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

Gene ID: 8653, updated on 9-Dec-2018

Summary

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
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

Genomic context

See DDX3Y in Genome Data Viewer
Location:
Yq11.221
Exon count:
19
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) Y NC_000024.10 (12903999..12920478)
105 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (15016019..15032390)

Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC112268311 Neighboring gene testis-specific 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

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • RIG-I-like Receptor Signaling, organism-specific biosystem (from WikiPathways)
    RIG-I-like Receptor Signaling, organism-specific biosystemViral pathogen RNA are recognized by host helicases called RIG-I-like receptors (RLRs) that include DDX58 (RIG-I), DHX58 (LGP2), IFIH1 (MDA5), SNW1, and DDX17. These RLR proteins then go on to initia...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
DNA binding IEA
Inferred from Electronic Annotation
more info
 
RNA binding IEA
Inferred from Electronic Annotation
more info
 
helicase activity IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
membrane HDA PubMed 
nucleus IDA
Inferred from Direct Assay
more info
 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_012831.1 RefSeqGene

    Range
    4892..21372
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001122665.3NP_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
    O15523
    UniProtKB/TrEMBL
    A0A024R9A4
    Related
    ENSP00000353284.4, ENST00000360160.8
    Conserved Domains (3) summary
    PTZ00424
    Location:171554
    PTZ00424; helicase 45; Provisional
    cd00268
    Location:180402
    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:424534
    Helicase_C; Helicase conserved C-terminal domain
  2. NM_001302552.2NP_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:168551
    PTZ00424; helicase 45; Provisional
    cd00268
    Location:177399
    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:421531
    Helicase_C; Helicase conserved C-terminal domain
  3. NM_001324195.1NP_001311124.1  ATP-dependent RNA helicase DDX3Y isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC244434
    Conserved Domains (3) summary
    smart00487
    Location:193416
    DEXDc; DEAD-like helicases superfamily
    cd00268
    Location:180402
    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:424534
    Helicase_C; Helicase conserved C-terminal domain
  4. NM_004660.5NP_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
    O15523
    UniProtKB/TrEMBL
    A0A024R9A4
    Related
    ENSP00000336725.3, ENST00000336079.7
    Conserved Domains (3) summary
    PTZ00424
    Location:171554
    PTZ00424; helicase 45; Provisional
    cd00268
    Location:180402
    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:424534
    Helicase_C; Helicase conserved C-terminal domain

RNA

  1. NR_136716.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC244434
  2. NR_136717.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC244434
  3. NR_136718.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC244434
  4. NR_136719.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC244434
  5. NR_136720.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC244434
  6. NR_136721.1 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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000024.10 Reference GRCh38.p12 Primary Assembly

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

RNA

  1. XR_001756014.2 RNA Sequence

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