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    CDYL chromodomain Y like [ Homo sapiens (human) ]

    Gene ID: 9425, updated on 27-Nov-2024

    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; AllianceGenome:HGNC:1811
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CDYL in Genome Data Viewer
    Location:
    6p25.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (4706138..4955544)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (4575080..4824553)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (4706372..4955778)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901549 Neighboring gene Sharpr-MPRA regulatory region 6592 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:4655389-4655960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:4655961-4656532 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4660676-4661494 Neighboring gene Sharpr-MPRA regulatory region 4929 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:4694403-4694656 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:4719503-4720314 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4725821-4726368 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:4732250-4733140 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:4733141-4734030 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:4735211-4735409 Neighboring gene proteasome 26S subunit, ATPase 1 pseudogene 11 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:4772853-4773404 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:4775329-4775982 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16862 Neighboring gene NANOG hESC enhancer GRCh37_chr6:4787179-4787707 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:4788958-4789502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23897 Neighboring gene CDYL antisense RNA 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:4864691-4865890 Neighboring gene uncharacterized LOC105374897 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:4903364-4903864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23898 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16863 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:4922310-4922536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:4922523-4923034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:4923035-4923546 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4925615-4926383 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4924846-4925614 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:4932371-4933089 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4947173-4947916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4971812-4972338 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4972339-4972863 Neighboring gene MPRA-validated peak5629 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16865 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?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association study of smoking behaviours in patients with COPD.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC131936, DKFZp586C1622

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables crotonyl-CoA hydratase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    NOT enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein-macromolecule adaptor activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription corepressor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables transcription corepressor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 random inactivation of X chromosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in spermatid development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in spermatogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in chromosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nuclear speck IDA
    Inferred from Direct Assay
    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 

    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
    XP_047275519.1
    XP_047275520.1
    XP_054212800.1
    XP_054212801.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001143970.2NP_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
      Consensus CDS
      CCDS93853.1
      UniProtKB/Swiss-Prot
      A8K6D6, B4DLG4, Q0VDG7, Q32NC5, Q5VX99, Q6P7T5, Q9BWZ2, Q9Y232, Q9Y424
      Related
      ENSP00000330512.5, ENST00000328908.9
    4. NM_001368126.1NP_001355055.1  chromodomain Y-like protein isoform f

      Status: REVIEWED

      Source sequence(s)
      AL022725, AL359643
      Conserved Domains (2) summary
      cd06558
      Location:268464
      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
    5. NM_001368127.1NP_001355056.1  chromodomain Y-like protein isoform g

      Status: REVIEWED

      Source sequence(s)
      AL022725, AL359643
      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. ...
    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. ...
      cd18634
      Location:657
      CD_CDY; chromodomain of the Chromodomain Y-like protein family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_047419563.1XP_047275519.1  chromodomain Y-like protein isoform X1

    2. XM_047419564.1XP_047275520.1  chromodomain Y-like protein isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      4575080..4824553
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356825.1XP_054212800.1  chromodomain Y-like protein isoform X1

    2. XM_054356826.1XP_054212801.1  chromodomain Y-like protein isoform X1

    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.