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

Gene ID: 12593, updated on 5-Mar-2024

Summary

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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 and 4-cell stage embryo. Used to study epilepsy. Orthologous to several human genes including CDYL (chromodomain Y like). [provided by Alliance of Genome Resources, Apr 2022]
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

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See Cdyl in Genome Data Viewer
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_000079.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 1700019C18 gene Neighboring gene STARR-seq mESC enhancer starr_34172 Neighboring gene predicted gene, 22674 Neighboring gene STARR-seq mESC enhancer starr_34173 Neighboring gene STARR-seq mESC enhancer starr_34176 Neighboring gene STARR-seq mESC enhancer starr_34177 Neighboring gene predicted gene, 22126 Neighboring gene STARR-seq mESC enhancer starr_34179 Neighboring gene STARR-positive B cell enhancer ABC_E10788 Neighboring gene STARR-seq mESC enhancer starr_34180 Neighboring gene STARR-seq mESC enhancer starr_34183 Neighboring gene ribonuclease P 40 subunit Neighboring gene protein phosphatase 1, regulatory subunit 3G Neighboring gene predicted gene, 30127

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Nuclear Condensation of CDYL Links Histone Crotonylation and Cystogenesis in Autosomal Dominant Polycystic Kidney Disease. Dang L, et al. J Am Soc Nephrol, 2022 Sep. PMID 35918147, Free PMC Article
  2. Circular RNA (circRNA) CDYL Induces Myocardial Regeneration by ceRNA After Myocardial Infarction. Zhang M, et al. Med Sci Monit, 2020 Jun 11. PMID 32522972, Free PMC Article
  3. Chromodomain Y-like Protein-Mediated Histone Crotonylation Regulates Stress-Induced Depressive Behaviors. Liu Y, et al. Biol Psychiatry, 2019 Apr 15. PMID 30665597
  4. Generation and neuronal differentiation of induced pluripotent stem cells in Cdyl-/- mice. Wan L, et al. Neuroreport, 2013 Feb 13. PMID 23282990
  5. CDYL reinforces male gonadal sex determination through epigenetically repressing Wnt4 transcription in mice. Okashita N, et al. Proc Natl Acad Sci U S A, 2023 May 16. PMID 37155872, Free PMC Article

See all (40) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. Disruption of Cdyl gene impairs mouse lung epithelium differentiation and maturation.
    Title: Disruption of Cdyl gene impairs mouse lung epithelium differentiation and maturation.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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)

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 MGI

Function Evidence Code Pubs
enables acyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables chromatin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables crotonyl-CoA hydratase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone acetyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
  
enables lyase activity IEA
Inferred from Electronic Annotation
more info
  
NOT enables methylated histone binding ISO
Inferred from Sequence Orthology
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 transferase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within cell differentiation 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 
acts_upstream_of_or_within spermatogenesis IEA
Inferred from Electronic Annotation
more info
  
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 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
NP_001365870.1
NP_001365871.1
NP_034011.1

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.

mRNA and Protein(s)

  1. 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

  2. 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

  3. 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. ...

  4. 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

RNA

  1. NR_166191.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC159209, AC162940

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

  1. NC_000079.7 Reference GRCm39 C57BL/6J

    Range
    35843801..36058047
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_382045.5 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9WTK2.1 GenPept UniProtKB/Swiss-Prot:Q9WTK2

Gene LinkOut

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