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 ... See more...

Aliases for DDX3Y Gene

Aliases for DDX3Y Gene

  • DEAD-Box Helicase 3 Y-Linked 2 3 5
  • 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
  • ATP-Dependent RNA Helicase DDX3Y 3 4
  • DBY 3 4
  • EC 3.6.4.13 4
  • EC 3.6.1 51
  • DDX3Y 5

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
  • GC0YP012940
  • GC0YP012945
  • GC0YP012948
  • GC0YP012963
  • GC0YP012905
  • GC0YP012911
  • GC0YP012919
  • GC0YP012925
  • GC0YP012930
  • GC0YP012935

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 Partial Deletion Of Y. 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 Summary for DDX3Y Gene

  • Probable ATP-dependent RNA helicase. During immune response, may enhance IFNB1 expression via IRF3/IRF7 pathway (By similarity).

Gene Wiki entry for DDX3Y Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for DDX3Y Gene

Genomics for DDX3Y Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for DDX3Y 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
GH0YJ012904 Enhancer 0.6 ENCODE 600.7 +1.5 1473 2.8 POLR2A SAP130 GABPB1 GATAD1 DRAP1 HOMEZ NFIL3 THAP11 DMAP1 NFYC DDX3Y piR-42731-002 RF00017-8849 UTY
GH0YJ012919 Enhancer 0.3 UCNEbase 0.4 +15.9 15921 0.3 piR-42731-002 KR153194-222 DDX3Y RF00017-8849 UTY
GH0YJ012984 Enhancer 0.3 ENCODE 0.2 +81.1 81130 1.1 TAF1 piR-48209-766 piR-61101-723 DDX3Y UTY
GH0YJ012661 Promoter/Enhancer 0.8 EPDnew ENCODE 0.1 -241.2 -241241 3.1 POLR2A YY1 TAF1 SPI1 ZNF384 MAFK ENSG00000286009 LOC112268311 lnc-UTY-5 lnc-UTY-6 TTTY15 RF00017-8849 RF00017-8850 USP9Y RF00017-8848 DDX3Y
GH0YJ012700 Enhancer 0.6 ENCODE 0.1 -203.8 -203772 0.2 CEBPA SOX13 FOXP1 SAP130 BCL6 NFIL3 RARA NR2F6 SOX5 CEBPG piR-42491-247 RF00017-8849 piR-33804-195 RF00017-8850 TTTY15 USP9Y DDX3Y RF00017-8848
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for DDX3Y

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

Genomic Locations for DDX3Y Gene

Genomic Locations for DDX3Y Gene
chrY:12,903,999-12,920,478
(GRCh38/hg38)
Size:
16,480 bases
Orientation:
Plus strand
chrY:15,016,019-15,032,390
(GRCh37/hg19)
Size:
16,372 bases
Orientation:
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:
    O15523-DDX3Y_HUMAN
    Recommended name:
    ATP-dependent RNA helicase DDX3Y
    Protein Accession:
    O15523
    Secondary Accessions:
    • B4DK29
    • B4DXX7
    • Q8IYV7

    Protein attributes for DDX3Y Gene

    Size:
    660 amino acids
    Molecular mass:
    73154 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for DDX3Y Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DDX3Y Gene

Selected DME Specific Peptides for DDX3Y Gene

O15523:
  • DMGFEPQ
  • NITKDLLDLLVEAKQEVPSWLE
  • VAARGLDI
  • YIPPHLR
  • LAPTREL
  • TGSGKTAAF
  • DEADRML
  • ENGRYGRRKQ
  • FSATFPKEIQ
  • RGFGGGGYGGFYN
  • DKDSSGWS
  • GSGSRGRFD
  • LVLDEADR
  • IHGDRSQ
  • NCPPHIE
  • VINFDLP
  • LVFVETK
  • VLDEADRM
  • YIFLAVGRVGS
  • VGSTSENITQ
  • IPVEATG
  • TRELAVQ
  • DREEALHQFRSG
  • DKDAYSSFGSR
  • DYRQSSG
  • VATPGRL
  • TGINFEKYDDIPV
  • AQTGSGKT
  • PTPVQKHAIPII
  • MGEIIMGNI
  • ADSLEDF
  • APTRELA
  • ATPGRLVD
  • HRIGRTGR
  • PCVVYGGA
  • VGRVGSTSENI
  • VYGGADI
  • TSIHGDR

Post-translational modifications for DDX3Y Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for DDX3Y Gene

Domains & Families for DDX3Y Gene

Gene Families for DDX3Y Gene

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

Protein Domains for DDX3Y Gene

Suggested Antigen Peptide Sequences for DDX3Y Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ50912, highly similar to ATP-dependent RNA helicase DDX3Y (EC 3.6.1.-) (B4DXX7_HUMAN)
  • cDNA FLJ53122, highly similar to ATP-dependent RNA helicase DDX3Y (EC 3.6.1.-) (B4E132_HUMAN)
  • DEAD box protein 3, Y-chromosomal (DDX3Y_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O15523

UniProtKB/Swiss-Prot:

DDX3Y_HUMAN :
  • Belongs to the DEAD box helicase family. DDX3/DED1 subfamily.
Family:
  • 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. During immune response, may enhance IFNB1 expression via IRF3/IRF7 pathway (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;.

Enzyme Numbers (IUBMB) for DDX3Y Gene

Gene Ontology (GO) - Molecular Function for DDX3Y Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding IBA 21873635
GO:0003724 RNA helicase activity IBA 21873635
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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DDX3Y

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 the

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

Gene Ontology (GO) - Cellular Components for DDX3Y Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA --
GO:0016020 membrane HDA 19946888
genes like me logo Genes that share ontologies with DDX3Y: view

No data available for Subcellular locations from COMPARTMENTS for DDX3Y Gene

Pathways & Interactions for DDX3Y Gene

PathCards logo

SuperPathways 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

Interacting Proteins for DDX3Y Gene

Gene Ontology (GO) - Biological Process for DDX3Y Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007276 gamete generation IBA 21873635
GO:0030154 cell differentiation IBA 21873635
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, Partial agonist, Antagonist, Full agonist, Gating inhibitor, Pore Blocker, Potentiation 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
Agonist, Full agonist, Partial agonist, Gating inhibitor, Antagonist 58-64-0
genes like me logo Genes that share compounds with DDX3Y: view

Transcripts for DDX3Y Gene

mRNA/cDNA for DDX3Y Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DDX3Y

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: -
SP10:
SP11:
SP12: -

ExUns: 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18a · 18b ^ 19 ^ 20a · 20b · 20c
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8: -
SP9:
SP10: -
SP11:
SP12:

Relevant External Links for DDX3Y Gene

GeneLoc Exon Structure for
DDX3Y

Expression for DDX3Y Gene

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



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for DDX3Y

SOURCE GeneReport for Unigene cluster for DDX3Y Gene:

Hs.99120

mRNA Expression by UniProt/SwissProt for DDX3Y Gene:

O15523-DDX3Y_HUMAN
Tissue specificity: Widely expressed at the mRNA level, with highest levels in testis (PubMed:9381176). Testis-specific (at protein level). Expressed predominantly in spermatogonia, but occasionally detected in some pre-leptotene/leptotene spermatocytes (PubMed:15294876).

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

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

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Evidence on tissue expression from TISSUES 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
Chimpanzee
(Pan troglodytes)
Mammalia DDX3Y 30 31
  • 99.24 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 90 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia DDX3Y 30 31
  • 88.8 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Ddx3y 30 17 31
  • 87.32 (n)
OneToOne
Chicken
(Gallus gallus)
Aves DDX3X 31
  • 88 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia -- 31
  • 78 (a)
OneToMany
Zebrafish
(Danio rerio)
Actinopterygii pl10 31
  • 74 (a)
ManyToMany
ddx3 31
  • 71 (a)
ManyToMany
Fruit Fly
(Drosophila melanogaster)
Insecta bel 31
  • 50 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea vbh-1 30
  • 56.71 (n)
ZC317.1 31
  • 26 (a)
ManyToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DED1 30 31
  • 57.38 (n)
OneToMany
DBP1 33
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_ADL273C 30
  • 56.3 (n)
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F01034g 30
  • 55.28 (n)
Rice
(Oryza sativa)
Liliopsida Os11g0599500 30
  • 53.26 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes sum3 30
  • 56.48 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU01369 30
  • 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 Vase (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

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

Paralogs for DDX3Y Gene

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

  • DDX3Y_HUMAN
  • B4DXX7_HUMAN
  • C9J081_HUMAN
  • C9J8G5_HUMAN

Pseudogenes.org Pseudogenes for DDX3Y Gene

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

Variants for DDX3Y Gene

Additional dbSNP identifiers (rs#s) for DDX3Y Gene

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)
DDX3Y
SNPedia medical, phenotypic, and genealogical associations of SNPs for
DDX3Y

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for DDX3Y Gene

Disorders for DDX3Y Gene

MalaCards: The human disease database

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

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

UniProtKB/Swiss-Prot

DDX3Y_HUMAN
  • Note=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.
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 23
  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 23
  3. Functional coherence of the human Y chromosome. (PMID: 9381176) Lahn BT … Page DC (Science (New York, N.Y.) 1997) 2 3 4
  4. 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 23
  5. Quantification of DDX3Y, RBMY1, DAZ and TSPY mRNAs in testes of patients with severe impairment of spermatogenesis. (PMID: 17881721) Lardone MC … Castro A (Molecular human reproduction 2007) 3 23

Products for DDX3Y Gene

Sources for DDX3Y Gene