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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

CDY2A Gene

protein-coding   GIFtS: 44
GCID: GC0YP020137

Chromodomain Protein, Y-Linked, 2A

(Previous names: chromodomain protein, Y chromosome, 2, chromodomain protein,...)
(Previous symbol: CDY2)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Chromodomain Protein, Y-Linked, 2A1 2     Chromodomain Protein, Y-Linked, 21
CDY21 2 3 5     CDY2
Chromodomain Protein, Y Chromosome, 21 2     Testis-Specific Chromodomain Protein Y 22
EC 2.3.1.483 8     Y Chromosome Chromodomain Protein 2A2

External Ids:    HGNC: 18101   Entrez Gene: 94262   Ensembl: ENSG000001824157   OMIM: 4000185   UniProtKB: Q9Y6F73   

Export aliases for CDY2A gene to outside databases

Previous GC identifers: GC0YP018576 GC0YP018648 GC0YM014436


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for CDY2A Gene:
This intronless gene encodes a protein containing a chromodomain and a histone acetyltransferase catalytic domain.
Chromodomain proteins are components of heterochromatin-like complexes and can act as gene repressors. This
protein is localized to the nucleus of late spermatids where histone hyperacetylation takes place. Histone
hyperacetylation is thought to facilitate the transition in which protamines replace histones as the major
DNA-packaging protein. Two nearly identical copies of this gene are found in a palindromic region on chromosome
Y; this record represents the telomeric copy. Chromosome Y also contains a pair of closely related genes in
another more telomeric palindrome as well as several related pseudogenes. (provided by RefSeq, Jul 2008)

GeneCards Summary for CDY2A Gene: 
CDY2A (chromodomain protein, Y-linked, 2A) is a protein-coding gene. Diseases associated with CDY2A include y chromosome infertility, and azoospermia. An important paralog of this gene is ECI2.

UniProtKB/Swiss-Prot: CDY2_HUMAN, Q9Y6F7
Function: May have histone acetyltransferase activity (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000024.9  NT_011875.12  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CDY2A gene promoter:
         Bach1   POU3F2 (N-Oct-5b)   POU3F2 (N-Oct-5a)   POU3F2   RORalpha2   N-Myc   Max   PPAR-gamma1   PPAR-gamma2   c-Myc   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for CDY2A

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CDY2A


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Yq11.221   Ensembl cytogenetic band:  Yq11.222   HGNC cytogenetic band: Yq11.222

CDY2A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CDY2A gene location

GeneLoc information about chromosome Y         GeneLoc Exon Structure

GeneLoc location for GC0YP020137:  view genomic region     (about GC identifiers)

Start:
20,137,667 bp from pter      End:
20,140,477 bp from pter
Size:
2,811 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: CDY2_HUMAN, Q9Y6F7 (See protein sequence)
Recommended Name: Testis-specific chromodomain protein Y 2  
Size: 541 amino acids; 60524 Da
Subcellular location: Nucleus (By similarity)
1 PDB 3D structure from and Proteopedia for CDY2A:
2FW2 (3D)    
Secondary accessions: A8K868

Explore the universe of human proteins at neXtProt for CDY2A: NX_Q9Y6F7

Explore proteomics data for CDY2A at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9Y6F7

  • 4/9 DME Specific Peptides for CDY2A (Q9Y6F7) (see all 9)
     KALVRCN  KGLVSQVF  YLVRWKGYD  DDTWEPEQHL 

    CDY2A Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    CDY2A Protein Expression
    REFSEQ proteins: NP_004816.1  
    ENSEMBL proteins: 
     ENSP00000402280   ENSP00000250838  

    Human Recombinant Protein Products for CDY2A: 
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    Cloud-Clone Corp. Proteins for CDY2A 

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus ----

    CDY2A for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    5/6 InterPro protein domains (see all 6):
     IPR000953 Chromo_domain/shadow
     IPR023780 Chromo_domain
     IPR016197 Chromodomain-like
     IPR023779 Chromodomain_CS
     IPR017984 Chromo_dom_subgr

    Graphical View of Domain Structure for InterPro Entry Q9Y6F7

    ProtoNet protein and cluster: Q9Y6F7

    1 Blocks protein domain: IPB000953 Chromo domain

    UniProtKB/Swiss-Prot: CDY2_HUMAN, Q9Y6F7
    Similarity: Contains 1 chromo domain


    CDY2A for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CDY2_HUMAN, Q9Y6F7
    Function: May have histone acetyltransferase activity (By similarity)
    Catalytic activity: Acetyl-CoA + [histone] = CoA + acetyl-[histone]

         Enzyme Number (IUBMB): EC 2.3.1.481 2

         Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003824catalytic activity ----
    GO:0004402histone acetyltransferase activity ----
         
    CDY2A for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for CDY2A 
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CDY2A

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007283spermatogenesis ----
    GO:0008152metabolic process ----

    CDY2A for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for CDY2A (CDY2)

    2 HMDB Compounds for CDY2A    About this table
    CompoundSynonyms CAS #PubMed Ids
    Acetyl-CoAS-Acetyl coenzyme A (see all 13)72-89-9--
    Coenzyme AAcetoacetyl coenzyme A sodium salt (see all 21)85-61-0--

    Search CenterWatch for drugs/clinical trials and news about CDY2A / CDY2

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for CDY2A gene: 
    NM_004825.2  

    Unigene Cluster for CDY2A:

    Chromodomain protein, Y-linked, 2A
    Hs.251375  [show with all ESTs]
    Unigene Representative Sequence: AF080598
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000426790 ENST00000250838(uc004ftm.1)
    miRNA
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    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
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    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat CDY2A
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    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat CDY2A
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CDY2A

    Additional mRNA sequence: 

    AF080598.1 AK292233.1 

    1 DOTS entry:

    DT.101963184 

    2 AceView cDNA sequences:

    NM_004825 AF080598 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    CDY2A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    CDY2A Expression
    About this image


    See CDY2A Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CDY2A

    SOURCE GeneReport for Unigene cluster: Hs.251375

    UniProtKB/Swiss-Prot: CDY2_HUMAN, Q9Y6F7
    Tissue specificity: Testis specific

        SABiosciences Custom PCR Arrays for CDY2A
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CDY2A

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

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

    Orthologs for CDY2A gene from 5/12 species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves --
    --
    60(a)
    1 → many
    2(65668286-65773998)
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    59(a)
    1 → many
    GL343209.1(12187-102820)
    zebrafish
    (Danio rerio)
    Actinopterygii cdyl6
    chromodomain protein, Y-like
    43(a)
    1 → many
    2(24187298-24239708)
    fruit fly
    (Drosophila melanogaster)
    Insecta CG138906
    --
    26(a)
    1 → many
    3L(851346-852673)
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes DCI16
    ECI16
    Peroxisomal protein; identification as a delta(3,5...
    Peroxisomal delta3,delta2-enoyl-CoA isomerase, hex...
    23(a)
    21(a)
    many ↔ many
    many ↔ many
    XV(674352-675167)
    XII(706198-707040)
            Species with no ortholog for CDY2A

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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CDY2A gene
    CDY2B1 2  CDY11 2  CDY1B1 2  ECI22  CDYL22  AUH2  ECHDC32  ECHS12  
    ECHDC22  CDYL2  ECH12  
    9 SIMAP similar genes for CDY2A using alignment to 2 protein entries:     CDY2_HUMAN (see all proteins):
    CDY2B    CDY1    CDY1B    CDYL    CDYL2    CBX5
    ECI2    PECI    ECHDC3

    CDY2A for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/14 SNPs in CDY2A are shown (see all 14)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr Y posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs39928781,2
    C--14438940(-) ctccaG/Ccctcg 1 -- us2k11Minor allele frequency- C:0.00NA 1
    rs25564461,2
    ----14436246(-) TCTTAC/TTTTTA 1 -- ds50010--------
    rs38762011,2
    ----14436801(-) ACAATC/GCAATT 2 P A mis10--------
    rs2006707241,2
    ----14438633(-) CCATAC/TAATCG 1 -- us2k10--------
    rs25564771,2
    ----14436176(+) TGATCA/GTTCTG 1 -- ds50010--------
    rs25564841,2
    ----14437889(+) AGAGAA/GTTGAA 3 N T S mis1 ese30--------
    rs25564471,2
    ----14436223(-) CCTCTA/GTTGGG 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for CDY2A (20137667 - 20140477 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for CDY2A:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv469874CNV Complex16826518
    esv1670141OTHER Inversion17803354

    SABiosciences Cancer Mutation PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing CDY2A
    DNA2.0 Custom Variant and Variant Library Synthesis for CDY2A

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 400018    OMIM disorders: --

    3 diseases for CDY2A:    About MalaCards
    y chromosome infertility    azoospermia    infertility

    1 disease from the University of Copenhagen DISEASES database for CDY2A:
    Male infertility

    CDY2A for disorders           About GeneDecksing


    Export disorders for CDY2A gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for CDY2A gene, integrated from 9 sources (see all 18):
    (articles sorted by number of sources associating them with CDY2A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Retroposition of autosomal mRNA yielded testis-specific gene family on human Y chromosome. (PubMed id 10192397)1, 2, 3 Lahn B.T. and Page D.C. (1999)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. Deletion or underexpression of the Y-chromosome genes CDY2 and HSFY is associated with maturation arrest in American men with nonobstr uctive azoospermia. (PubMed id 22820855)1 Stahl P.J....Paduch D.A. (2012)
    4. Dynamics of cullin-RING ubiquitin ligase network revea led by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (2010)
    5. Crystal structures of human CDY proteins reveal a crotonase-like fold. (PubMed id 19507244)2 Wu H.... Plotnikov A.N. (2009)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
    7. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. (PubMed id 12815422)1 Skaletsky H.... Page D.C. (2003)
    8. Comparative mapping of CDY and DAZ in higher primates. (PubMed id 12438810)1 Wimmer R....Schempp W. (2002)
    9. Identification and characterization of the cynomolgus monkey chromodomain gene cynCDY, an orthologue of the human CDY gene family. (PubMed id 12149400)1 Kostova E....Gromoll J. (2002)
    10. Previously uncharacterized histone acetyltransferases implicated in mammalian spermatogenesis. (PubMed id 12072557)1 Lahn B.T....Page D.C. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 9426 HGNC: 1810 AceView: CDY2 Ensembl:ENSG00000182415 euGenes: HUgn9426
    ECgene: CDY2A H-InvDB: CDY2A

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for CDY2A Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for CDY2A gene:
    Search GeneIP for patents involving CDY2A

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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     inGenious Targeting Laboratory - Custom generated mouse model solutions for CDY2A
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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