Cdyl chromodomain protein, Y chromosome-like [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Cdylprovided by MGI
Official Full Name: chromodomain protein, Y chromosome-likeprovided by MGI
Primary source: MGI:MGI:1339956
See related: Ensembl:ENSMUSG00000059288 AllianceGenome:MGI:1339956
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
Summary: Enables chromatin binding activity. Involved in negative regulation of peptidyl-lysine crotonylation; random inactivation of X chromosome; and spermatid development. Located in chromosome; cytoplasm; and nucleus. Is expressed in 2-cell stage embryo; 4-cell stage embryo; cap mesenchyme; and ureteric tip. Used to study epilepsy. Orthologous to human CDYL (chromodomain Y like). [provided by Alliance of Genome Resources, Oct 2024]
Expression: Biased expression in testis adult (RPKM 40.9), limb E14.5 (RPKM 5.9) and 13 other tissues See more
Orthologs: human all
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Genomic context

Location:: 13 A3.3; 13 14.39 cM

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	13	NC_000079.7 (35843801..36058047)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	13	NC_000079.6 (35659818..35874064)

Chromosome 13 - NC_000079.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data 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?

CDYL reinforces male gonadal sex determination through epigenetically repressing Wnt4 transcription in mice.
Title: CDYL reinforces male gonadal sex determination through epigenetically repressing Wnt4 transcription in mice.
Nuclear Condensation of CDYL Links Histone Crotonylation and Cystogenesis in Autosomal Dominant Polycystic Kidney Disease.
Title: Nuclear Condensation of CDYL Links Histone Crotonylation and Cystogenesis in Autosomal Dominant Polycystic Kidney Disease.
Disruption of Cdyl gene impairs mouse lung epithelium differentiation and maturation.
Title: Disruption of Cdyl gene impairs mouse lung epithelium differentiation and maturation.
Cdyl Deficiency Brakes Neuronal Excitability and Nociception through Promoting Kcnb1 Transcription in Peripheral Sensory Neurons.
Title: Cdyl Deficiency Brakes Neuronal Excitability and Nociception through Promoting Kcnb1 Transcription in Peripheral Sensory Neurons.
Circular RNA (circRNA) CDYL Induces Myocardial Regeneration by ceRNA After Myocardial Infarction.
Title: Circular RNA (circRNA) CDYL Induces Myocardial Regeneration by ceRNA After Myocardial Infarction.
Cdyl is crucial for spermatogenesis and male fertility, which provides novel insights into the function of CDY gene, as well as the pathogenesis of Y chromosome microdeletion-related reproductive failure.
Title: Germline deletion of Cdyl causes teratozoospermia and progressive infertility in male mice.
results demonstrate that CDYL-mediated histone crotonylation plays a critical role in regulating stress-induced depression.
Title: Chromodomain Y-like Protein-Mediated Histone Crotonylation Regulates Stress-Induced Depressive Behaviors.
These results demonstrate that CDYL is a regulator of neuronal migration and shed light on the pathogenesis of seizure-related neurodevelopmental disorders.
Title: CDYL Deficiency Disrupts Neuronal Migration and Increases Susceptibility to Epilepsy.
CDYL negatively regulates histone crotonylation by acting as a crotonyl-CoA hydratase to convert crotonyl-CoA to beta-hydroxybutyryl-CoA and suggest role in spermatogenesis.
Title: Chromodomain Protein CDYL Acts as a Crotonyl-CoA Hydratase to Regulate Histone Crotonylation and Spermatogenesis.
A combination of H3K9me2 and H3K27me3 recruits Cdyl to the inactivated X chromosome, and this, in turn, may facilitate propagation of the H3K9me2 mark by anchoring G9a.
Title: Cdyl, a new partner of the inactive X chromosome and potential reader of H3K27me3 and H3K9me2.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Variation

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Alleles

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

Endonuclease-mediated (5) 1 citation
Gene trapped (1)
Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI325931 (e-PCR)
- UniSTS:160284

D13Mit274 (e-PCR), detects polymorphism
- UniSTS:127092

NoName (e-PCR)
- UniSTS:236992

D13Mit85 (e-PCR), detects polymorphism
- UniSTS:127183

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables crotonyl-CoA hydratase activity	ISO Inferred from Sequence Orthology more info
enables crotonyl-CoA hydratase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
NOT enables methylated histone binding	ISO Inferred from Sequence Orthology more info
enables methylated histone binding	ISO Inferred from Sequence Orthology more info
enables methylated histone binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-macromolecule adaptor activity	ISO Inferred from Sequence Orthology more info
enables transcription corepressor activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription corepressor activity	ISO Inferred from Sequence Orthology more info
enables transcription corepressor activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of peptidyl-lysine crotonylation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of peptidyl-lysine crotonylation	ISO Inferred from Sequence Orthology more info
involved_in random inactivation of X chromosome	IDA Inferred from Direct Assay more info	PubMed
involved_in spermatid development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in chromosome	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: chromodomain Y-like protein

Names: CDY-like; crotonyl-CoA hydratase; putative histone acetyltransferase Cdyl

NP_001116858.1

EC 2.3.1.48

NP_001365870.1

EC 2.3.1.48

NP_001365871.1

EC 2.3.1.48

NP_034011.1

EC 2.3.1.48

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_001123386.1 → NP_001116858.1 chromodomain Y-like protein isoform 2

See identical proteins and their annotated locations for NP_001116858.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks several 5' exons but has an alternate 5' exon, as compared to variant 1. The resulting isoform (2) has a different and shorter N-terminus, as compared to isoform 1.

Source sequence(s)

AK028162, BC062123, BG229669

Consensus CDS

CCDS49236.1

UniProtKB/Swiss-Prot

Q9WTK2

Related

ENSMUSP00000131784.3, ENSMUST00000163595.3

Conserved Domains (2) summary

cd06558
Location:290 → 486

crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...

cd18634
Location:6 → 57

CD_CDY; chromodomain of the Chromodomain Y-like protein family
NM_001378941.1 → NP_001365870.1 chromodomain Y-like protein isoform 3

Status: VALIDATED

Source sequence(s)

AC141476, AC159209, AC162940

Conserved Domains (2) summary

cd06558
Location:315 → 511

crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...

cd18634
Location:33 → 82

CD_CDY; chromodomain of the Chromodomain Y-like protein family
NM_001378942.1 → NP_001365871.1 chromodomain Y-like protein isoform 4

Status: VALIDATED

Source sequence(s)

AC159209, AC162940

UniProtKB/TrEMBL

Q3TSA1

Conserved Domains (1) summary

cd06558
Location:55 → 251

crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...
NM_009881.3 → NP_034011.1 chromodomain Y-like protein isoform 1

See identical proteins and their annotated locations for NP_034011.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AK028162, BC055103, BG229669, BY090531

Consensus CDS

CCDS49235.1

UniProtKB/Swiss-Prot

Q3U0W2, Q6P6N3, Q9WTK2

Related

ENSMUSP00000074707.7, ENSMUST00000075220.14

Conserved Domains (2) summary

cd06558
Location:339 → 535

crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...

smart00298
Location:55 → 109

CHROMO; Chromatin organization modifier domain