| Name | chromodomain protein, Y-linked, 1 |
| Description | 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] |
| Summary |
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nCDY1, a member of the chromodomain Y gene family, is expressed selectively during the late phases of spermatogenesis. In testicular tissues from infertile men, detailed transcript analyses revealed that unlike its paralog CDY2—which is detectable as long as germ cells are present—CDY1 transcripts (including its major, minor, and short isoforms) are found almost exclusively when mature spermatids or spermatozoa are present. This expression pattern indicates a pivotal role for CDY1 in chromatin remodeling events required for spermiogenesis and suggests that its activity is tightly linked to the later stages of sperm development."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": "\n \nDisruptions in the normal copy number of CDY1, often resulting from partial AZFc rearrangements such as gr/gr deletions, have been implicated as a risk factor for impaired spermatogenesis. Multiple studies across diverse populations—including Caucasian, Chinese, Japanese, and Tunisian cohorts—have demonstrated that deletions affecting CDY1 (either alone or in conjunction with other AZFc genes) are associated with reductions in sperm production. Moreover, variations in the phenotypic expression of these microdeletions appear to be influenced by the Y-chromosomal haplogroup background, thereby underlining the importance of copy number analyses in genetic counseling for male infertility."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "2", "end_ref": "7"}]}, {"type": "t", "text": "\n \nThe clinical utility of CDY1 is further highlighted by its incorporation as a molecular marker in testicular biopsies; its expression correlates strongly with the presence of advanced spermatogenic activity and can thereby aid in predicting successful sperm retrieval in azoospermic men. Together, these findings emphasize that CDY1 is not only essential for the proper progression of late spermiogenesis but also serves as a valuable biomarker for assessing testicular function in the context of male infertility."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "8"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Sandra E Kleiman, Leah Yogev, Ron Hauser, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Members of the CDY family have different expression patterns: CDY1 transcripts have the best correlation with complete spermatogenesis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Hum Genet (2003)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s00439-003-0990-9"}], "href": "https://doi.org/10.1007/s00439-003-0990-9"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "14569460"}], "href": "https://pubmed.ncbi.nlm.nih.gov/14569460"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Katrien Stouffs, Herman Tournaye, Josiane Van der Elst, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Do we need to search for gr/gr deletions in infertile men in a clinical setting?"}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Hum Reprod (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/humrep/den069"}], "href": "https://doi.org/10.1093/humrep/den069"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18326516"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18326516"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Claudia Giachini, Ilaria Laface, Elena Guarducci, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Partial AZFc deletions and duplications: clinical correlates in the Italian population."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Hum Genet (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s00439-008-0561-1"}], "href": "https://doi.org/10.1007/s00439-008-0561-1"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18807255"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18807255"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Y Yang, M Ma, L Li, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Differential effect of specific gr/gr deletion subtypes on spermatogenesis in the Chinese Han population."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Int J Androl (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1111/j.1365-2605.2009.01015.x"}], "href": "https://doi.org/10.1111/j.1365-2605.2009.01015.x"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20039973"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20039973"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Ho-Su Sin, Eitetsu Koh, Kazuyoshi Shigehara, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Features of constitutive gr/gr deletion in a Japanese population."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Hum Reprod (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/humrep/deq191"}], "href": "https://doi.org/10.1093/humrep/deq191"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20663794"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20663794"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Myriam Ghorbel, Siwar Baklouti-Gargouri, Rim Keskes, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Deletion of CDY1b copy of Y chromosome CDY1 gene is a risk factor of male infertility in Tunisian men."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Gene (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.gene.2014.07.042"}], "href": "https://doi.org/10.1016/j.gene.2014.07.042"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25042452"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25042452"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Myriam Ghorbel, Siwar Baklouti-Gargouri, Rim Keskes, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Y-chromosome haplogroups and Azoospermia Factor (AZF) analysis in Tunisian infertile male."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Hum Fertil (Camb) (2023)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1080/14647273.2022.2163194"}], "href": "https://doi.org/10.1080/14647273.2022.2163194"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "36591797"}], "href": "https://pubmed.ncbi.nlm.nih.gov/36591797"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Sandra E Kleiman, Ofer Lehavi, Ron Hauser, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CDY1 and BOULE transcripts assessed in the same biopsy as predictive markers for successful testicular sperm retrieval."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Fertil Steril (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.fertnstert.2011.03.020"}], "href": "https://doi.org/10.1016/j.fertnstert.2011.03.020"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21474125"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21474125"}]}]}]}
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| Synonyms | CDY1A |
| Proteins | CDY1_HUMAN |
| NCBI Gene ID | 9085 |
| API | |
| Download Associations | |
| Predicted Functions |
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| Co-expressed Genes |
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| Expression in Tissues and Cell Lines |
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CDY1 has 1,268 functional associations with biological entities spanning 6 categories (molecular profile, chemical, functional term, phrase or reference, disease, phenotype or trait, cell line, cell type or tissue, gene, protein or microRNA) extracted from 51 datasets.
Click the + buttons to view associations for CDY1 from the datasets below.
If available, associations are ranked by standardized value
| Dataset | Summary | |
|---|---|---|
| Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles | tissue samples with high or low expression of CDY1 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset. | |
| BioGPS Cell Line Gene Expression Profiles | cell lines with high or low expression of CDY1 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset. | |
| BioGPS Human Cell Type and Tissue Gene Expression Profiles | cell types and tissues with high or low expression of CDY1 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset. | |
| Carcinogenome Chemical Perturbation Carcinogenicity Signatures | small molecule perturbations changing expression of CDY1 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset. | |
| ChEA Transcription Factor Binding Site Profiles | transcription factor binding site profiles with transcription factor binding evidence at the promoter of CDY1 gene from the CHEA Transcription Factor Binding Site Profiles dataset. | |
| ChEA Transcription Factor Targets | transcription factors binding the promoter of CDY1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset. | |
| ChEA Transcription Factor Targets 2022 | transcription factors binding the promoter of CDY1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset. | |
| CMAP Signatures of Differentially Expressed Genes for Small Molecules | small molecule perturbations changing expression of CDY1 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset. | |
| COMPARTMENTS Curated Protein Localization Evidence Scores | cellular components containing CDY1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset. | |
| COMPARTMENTS Curated Protein Localization Evidence Scores 2025 | cellular components containing CDY1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset. | |
| COMPARTMENTS Text-mining Protein Localization Evidence Scores | cellular components co-occuring with CDY1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset. | |
| COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 | cellular components co-occuring with CDY1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset. | |
| CTD Gene-Chemical Interactions | chemicals interacting with CDY1 gene/protein from the curated CTD Gene-Chemical Interactions dataset. | |
| DISEASES Text-mining Gene-Disease Association Evidence Scores | diseases co-occuring with CDY1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset. | |
| DISEASES Text-mining Gene-Disease Association Evidence Scores 2025 | diseases co-occuring with CDY1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset. | |
| DisGeNET Gene-Disease Associations | diseases associated with CDY1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset. | |
| DisGeNET Gene-Phenotype Associations | phenotypes associated with CDY1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset. | |
| ENCODE Transcription Factor Binding Site Profiles | transcription factor binding site profiles with transcription factor binding evidence at the promoter of CDY1 gene from the ENCODE Transcription Factor Binding Site Profiles dataset. | |
| ENCODE Transcription Factor Targets | transcription factors binding the promoter of CDY1 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset. | |
| GAD Gene-Disease Associations | diseases associated with CDY1 gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset. | |
| GAD High Level Gene-Disease Associations | diseases associated with CDY1 gene in GWAS and other genetic association datasets from the GAD High Level Gene-Disease Associations dataset. | |
| GeneRIF Biological Term Annotations | biological terms co-occuring with CDY1 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset. | |
| GeneSigDB Published Gene Signatures | PubMedIDs of publications reporting gene signatures containing CDY1 from the GeneSigDB Published Gene Signatures dataset. | |
| GEO Signatures of Differentially Expressed Genes for Diseases | disease perturbations changing expression of CDY1 gene from the GEO Signatures of Differentially Expressed Genes for Diseases dataset. | |
| GEO Signatures of Differentially Expressed Genes for Gene Perturbations | gene perturbations changing expression of CDY1 gene from the GEO Signatures of Differentially Expressed Genes for Gene Perturbations dataset. | |
| GEO Signatures of Differentially Expressed Genes for Kinase Perturbations | kinase perturbations changing expression of CDY1 gene from the GEO Signatures of Differentially Expressed Genes for Kinase Perturbations dataset. | |
| GEO Signatures of Differentially Expressed Genes for Small Molecules | small molecule perturbations changing expression of CDY1 gene from the GEO Signatures of Differentially Expressed Genes for Small Molecules dataset. | |
| GO Cellular Component Annotations 2023 | cellular components containing CDY1 protein from the curated GO Cellular Component Annotations 2023 dataset. | |
| GO Cellular Component Annotations 2025 | cellular components containing CDY1 protein from the curated GO Cellular Component Annotations 2025 dataset. | |
| GO Molecular Function Annotations 2023 | molecular functions performed by CDY1 gene from the curated GO Molecular Function Annotations 2023 dataset. | |
| GO Molecular Function Annotations 2025 | molecular functions performed by CDY1 gene from the curated GO Molecular Function Annotations 2025 dataset. | |
| Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles | cell lines with high or low expression of CDY1 gene relative to other cell lines from the Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles dataset. | |
| HMDB Metabolites of Enzymes | interacting metabolites for CDY1 protein from the curated HMDB Metabolites of Enzymes dataset. | |
| HuGE Navigator Gene-Phenotype Associations | phenotypes associated with CDY1 gene by text-mining GWAS publications from the HuGE Navigator Gene-Phenotype Associations dataset. | |
| JASPAR Predicted Human Transcription Factor Targets 2025 | transcription factors regulating expression of CDY1 gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Human Transcription Factor Targets dataset. | |
| JASPAR Predicted Transcription Factor Targets | transcription factors regulating expression of CDY1 gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Transcription Factor Targets dataset. | |
| Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles | cell lines with high or low copy number of CDY1 gene relative to other cell lines from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles dataset. | |
| KnockTF Gene Expression Profiles with Transcription Factor Perturbations | transcription factor perturbations changing expression of CDY1 gene from the KnockTF Gene Expression Profiles with Transcription Factor Perturbations dataset. | |
| LINCS L1000 CMAP Chemical Perturbation Consensus Signatures | small molecule perturbations changing expression of CDY1 gene from the LINCS L1000 CMAP Chemical Perturbations Consensus Signatures dataset. | |
| LOCATE Curated Protein Localization Annotations | cellular components containing CDY1 protein in low- or high-throughput protein localization assays from the LOCATE Curated Protein Localization Annotations dataset. | |
| LOCATE Predicted Protein Localization Annotations | cellular components predicted to contain CDY1 protein from the LOCATE Predicted Protein Localization Annotations dataset. | |
| NURSA Protein Complexes | protein complexs containing CDY1 protein recovered by IP-MS from the NURSA Protein Complexes dataset. | |
| Pathway Commons Protein-Protein Interactions | interacting proteins for CDY1 from the Pathway Commons Protein-Protein Interactions dataset. | |
| PFOCR Pathway Figure Associations 2024 | pathways involving CDY1 protein from the Wikipathways PFOCR 2024 dataset. | |
| Rummagene Transcription Factor Associations 2026 | transcription factors regulating expression of CDY1 gene from the Rummagene Transcription Factor Associations 2026 dataset. | |
| TargetScan Predicted Nonconserved microRNA Targets | microRNAs regulating expression of CDY1 gene predicted using nonconserved miRNA seed sequences from the TargetScan Predicted Nonconserved microRNA Targets dataset. | |
| TCGA Signatures of Differentially Expressed Genes for Tumors | tissue samples with high or low expression of CDY1 gene relative to other tissue samples from the TCGA Signatures of Differentially Expressed Genes for Tumors dataset. | |
| TISSUES Curated Tissue Protein Expression Evidence Scores | tissues with high expression of CDY1 protein from the TISSUES Curated Tissue Protein Expression Evidence Scores dataset. | |
| TISSUES Curated Tissue Protein Expression Evidence Scores 2025 | tissues with high expression of CDY1 protein from the TISSUES Curated Tissue Protein Expression Evidence Scores 2025 dataset. | |
| TISSUES Text-mining Tissue Protein Expression Evidence Scores | tissues co-occuring with CDY1 protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores dataset. | |
| TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 | tissues co-occuring with CDY1 protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 dataset. | |
