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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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