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    CDYL chromodomain Y like [ Homo sapiens (human) ]

    Gene ID: 9425, updated on 17-Jun-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
    109.20190607 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 uncharacterized LOC101927913 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 FunctionsWhat'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
     
    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
    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

    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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