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

    Gene ID: 8653, updated on 14-Nov-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_2024_08 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (12903999..12920478)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (13812270..13828749)
    RS_2024_09 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 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 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
    2. Translational control of the AZFa gene DDX3Y by 5'UTR exon-T extension. Jaroszynski L, et al. Int J Androl, 2011 Aug. PMID 20561090
    3. Combined CD4 T-cell and antibody response to human minor histocompatibility antigen DBY after allogeneic stem-cell transplantation. Porcheray F, et al. Transplantation, 2011 Aug 15. PMID 21709606, Free PMC Article
    4. DDX3Y encodes a class I MHC-restricted H-Y antigen that is expressed in leukemic stem cells. Rosinski KV, et al. Blood, 2008 May 1. PMID 18299450, Free PMC Article
    5. The DDX3 subfamily of the DEAD box helicases: divergent roles as unveiled by studying different organisms and in vitro assays. Rosner A, et al. Curr Med Chem, 2007. PMID 17979704

    See all (91) 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
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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 ATP-dependent H2AZ histone chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent H3-H4 histone complex chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA clamp loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA helicase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin extrusion motor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cohesin loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chromatin looping IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    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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    NEW Try the new Transcript table

    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_2024_08

    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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