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Aliases for CDY2A Gene

Aliases for CDY2A Gene

  • Chromodomain Y-Linked 2A 2 3 5
  • Chromodomain Protein, Y Chromosome, 2 2 3
  • EC 4 56
  • CDY2 3 4
  • Testis-Specific Chromodomain Protein Y 2 3
  • Y Chromosome Chromodomain Protein 2A 3
  • Chromodomain Protein, Y-Linked, 2A 3
  • Chromodomain Protein, Y-Linked, 2 2
  • CDY2A CDY2B 4
  • CDY 3

External Ids for CDY2A Gene

Previous HGNC Symbols for CDY2A Gene

  • CDY2

Previous GeneCards Identifiers for CDY2A Gene

  • GC0YP018576
  • GC0YP018648
  • GC0YP020137
  • GC0YM014436

Summaries for CDY2A Gene

Entrez Gene Summary for CDY2A Gene

  • This intronless 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. Two nearly identical copies of this gene are found in a palindromic region on chromosome Y; this record represents the telomeric copy. Chromosome Y also contains a pair of closely related genes in another more telomeric palindrome as well as several related pseudogenes. [provided by RefSeq, Jul 2008]

GeneCards Summary for CDY2A Gene

CDY2A (Chromodomain Y-Linked 2A) is a Protein Coding gene. Diseases associated with CDY2A include Spermatogenic Failure, Y-Linked, 2. Gene Ontology (GO) annotations related to this gene include histone acetyltransferase activity. An important paralog of this gene is CDY2B.

UniProtKB/Swiss-Prot for CDY2A Gene

  • May have histone acetyltransferase activity.

Additional gene information for CDY2A Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CDY2A Gene

Genomics for CDY2A Gene

GeneHancer (GH) Regulatory Elements for CDY2A Gene

Promoters and enhancers for CDY2A Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0YI018025 Promoter 0.5 EPDnew 550.8 +0.0 36 0.1 CDY2A ELOCP12
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CDY2A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CDY2A gene promoter:

Genomic Locations for CDY2A Gene

Genomic Locations for CDY2A Gene
2,811 bases
Plus strand

Genomic View for CDY2A Gene

Genes around CDY2A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDY2A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDY2A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CDY2A Gene

Proteins for CDY2A Gene

  • Protein details for CDY2A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Testis-specific chromodomain protein Y 2
    Protein Accession:
    Secondary Accessions:
    • A8K868

    Protein attributes for CDY2A Gene

    541 amino acids
    Molecular mass:
    60524 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for CDY2A Gene

neXtProt entry for CDY2A Gene

Selected DME Specific Peptides for CDY2A Gene


Post-translational modifications for CDY2A Gene

No Post-translational modifications

Other Protein References for CDY2A Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for CDY2A Gene

Gene Families for CDY2A Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CDY2A: view

No data available for Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for CDY2A Gene

Function for CDY2A Gene

Molecular function for CDY2A Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N(6)-acetyl-L-lysine.
UniProtKB/Swiss-Prot Function:
May have histone acetyltransferase activity.

Enzyme Numbers (IUBMB) for CDY2A Gene

Gene Ontology (GO) - Molecular Function for CDY2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004402 histone acetyltransferase activity IEA --
GO:0016740 transferase activity IEA --
GO:0016746 transferase activity, transferring acyl groups IEA --
genes like me logo Genes that share ontologies with CDY2A: view
genes like me logo Genes that share phenotypes with CDY2A: view

Human Phenotype Ontology for CDY2A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Phenotypes From GWAS Catalog , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CDY2A Gene

Localization for CDY2A Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDY2A Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CDY2A gene
Compartment Confidence
nucleus 3

Gene Ontology (GO) - Cellular Components for CDY2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with CDY2A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CDY2A Gene

Pathways & Interactions for CDY2A Gene

SuperPathways for CDY2A Gene

No Data Available

Gene Ontology (GO) - Biological Process for CDY2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007283 spermatogenesis TAS 9381176
GO:0008152 metabolic process IEA --
GO:0016573 histone acetylation IEA --
genes like me logo Genes that share ontologies with CDY2A: view

No data available for Pathways by source and SIGNOR curated interactions for CDY2A Gene

Drugs & Compounds for CDY2A Gene

(1) Drugs for CDY2A Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Coenzyme A Investigational Nutra 0

(1) Additional Compounds for CDY2A Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • Ac-CoA
  • Ac-Coenzyme A
  • Ac-S-CoA
  • Ac-S-Coenzyme A
  • Acetyl coenzyme-A
genes like me logo Genes that share compounds with CDY2A: view

Transcripts for CDY2A Gene

mRNA/cDNA for CDY2A Gene

(1) REFSEQ mRNAs :
(2) Additional mRNA sequences :
(2) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CDY2A Gene

Chromodomain protein, Y-linked, 2A:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for CDY2A Gene

No ASD Table

Relevant External Links for CDY2A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CDY2A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CDY2A Gene

mRNA differential expression in normal tissues according to GTEx for CDY2A Gene

This gene is overexpressed in Testis (x53.0).

Protein differential expression in normal tissues from HIPED for CDY2A Gene

This gene is overexpressed in Urine (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for CDY2A Gene

Protein tissue co-expression partners for CDY2A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CDY2A Gene:


SOURCE GeneReport for Unigene cluster for CDY2A Gene:


mRNA Expression by UniProt/SwissProt for CDY2A Gene:

Tissue specificity: Testis specific.
genes like me logo Genes that share expression patterns with CDY2A: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for CDY2A Gene

Orthologs for CDY2A Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for CDY2A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CDY1 33 34 34
  • 98.15 (n)
-- 34
  • 92 (a)
-- 34
  • 92 (a)
-- 34
  • 92 (a)
(Canis familiaris)
Mammalia -- 34
  • 61 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 60 (a)
(Bos Taurus)
Mammalia CDYL 34
  • 59 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 59 (a)
(Gallus gallus)
Aves -- 34
  • 61 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 60 (a)
(Danio rerio)
Actinopterygii cdyl 34
  • 45 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG3680 34
  • 9 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DCI1 34
  • 22 (a)
ECI1 34
  • 21 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2946 34
  • 26 (a)
Species where no ortholog for CDY2A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CDY2A Gene

Gene Tree for CDY2A (if available)
Gene Tree for CDY2A (if available)

Paralogs for CDY2A Gene

Paralogs for CDY2A Gene

(10) SIMAP similar genes for CDY2A Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with CDY2A: view

Variants for CDY2A Gene

Sequence variations from dbSNP and Humsavar for CDY2A Gene

SNP ID Clin Chr 0Y pos Variation AA Info Type
rs200670724 -- 18,025,744(+) T/C upstream_transcript_variant
rs779899525 -- 18,026,284(+) G/A coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for CDY2A Gene

Variant ID Type Subtype PubMed ID
nsv469874 CNV gain+loss 16826518
esv3577589 CNV gain 25503493
esv3577586 CNV gain 25503493
esv3575095 CNV loss 25503493
esv1670141 OTHER inversion 17803354

Additional Variant Information for CDY2A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for CDY2A Gene

Disorders for CDY2A Gene

MalaCards: The human disease database

(1) MalaCards diseases for CDY2A Gene - From: GTR

Disorder Aliases PubMed IDs
spermatogenic failure, y-linked, 2
  • spgfy2
- elite association - COSMIC cancer census association via MalaCards
Search CDY2A in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CDY2A

genes like me logo Genes that share disorders with CDY2A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CDY2A Gene

Publications for CDY2A Gene

  1. Retroposition of autosomal mRNA yielded testis-specific gene family on human Y chromosome. (PMID: 10192397) Lahn BT … Page DC (Nature genetics 1999) 2 3 4 58
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  3. Deletion or underexpression of the Y-chromosome genes CDY2 and HSFY is associated with maturation arrest in American men with nonobstructive azoospermia. (PMID: 22820855) Stahl PJ … Paduch DA (Asian journal of andrology 2012) 3 58
  4. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. (PMID: 21145461) Bennett EJ … Harper JW (Cell 2010) 3 58
  5. Crystal structures of human CDY proteins reveal a crotonase-like fold. (PMID: 19507244) Wu H … Plotnikov AN (Proteins 2009) 4 58

Products for CDY2A Gene

Sources for CDY2A Gene

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