Ddx3y DEAD box helicase 3, Y-linked [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ddx3yprovided by MGI
Official Full Name: DEAD box helicase 3, Y-linkedprovided by MGI
Primary source: MGI:MGI:1349406
See related: Ensembl:ENSMUSG00000069045 AllianceGenome:MGI:1349406
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Dby; D1Pas1-rs1; 8030469F12Rik
Summary: Predicted to enable RNA helicase activity and mRNA binding activity. Predicted to be involved in cell differentiation; gamete generation; and negative regulation of gene expression. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in P granule and nucleus. Is expressed in several structures, including heart; hemolymphoid system gland; liver; lung; and reproductive system. Orthologous to human DDX3Y (DEAD-box helicase 3 Y-linked). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in CNS E18 (RPKM 5.2), liver E14.5 (RPKM 4.5) and 17 other tissues See more
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Genomic context

Location:: Y; Ypter

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	Y	NC_000087.8 (1260715..1286630, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	Y	NC_000087.7 (1260715..1286628, complement)

Chromosome Y - NC_000087.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Regulatory effects of the Uty/Ddx3y locus on neighboring chromosome Y genes and autosomal mRNA transcripts in adult mouse non-reproductive cells.
Title: Regulatory effects of the Uty/Ddx3y locus on neighboring chromosome Y genes and autosomal mRNA transcripts in adult mouse non-reproductive cells.
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.
Ddx3x and Ddx3y are dispensable for spermatogenesis at least in mice. Unlike human, mice have an additional Ddx3y paralog D1pas1, that has been reported to be essential for spermatogenesis. Human and mouse DDX3 related proteins have distinct differences in their functions.
Title: An azoospermic factor gene, Ddx3y and its paralog, Ddx3x are dispensable in germ cells for male fertility.
Research suggests that arsenic induces testicular steroidogenic toxicity and inhibits the expression of ABP and Ddx3y mRNA in testes, leading to spermatogenesis disturbance.
Title: Reduced testosterone and Ddx3y expression caused by long-term exposure to arsenic and its effect on spermatogenesis in mice.
Dby mRNA is selectively retained in capacitated mouse spermatozoa. It has an important role in the early zygotic development of male mouse zygotes. This might imply that spermatozoa mRNA is involved in early zygotic and embryonic stages of reproduction.
Title: The role of Dby mRNA in early development of male mouse zygotes.
unlike DBY in humans, the role of Dby in spermatogenesis is less obvious in the mouse and its biologic activity may be replaced by that of Ddx3 and D1Pas1.
Title: Structural characterization and expression studies of Dby and its homologs in the mouse.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (5) 1 citation
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH126528 (e-PCR)
- UniSTS:209668

Dby (e-PCR), detects polymorphism
- UniSTS:256391

Gene Ontology Provided by MGI

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 clamp loader activity	IEA Inferred from Electronic Annotation more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA helicase activity	IEA Inferred from Electronic Annotation 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

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	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology 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: D1Pas1 related sequence 1; DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked; DEAD (aspartate-glutamate-alanine-aspartate) box polypeptide, Y chromosome; DEAD box protein 3, Y-chromosomal; DEAD-box RNA helicase DEAD2; mDEAD2

NP_036138.1

EC 3.6.4.13

XP_006531666.1

EC 3.6.4.13

XP_006531670.1

EC 3.6.4.13

XP_011246894.1

EC 3.6.4.13

XP_030107428.1

EC 3.6.4.13

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.

mRNA and Protein(s)

NM_012008.2 → NP_036138.1 ATP-dependent RNA helicase DDX3Y

See identical proteins and their annotated locations for NP_036138.1

Status: VALIDATED

Source sequence(s)

AJ007376, AK160604, AK162630, BB671323, BC051046, CD552910

Consensus CDS

CCDS30543.1

UniProtKB/Swiss-Prot

Q62095, Q9QWS9

UniProtKB/TrEMBL

Q3U484

Related

ENSMUSP00000088729.6, ENSMUST00000091190.12

Conserved Domains (4) summary

cd00268
Location:181 → 403

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 ...

PTZ00110
Location:66 → 609

PTZ00110; helicase; Provisional

pfam00271
Location:425 → 535

Helicase_C; Helicase conserved C-terminal domain

pfam06273
Location:87 → 171

eIF-4B; Plant specific eukaryotic initiation factor 4B

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000087.8 Reference GRCm39 C57BL/6J

Range

1260715..1286630 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006531603.3 → XP_006531666.1 ATP-dependent RNA helicase DDX3Y isoform X1

UniProtKB/TrEMBL

Q3U484

Conserved Domains (2) summary

PTZ00110
Location:66 → 608

PTZ00110; helicase; Provisional

cd18051
Location:159 → 409

DEADc_DDX3; DEAD-box helicase domain of DEAD box protein 3
XM_011248592.4 → XP_011246894.1 ATP-dependent RNA helicase DDX3Y isoform X2

UniProtKB/TrEMBL

Q3U484

Conserved Domains (2) summary

PTZ00110
Location:52 → 595

PTZ00110; helicase; Provisional

cd18051
Location:145 → 395

DEADc_DDX3; DEAD-box helicase domain of DEAD box protein 3
XM_030251568.2 → XP_030107428.1 ATP-dependent RNA helicase DDX3Y isoform X4

Conserved Domains (2) summary

cd18787
Location:229 → 359

SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases

cd18051
Location:1 → 224

DEADc_DDX3; DEAD-box helicase domain of DEAD box protein 3
XM_006531607.5 → XP_006531670.1 ATP-dependent RNA helicase DDX3Y isoform X3

Conserved Domains (2) summary

cd18787
Location:229 → 359

SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases

cd18051
Location:1 → 224

DEADc_DDX3; DEAD-box helicase domain of DEAD box protein 3