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

    Gene ID: 9085, updated on 3-Apr-2024

    Summary

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    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

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    Location:
    Yq11.23
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (25622115..25625511)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (26434508..26437904)
    105.20220307 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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Deletion of CDY1b copy of Y chromosome CDY1 gene is a risk factor of male infertility in Tunisian men. Ghorbel M, et al. Gene, 2014 Sep 15. PMID 25042452
    2. CDY1 and BOULE transcripts assessed in the same biopsy as predictive markers for successful testicular sperm retrieval. Kleiman SE, et al. Fertil Steril, 2011 Jun. PMID 21474125
    3. Features of constitutive gr/gr deletion in a Japanese population. Sin HS, et al. Hum Reprod, 2010 Sep. PMID 20663794
    4. Partial AZFc deletions and duplications: clinical correlates in the Italian population. Giachini C, et al. Hum Genet, 2008 Nov. PMID 18807255
    5. Do we need to search for gr/gr deletions in infertile men in a clinical setting? Stouffs K, et al. Hum Reprod, 2008 May. PMID 18326516

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Y-chromosome haplogroups and Azoospermia Factor (AZF) analysis in Tunisian infertile male.
      Title: Y-chromosome haplogroups and Azoospermia Factor (AZF) analysis in Tunisian infertile male.
    2. Findings showed that deletion of CDY1b copy gene is a significant risk factor for male infertility independent of sperm concentration, whereas deletion of CDY1a gene seems to have no effect on fertility in the Tunisian population.
      Title: Deletion of CDY1b copy of Y chromosome CDY1 gene is a risk factor of male infertility in Tunisian men.
    3. Assessing the expression of both CDY1 and BOULE by qualitative RT-PCR is a sensitive and feasible test for predicting the presence of sperm cells in testicular tissue biopsies.
      Title: CDY1 and BOULE transcripts assessed in the same biopsy as predictive markers for successful testicular sperm retrieval.
    4. Partial AZFc deletions including CDY1-DAZ gene is associated with impaired spermatogenesis.
      Title: Partial AZFc deletions and duplications: clinical correlates in the Italian population.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Features of constitutive gr/gr deletion in a Japanese population.
    6. different functional roles for CDY isoforms during spermatogenesis
      Title: Members of the CDY family have different expression patterns: CDY1 transcripts have the best correlation with complete spermatogenesis.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ77185

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables histone 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

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    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_2023_10

    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

    RNA

    1. XR_008485531.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y6F8.1 GenPept UniProtKB/Swiss-Prot:Q9Y6F8

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