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DDX3Y DEAD-box helicase 3 Y-linked [ Homo sapiens (human) ]

Gene ID: 8653, updated on 7-Apr-2024

Summary

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Official Symbol
DDX3Yprovided by HGNC
Official Full Name
DEAD-box helicase 3 Y-linkedprovided by HGNC
Primary source
HGNC:HGNC:2699
See related
Ensembl:ENSG00000067048 MIM:400010; AllianceGenome:HGNC:2699
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DBY
Summary
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]
Expression
Broad expression in bone marrow (RPKM 32.5), testis (RPKM 29.4) and 19 other tissues See more
Orthologs
all
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Genomic context

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See DDX3Y in Genome Data Viewer
Location:
Yq11.221
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (12903999..12920478)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (13812270..13828749)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (15015910..15032390)

Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC112268311 Neighboring gene testis expressed transcript, Y-linked 15 Neighboring gene ubiquitin specific peptidase 9 Y-linked Neighboring gene chromodomain Y-linked 4 pseudogene Neighboring gene calcium/calmodulin dependent serine protein kinase pseudogene 1 Neighboring gene splicing factor proline and glutamine rich pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. AZFa Y gene, DDX3Y, evolved novel testis transcript variants in primates with proximal 3´UTR polyadenylation for germ cell specific translation. Vogt PH, et al. Sci Rep, 2022 May 27. PMID 35624115, Free PMC Article
  2. Computational Analysis of High-Risk SNPs in Human DBY Gene Responsible for Male Infertility: A Functional and Structural Impact. Nailwal M, et al. Interdiscip Sci, 2019 Sep. PMID 29520635
  3. DDX3Y gene rescue of a Y chromosome AZFa deletion restores germ cell formation and transcriptional programs. Ramathal C, et al. Sci Rep, 2015 Oct 12. PMID 26456624, Free PMC Article
  4. DDX3Y, a Male-Specific Region of Y Chromosome Gene, May Modulate Neuronal Differentiation. Vakilian H, et al. J Proteome Res, 2015 Sep 4. PMID 26144214
  5. AZFa protein DDX3Y is differentially expressed in human male germ cells during development and in testicular tumours: new evidence for phenotypic plasticity of germ cells. Gueler B, et al. Hum Reprod, 2012 Jun. PMID 22466863

See all (80) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Antioncogenic roles of USP9Y and DDX3Y in lung cancer: USP9Y stabilizes DDX3Y by preventing its degradation through deubiquitination.
    Title: Antioncogenic roles of USP9Y and DDX3Y in lung cancer: USP9Y stabilizes DDX3Y by preventing its degradation through deubiquitination.
  2. Antibody-mediated pathogenesis of chronic GVHD through DBY/HLA class II complexes and induction of a GVL effect.
    Title: Antibody-mediated pathogenesis of chronic GVHD through DBY/HLA class II complexes and induction of a GVL effect.
  3. DDX3Y is likely the key spermatogenic factor in the AZFa region that contributes to human non-obstructive azoospermia.
    Title: DDX3Y is likely the key spermatogenic factor in the AZFa region that contributes to human non-obstructive azoospermia.
  4. Sexually dimorphic RNA helicases DDX3X and DDX3Y differentially regulate RNA metabolism through phase separation.
    Title: Sexually dimorphic RNA helicases DDX3X and DDX3Y differentially regulate RNA metabolism through phase separation.
  5. AZFa Y gene, DDX3Y, evolved novel testis transcript variants in primates with proximal 3 UTR polyadenylation for germ cell specific translation.
    Title: AZFa Y gene, DDX3Y, evolved novel testis transcript variants in primates with proximal 3´UTR polyadenylation for germ cell specific translation.
  6. Sequential inverse dysregulation of the RNA helicases DDX3X and DDX3Y facilitates MYC-driven lymphomagenesis.
    Title: Sequential inverse dysregulation of the RNA helicases DDX3X and DDX3Y facilitates MYC-driven lymphomagenesis.
  7. Sex matters: XIST and DDX3Y gene expression as a tool to determine fetal sex in human first trimester placenta.
    Title: Sex matters: XIST and DDX3Y gene expression as a tool to determine fetal sex in human first trimester placenta.
  8. MicroRNA-497 functions as an inflammatory suppressor via targeting DDX3Y and modulating toll-like receptor 4/NF-kappaB in cigarette smoke extract-stimulated human bronchial epithelial cells.
    Title: MicroRNA-497 functions as an inflammatory suppressor via targeting DDX3Y and modulating toll-like receptor 4/NF-κB in cigarette smoke extract-stimulated human bronchial epithelial cells.
  9. intercellular antigen transfer of DBY is tightly regulated via binding to HSC70 and that this mechanism influences recognition and rejection of MHC-II-negative tumors in vivo.
    Title: Chaperone protein HSC70 regulates intercellular transfer of Y chromosome antigen DBY.
  10. a significant nsSNP in DBY was identified through computational approaches; this deleterious mutation may interfere with spermatogenesis
    Title: Computational Analysis of High-Risk SNPs in Human DBY Gene Responsible for Male Infertility: A Functional and Structural Impact.
Submit: New GeneRIF Correction See all GeneRIFs (21)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Spermatogenic failure, Y-linked, 2
MedGen: C1839071 OMIM: 415000 GeneReviews: Y Chromosome Infertility
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP hydrolysis activity IEA
Inferred from Electronic Annotation
more info
  
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA helicase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in gamete generation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in P granule IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in membrane HDA PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
ATP-dependent RNA helicase DDX3Y
Names
DEAD (Asp-Glu-Ala-Asp) box helicase 3, Y-linked
DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked
DEAD box protein 3, Y-chromosomal
DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide, Y chromosome
NP_001116137.1
NP_001289481.1
NP_001311124.1
NP_004651.2
XP_047298731.1
XP_047298732.1
XP_047298733.1
XP_047298734.1
XP_054184360.1
XP_054184361.1
XP_054184362.1
XP_054184363.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_012831.2 RefSeqGene

    Range
    5871..21481
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001122665.3 → NP_001116137.1  ATP-dependent RNA helicase DDX3Y isoform 1

    See identical proteins and their annotated locations for NP_001116137.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC244434, BC034942, HY048505
    Consensus CDS
    CCDS14782.1
    UniProtKB/Swiss-Prot
    B4DK29, B4DXX7, O15523, Q8IYV7
    Related
    ENSP00000353284.4, ENST00000360160.8
    Conserved Domains (3) summary
    PTZ00424
    Location:171 → 554
    PTZ00424; helicase 45; Provisional
    cd00268
    Location:180 → 402
    DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...
    pfam00271
    Location:424 → 534
    Helicase_C; Helicase conserved C-terminal domain

  2. NM_001302552.3 → NP_001289481.1  ATP-dependent RNA helicase DDX3Y isoform 2

    See identical proteins and their annotated locations for NP_001289481.1

    Status: REVIEWED

    Source sequence(s)
    AC244434, AK302172
    UniProtKB/Swiss-Prot
    O15523
    Conserved Domains (3) summary
    PTZ00424
    Location:168 → 551
    PTZ00424; helicase 45; Provisional
    cd00268
    Location:177 → 399
    DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...
    pfam00271
    Location:421 → 531
    Helicase_C; Helicase conserved C-terminal domain

  3. NM_001324195.2 → NP_001311124.1  ATP-dependent RNA helicase DDX3Y isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC244434
    Conserved Domains (3) summary
    smart00487
    Location:193 → 416
    DEXDc; DEAD-like helicases superfamily
    cd00268
    Location:180 → 402
    DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...
    pfam00271
    Location:424 → 534
    Helicase_C; Helicase conserved C-terminal domain

  4. NM_004660.5 → NP_004651.2  ATP-dependent RNA helicase DDX3Y isoform 1

    See identical proteins and their annotated locations for NP_004651.2

    Status: REVIEWED

    Source sequence(s)
    BC034942, BM055220, BM995760, BQ718381, CR981580, CX783434, DC394594, DR421958
    Consensus CDS
    CCDS14782.1
    UniProtKB/Swiss-Prot
    B4DK29, B4DXX7, O15523, Q8IYV7
    Related
    ENSP00000336725.3, ENST00000336079.8
    Conserved Domains (3) summary
    PTZ00424
    Location:171 → 554
    PTZ00424; helicase 45; Provisional
    cd00268
    Location:180 → 402
    DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...
    pfam00271
    Location:424 → 534
    Helicase_C; Helicase conserved C-terminal domain

RNA

  1. NR_136716.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC244434

  2. NR_136717.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC244434

  3. NR_136718.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC244434

  4. NR_136719.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC244434

  5. NR_136720.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC244434

  6. NR_136721.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC244434

  7. NR_136722.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC244434

  8. NR_136723.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC244434

  9. NR_136724.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC244434

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

    Range
    12903999..12920478
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047442775.1 → XP_047298731.1  ATP-dependent RNA helicase DDX3Y isoform X1

    UniProtKB/Swiss-Prot
    B4DK29, B4DXX7, O15523, Q8IYV7

  2. XM_047442777.1 → XP_047298733.1  ATP-dependent RNA helicase DDX3Y isoform X3

  3. XM_047442776.1 → XP_047298732.1  ATP-dependent RNA helicase DDX3Y isoform X2

  4. XM_047442778.1 → XP_047298734.1  ATP-dependent RNA helicase DDX3Y isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060948.1 Alternate T2T-CHM13v2.0

    Range
    13812270..13828749
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054328385.1 → XP_054184360.1  ATP-dependent RNA helicase DDX3Y isoform X1

    UniProtKB/Swiss-Prot
    B4DK29, B4DXX7, O15523, Q8IYV7

  2. XM_054328387.1 → XP_054184362.1  ATP-dependent RNA helicase DDX3Y isoform X3

  3. XM_054328386.1 → XP_054184361.1  ATP-dependent RNA helicase DDX3Y isoform X2

  4. XM_054328388.1 → XP_054184363.1  ATP-dependent RNA helicase DDX3Y isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O15523.2 GenPept UniProtKB/Swiss-Prot:O15523

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