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 fami... See more...

Aliases for DDX4 Gene

Aliases for DDX4 Gene

  • DEAD-Box Helicase 4 2 3 5
  • VASA 2 3 4
  • DEAD/H (Asp-Glu-Ala-Asp/His) Box Polypeptide 4 2 3
  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 4 2 3
  • Probable ATP-Dependent RNA Helicase DDX4 3 4
  • DEAD Box Protein 4 3 4
  • Vasa Homolog 3 4
  • EC 3.6.4.13 4
  • EC 3.6.1 50
  • DDX4 5

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. Diseases associated with DDX4 include Male Infertility and Spermatogenic Failure, X-Linked, 1. Among its related pathways are PIWI-interacting RNA (piRNA) biogenesis and Translational Control. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and ATP-dependent helicase activity. An important paralog of this gene is DDX3Y.

UniProtKB/Swiss-Prot Summary 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).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for DDX4 Gene

Genomics for DDX4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for DDX4 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around DDX4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for DDX4

Top Transcription factor binding sites by QIAGEN in the DDX4 gene promoter:
  • aMEF-2
  • ER-alpha
  • FOXF2
  • MEF-2A
  • POU3F2
  • POU3F2 (N-Oct-5a)

Genomic Locations for DDX4 Gene

Latest Assembly
chr5:55,737,994-55,817,157
(GRCh38/hg38)
Size:
79,164 bases
Orientation:
Plus strand

Previous Assembly
chr5:55,033,889-55,112,985
(GRCh37/hg19 by Entrez Gene)
Size:
79,097 bases
Orientation:
Plus strand

chr5:55,033,845-55,112,985
(GRCh37/hg19 by Ensembl)
Size:
79,141 bases
Orientation:
Plus strand

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 (By similarity). Interacts with RANBP9 (PubMed:27622290). Interacts with RANBP10. Interacts with PIWIL2 and MAEL. Interacts with ARNTL/BMAL1 and CLOCK. Interacts with Tex19.1 and, probably, Tex19.2 (By similarity).

    Alternative splice isoforms for DDX4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DDX4 Gene

Selected DME Specific Peptides for DDX4 Gene

Q9NQI0:
  • PPAILTFEEANLC
  • VAARGLDI
  • GINFDKY
  • NVQHVIN
  • DEADRML
  • PEMKKLI
  • RQTLMFSATFP
  • TPGRLMD
  • ATSVAARGLD
  • VINFDLP
  • VLDEADRM
  • DAQQDVPAWLEEIAFSTY
  • GGYRDGN
  • AQTGSGKT
  • TPVQKYSIPI
  • HRIGRTGR
  • VFASVDTRK
  • TGSGKTAAF
  • TKKKADFIA
  • IVAPTREL
  • LVLDEADR
  • RRGGRGSFRGCRGGFG
  • VTYIPPPPP
  • TSIHGDR

Post-translational modifications for DDX4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for DDX4 Gene

Gene Families for DDX4 Gene

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

Protein Domains for DDX4 Gene

Suggested Antigen Peptide Sequences for DDX4 Gene

GenScript: Design optimal peptide antigens:
  • Vasa homolog (DDX4_HUMAN)

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:
Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13; Evidence={ECO:0000250|UniProtKB:Q61496};.

Enzyme Numbers (IUBMB) for DDX4 Gene

Phenotypes From GWAS Catalog for DDX4 Gene

Gene Ontology (GO) - Molecular Function for DDX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IBA 21873635
GO:0003724 RNA helicase activity IBA 21873635
GO:0004386 helicase 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:

Inhibitory RNAs for research

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

Clone products for research

No data available for 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 4
cytosol 3
extracellular 2
cytoskeleton 2
mitochondrion 2
plasma membrane 1
endoplasmic reticulum 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for DDX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005737 cytoplasm IEA,IDA 21421998
GO:0043186 P granule IBA 21873635
GO:0048471 perinuclear region of cytoplasm IEA --
GO:0071546 pi-body ISS --
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:0007276 gamete generation IBA 21873635
GO:0007283 spermatogenesis ISS --
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
Water Approved Pharma 0
Phosphate Experimental Pharma 0
ATP Investigational Nutra 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
58-64-0
genes like me logo Genes that share compounds with DDX4: view

Transcripts for DDX4 Gene

mRNA/cDNA for DDX4 Gene

5 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
14 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

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

Clone products for research

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

No ASD Table

Relevant External Links for DDX4 Gene

GeneLoc Exon Structure for
DDX4

Expression for DDX4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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.

Evidence on tissue expression from TISSUES for DDX4 Gene

  • Blood(2.3)
  • Liver(2.1)
  • Pancreas(2.1)
  • Nervous system(2.1)
  • Heart(2)
genes like me logo Genes that share expression patterns with DDX4: view

Primer products for research

No data available for 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 29 30
  • 99.68 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia DDX4 29 30
  • 92.45 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia DDX4 29 30
  • 92.39 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Ddx4 29 16 30
  • 87.98 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ddx4 29
  • 87.46 (n)
Oppossum
(Monodelphis domestica)
Mammalia DDX4 30
  • 83 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia DDX4 30
  • 82 (a)
OneToOne
Chicken
(Gallus gallus)
Aves DDX4 29 30
  • 71.37 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia DDX4 30
  • 64 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ddx4 29
  • 63.91 (n)
Str.4894 29
African clawed frog
(Xenopus laevis)
Amphibia VLG1 29
Zebrafish
(Danio rerio)
Actinopterygii vasa 29 30
  • 63.81 (n)
OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.190 29
Fruit Fly
(Drosophila melanogaster)
Insecta vas 29 31
  • 54.39 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008578 29
  • 52.31 (n)
Worm
(Caenorhabditis elegans)
Secernentea glh-2 31
  • 43 (a)
glh-1 31
  • 42 (a)
vbh-1 30 31
  • 37 (a)
ManyToMany
glh-3 31
  • 37 (a)
glh-4 31
  • 36 (a)
T08D2.3 31
  • 34 (a)
F58G11.2 30 31
  • 21 (a)
ManyToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DED1 30
  • 41 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 44 (a)
OneToOne
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.8121 29
Species where no ortholog for DDX4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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
Alliance of Genome Resources:
Additional Orthologs for DDX4

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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for DDX4 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
rs139850021 Benign: not provided 55,792,752(+) A/G
NM_024415.3(DDX4):c.1414A>G (p.Lys472Glu)
MISSENSE
rs145819871 Benign: not provided 55,792,682(+) T/G
NM_024415.3(DDX4):c.1344T>G (p.Ala448=)
SYNONYMOUS
rs73131156 Benign: not provided 55,788,009(+) A/G
NM_024415.3(DDX4):c.1172+9A>G
INTRON
rs2305123 -- p.Ile287Val
rs2306259 -- p.Gly148Asp

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for DDX4 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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
Leiden Open Variation Database (LOVD)
DDX4

SNP Genotyping and Copy Number Assays for research

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

Disorders for DDX4 Gene

MalaCards: The human disease database

(8) MalaCards diseases for DDX4 Gene - From: COP and GCD

- elite association - COSMIC cancer census association via MalaCards
Search DDX4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for DDX4

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

No data available for 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
  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
  3. Structural Basis for the Interaction between the IUS-SPRY Domain of RanBPM and DDX-4 in Germ Cell Development. (PMID: 27622290) Hong SK … Kim EE (Journal of molecular biology 2016) 3 4
  4. NANOS3 function in human germ cell development. (PMID: 21421998) Julaton VT … Reijo Pera RA (Human molecular genetics 2011) 3 4
  5. Spermatozoal protein profiles in male infertility with asthenozoospermia. (PMID: 21034600) Li HJ … Li HZ (Chinese medical journal 2010) 3 4

Products for DDX4 Gene

Sources for DDX4 Gene