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    CDY1 chromodomain Y-linked 1 [ Homo sapiens (human) ]

    Gene ID: 9085, updated on 10-Dec-2024

    Summary

    Official Symbol
    CDY1provided by HGNC
    Official Full Name
    chromodomain Y-linked 1provided by HGNC
    Primary source
    HGNC:HGNC:1809
    See related
    Ensembl:ENSG00000172288 MIM:400016; AllianceGenome:HGNC:1809
    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
    CDY; CDY1A
    Summary
    This gene encodes a protein containing a chromodomain and a histone acetyltransferase catalytic domain. Chromodomain proteins are components of heterochromatin-like complexes and can act as gene repressors. This protein is localized to the nucleus of late spermatids where histone hyperacetylation takes place. Histone hyperacetylation is thought to facilitate the transition in which protamines replace histones as the major DNA-packaging protein. The human chromosome Y has two identical copies of this gene within a palindromic region; this record represents the more telomeric copy. Chromosome Y also contains a pair of closely related genes in another more telomeric palindrome as well as several related pseudogenes. Two protein isoforms are encoded by transcript variants of this gene. Additional transcript variants have been described, but their full-length nature has not been determined. [provided by RefSeq, Jul 2008]
    Expression
    Restricted expression toward testis (RPKM 2.1) See more
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    Genomic context

    See CDY1 in Genome Data Viewer
    Location:
    Yq11.23
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (25622115..25625511)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (26434508..26437904)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (27768264..27771049)

    Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene USP9Y pseudogene 33 Neighboring gene chromodomain Y-linked 20 pseudogene Neighboring gene elongin C pseudogene 34 Neighboring gene OFD1 pseudogene 13 Y-linked

    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

    Associated conditions

    Description Tests
    Spermatogenic failure, Y-linked, 2
    MedGen: C1839071 OMIM: 415000 GeneReviews: Y Chromosome Infertility
    Compare labs

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2012-08-22)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2012-08-22)

    ClinGen Genome Curation Page

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ77185

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables histone H2AK5 acetyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H2AK9 acetyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H2BK12 acetyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H2BK5 acetyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3K122 acetyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3K14 acetyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3K18 acetyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3K23 acetyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3K27 acetyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3K36 acetyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3K4 acetyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3K56 acetyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3K9 acetyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H4K12 acetyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H4K16 acetyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H4K5 acetyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H4K8 acetyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription corepressor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in spermatogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    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
    testis-specific chromodomain protein Y 1
    Names
    chromodomain protein, Y chromosome, 1
    chromodomain protein, Y-linked, 1
    testis-specific chromodomain protein on Y
    NP_004671.1
    NP_733841.1
    XP_011529814.1
    XP_054184366.1

    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.

    Genomic

    1. NG_011754.1 RefSeqGene

      Range
      5001..7786
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_004680.3 → NP_004671.1  testis-specific chromodomain protein Y 1 isoform b

      See identical proteins and their annotated locations for NP_004671.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2), also called the minor variant, lacks a segment in the 3' end of the coding sequence, compared to variant 1. Variant 2 encodes isoform b which has a longer and distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AC007562
      Consensus CDS
      CCDS14801.1
      UniProtKB/TrEMBL
      A8K8F3
      Related
      ENSP00000302968.4, ENST00000306609.5
      Conserved Domains (2) summary
      cd06558
      Location:286 → 482
      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:5 → 58
      CHROMO; Chromatin organization modifier domain
    2. NM_170723.2 → NP_733841.1  testis-specific chromodomain protein Y 1 isoform a

      See identical proteins and their annotated locations for NP_733841.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1), also called the major transcript, is unspliced. It encodes isoform a.
      Source sequence(s)
      AC007562
      Consensus CDS
      CCDS14802.1
      UniProtKB/Swiss-Prot
      A2RUK1, O14600, Q9Y6F8
      UniProtKB/TrEMBL
      A8K8L0
      Related
      ENSP00000354799.2, ENST00000361963.3
      Conserved Domains (2) summary
      cd06558
      Location:286 → 482
      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:5 → 58
      CHROMO; Chromatin organization modifier domain

    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_000024.10 Reference GRCh38.p14 Primary Assembly

      Range
      25622115..25625511
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011531512.3 → XP_011529814.1  testis-specific chromodomain protein Y 1 isoform X1

      See identical proteins and their annotated locations for XP_011529814.1

      UniProtKB/TrEMBL
      A8K8L0
      Conserved Domains (2) summary
      cd06558
      Location:286 → 464
      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:5 → 58
      CHROMO; Chromatin organization modifier domain

    RNA

    1. XR_938657.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060948.1 Alternate T2T-CHM13v2.0

      Range
      26434508..26437904
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328391.1 → XP_054184366.1  testis-specific chromodomain protein Y 1 isoform X1

      UniProtKB/TrEMBL
      A8K8L0

    RNA

    1. XR_008485531.1 RNA Sequence