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Aliases for CDY1 Gene

Aliases for CDY1 Gene

  • Chromodomain Y-Linked 1 2 3 5
  • Chromodomain Protein, Y Chromosome, 1 2 3
  • CDY1A 3 4
  • Testis-Specific Chromodomain Protein On Y 3
  • Testis-Specific Chromodomain Protein Y 1 3
  • Chromodomain Protein, Y-Linked, 1 3
  • EC 4
  • CDY 3

External Ids for CDY1 Gene

Previous GeneCards Identifiers for CDY1 Gene

  • GC0YP026933
  • GC0YM025438
  • GC0YM025036
  • GC0YP026106
  • GC0YP026177
  • GC0YP027768
  • GC0YM018183

Summaries for CDY1 Gene

Entrez Gene Summary for CDY1 Gene

  • 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]

GeneCards Summary for CDY1 Gene

CDY1 (Chromodomain Y-Linked 1) is a Protein Coding gene. Diseases associated with CDY1 include Spermatogenic Failure, Y-Linked, 2 and Male Reproductive System Disease. Gene Ontology (GO) annotations related to this gene include histone acetyltransferase activity and methylated histone binding. An important paralog of this gene is CDY1B.

UniProtKB/Swiss-Prot for CDY1 Gene

  • Has histone acetyltransferase activity, with a preference for histone H4.

Gene Wiki entry for CDY1 Gene

Additional gene information for CDY1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CDY1 Gene

Genomics for CDY1 Gene

GeneHancer (GH) Regulatory Elements for CDY1 Gene

Top Transcription factor binding sites by QIAGEN in the CDY1 gene promoter:
  • GR-alpha
  • GR
  • GR-beta

Genomic Locations for CDY1 Gene

Genomic Locations for CDY1 Gene
12,631 bases
Plus strand
2,786 bases
Plus strand

Genomic View for CDY1 Gene

Genes around CDY1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDY1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDY1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CDY1 Gene

Proteins for CDY1 Gene

  • Protein details for CDY1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Testis-specific chromodomain protein Y 1
    Protein Accession:
    Secondary Accessions:
    • A2RUK1
    • O14600
    • A2RUK1
    • O14600

    Protein attributes for CDY1 Gene

    540 amino acids
    Molecular mass:
    60473 Da
    Quaternary structure:
    • Interacts (via chromo domain) with histone H3K9me3.
    • Interacts (via chromo domain) with histone H3K9me3.

    Three dimensional structures from OCA and Proteopedia for CDY1 Gene

    Alternative splice isoforms for CDY1 Gene


neXtProt entry for CDY1 Gene

Post-translational modifications for CDY1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CDY1 Gene

No data available for DME Specific Peptides for CDY1 Gene

Domains & Families for CDY1 Gene

Gene Families for CDY1 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 CDY1: view

No data available for Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for CDY1 Gene

Function for CDY1 Gene

Molecular function for CDY1 Gene

UniProtKB/Swiss-Prot Function:
Has histone acetyltransferase activity, with a preference for histone H4.
UniProtKB/Swiss-Prot CatalyticActivity:
Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N(6)-acetyl-L-lysine.
GENATLAS Biochemistry:
DNA binding protein with a chromatin organization modifier (chromo) domain,involved in compaction during spermatogenesis,testis specific,CHD family,1,in a AZF deleted region

Enzyme Numbers (IUBMB) for CDY1 Gene

Gene Ontology (GO) - Molecular Function for CDY1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003714 transcription corepressor activity IBA --
GO:0004402 histone acetyltransferase activity IEA --
GO:0016740 transferase activity IEA --
GO:0016746 transferase activity, transferring acyl groups IEA --
GO:0035064 methylated histone binding IDA 18450745
genes like me logo Genes that share ontologies with CDY1: view
genes like me logo Genes that share phenotypes with CDY1: view

Human Phenotype Ontology for CDY1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CDY1

No data available for Phenotypes From GWAS Catalog , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CDY1 Gene

Localization for CDY1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDY1 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 CDY1 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for CDY1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 18450745
genes like me logo Genes that share ontologies with CDY1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CDY1 Gene

Pathways & Interactions for CDY1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CDY1 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 CDY1: view

No data available for Pathways by source and SIGNOR curated interactions for CDY1 Gene

Drugs & Compounds for CDY1 Gene

(1) Drugs for CDY1 Gene - From: HMDB

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

(1) Additional Compounds for CDY1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • AcCoA
  • Acetyl coenzyme A
  • S-Acetyl-CoA
  • S-Acetyl-coenzyme A
  • Ac-CoA
genes like me logo Genes that share compounds with CDY1: view

Transcripts for CDY1 Gene

mRNA/cDNA for CDY1 Gene

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

Unigene Clusters for CDY1 Gene

Chromodomain protein, Y-linked, 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CDY1

Alternative Splicing Database (ASD) splice patterns (SP) for CDY1 Gene

No ASD Table

Relevant External Links for CDY1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CDY1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CDY1 Gene

Protein differential expression in normal tissues from HIPED for CDY1 Gene

This gene is overexpressed in Monocytes (54.6) and Adipocyte (14.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CDY1 Gene

Protein tissue co-expression partners for CDY1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CDY1 Gene:


SOURCE GeneReport for Unigene cluster for CDY1 Gene:


mRNA Expression by UniProt/SwissProt for CDY1 Gene:

Tissue specificity: Testis-specific. Detected in spermatids (at protein level).
genes like me logo Genes that share expression patterns with CDY1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for CDY1 Gene

Orthologs for CDY1 Gene

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

Orthologs for CDY1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CDY1 34 34 33
  • 98.4 (n)
-- 34
  • 97 (a)
-- 34
  • 97 (a)
-- 34
  • 97 (a)
(Canis familiaris)
Mammalia -- 34
  • 60 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 60 (a)
(Bos Taurus)
Mammalia CDYL 34
  • 59 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 58 (a)
(Gallus gallus)
Aves -- 34
  • 60 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 59 (a)
(Danio rerio)
Actinopterygii cdyl 34
  • 44 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG3680 34
  • 9 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DCI1 36 34
  • 23 (a)
ECI1 34
  • 21 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2946 34
  • 26 (a)
Species where no ortholog for CDY1 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 CDY1 Gene

Gene Tree for CDY1 (if available)
Gene Tree for CDY1 (if available)

Paralogs for CDY1 Gene

Variants for CDY1 Gene

Sequence variations from dbSNP and Humsavar for CDY1 Gene

SNP ID Clin Chr 0Y pos Variation AA Info Type
rs112604390 -- 25,621,799(+) A/G upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for CDY1 Gene

Variant ID Type Subtype PubMed ID
dgv2564e212 CNV gain 25503493
dgv2577e212 CNV gain 25503493
dgv2579e212 CNV gain 25503493
dgv2580e212 CNV loss 25503493
dgv2581e212 CNV loss 25503493
esv3575148 CNV loss 25503493
esv3575152 CNV loss 25503493
esv3575154 CNV loss 25503493
esv3575179 CNV loss 25503493
esv3575190 CNV loss 25503493
esv3577652 CNV gain 25503493
esv3577653 CNV gain 25503493
nsv442824 CNV gain+loss 18776908
nsv442826 CNV gain+loss 18776908
nsv469828 CNV gain+loss 16826518
nsv515229 CNV loss 21397061
nsv515231 CNV loss 21397061

Additional Variant Information for CDY1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for CDY1 Gene

Disorders for CDY1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for CDY1 Gene - From: GTR and DISEASES

Disorder Aliases PubMed IDs
spermatogenic failure, y-linked, 2
  • spgfy2
male reproductive system disease
  • genital diseases, male
- elite association - COSMIC cancer census association via MalaCards
Search CDY1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CDY1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CDY1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CDY1 Gene

Publications for CDY1 Gene

  1. Specificity of the chromodomain Y chromosome family of chromodomains for lysine-methylated ARK(S/T) motifs. (PMID: 18450745) Fischle W … Khorasanizadeh S (The Journal of biological chemistry 2008) 3 4 22 58
  2. Functional coherence of the human Y chromosome. (PMID: 9381176) Lahn BT … Page DC (Science (New York, N.Y.) 1997) 2 3 4 58
  3. Features of constitutive gr/gr deletion in a Japanese population. (PMID: 20663794) Sin HS … Namiki M (Human reproduction (Oxford, England) 2010) 3 44 58
  4. Differential effect of specific gr/gr deletion subtypes on spermatogenesis in the Chinese Han population. (PMID: 20039973) Yang Y … Zhang S (International journal of andrology 2010) 3 44 58
  5. Do we need to search for gr/gr deletions in infertile men in a clinical setting? (PMID: 18326516) Stouffs K … Lissens W (Human reproduction (Oxford, England) 2008) 3 44 58

Products for CDY1 Gene

Sources for CDY1 Gene

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