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Entry
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- *400016 - CHROMODOMAIN PROTEIN, Y-LINKED, 1; CDY1
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- OMIM
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<p>
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<span class="h4">*400016</span>
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<br />
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<strong>Table of Contents</strong>
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<a href="#title"><strong>Title</strong></a>
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<a href="#text"><strong>Text</strong></a>
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<li role="presentation" style="margin-left: 1em">
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<a href="#description">Description</a>
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<a href="#cloning">Cloning and Expression</a>
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<a href="#mapping">Mapping</a>
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<a href="#geneFunction">Gene Function</a>
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<a href="#molecularGenetics">Molecular Genetics</a>
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<a href="#evolution">Evolution</a>
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<a href="#references"><strong>References</strong></a>
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<a href="#contributors"><strong>Contributors</strong></a>
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<a href="#creationDate"><strong>Creation Date</strong></a>
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<a href="#editHistory"><strong>Edit History</strong></a>
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<h4 class="panel-title">
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<div id="mimExternalLinksToggleTriangle" class="small" style="color: white; display: table-cell;">▼</div>
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<div style="display: table-cell;">External Links</div>
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</a>
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</h4>
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<div class="panel-heading mim-panel-heading" role="tab" id="mimGenome">
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<span class="panel-title">
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<a href="#mimGenomeLinksFold" id="mimGenomeLinksToggle" class="collapsed mimSingletonTriangleToggle" role="button" data-toggle="collapse" data-parent="#mimExternalLinksAccordion">
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<span id="mimGenomeLinksToggleTriangle" class="small mimSingletonTriangle" style="color: #337CB5">►</span> Genome
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</a>
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</span>
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</span>
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</div>
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<div id="mimGenomeLinksFold" class="panel-collapse collapse mimLinksFold" role="tabpanel" aria-labelledby="genome">
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<div class="panel-body small mim-panel-body">
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<div><a href="https://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000172288;t=ENST00000306609" class="mim-tip-hint" title="Genome databases for vertebrates and other eukaryotic species." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'Ensembl', 'domain': 'ensembl.org'})">Ensembl</a></div>
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<div><a href="https://www.ncbi.nlm.nih.gov/genome/gdv/browser/gene/?id=9085" class="mim-tip-hint" title="Detailed views of the complete genomes of selected organisms from vertebrates to protozoa." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'NCBI Genome Viewer', 'domain': 'ncbi.nlm.nih.gov'})">NCBI Genome Viewer</a></div>
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<div><a href="https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgFind=omimGeneAcc&position=400016" class="mim-tip-hint" title="UCSC Genome Browser; reference sequences and working draft assemblies for a large collection of genomes." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'UCSC Genome Browser', 'domain': 'genome.ucsc.edu'})">UCSC Genome Browser</a></div>
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</div>
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</div>
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</div>
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<div class="panel panel-default" style="margin-top: 0px; border-radius: 0px">
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<div class="panel-heading mim-panel-heading" role="tab" id="mimDna">
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<span class="panel-title">
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<span class="small">
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<a href="#mimDnaLinksFold" id="mimDnaLinksToggle" class="collapsed mimSingletonTriangleToggle" role="button" data-toggle="collapse" data-parent="#mimExternalLinksAccordion">
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<span id="mimDnaLinksToggleTriangle" class="small mimSingletonTriangle" style="color: #337CB5">►</span> DNA
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</a>
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<div id="mimDnaLinksFold" class="panel-collapse collapse mimLinksFold" role="tabpanel">
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<div class="panel-body small mim-panel-body">
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<div><a href="https://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000172288;t=ENST00000306609" class="mim-tip-hint" title="Transcript-based views for coding and noncoding DNA." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'Ensembl', 'domain': 'ensembl.org'})">Ensembl (MANE Select)</a></div>
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<div><a href="https://www.ncbi.nlm.nih.gov/nuccore/NM_004680,NM_170723,XM_011531512,XR_938657" class="mim-tip-hint" title="A collection of genome, gene, and transcript sequence data from several sources, including GenBank, RefSeq." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'NCBI RefSeq', 'domain': 'ncbi.nlm.nih'})">NCBI RefSeq</a></div>
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<div><a href="https://www.ncbi.nlm.nih.gov/nuccore/NM_004680" class="mim-tip-hint" title="A collection of genome, gene, and transcript sequence data from several sources, including GenBank, RefSeq." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'NCBI RefSeq (MANE)', 'domain': 'ncbi.nlm.nih'})">NCBI RefSeq (MANE Select)</a></div>
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<div><a href="https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgFind=omimGeneAcc&position=400016" class="mim-tip-hint" title="UCSC Genome Browser; reference sequences and working draft assemblies for a large collection of genomes." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'UCSC Genome Browser', 'domain': 'genome.ucsc.edu'})">UCSC Genome Browser</a></div>
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</div>
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</div>
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</div>
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<div class="panel panel-default" style="margin-top: 0px; border-radius: 0px">
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<div class="panel-heading mim-panel-heading" role="tab" id="mimProtein">
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<span class="panel-title">
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<span class="small">
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<a href="#mimProteinLinksFold" id="mimProteinLinksToggle" class="collapsed mimSingletonTriangleToggle" role="button" data-toggle="collapse" data-parent="#mimExternalLinksAccordion">
|
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<span id="mimProteinLinksToggleTriangle" class="small mimSingletonTriangle" style="color: #337CB5">►</span> Protein
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</a>
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</span>
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</div>
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<div id="mimProteinLinksFold" class="panel-collapse collapse mimLinksFold" role="tabpanel">
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<div class="panel-body small mim-panel-body">
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<div><a href="https://hprd.org/summary?hprd_id=02457&isoform_id=02457_1&isoform_name=Isoform_1" class="mim-tip-hint" title="The Human Protein Reference Database; manually extracted and visually depicted information on human proteins." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'HPRD', 'domain': 'hprd.org'})">HPRD</a></div>
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<div><a href="https://www.proteinatlas.org/search/CDY1" class="mim-tip-hint" title="The Human Protein Atlas contains information for a large majority of all human protein-coding genes regarding the expression and localization of the corresponding proteins based on both RNA and protein data." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'HumanProteinAtlas', 'domain': 'proteinatlas.org'})">Human Protein Atlas</a></div>
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<div><a href="https://www.ncbi.nlm.nih.gov/protein/3342716,4558752,4757966,20138089,25453481,124376226,158258182,768041178,2462632197" class="mim-tip-hint" title="NCBI protein data." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'NCBI Protein', 'domain': 'ncbi.nlm.nih.gov'})">NCBI Protein</a></div>
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<div><a href="https://www.uniprot.org/uniprotkb/Q9Y6F8" class="mim-tip-hint" title="Comprehensive protein sequence and functional information, including supporting data." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'UniProt', 'domain': 'uniprot.org'})">UniProt</a></div>
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</div>
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</div>
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<div class="panel panel-default" style="margin-top: 0px; border-radius: 0px">
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<div class="panel-heading mim-panel-heading" role="tab" id="mimGeneInfo">
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<span class="panel-title">
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<span class="small">
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<a href="#mimGeneInfoLinksFold" id="mimGeneInfoLinksToggle" class="collapsed mimSingletonTriangleToggle" role="button" data-toggle="collapse" data-parent="#mimExternalLinksAccordion">
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<div style="display: table-row">
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<div id="mimGeneInfoLinksToggleTriangle" class="small mimSingletonTriangle" style="color: #337CB5; display: table-cell;">►</div>
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<div style="display: table-cell;">Gene Info</div>
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</a>
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<div id="mimGeneInfoLinksFold" class="panel-collapse collapse mimLinksFold" role="tabpanel">
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<div class="panel-body small mim-panel-body">
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<div><a href="http://biogps.org/#goto=genereport&id=9085" class="mim-tip-hint" title="The Gene Portal Hub; customizable portal of gene and protein function information." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'BioGPS', 'domain': 'biogps.org'})">BioGPS</a></div>
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<div><a href="https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000172288;t=ENST00000306609" class="mim-tip-hint" title="Orthologs, paralogs, regulatory regions, and splice variants." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'Ensembl', 'domain': 'ensembl.org'})">Ensembl</a></div>
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<div><a href="https://www.genecards.org/cgi-bin/carddisp.pl?gene=CDY1" class="mim-tip-hint" title="The Human Genome Compendium; web-based cards integrating automatically mined information on human genes." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'GeneCards', 'domain': 'genecards.org'})">GeneCards</a></div>
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<div><a href="http://amigo.geneontology.org/amigo/search/annotation?q=CDY1" class="mim-tip-hint" title="Terms, defined using controlled vocabulary, representing gene product properties (biologic process, cellular component, molecular function) across species." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'GeneOntology', 'domain': 'amigo.geneontology.org'})">Gene Ontology</a></div>
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<div><a href="https://www.genome.jp/dbget-bin/www_bget?hsa+9085" class="mim-tip-hint" title="Kyoto Encyclopedia of Genes and Genomes; diagrams of signaling pathways." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'KEGG', 'domain': 'genome.jp'})">KEGG</a></div>
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<dd><a href="http://v1.marrvel.org/search/gene/CDY1" class="mim-tip-hint" title="Model organism Aggregated Resources for Rare Variant ExpLoration." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'MARRVEL', 'domain': 'marrvel.org'})">MARRVEL</a></dd>
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<div><a href="https://www.ncbi.nlm.nih.gov/gene/9085" class="mim-tip-hint" title="Gene-specific map, sequence, expression, structure, function, citation, and homology data." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'NCBI Gene', 'domain': 'ncbi.nlm.nih.gov'})">NCBI Gene</a></div>
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<div><a href="https://genome.ucsc.edu/cgi-bin/hgGene?db=hg38&hgg_chrom=chrY&hgg_gene=ENST00000306609.5&hgg_start=25622115&hgg_end=25625511&hgg_type=knownGene" class="mim-tip-hint" title="UCSC Genome Bioinformatics; gene-specific structure and function information with links to other databases." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'UCSC', 'domain': 'genome.ucsc.edu'})">UCSC</a></div>
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</div>
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<div class="panel panel-default" style="margin-top: 0px; border-radius: 0px">
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<div class="panel-heading mim-panel-heading" role="tab" id="mimClinicalResources">
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<span class="panel-title">
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<span class="small">
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<a href="#mimClinicalResourcesLinksFold" id="mimClinicalResourcesLinksToggle" class="collapsed mimSingletonTriangleToggle" role="button" data-toggle="collapse" data-parent="#mimExternalLinksAccordion">
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<div style="display: table-row">
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<div id="mimClinicalResourcesLinksToggleTriangle" class="small mimSingletonTriangle" style="color: #337CB5; display: table-cell;">►</div>
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<div style="display: table-cell;">Clinical Resources</div>
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</div>
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</span>
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</div>
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<div id="mimClinicalResourcesLinksFold" class="panel-collapse collapse mimLinksFold" role="tabpanel" aria-labelledby="clinicalResources">
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<div class="panel-body small mim-panel-body">
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<div><a href="https://search.clinicalgenome.org/kb/gene-dosage/HGNC:1809" class="mim-tip-hint" title="A ClinGen curated resource of genes and regions of the genome that are dosage sensitive and should be targeted on a cytogenomic array." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'ClinGen Dosage', 'domain': 'dosage.clinicalgenome.org'})">ClinGen Dosage</a></div>
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<span id="mimVariationLinksToggleTriangle" class="small mimSingletonTriangle" style="color: #337CB5">▼</span> Variation
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<div><a href="https://www.ncbi.nlm.nih.gov/clinvar?term=400016[MIM]" class="mim-tip-hint" title="ClinVar aggregates information about sequence variation and its relationship to human health." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'ClinVar', 'domain': 'ncbi.nlm.nih.gov'})">ClinVar</a></div>
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<div><a href="https://gnomad.broadinstitute.org/gene/ENSG00000172288" class="mim-tip-hint" title="The Genome Aggregation Database (gnomAD), Broad Institute." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'gnomAD', 'domain': 'gnomad.broadinstitute.org'})">gnomAD</a></div>
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<div><a href="https://www.gwascentral.org/search?q=CDY1" class="mim-tip-hint" title="GWAS Central; summary level genotype-to-phenotype information from genetic association studies." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'GWAS Central', 'domain': 'gwascentral.org'})">GWAS Central </a></div>
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<div><a href="https://evs.gs.washington.edu/EVS/PopStatsServlet?searchBy=Gene+Hugo&target=CDY1&upstreamSize=0&downstreamSize=0&x=0&y=0" class="mim-tip-hint" title="National Heart, Lung, and Blood Institute Exome Variant Server." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'NHLBI EVS', 'domain': 'evs.gs.washington.edu'})">NHLBI EVS</a></div>
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<div><a href="https://www.pharmgkb.org/gene/PA26354" class="mim-tip-hint" title="Pharmacogenomics Knowledge Base; curated and annotated information regarding the effects of human genetic variations on drug response." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PharmGKB', 'domain': 'pharmgkb.org'})">PharmGKB</a></div>
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<div style="display: table-cell;">Animal Models</div>
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<div><a href="https://www.alliancegenome.org/gene/HGNC:1809" class="mim-tip-hint" title="Search Across Species; explore model organism and human comparative genomics." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'Alliance Genome', 'domain': 'alliancegenome.org'})">Alliance Genome</a></div>
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<div><a href="https://flybase.org/reports/FBgn0035169.html" class="mim-tip-hint" title="A Database of Drosophila Genes and Genomes." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'FlyBase', 'domain': 'flybase.org'})">FlyBase</a></div>
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<div><a href="http://v1.marrvel.org/search/gene/CDY1#HomologGenesPanel" class="mim-tip-hint" title="Model organism Aggregated Resources for Rare Variant ExpLoration." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'MARRVEL', 'domain': 'marrvel.org'})">MARRVEL</a></div>
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<div><a href="https://www.ncbi.nlm.nih.gov/gene/9085/ortholog/" class="mim-tip-hint" title="Orthologous genes at NCBI." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'NCBI Orthologs', 'domain': 'ncbi.nlm.nih.gov'})">NCBI Orthologs</a></div>
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<div><a href="https://www.orthodb.org/?ncbi=9085" class="mim-tip-hint" title="Hierarchical catalogue of orthologs." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'OrthoDB', 'domain': 'orthodb.org'})">OrthoDB</a></div>
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<div><a href="https://wormbase.org/db/gene/gene?name=WBGene00007130;class=Gene" class="mim-tip-hint" title="Database of the biology and genome of Caenorhabditis elegans and related nematodes." target="_blank" onclick="gtag('event', 'mim_outbound', {'name'{'name': 'Wormbase Gene', 'domain': 'wormbase.org'})">Wormbase Gene</a></div>
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<div style="display: table-cell;">Cellular Pathways</div>
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<div><a href="https://reactome.org/content/query?q=CDY1&species=Homo+sapiens&types=Reaction&types=Pathway&cluster=true" class="definition" title="Protein-specific information in the context of relevant cellular pathways." target="_blank" onclick="gtag('event', 'mim_outbound', {{'name': 'Reactome', 'domain': 'reactome.org'}})">Reactome</a></div>
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<span class="mim-font mim-tip-hint" title="Gene description">
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<span class="text-danger"><strong>*</strong></span>
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400016
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<a id="preferredTitle" class="mim-anchor"></a>
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CHROMODOMAIN PROTEIN, Y-LINKED, 1; CDY1
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<br />
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<span class="mim-font">
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CHROMODOMAIN PROTEIN, Y CHROMOSOME; CDY
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<strong><em>HGNC Approved Gene Symbol: <a href="https://www.genenames.org/tools/search/#!/genes?query=CDY1" class="mim-tip-hint" title="HUGO Gene Nomenclature Committee." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'HGNC', 'domain': 'genenames.org'})">CDY1</a></em></strong>
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Cytogenetic location: <a href="/geneMap/Y/52?start=-3&limit=10&highlight=52">Yq11.23</a>
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Genomic coordinates <span class="small">(GRCh38)</span> : <a href="https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chrY:25622115-25625511&dgv=pack&knownGene=pack&omimGene=pack" class="mim-tip-hint" title="UCSC Genome Browser; reference sequences and working draft assemblies for a large collection of genomes." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'UCSC Genome Browser', 'domain': 'genome.ucsc.edu'})">Y:25,622,115-25,625,511</a> </span>
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</strong>
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<a href="https://www.ncbi.nlm.nih.gov/" target="_blank" class="small"> (from NCBI) </a>
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<span class="mim-font">
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<span class="mim-tip-floating" qtip_title="<strong>Looking For More References?</strong>" qtip_text="Click the 'reference plus' icon <span class='glyphicon glyphicon-plus-sign'></span> at the end of each OMIM text paragraph to see more references related to the content of the preceding paragraph.">
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<strong>TEXT</strong>
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<span id="mimDescriptionToggleTriangle" class="small mimTextToggleTriangle">▼</span>
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<strong>Description</strong>
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<p>CDY family proteins, such as CDY1, each contain a chromodomain and catalytic domain that are highly conserved and implicated in histone modification and recognition. However, due to subtle amino acid changes in their chromodomains, CDY proteins display substantial differences in chromatin recognition and binding, thereby diversifying the epigenetic regulatory roles they play (<a href="#2" class="mim-tip-reference" title="Fischle, W., Franz, H., Jacobs, S. A., Allis, C. D., Khorasanizadeh, S. <strong>Specificity of the chromodomain Y chromosome family of chromodomains for lysine-methylated ARK(S/T) motifs.</strong> J. Biol. Chem. 283: 19626-19635, 2008.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/18450745/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">18450745</a>] [<a href="https://doi.org/10.1074/jbc.M802655200" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="18450745">Fischle et al., 2008</a>). <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=18450745" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})"><span class="glyphicon glyphicon-plus-sign mim-tip-hint" title="Click this 'reference-plus' icon to see articles related to this paragraph in PubMed."></span></a></p>
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<strong>Cloning and Expression</strong>
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<p><a href="#4" class="mim-tip-reference" title="Lahn, B. T., Page, D. C. <strong>Functional coherence of the human Y chromosome.</strong> Science 278: 675-680, 1997.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/9381176/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">9381176</a>] [<a href="https://doi.org/10.1126/science.278.5338.675" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="9381176">Lahn and Page (1997)</a> isolated testis cDNAs corresponding to CDY (chromodomain on Y chromosome) and other genes located in the nonrecombining portion of the Y chromosome (NRY). The predicted CDY protein contains a chromodomain (see <a href="/entry/603079">603079</a>) and a putative catalytic domain. The authors noted that CDY was 1 of 7 novel genes that appeared to exist in multiple copies on the Y chromosome and were expressed specifically in testis. See BPY1 (<a href="/entry/400012">400012</a>). <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=9381176" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})"><span class="glyphicon glyphicon-plus-sign mim-tip-hint" title="Click this 'reference-plus' icon to see articles related to this paragraph in PubMed."></span></a></p><p><a href="#5" class="mim-tip-reference" title="Lahn, B. T., Page, D. C. <strong>Retroposition of autosomal mRNA yielded testis-specific gene family on human Y chromosome.</strong> Nature Genet. 21: 429-433, 1999. Note: Erratum: Nature Genet. 22: 209 only, 1999.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/10192397/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">10192397</a>] [<a href="https://doi.org/10.1038/7771" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="10192397">Lahn and Page (1999)</a> isolated 2 distinct species of CDY cDNAs from testis, CDY1 and CDY2 (<a href="/entry/400018">400018</a>). The predicted 540-amino acid CDY1 protein is 98% identical to CDY2. These authors also isolated a minor, alternatively spliced CDY1 transcript encoding a 554-amino acid isoform with a divergent C terminus. The CDY1 gene coding region corresponding to the major transcript does not contain any introns, although a single intron is excised to form the minor mRNA. The authors stated that there might be multiple CDY1 and CDY2 genes. They proposed that these Y-linked CDY genes arose by retroposition of an mRNA from the autosomal CDYL (<a href="/entry/603778">603778</a>) gene, followed by amplification of the retroposed gene. Since no Y-linked CDY homolog was found in the mouse, <a href="#5" class="mim-tip-reference" title="Lahn, B. T., Page, D. C. <strong>Retroposition of autosomal mRNA yielded testis-specific gene family on human Y chromosome.</strong> Nature Genet. 21: 429-433, 1999. Note: Erratum: Nature Genet. 22: 209 only, 1999.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/10192397/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">10192397</a>] [<a href="https://doi.org/10.1038/7771" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="10192397">Lahn and Page (1999)</a> suggested that CDYL may have given rise to CDY some time after the divergence of the mouse and human lineages. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=10192397" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})"><span class="glyphicon glyphicon-plus-sign mim-tip-hint" title="Click this 'reference-plus' icon to see articles related to this paragraph in PubMed."></span></a></p><p><a href="#2" class="mim-tip-reference" title="Fischle, W., Franz, H., Jacobs, S. A., Allis, C. D., Khorasanizadeh, S. <strong>Specificity of the chromodomain Y chromosome family of chromodomains for lysine-methylated ARK(S/T) motifs.</strong> J. Biol. Chem. 283: 19626-19635, 2008.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/18450745/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">18450745</a>] [<a href="https://doi.org/10.1074/jbc.M802655200" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="18450745">Fischle et al. (2008)</a> showed that FLAG-tagged human CDY and CDYL and mouse Cdyl2 (<a href="/entry/618816">618816</a>) localized exclusively in nuclei of mouse fibroblasts. Cdyl2 was found throughout nucleus in a punctate distribution pattern and colocalized with regions of trimethylated histone H3 (see <a href="/entry/602810">602810</a>) lys9 (H3K9me3). CDY was excluded from nucleoli, but overlapped in chromatin with regions of H3K9me3. CDYL was also excluded from nucleoli, but it did not overlap with regions of H3K9me3. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=18450745" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})"><span class="glyphicon glyphicon-plus-sign mim-tip-hint" title="Click this 'reference-plus' icon to see articles related to this paragraph in PubMed."></span></a></p>
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<p>By analysis of a panel of partial Y chromosomes, <a href="#4" class="mim-tip-reference" title="Lahn, B. T., Page, D. C. <strong>Functional coherence of the human Y chromosome.</strong> Science 278: 675-680, 1997.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/9381176/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">9381176</a>] [<a href="https://doi.org/10.1126/science.278.5338.675" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="9381176">Lahn and Page (1997)</a> found that CDY genes mapped to both the 6F and 5L regions on the long arm of the human Y chromosome. Using the same technique, <a href="#5" class="mim-tip-reference" title="Lahn, B. T., Page, D. C. <strong>Retroposition of autosomal mRNA yielded testis-specific gene family on human Y chromosome.</strong> Nature Genet. 21: 429-433, 1999. Note: Erratum: Nature Genet. 22: 209 only, 1999.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/10192397/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">10192397</a>] [<a href="https://doi.org/10.1038/7771" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="10192397">Lahn and Page (1999)</a> mapped the CDY1 gene to the Y-chromosome 6F region. <a href="#8" class="mim-tip-reference" title="Yen, P. H. <strong>A long-range restriction map of deletion interval 6 of the human Y chromosome: a region frequently deleted in azoospermic males.</strong> Genomics 54: 5-12, 1998.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/9806824/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">9806824</a>] [<a href="https://doi.org/10.1006/geno.1998.5526" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="9806824">Yen (1998)</a> detected 2 CDY genes in deletion interval 6 of the human Y chromosome. <a href="https://pubmed.ncbi.nlm.nih.gov/?term=10192397+9806824+9381176" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})"><span class="glyphicon glyphicon-plus-sign mim-tip-hint" title="Click this 'reference-plus' icon to see articles related to this paragraph in PubMed."></span></a></p><p><a href="#3" class="mim-tip-reference" title="Gross, M. B. <strong>Personal Communication.</strong> Baltimore, Md. 3/17/2020."None>Gross (2020)</a> mapped the CDY1 gene to chromosome Yq11.23 based on an alignment of the CDY1 sequence (GenBank <a href="https://www.ncbi.nlm.nih.gov/search/all/?term=BC132955" target="_blank" onclick="gtag(\'event\', \'mim_outbound\', {\'name\': \'GENBANK\', \'domain\': \'ncbi.nlm.nih.gov\'})">BC132955</a>) with the genomic sequence (GRCh38).</p>
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<p><a href="#2" class="mim-tip-reference" title="Fischle, W., Franz, H., Jacobs, S. A., Allis, C. D., Khorasanizadeh, S. <strong>Specificity of the chromodomain Y chromosome family of chromodomains for lysine-methylated ARK(S/T) motifs.</strong> J. Biol. Chem. 283: 19626-19635, 2008.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/18450745/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">18450745</a>] [<a href="https://doi.org/10.1074/jbc.M802655200" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="18450745">Fischle et al. (2008)</a> noted that the chromodomain of human CDY interacts with methylated H3K9. They found that, despite their high homology and similar tertiary structures, the chromodomains of CDY, CDYL, and CDYL2 displayed variability in binding to H3K9me3. Both the CDY and CDYL2 chromodomains bound to a similar fragment of the H3 tail, but the CDY chromodomain bound more avidly than the CDYL2 chromodomain. The CDY and CDYL2 chromodomains also displayed different sensitivities to H3K9 methylation level. The affinity of the CDYL2 chromodomain increased with methylation level, whereas binding of the CDY chromodomain to the H3K9me1 peptide was as efficient as binding of the CDYL2 chromodomain to the H3K9me3 peptide. Phosphorylation of ser10 adjacent to H3K9 weakened binding of CDY and CDYL2 to the H3K9me3 peptide. The CDYL chromodomain did not bind to the H3K9me3 peptide, but efficient binding could be established by point mutations in the chromodomain. In addition to H3K9me3, other lysine-methylated binding sites were identified for the CDY and CDYL2 chromodomains, but the CDY chromodomain displayed substantially higher selectivity for binding compared with the CDYL2 chromodomain. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=18450745" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})"><span class="glyphicon glyphicon-plus-sign mim-tip-hint" title="Click this 'reference-plus' icon to see articles related to this paragraph in PubMed."></span></a></p>
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<p><a href="#7" class="mim-tip-reference" title="Repping, S., van Daalen, S. K. M., Korver, C. M., Brown, L. G., Marszalek, J. D., Gianotten, J., Oates, R. D., Silber, S., van der Veen, F., Page, D. C., Rozen, S. <strong>A family of human Y chromosomes has dispersed throughout northern Eurasia despite a 1.8-Mb deletion in the azoospermia factor c region.</strong> Genomics 83: 1046-1052, 2004.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/15177557/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">15177557</a>] [<a href="https://doi.org/10.1016/j.ygeno.2003.12.018" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="15177557">Repping et al. (2004)</a> identified the b2/b3 deletion within the AZFc region (<a href="/entry/415000">415000</a>) of the Y chromosome, in which 1 of the 2 copies of the CDY1 gene is deleted. The b2/b3 deletion has no obvious effect on fitness. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=15177557" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})"><span class="glyphicon glyphicon-plus-sign mim-tip-hint" title="Click this 'reference-plus' icon to see articles related to this paragraph in PubMed."></span></a></p><p>To determine the incidence of various partial AZFc deletions and their effect on fertility, <a href="#6" class="mim-tip-reference" title="Machev, N., Saut, N., Longepied, G., Terriou, P., Navarro, A., Levy, N., Guichaoua, M., Metzler-Guillemain, C., Collignon, P., Frances, A.-M., Belougne, J., Clemente, E., Chiaroni, J., Chevillard, C., Durand, C., Ducourneau, A., Pech, N., McElreavey, K., Mattei, M.-G., Mitchell, M. J. <strong>Sequence family variant loss from the AZFc interval of the human Y chromosome, but not gene copy loss, is strongly associated with male infertility.</strong> J. Med. Genet. 41: 814-825, 2004. Note: Erratum: J. Med. Genet. 41: 960 only, 2004.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/15520406/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">15520406</a>] [<a href="https://doi.org/10.1136/jmg.2004.022111" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="15520406">Machev et al. (2004)</a> discriminated 4 types of DAZ-CDY1 partial deletions and performed combined quantitative and qualitative analyses of the AZFc region in 300 infertile men and 399 controls. Only one deletion type, DAZ3/4 (<a href="/entry/400027">400027</a>, <a href="/entry/400003">400003</a>)-CDY1a, was associated with male infertility (p = 0.042), suggesting that most of the partial deletions are neutral variants. A stronger association, however, was found between loss of the CDY1a sequence family variant (SFV) and infertility (p = 0.002). <a href="#6" class="mim-tip-reference" title="Machev, N., Saut, N., Longepied, G., Terriou, P., Navarro, A., Levy, N., Guichaoua, M., Metzler-Guillemain, C., Collignon, P., Frances, A.-M., Belougne, J., Clemente, E., Chiaroni, J., Chevillard, C., Durand, C., Ducourneau, A., Pech, N., McElreavey, K., Mattei, M.-G., Mitchell, M. J. <strong>Sequence family variant loss from the AZFc interval of the human Y chromosome, but not gene copy loss, is strongly associated with male infertility.</strong> J. Med. Genet. 41: 814-825, 2004. Note: Erratum: J. Med. Genet. 41: 960 only, 2004.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/15520406/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">15520406</a>] [<a href="https://doi.org/10.1136/jmg.2004.022111" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="15520406">Machev et al. (2004)</a> concluded that loss of this SFV through deletion or gene conversion could be a major risk factor for male infertility. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=15520406" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})"><span class="glyphicon glyphicon-plus-sign mim-tip-hint" title="Click this 'reference-plus' icon to see articles related to this paragraph in PubMed."></span></a></p>
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<p><a href="#1" class="mim-tip-reference" title="Dorus, S., Gilbert, S. L., Forster, M. L., Barndt, R. J., Lahn, B. T. <strong>The CDY-related gene family: coordinated evolution in copy number, expression profile and protein sequence.</strong> Hum. Molec. Genet. 12: 1643-1650, 2003.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/12837688/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">12837688</a>] [<a href="https://doi.org/10.1093/hmg/ddg185" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="12837688">Dorus et al. (2003)</a> showed that the progenitor of the CDY gene family arose de novo in the mammalian ancestor via domain accretion. This progenitor later duplicated to generate CDYL and CDYL2, 2 autosomal genes found in all extant mammals. Prior to human-mouse divergence, a processed CDYL transcript retroposed onto the Y chromosome to create CDY. In the simian lineage, CDY was retained and subsequently amplified on the Y. In nonsimian mammals, however, CDY appears to have been lost. The retention of the Y-linked CDY genes in simians spurred the process of subfunctionalization and possibly neofunctionalization. Subfunctionalization is evidenced by the observation that simian CDYL and CDYL2 retained their somatic housekeeping transcripts but lost the spermatogenic transcripts to the newly arisen CDY. Neofunctionalization is suggested by the rapid evolution of the CDY protein sequence. <a href="#1" class="mim-tip-reference" title="Dorus, S., Gilbert, S. L., Forster, M. L., Barndt, R. J., Lahn, B. T. <strong>The CDY-related gene family: coordinated evolution in copy number, expression profile and protein sequence.</strong> Hum. Molec. Genet. 12: 1643-1650, 2003.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/12837688/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">12837688</a>] [<a href="https://doi.org/10.1093/hmg/ddg185" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="12837688">Dorus et al. (2003)</a> concluded that the CDY-related family offers an example of how duplicated genes undergo functional diversification in both expression profile and protein sequence and supports the hypothesis that there is a tendency for spermatogenic functions to transfer from autosomes to the Y chromosome. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=12837688" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})"><span class="glyphicon glyphicon-plus-sign mim-tip-hint" title="Click this 'reference-plus' icon to see articles related to this paragraph in PubMed."></span></a></p>
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Dorus, S., Gilbert, S. L., Forster, M. L., Barndt, R. J., Lahn, B. T.
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<strong>The CDY-related gene family: coordinated evolution in copy number, expression profile and protein sequence.</strong>
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Hum. Molec. Genet. 12: 1643-1650, 2003.
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[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/12837688/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">12837688</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=12837688" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
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[<a href="https://doi.org/10.1093/hmg/ddg185" target="_blank">Full Text</a>]
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Fischle, W., Franz, H., Jacobs, S. A., Allis, C. D., Khorasanizadeh, S.
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<strong>Specificity of the chromodomain Y chromosome family of chromodomains for lysine-methylated ARK(S/T) motifs.</strong>
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J. Biol. Chem. 283: 19626-19635, 2008.
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[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/18450745/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">18450745</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=18450745" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
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[<a href="https://doi.org/10.1074/jbc.M802655200" target="_blank">Full Text</a>]
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Baltimore, Md. 3/17/2020.
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Lahn, B. T., Page, D. C.
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<strong>Functional coherence of the human Y chromosome.</strong>
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Science 278: 675-680, 1997.
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[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/9381176/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">9381176</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=9381176" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
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[<a href="https://doi.org/10.1126/science.278.5338.675" target="_blank">Full Text</a>]
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Lahn, B. T., Page, D. C.
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<strong>Retroposition of autosomal mRNA yielded testis-specific gene family on human Y chromosome.</strong>
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Nature Genet. 21: 429-433, 1999. Note: Erratum: Nature Genet. 22: 209 only, 1999.
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[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/10192397/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">10192397</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=10192397" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
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[<a href="https://doi.org/10.1038/7771" target="_blank">Full Text</a>]
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Machev, N., Saut, N., Longepied, G., Terriou, P., Navarro, A., Levy, N., Guichaoua, M., Metzler-Guillemain, C., Collignon, P., Frances, A.-M., Belougne, J., Clemente, E., Chiaroni, J., Chevillard, C., Durand, C., Ducourneau, A., Pech, N., McElreavey, K., Mattei, M.-G., Mitchell, M. J.
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<strong>Sequence family variant loss from the AZFc interval of the human Y chromosome, but not gene copy loss, is strongly associated with male infertility.</strong>
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J. Med. Genet. 41: 814-825, 2004. Note: Erratum: J. Med. Genet. 41: 960 only, 2004.
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[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/15520406/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">15520406</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=15520406" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
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[<a href="https://doi.org/10.1136/jmg.2004.022111" target="_blank">Full Text</a>]
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Repping, S., van Daalen, S. K. M., Korver, C. M., Brown, L. G., Marszalek, J. D., Gianotten, J., Oates, R. D., Silber, S., van der Veen, F., Page, D. C., Rozen, S.
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<strong>A family of human Y chromosomes has dispersed throughout northern Eurasia despite a 1.8-Mb deletion in the azoospermia factor c region.</strong>
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Genomics 83: 1046-1052, 2004.
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[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/15177557/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">15177557</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=15177557" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
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[<a href="https://doi.org/10.1016/j.ygeno.2003.12.018" target="_blank">Full Text</a>]
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Yen, P. H.
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<strong>A long-range restriction map of deletion interval 6 of the human Y chromosome: a region frequently deleted in azoospermic males.</strong>
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Genomics 54: 5-12, 1998.
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[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/9806824/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">9806824</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=9806824" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
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[<a href="https://doi.org/10.1006/geno.1998.5526" target="_blank">Full Text</a>]
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<div class="col-lg-6 col-md-6 col-sm-6 col-xs-6">
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<span class="mim-text-font">
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Matthew B. Gross - updated : 03/17/2020
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Bao Lige - updated : 03/17/2020<br>George E. Tiller - updated : 5/3/2005<br>Victor A. McKusick - updated : 12/16/2004<br>Patricia A. Hartz - updated : 7/6/2004
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Creation Date:
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<span class="mim-text-font">
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Rebekah S. Rasooly : 4/27/1999
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mgross : 03/27/2020
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mgross : 03/17/2020<br>mgross : 03/17/2020<br>mgross : 03/17/2020<br>alopez : 04/30/2013<br>tkritzer : 5/3/2005<br>ckniffin : 1/25/2005<br>carol : 12/29/2004<br>carol : 12/28/2004<br>terry : 12/16/2004<br>mgross : 7/8/2004<br>terry : 7/6/2004<br>alopez : 4/28/1999<br>alopez : 4/27/1999
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<strong>*</strong> 400016
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CHROMODOMAIN PROTEIN, Y-LINKED, 1; CDY1
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CHROMODOMAIN PROTEIN, Y CHROMOSOME; CDY
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<strong><em>HGNC Approved Gene Symbol: CDY1</em></strong>
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Cytogenetic location: Yq11.23
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Genomic coordinates <span class="small">(GRCh38)</span> : Y:25,622,115-25,625,511 </span>
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<span class="small">(from NCBI)</span>
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<p>CDY family proteins, such as CDY1, each contain a chromodomain and catalytic domain that are highly conserved and implicated in histone modification and recognition. However, due to subtle amino acid changes in their chromodomains, CDY proteins display substantial differences in chromatin recognition and binding, thereby diversifying the epigenetic regulatory roles they play (Fischle et al., 2008). </p>
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<strong>Cloning and Expression</strong>
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<p>Lahn and Page (1997) isolated testis cDNAs corresponding to CDY (chromodomain on Y chromosome) and other genes located in the nonrecombining portion of the Y chromosome (NRY). The predicted CDY protein contains a chromodomain (see 603079) and a putative catalytic domain. The authors noted that CDY was 1 of 7 novel genes that appeared to exist in multiple copies on the Y chromosome and were expressed specifically in testis. See BPY1 (400012). </p><p>Lahn and Page (1999) isolated 2 distinct species of CDY cDNAs from testis, CDY1 and CDY2 (400018). The predicted 540-amino acid CDY1 protein is 98% identical to CDY2. These authors also isolated a minor, alternatively spliced CDY1 transcript encoding a 554-amino acid isoform with a divergent C terminus. The CDY1 gene coding region corresponding to the major transcript does not contain any introns, although a single intron is excised to form the minor mRNA. The authors stated that there might be multiple CDY1 and CDY2 genes. They proposed that these Y-linked CDY genes arose by retroposition of an mRNA from the autosomal CDYL (603778) gene, followed by amplification of the retroposed gene. Since no Y-linked CDY homolog was found in the mouse, Lahn and Page (1999) suggested that CDYL may have given rise to CDY some time after the divergence of the mouse and human lineages. </p><p>Fischle et al. (2008) showed that FLAG-tagged human CDY and CDYL and mouse Cdyl2 (618816) localized exclusively in nuclei of mouse fibroblasts. Cdyl2 was found throughout nucleus in a punctate distribution pattern and colocalized with regions of trimethylated histone H3 (see 602810) lys9 (H3K9me3). CDY was excluded from nucleoli, but overlapped in chromatin with regions of H3K9me3. CDYL was also excluded from nucleoli, but it did not overlap with regions of H3K9me3. </p>
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<strong>Mapping</strong>
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<p>By analysis of a panel of partial Y chromosomes, Lahn and Page (1997) found that CDY genes mapped to both the 6F and 5L regions on the long arm of the human Y chromosome. Using the same technique, Lahn and Page (1999) mapped the CDY1 gene to the Y-chromosome 6F region. Yen (1998) detected 2 CDY genes in deletion interval 6 of the human Y chromosome. </p><p>Gross (2020) mapped the CDY1 gene to chromosome Yq11.23 based on an alignment of the CDY1 sequence (GenBank BC132955) with the genomic sequence (GRCh38).</p>
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<strong>Gene Function</strong>
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<p>Fischle et al. (2008) noted that the chromodomain of human CDY interacts with methylated H3K9. They found that, despite their high homology and similar tertiary structures, the chromodomains of CDY, CDYL, and CDYL2 displayed variability in binding to H3K9me3. Both the CDY and CDYL2 chromodomains bound to a similar fragment of the H3 tail, but the CDY chromodomain bound more avidly than the CDYL2 chromodomain. The CDY and CDYL2 chromodomains also displayed different sensitivities to H3K9 methylation level. The affinity of the CDYL2 chromodomain increased with methylation level, whereas binding of the CDY chromodomain to the H3K9me1 peptide was as efficient as binding of the CDYL2 chromodomain to the H3K9me3 peptide. Phosphorylation of ser10 adjacent to H3K9 weakened binding of CDY and CDYL2 to the H3K9me3 peptide. The CDYL chromodomain did not bind to the H3K9me3 peptide, but efficient binding could be established by point mutations in the chromodomain. In addition to H3K9me3, other lysine-methylated binding sites were identified for the CDY and CDYL2 chromodomains, but the CDY chromodomain displayed substantially higher selectivity for binding compared with the CDYL2 chromodomain. </p>
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<span class="mim-font">
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<strong>Molecular Genetics</strong>
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<p>Repping et al. (2004) identified the b2/b3 deletion within the AZFc region (415000) of the Y chromosome, in which 1 of the 2 copies of the CDY1 gene is deleted. The b2/b3 deletion has no obvious effect on fitness. </p><p>To determine the incidence of various partial AZFc deletions and their effect on fertility, Machev et al. (2004) discriminated 4 types of DAZ-CDY1 partial deletions and performed combined quantitative and qualitative analyses of the AZFc region in 300 infertile men and 399 controls. Only one deletion type, DAZ3/4 (400027, 400003)-CDY1a, was associated with male infertility (p = 0.042), suggesting that most of the partial deletions are neutral variants. A stronger association, however, was found between loss of the CDY1a sequence family variant (SFV) and infertility (p = 0.002). Machev et al. (2004) concluded that loss of this SFV through deletion or gene conversion could be a major risk factor for male infertility. </p>
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<strong>Evolution</strong>
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<p>Dorus et al. (2003) showed that the progenitor of the CDY gene family arose de novo in the mammalian ancestor via domain accretion. This progenitor later duplicated to generate CDYL and CDYL2, 2 autosomal genes found in all extant mammals. Prior to human-mouse divergence, a processed CDYL transcript retroposed onto the Y chromosome to create CDY. In the simian lineage, CDY was retained and subsequently amplified on the Y. In nonsimian mammals, however, CDY appears to have been lost. The retention of the Y-linked CDY genes in simians spurred the process of subfunctionalization and possibly neofunctionalization. Subfunctionalization is evidenced by the observation that simian CDYL and CDYL2 retained their somatic housekeeping transcripts but lost the spermatogenic transcripts to the newly arisen CDY. Neofunctionalization is suggested by the rapid evolution of the CDY protein sequence. Dorus et al. (2003) concluded that the CDY-related family offers an example of how duplicated genes undergo functional diversification in both expression profile and protein sequence and supports the hypothesis that there is a tendency for spermatogenic functions to transfer from autosomes to the Y chromosome. </p>
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<h4>
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<span class="mim-font">
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<strong>REFERENCES</strong>
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</span>
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</h4>
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<div>
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<p />
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</div>
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<ol>
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<p class="mim-text-font">
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Dorus, S., Gilbert, S. L., Forster, M. L., Barndt, R. J., Lahn, B. T.
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<strong>The CDY-related gene family: coordinated evolution in copy number, expression profile and protein sequence.</strong>
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Hum. Molec. Genet. 12: 1643-1650, 2003.
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[PubMed: 12837688]
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[Full Text: https://doi.org/10.1093/hmg/ddg185]
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Fischle, W., Franz, H., Jacobs, S. A., Allis, C. D., Khorasanizadeh, S.
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<strong>Specificity of the chromodomain Y chromosome family of chromodomains for lysine-methylated ARK(S/T) motifs.</strong>
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J. Biol. Chem. 283: 19626-19635, 2008.
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[PubMed: 18450745]
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[Full Text: https://doi.org/10.1074/jbc.M802655200]
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<li>
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<p class="mim-text-font">
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Gross, M. B.
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<strong>Personal Communication.</strong>
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Baltimore, Md. 3/17/2020.
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</p>
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</li>
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<li>
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<p class="mim-text-font">
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Lahn, B. T., Page, D. C.
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<strong>Functional coherence of the human Y chromosome.</strong>
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Science 278: 675-680, 1997.
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[PubMed: 9381176]
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[Full Text: https://doi.org/10.1126/science.278.5338.675]
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<p class="mim-text-font">
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Lahn, B. T., Page, D. C.
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<strong>Retroposition of autosomal mRNA yielded testis-specific gene family on human Y chromosome.</strong>
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Nature Genet. 21: 429-433, 1999. Note: Erratum: Nature Genet. 22: 209 only, 1999.
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[PubMed: 10192397]
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[Full Text: https://doi.org/10.1038/7771]
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<p class="mim-text-font">
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Machev, N., Saut, N., Longepied, G., Terriou, P., Navarro, A., Levy, N., Guichaoua, M., Metzler-Guillemain, C., Collignon, P., Frances, A.-M., Belougne, J., Clemente, E., Chiaroni, J., Chevillard, C., Durand, C., Ducourneau, A., Pech, N., McElreavey, K., Mattei, M.-G., Mitchell, M. J.
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<strong>Sequence family variant loss from the AZFc interval of the human Y chromosome, but not gene copy loss, is strongly associated with male infertility.</strong>
|
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J. Med. Genet. 41: 814-825, 2004. Note: Erratum: J. Med. Genet. 41: 960 only, 2004.
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[PubMed: 15520406]
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[Full Text: https://doi.org/10.1136/jmg.2004.022111]
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Repping, S., van Daalen, S. K. M., Korver, C. M., Brown, L. G., Marszalek, J. D., Gianotten, J., Oates, R. D., Silber, S., van der Veen, F., Page, D. C., Rozen, S.
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<strong>A family of human Y chromosomes has dispersed throughout northern Eurasia despite a 1.8-Mb deletion in the azoospermia factor c region.</strong>
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Genomics 83: 1046-1052, 2004.
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[PubMed: 15177557]
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[Full Text: https://doi.org/10.1016/j.ygeno.2003.12.018]
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Yen, P. H.
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<strong>A long-range restriction map of deletion interval 6 of the human Y chromosome: a region frequently deleted in azoospermic males.</strong>
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Genomics 54: 5-12, 1998.
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[PubMed: 9806824]
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[Full Text: https://doi.org/10.1006/geno.1998.5526]
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Matthew B. Gross - updated : 03/17/2020<br>Bao Lige - updated : 03/17/2020<br>George E. Tiller - updated : 5/3/2005<br>Victor A. McKusick - updated : 12/16/2004<br>Patricia A. Hartz - updated : 7/6/2004
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