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Aliases for DDX3Y Gene

Aliases for DDX3Y Gene

  • DEAD-Box Helicase 3 Y-Linked 2 3
  • DEAD/H (Asp-Glu-Ala-Asp/His) Box Polypeptide, Y Chromosome 2 3
  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 3, Y-Linked 2 3
  • DEAD (Asp-Glu-Ala-Asp) Box Helicase 3, Y-Linked 2 3
  • DEAD Box Protein 3, Y-Chromosomal 3 4
  • DBY 3 4
  • ATP-Dependent RNA Helicase DDX3Y 3
  • DEAD-Box Helicase 3, Y-Linked 5
  • EC 4

External Ids for DDX3Y Gene

Previous HGNC Symbols for DDX3Y Gene

  • DBY

Previous GeneCards Identifiers for DDX3Y Gene

  • GC0YP014327
  • GC0YP014024
  • GC0YP014025
  • GC0YP013454
  • GC0YP013526
  • GC0YP015016
  • GC0YP009668
  • GC0YP012903
  • GC0YP012905
  • GC0YP012911
  • GC0YP012919
  • GC0YP012925

Summaries for DDX3Y Gene

Entrez Gene Summary for DDX3Y Gene

  • The protein encoded by this gene is a member of the DEAD-box RNA helicase family, characterized by nine conserved motifs, included the conserved Asp-Glu-Ala-Asp (DEAD) motif. These motifs are thought to be involved in ATP binding, hydrolysis, RNA binding, and in the formation of intramolecular interactions. This protein shares high similarity to DDX3X, on the X chromosome, but a deletion of this gene is not complemented by DDX3X. Mutations in this gene result in male infertility, a reduction in germ cell numbers, and can result in Sertoli-cell only sydrome. Pseudogenes sharing similarity to both this gene and the DDX3X paralog are found on chromosome 4 and the X chromosome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2014]

GeneCards Summary for DDX3Y Gene

DDX3Y (DEAD-Box Helicase 3 Y-Linked) is a Protein Coding gene. Diseases associated with DDX3Y include Spermatogenic Failure, Y-Linked, 2 and Male Infertility. Among its related pathways are RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and ATP-dependent RNA helicase activity. An important paralog of this gene is DDX3X.

UniProtKB/Swiss-Prot for DDX3Y Gene

  • Probable ATP-dependent RNA helicase. May play a role in spermatogenesis.

Gene Wiki entry for DDX3Y Gene

Additional gene information for DDX3Y Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DDX3Y Gene

Genomics for DDX3Y Gene

GeneHancer (GH) Regulatory Elements for DDX3Y Gene

Promoters and enhancers for DDX3Y Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0YJ012904 Enhancer 0.4 ENCODE 650.7 +1.4 1364 2.8 POLR2A ETV5 DDX3Y PIR35730
GH0YJ012919 Enhancer 0.4 UCNEbase 0.4 +15.8 15812 0.3 PIR35730 DDX3Y CASKP1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around DDX3Y on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the DDX3Y gene promoter:
  • Tal-1beta
  • E47
  • AP-1
  • AREB6
  • PPAR-gamma2

Genomic Locations for DDX3Y Gene

Genomic Locations for DDX3Y Gene
16,371 bases
Plus strand
16,372 bases
Plus strand

Genomic View for DDX3Y Gene

Genes around DDX3Y on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DDX3Y Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DDX3Y Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DDX3Y Gene

Proteins for DDX3Y Gene

  • Protein details for DDX3Y Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    ATP-dependent RNA helicase DDX3Y
    Protein Accession:
    Secondary Accessions:
    • B4DK29
    • B4DXX7
    • Q8IYV7

    Protein attributes for DDX3Y Gene

    660 amino acids
    Molecular mass:
    73154 Da
    Quaternary structure:
    • May interact with TDRD3.

    Alternative splice isoforms for DDX3Y Gene


neXtProt entry for DDX3Y Gene

Post-translational modifications for DDX3Y Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for DDX3Y Gene

No data available for DME Specific Peptides for DDX3Y Gene

Domains & Families for DDX3Y Gene

Gene Families for DDX3Y Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the DEAD box helicase family. DDX3/DED1 subfamily.
  • Belongs to the DEAD box helicase family. DDX3/DED1 subfamily.
genes like me logo Genes that share domains with DDX3Y: view

Function for DDX3Y Gene

Molecular function for DDX3Y Gene

UniProtKB/Swiss-Prot Function:
Probable ATP-dependent RNA helicase. May play a role in spermatogenesis.
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.

Enzyme Numbers (IUBMB) for DDX3Y Gene

Gene Ontology (GO) - Molecular Function for DDX3Y Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding IEA --
GO:0004004 ATP-dependent RNA helicase activity IBA --
GO:0004386 helicase activity IEA --
genes like me logo Genes that share ontologies with DDX3Y: view
genes like me logo Genes that share phenotypes with DDX3Y: view

Human Phenotype Ontology for DDX3Y Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Clone Products

No data available for Phenotypes From GWAS Catalog , Animal Models , Transcription Factor Targets and HOMER Transcription for DDX3Y Gene

Localization for DDX3Y Gene

Subcellular locations from UniProtKB/Swiss-Prot for DDX3Y Gene

Cytoplasm. Nucleus. Note=Shuttles between the nucleus and the cytoplasm in an XPO1-dependent manner.

Subcellular locations from

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 DDX3Y gene
Compartment Confidence
nucleus 5
cytosol 5
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for DDX3Y Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005730 nucleolus IBA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA --
GO:0016020 membrane HDA 19946888
genes like me logo Genes that share ontologies with DDX3Y: view

Pathways & Interactions for DDX3Y Gene

genes like me logo Genes that share pathways with DDX3Y: view

Pathways by source for DDX3Y Gene

1 BioSystems pathway for DDX3Y Gene

Gene Ontology (GO) - Biological Process for DDX3Y Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006413 translational initiation IBA --
GO:0007059 chromosome segregation IBA --
GO:0010468 regulation of gene expression IBA --
GO:0010501 RNA secondary structure unwinding IBA --
genes like me logo Genes that share ontologies with DDX3Y: view

No data available for SIGNOR curated interactions for DDX3Y Gene

Drugs & Compounds for DDX3Y Gene

(3) Drugs for DDX3Y 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, Activator, Full agonist, Antagonist, Potentiation, Pore Blocker 0

(1) Additional Compounds for DDX3Y Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • 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 DDX3Y: view

Transcripts for DDX3Y Gene

Unigene Clusters for DDX3Y Gene

DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for DDX3Y Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c · 2d · 2e · 2f ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10 ^ 11a · 11b · 11c ^ 12a · 12b ^ 13 ^
SP1: - - - - - - - -
SP2: - - -
SP3: -
SP4: - - - -
SP5: - - - - - - -
SP6: - - - - - - - - - -
SP7: - -
SP8: - - - - - - - - - - - - - - -
SP9: -
SP12: -

ExUns: 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18a · 18b ^ 19 ^ 20a · 20b · 20c
SP8: -
SP10: -

Relevant External Links for DDX3Y Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for DDX3Y Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for DDX3Y Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for DDX3Y Gene

This gene is overexpressed in Peripheral blood mononuclear cells (19.9) and Ovary (10.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for DDX3Y Gene

NURSA nuclear receptor signaling pathways regulating expression of DDX3Y Gene:


SOURCE GeneReport for Unigene cluster for DDX3Y Gene:


mRNA Expression by UniProt/SwissProt for DDX3Y Gene:

Tissue specificity: Testis-specific. Expressed predominantly in spermatogonia.

Evidence on tissue expression from TISSUES for DDX3Y Gene

  • Nervous system(4.8)
  • Spleen(2.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for DDX3Y Gene

Germ Layers:
  • mesoderm
  • reproductive
  • testicle
genes like me logo Genes that share expression patterns with DDX3Y: view

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for DDX3Y Gene

Orthologs for DDX3Y Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for DDX3Y Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia DDX3Y 34 33
  • 99.24 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 90 (a)
(Bos Taurus)
Mammalia DDX3Y 34 33
  • 88.8 (n)
(Mus musculus)
Mammalia Ddx3y 16 34 33
  • 87.32 (n)
(Gallus gallus)
Aves DDX3X 34
  • 88 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 78 (a)
(Danio rerio)
Actinopterygii pl10 34
  • 74 (a)
ddx3 34
  • 71 (a)
fruit fly
(Drosophila melanogaster)
Insecta bel 34
  • 50 (a)
(Caenorhabditis elegans)
Secernentea vbh-1 33
  • 56.71 (n)
ZC317.1 34
  • 26 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DED1 36 34 33
  • 57.38 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADL273C 33
  • 56.3 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F01034g 33
  • 55.28 (n)
(Oryza sativa)
Liliopsida Os11g0599500 33
  • 53.26 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes sum3 33
  • 56.48 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU01369 33
  • 53.17 (n)
Species where no ortholog for DDX3Y was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for DDX3Y Gene

Gene Tree for DDX3Y (if available)
Gene Tree for DDX3Y (if available)
Evolutionary constrained regions (ECRs) for DDX3Y: view image

Paralogs for DDX3Y Gene

Paralogs for DDX3Y Gene

(21) SIMAP similar genes for DDX3Y Gene using alignment to 4 proteins:

  • C9J081_HUMAN
  • C9J8G5_HUMAN Pseudogenes for DDX3Y Gene

genes like me logo Genes that share paralogs with DDX3Y: view

Variants for DDX3Y Gene

Sequence variations from dbSNP and Humsavar for DDX3Y Gene

SNP ID Clin Chr 0Y pos Variation AA Info Type
rs1000822330 -- 12,902,522(+) C/A upstream_transcript_variant
rs1001249661 -- 12,918,794(+) G/C 3_prime_UTR_variant, non_coding_transcript_variant
rs1001741722 -- 12,920,311(+) T/C 3_prime_UTR_variant, non_coding_transcript_variant
rs1002744552 -- 12,911,658(+) A/G intron_variant
rs1003594315 -- 12,910,568(+) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for DDX3Y Gene

Variant ID Type Subtype PubMed ID
esv2740672 CNV deletion 23290073

Variation tolerance for DDX3Y Gene

Gene Damage Index Score: 0.30; 6.63% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DDX3Y Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DDX3Y Gene

Disorders for DDX3Y Gene

MalaCards: The human disease database

(8) MalaCards diseases for DDX3Y Gene - From: HGMD, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
spermatogenic failure, y-linked, 2
  • spgfy2
male infertility
  • infertility male
  • spermatogenic failure
partial deletion of y
  • partial deletion of chromosome y
spermatogenic failure, x-linked, 1
  • spgfx1
- elite association - COSMIC cancer census association via MalaCards
Search DDX3Y in MalaCards View complete list of genes associated with diseases


  • Note=DDX3Y is located in the azoospermia factor a (AZFa) region on chromosome Y which is deleted in Sertoli cell-only syndrome. This is an infertility disorder in which no germ cells are visible in seminiferous tubules leading to azoospermia.

Additional Disease Information for DDX3Y

genes like me logo Genes that share disorders with DDX3Y: view

No data available for Genatlas for DDX3Y Gene

Publications for DDX3Y Gene

  1. The AZFa gene DBY (DDX3Y) is widely transcribed but the protein is limited to the male germ cells by translation control. (PMID: 15294876) Ditton HJ … Vogt PH (Human molecular genetics 2004) 3 4 22 58
  2. Human DDX3Y, the Y-encoded isoform of RNA helicase DDX3, rescues a hamster temperature-sensitive ET24 mutant cell line with a DDX3X mutation. (PMID: 15383328) Sekiguchi T … Nishimoto T (Experimental cell research 2004) 3 4 22 58
  3. Functional coherence of the human Y chromosome. (PMID: 9381176) Lahn BT … Page DC (Science (New York, N.Y.) 1997) 2 3 4 58
  4. TDRD3, a novel Tudor domain-containing protein, localizes to cytoplasmic stress granules. (PMID: 18632687) Goulet I … Côté J (Human molecular genetics 2008) 3 4 58
  5. DDX3Y encodes a class I MHC-restricted H-Y antigen that is expressed in leukemic stem cells. (PMID: 18299450) Rosinski KV … Warren EH (Blood 2008) 3 22 58

Products for DDX3Y Gene

Sources for DDX3Y Gene

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