX4 (DEAD-Box Helicase 4) is a Protein Coding gene. Among its related pathways are Translational Control and Gene Expression. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and ATP-dependent helicase activity. An important paralog of this gene is DDX3X.

UniProtKB/Swiss-Prot for DDX4 Gene

  • ATP-dependent RNA helicase required during spermatogenesis (PubMed:10920202, PubMed:21034600). Required to repress transposable elements and preventing their mobilization, which is essential for the germline integrity (By similarity). Acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposons (By similarity). Involved in the secondary piRNAs metabolic process, the production of piRNAs in fetal male germ cells through a ping-pong amplification cycle (By similarity). Required for PIWIL2 slicing-triggered piRNA biogenesis: helicase activity enables utilization of one of the slice cleavage fragments generated by PIWIL2 and processing these pre-piRNAs into piRNAs (By similarity).

Additional gene information for DDX4 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DDX4 Gene

Genomics for DDX4 Gene

GeneHancer (GH) Regulatory Elements for DDX4 Gene

Promoters and enhancers for DDX4 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
GH05J055737 Promoter 0.7 EPDnew 650.7 0.0 -17 0.1 EGR1 ZBTB33 DDX4 SLC38A9 GC05P055648
GH05J055711 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 18.3 -25.6 -25570 2 HDGF PKNOX1 SMAD1 ARID4B SIN3A DMAP1 YY1 SLC30A9 POLR2B ZNF766 SLC38A9 DDX4 IL31RA DHX29 MTREX RNA5SP183 GC05P055648
GH05J055902 Enhancer 1.3 FANTOM5 Ensembl ENCODE 10.7 +165.7 165711 1.9 HDGF PKNOX1 BACH1 EBF1 BATF RELA FOSL1 POLR2A NFATC1 EED IL31RA RNA5SP183 SLC38A9 DDX4 ENSG00000262211 GC05P055845
GH05J055933 Enhancer 1.2 ENCODE dbSUPER 9.9 +196.3 196276 2.3 CLOCK FOXA2 MLX ARID4B SIN3A DMAP1 YY1 SLC30A9 FOS SP5 ENSG00000262211 MTREX ENSG00000238326 RNA5SP183 SLC38A9 DDX4 RPL26P19 IL6ST GC05P055845
GH05J055596 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 6.6 -137.1 -137128 9.3 PKNOX1 FOXA2 SIN3A FEZF1 YY1 GATA2 FOS RXRA SP5 REST DDX4 SLC38A9 RNF138P1 PLPP1 IL6ST LOC105378975 AK4P2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around DDX4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the DDX4 gene promoter:

Genomic Locations for DDX4 Gene

Genomic Locations for DDX4 Gene
chr5:55,737,995-55,817,157
(GRCh38/hg38)
Size:
79,163 bases
Orientation:
Plus strand
chr5:55,033,845-55,112,985
(GRCh37/hg19)

Genomic View for DDX4 Gene

Genes around DDX4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DDX4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DDX4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DDX4 Gene

Proteins for DDX4 Gene

  • Protein details for DDX4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NQI0-DDX4_HUMAN
    Recommended name:
    Probable ATP-dependent RNA helicase DDX4
    Protein Accession:
    Q9NQI0
    Secondary Accessions:
    • A8K8Q2
    • B3KSF4
    • D6RDK4
    • E9PCD8
    • Q5M7Z3
    • Q86VX0
    • Q9NT92
    • Q9NYB1

    Protein attributes for DDX4 Gene

    Size:
    724 amino acids
    Molecular mass:
    79308 Da
    Quaternary structure:
    • Found in a mRNP complex, at least composed of TDRD1, TDRD6, TDRD7 and DDX4. N-terminus interacts with RANBP9. Interacts with PIWIL2 and MAEL. Interacts with ARNTL/BMAL1 and CLOCK. Interacts with TEX19 (By similarity).

    Alternative splice isoforms for DDX4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DDX4 Gene

Post-translational modifications for DDX4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Boster Bio Antibodies for DDX4

No data available for DME Specific Peptides for DDX4 Gene

Domains & Families for DDX4 Gene

Gene Families for DDX4 Gene

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

Suggested Antigen Peptide Sequences for DDX4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NQI0

UniProtKB/Swiss-Prot:

DDX4_HUMAN :
  • Belongs to the DEAD box helicase family. DDX4/VASA subfamily.
Family:
  • Belongs to the DEAD box helicase family. DDX4/VASA subfamily.
genes like me logo Genes that share domains with DDX4: view

Function for DDX4 Gene

Molecular function for DDX4 Gene

UniProtKB/Swiss-Prot Function:
ATP-dependent RNA helicase required during spermatogenesis (PubMed:10920202, PubMed:21034600). Required to repress transposable elements and preventing their mobilization, which is essential for the germline integrity (By similarity). Acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposons (By similarity). Involved in the secondary piRNAs metabolic process, the production of piRNAs in fetal male germ cells through a ping-pong amplification cycle (By similarity). Required for PIWIL2 slicing-triggered piRNA biogenesis: helicase activity enables utilization of one of the slice cleavage fragments generated by PIWIL2 and processing these pre-piRNAs into piRNAs (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.

Enzyme Numbers (IUBMB) for DDX4 Gene

Gene Ontology (GO) - Molecular Function for DDX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0004004 ATP-dependent RNA helicase activity IBA --
GO:0004386 helicase activity IEA --
GO:0005524 ATP binding IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with DDX4: view
genes like me logo Genes that share phenotypes with DDX4: view

Animal Models for DDX4 Gene

MGI Knock Outs for DDX4:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DDX4

Clone Products

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for DDX4 Gene

Localization for DDX4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DDX4 Gene

Cytoplasm. Cytoplasm, perinuclear region. Note=Component of the meiotic nuage, also named P granule, a germ-cell-specific organelle required to repress transposon activity during meiosis. {ECO:0000250 UniProtKB:Q61496}.

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 DDX4 gene
Compartment Confidence
nucleus 5
cytosol 2
extracellular 1

Gene Ontology (GO) - Cellular Components for DDX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005730 nucleolus IBA --
GO:0005737 cytoplasm IDA,IEA 21421998
GO:0036464 cytoplasmic ribonucleoprotein granule IBA --
GO:0043186 P granule IBA --
GO:0048471 perinuclear region of cytoplasm IBA --
genes like me logo Genes that share ontologies with DDX4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for DDX4 Gene

Pathways & Interactions for DDX4 Gene

genes like me logo Genes that share pathways with DDX4: view

Pathways by source for DDX4 Gene

1 Cell Signaling Technology pathway for DDX4 Gene

Gene Ontology (GO) - Biological Process for DDX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007140 male meiotic nuclear division ISS --
GO:0007141 male meiosis I ISS --
GO:0007275 multicellular organism development IEA --
GO:0007283 spermatogenesis ISS --
GO:0010468 regulation of gene expression IBA --
genes like me logo Genes that share ontologies with DDX4: view

No data available for SIGNOR curated interactions for DDX4 Gene

Drugs & Compounds for DDX4 Gene

(3) Drugs for DDX4 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
ATP Investigational Nutra Agonist, Activator, Full agonist, Antagonist, Potentiation, Pore Blocker 0

(2) Additional Compounds for DDX4 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
Full agonist, Agonist, Partial agonist, Antagonist, Gating inhibitor 58-64-0
genes like me logo Genes that share compounds with DDX4: view

Transcripts for DDX4 Gene

Unigene Clusters for DDX4 Gene

DEAD (Asp-Glu-Ala-Asp) box polypeptide 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DDX4

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for DDX4 Gene

No ASD Table

Relevant External Links for DDX4 Gene

GeneLoc Exon Structure for
DDX4
ECgene alternative splicing isoforms for
DDX4

Expression for DDX4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for DDX4 Gene

mRNA differential expression in normal tissues according to GTEx for DDX4 Gene

This gene is overexpressed in Testis (x50.2).

Protein differential expression in normal tissues from HIPED for DDX4 Gene

This gene is overexpressed in Ovary (34.8) and Testis (31.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for DDX4 Gene



Protein tissue co-expression partners for DDX4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of DDX4 Gene:

DDX4

SOURCE GeneReport for Unigene cluster for DDX4 Gene:

Hs.223581

mRNA Expression by UniProt/SwissProt for DDX4 Gene:

Q9NQI0-DDX4_HUMAN
Tissue specificity: Expressed only in ovary and testis. Expressed in migratory primordial germ cells in the region of the gonadal ridge in both sexes.
genes like me logo Genes that share expression patterns with DDX4: view

No data available for Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for DDX4 Gene

Orthologs for DDX4 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for DDX4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia DDX4 34 33
  • 99.68 (n)
OneToOne
cow
(Bos Taurus)
Mammalia DDX4 34 33
  • 92.45 (n)
OneToOne
dog
(Canis familiaris)
Mammalia DDX4 34 33
  • 92.39 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Ddx4 16 34 33
  • 87.98 (n)
rat
(Rattus norvegicus)
Mammalia Ddx4 33
  • 87.46 (n)
oppossum
(Monodelphis domestica)
Mammalia DDX4 34
  • 83 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia DDX4 34
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves DDX4 34 33
  • 71.37 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia DDX4 34
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ddx4 33
  • 63.91 (n)
Str.4894 33
African clawed frog
(Xenopus laevis)
Amphibia VLG1 33
zebrafish
(Danio rerio)
Actinopterygii vasa 34 33 33
  • 63.81 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.190 33
fruit fly
(Drosophila melanogaster)
Insecta vas 35 33
  • 54.39 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008578 33
  • 52.31 (n)
worm
(Caenorhabditis elegans)
Secernentea glh-2 35
  • 43 (a)
glh-1 35
  • 42 (a)
vbh-1 34 35
  • 37 (a)
ManyToMany
glh-3 35
  • 37 (a)
glh-4 35
  • 36 (a)
T08D2.3 35
  • 34 (a)
F58G11.2 34 35
  • 21 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DED1 34
  • 41 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 44 (a)
OneToOne
Cin.8121 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.8121 33
Species where no ortholog for DDX4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for DDX4 Gene

ENSEMBL:
Gene Tree for DDX4 (if available)
TreeFam:
Gene Tree for DDX4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for DDX4: view image

Paralogs for DDX4 Gene

Paralogs for DDX4 Gene

(8) SIMAP similar genes for DDX4 Gene using alignment to 8 proteins:

  • DDX4_HUMAN
  • D6RAF5_HUMAN
  • D6RAT7_HUMAN
  • D6RBL3_HUMAN
  • D6RCM4_HUMAN
  • D6RIB2_HUMAN
  • H0Y960_HUMAN
  • H0YBW0_HUMAN

Pseudogenes.org Pseudogenes for DDX4 Gene

genes like me logo Genes that share paralogs with DDX4: view

Variants for DDX4 Gene

Sequence variations from dbSNP and Humsavar for DDX4 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000085745 -- 55,789,489(+) C/A intron_variant
rs1000087669 -- 55,748,259(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000104609 -- 55,756,476(+) A/G genic_upstream_transcript_variant, intron_variant
rs1000154219 -- 55,740,580(+) A/G genic_upstream_transcript_variant, intron_variant
rs1000160268 -- 55,753,244(+) C/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for DDX4 Gene

Variant ID Type Subtype PubMed ID
esv2759343 CNV gain 17122850
nsv10698 CNV gain 18304495
nsv4835 CNV insertion 18451855
nsv525146 CNV loss 19592680
nsv830305 CNV loss 17160897
nsv830306 CNV gain 17160897

Variation tolerance for DDX4 Gene

Residual Variation Intolerance Score: 24.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.72; 73.23% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DDX4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
DDX4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DDX4 Gene

Disorders for DDX4 Gene

Additional Disease Information for DDX4

No disorders were found for DDX4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for DDX4 Gene

Publications for DDX4 Gene

  1. The human VASA gene is specifically expressed in the germ cell lineage. (PMID: 10920202) Castrillon DH … Crum CP (Proceedings of the National Academy of Sciences of the United States of America 2000) 2 3 4 22 58
  2. VASA is a specific marker for both normal and malignant human germ cells. (PMID: 11850529) Zeeman AM … Looijenga LH (Laboratory investigation; a journal of technical methods and pathology 2002) 2 3 22 58
  3. NANOS3 function in human germ cell development. (PMID: 21421998) Julaton VT … Reijo Pera RA (Human molecular genetics 2011) 3 4 58
  4. Spermatozoal protein profiles in male infertility with asthenozoospermia. (PMID: 21034600) Li HJ … Li HZ (Chinese medical journal 2010) 3 4 58
  5. Tissue-specific differentially methylated regions of the human VASA gene are potentially associated with maturation arrest phenotype in the testis. (PMID: 19629140) Sugimoto K … Namiki M (Journal of human genetics 2009) 3 22 58

Products for DDX4 Gene

Sources for DDX4 Gene

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