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CDYL chromodomain Y like [ Homo sapiens (human) ]

Gene ID: 9425, updated on 10-Oct-2019

Summary

Official Symbol
CDYLprovided by HGNC
Official Full Name
chromodomain Y likeprovided by HGNC
Primary source
HGNC:HGNC:1811
See related
Ensembl:ENSG00000153046 MIM:603778
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
CDYL1
Summary
Chromodomain Y is a primate-specific Y-chromosomal gene family expressed exclusively in the testis and implicated in infertility. Although the Y-linked genes are testis-specific, this autosomal gene is ubiquitously expressed. The Y-linked genes arose by retrotransposition of an mRNA from this gene, followed by amplification of the retroposed gene. Proteins encoded by this gene superfamily possess a chromodomain, a motif implicated in chromatin binding and gene suppression, and a catalytic domain believed to be involved in histone acetylation. Multiple proteins are encoded by transcript variants of this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in placenta (RPKM 8.5), endometrium (RPKM 8.1) and 25 other tissues See more
Orthologs

Genomic context

See CDYL in Genome Data Viewer
Location:
6p25.1
Exon count:
12
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (4706138..4955544)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (4706393..4955778)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 4929 Neighboring gene proteasome 26S subunit, ATPase 1 pseudogene 11 Neighboring gene CDYL antisense RNA 1 Neighboring gene uncharacterized LOC105374897 Neighboring gene ribosomal protein S18 pseudogene 8 Neighboring gene LYRM4 antisense RNA 1 Neighboring gene ribonuclease P/MRP subunit p40

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 Functions

What's a GeneRIF?

Pathways from BioSystems

  • Endoderm Differentiation, organism-specific biosystem (from WikiPathways)
    Endoderm Differentiation, organism-specific biosystemModel depicting endoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC131936, DKFZp586C1622

Gene Ontology Provided by GOA

Function Evidence Code Pubs
chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
crotonyl-CoA hydratase activity IDA
Inferred from Direct Assay
more info
PubMed 
methylated histone binding IDA
Inferred from Direct Assay
more info
PubMed 
NOT methylated histone binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding, bridging IPI
Inferred from Physical Interaction
more info
PubMed 
transcription corepressor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription corepressor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
negative regulation of nucleic acid-templated transcription IEA
Inferred from Electronic Annotation
more info
 
negative regulation of peptidyl-lysine crotonylation IDA
Inferred from Direct Assay
more info
PubMed 
random inactivation of X chromosome ISS
Inferred from Sequence or Structural Similarity
more info
 
spermatid development ISS
Inferred from Sequence or Structural Similarity
more info
 
spermatogenesis TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
chromosome ISS
Inferred from Sequence or Structural Similarity
more info
 
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear speck IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
chromodomain Y-like protein
Names
CDY-like, autosomal
chromodomain protein, Y-like
crotonyl-CoA hydratase
testis-specific chromodomain Y-like protein
NP_001137442.1
NP_001137443.1
NP_001355054.1
NP_001355055.1
NP_001355056.1
NP_004815.3

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.

mRNA and Protein(s)

  1. NM_001143970.1NP_001137442.1  chromodomain Y-like protein isoform d

    See identical proteins and their annotated locations for NP_001137442.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (d) has a shorter N-terminus compared to isoform a. Variants 4 and 5 both encode isoform d.
    Source sequence(s)
    AK296985, BC043397, BE874176
    Consensus CDS
    CCDS47364.1
    UniProtKB/Swiss-Prot
    Q9Y232
    Related
    ENSP00000394076.2, ENST00000449732.6
    Conserved Domains (1) summary
    cd06558
    Location:158354
    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. ...
  2. NM_001143971.2NP_001137443.1  chromodomain Y-like protein isoform d

    See identical proteins and their annotated locations for NP_001137443.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (d) has a shorter N-terminus compared to isoform a. Variants 4 and 5 both encode isoform d.
    Source sequence(s)
    AF081258, BC043397, BE874176
    Consensus CDS
    CCDS47364.1
    UniProtKB/Swiss-Prot
    Q9Y232
    Related
    ENSP00000340908.5, ENST00000343762.5
    Conserved Domains (1) summary
    cd06558
    Location:158354
    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. ...
  3. NM_001368125.1NP_001355054.1  chromodomain Y-like protein isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) is predicted to encode the longest isoform (e). However, the presence of an upstream ORF may interfere with translation of the longest ORF. Translation of the upstream ORF would render the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL022725, AL356747, AL359643
    Related
    ENSP00000330512.5, ENST00000328908.9
  4. NM_001368126.1NP_001355055.1  chromodomain Y-like protein isoform f

    Status: REVIEWED

    Source sequence(s)
    AL022725, AL359643
  5. NM_001368127.1NP_001355056.1  chromodomain Y-like protein isoform g

    Status: REVIEWED

    Source sequence(s)
    AL022725, AL359643
  6. NM_004824.4NP_004815.3  chromodomain Y-like protein isoform a

    See identical proteins and their annotated locations for NP_004815.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AL022725, BC043397, BC108725, BE874176
    Consensus CDS
    CCDS4491.2
    UniProtKB/Swiss-Prot
    Q9Y232
    Related
    ENSP00000380718.3, ENST00000397588.8
    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. ...
    smart00298
    Location:759
    CHROMO; Chromatin organization modifier domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    4706138..4955544
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_170752.1: Suppressed sequence

    Description
    NM_170752.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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