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

Gene ID: 12593, updated on 12-May-2024

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 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
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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_000079.7Genomic 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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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
 
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

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_001123386.1NP_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:290486
    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:657
    CD_CDY; chromodomain of the Chromodomain Y-like protein family
  2. NM_001378941.1NP_001365870.1  chromodomain Y-like protein isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC141476, AC159209, AC162940
    Conserved Domains (2) summary
    cd06558
    Location:315511
    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:3382
    CD_CDY; chromodomain of the Chromodomain Y-like protein family
  3. NM_001378942.1NP_001365871.1  chromodomain Y-like protein isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC159209, AC162940
    UniProtKB/TrEMBL
    Q3TSA1
    Conserved Domains (1) summary
    cd06558
    Location:55251
    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_009881.3NP_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:339535
    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:55109
    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