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CDY1 Gene

protein-coding   GIFtS: 50
GCID: GC0YP027768

Chromodomain Protein, Y-Linked, 1

(Previous names: chromodomain protein, Y chromosome, 1)
  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)
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Aliases
Chromodomain Protein, Y-Linked, 11 2     CDY2 5
Chromodomain Protein, Y Chromosome, 11 2     Testis-Specific Chromodomain Protein On Y2
CDY1A2 3     Testis-Specific Chromodomain Protein Y 12
EC 2.3.1.483 8     

External Ids:    HGNC: 18091   Entrez Gene: 90852   Ensembl: ENSG000001722887   OMIM: 4000165   UniProtKB: Q9Y6F83   

Export aliases for CDY1 gene to outside databases

Previous GC identifers: GC0YP026933 GC0YM025438 GC0YM025036 GC0YP026106 GC0YP026177 GC0YM018183


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for CDY1 Gene:
This gene encodes a protein containing a chromodomain and a histone acetyltransferase catalytic domain.
Chromodomain proteins are components of heterochromatin-like complexes and can act as gene repressors. This
protein is localized to the nucleus of late spermatids where histone hyperacetylation takes place. Histone
hyperacetylation is thought to facilitate the transition in which protamines replace histones as the major
DNA-packaging protein. The human chromosome Y has two identical copies of this gene within a palindromic region;
this record represents the more telomeric copy. Chromosome Y also contains a pair of closely related genes in
another more telomeric palindrome as well as several related pseudogenes. Two protein isoforms are encoded by
transcript variants of this gene. Additional transcript variants have been described, but their full-length
nature has not been determined. (provided by RefSeq, Jul 2008)

GeneCards Summary for CDY1 Gene:
CDY1 (chromodomain protein, Y-linked, 1) is a protein-coding gene. Diseases associated with CDY1 include y chromosome infertility, and gonadoblastoma. An important paralog of this gene is CDY2A.

UniProtKB/Swiss-Prot: CDY1_HUMAN, Q9Y6F8
Function: Has histone acetyltransferase activity, with a preference for histone H4

Gene Wiki entry for CDY1 Gene


(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000024.10  NT_011903.12  
Regulatory elements:
   Regulatory transcription factor binding sites in the CDY1 gene promoter:
         GR   GR-beta   GR-alpha   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CDY1


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

Entrez Gene cytogenetic band: Yq11.23   Ensembl cytogenetic band:  Yq11.23   HGNC cytogenetic band: Yq11.22

CDY1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CDY1 gene location

GeneLoc information about chromosome Y         GeneLoc Exon Structure

GeneLoc location for GC0YP027768:  view genomic region     (about GC identifiers)

Start:
27,768,264 bp from pter      End:
27,771,049 bp from pter
Size:
2,786 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: CDY1_HUMAN, Q9Y6F8 (See protein sequence)
Recommended Name: Testis-specific chromodomain protein Y 1  
Size: 540 amino acids; 60473 Da
Subunit: Interacts (via chromo domain) with histone H3K9me3
1 PDB 3D structure from and Proteopedia for CDY1:
2FBM (3D)    
Secondary accessions: A2RUK1 O14600
Alternative splicing: 2 isoforms:  Q9Y6F8-1   Q9Y6F8-2   

Explore the universe of human proteins at neXtProt for CDY1: NX_Q9Y6F8

Explore proteomics data for CDY1 at MOPED

Selected DME Specific Peptides for CDY1 (Q9Y6F8) (see all 9)
 KALVRCN  KGLVSQVF  YLVRWKGYD  DDTWEPEQHL 


See CDY1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_004671.1  NP_733841.1  

ENSEMBL proteins: 
 ENSP00000302968   ENSP00000354799  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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Selected 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 Q9Y6F8

ProtoNet protein and cluster: Q9Y6F8

1 Blocks protein domain: IPB000953 Chromo domain

UniProtKB/Swiss-Prot: CDY1_HUMAN, Q9Y6F8
Similarity: Contains 1 chromo domain


CDY1 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,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: CDY1_HUMAN, Q9Y6F8
Function: Has histone acetyltransferase activity, with a preference for histone H4
Catalytic activity: Acetyl-CoA + [histone] = CoA + acetyl-[histone]

     Genatlas biochemistry entry for CDY1:
DNA binding protein with a chromatin organization modifier (chromo) domain,involved in compaction during
spermatogenesis,testis specific,CHD family,1,in a AZF deleted region

     Enzyme Number (IUBMB): EC 2.3.1.481 2

     Gene Ontology (GO): 3 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003824catalytic activity ----
GO:0004402histone acetyltransferase activity ----
GO:0035064methylated histone residue binding ----
     
CDY1 for ontologies           About GeneDecksing


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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
CDY1_HUMAN, Q9Y6F8: Nucleus
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus3
mitochondrion1

Gene Ontology (GO): 1 cellular component term:    About this table

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

CDY1 for ontologies           About GeneDecksing


(SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for CDY1
Interactions:

    Search GeneGlobe Interaction Network for CDY1

STRING Interaction Network Preview (showing 5 interactants - click image to see 14)

Selected Interacting proteins for CDY1 (Q9Y6F83 ENSP000003029684) via UniProtKB, MINT, STRING, and/or I2D (see all 29)
InteractantInteraction Details
GeneCardExternal ID(s)
HIST1H4AP628053I2D: score=1 
HIST1H4BP628053I2D: score=1 
HIST1H4CP628053I2D: score=1 
HIST1H4DP628053I2D: score=1 
HIST1H4EP628053I2D: score=1 
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Gene Ontology (GO): 2 biological process terms:    About this table

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

CDY1 for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
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Browse Tocris compounds for CDY1

2 HMDB Compounds for CDY1    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--



(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,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for CDY1 gene (2 alternative transcripts): 
NM_004680.2  NM_170723.1  

Unigene Cluster for CDY1:

Chromodomain protein, Y-linked, 1
Hs.159281
Unigene Representative Sequence: NM_004680
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000306609(uc004fxf.3) ENST00000361963(uc004fxe.3)
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Additional mRNA sequence: 

AF000981.1 AF080597.1 AK292375.1 BC033041.1 BC132955.1 

4 DOTS entries:

DT.105323  DT.120653220  DT.120654013  DT.92059991 

12 AceView cDNA sequences:

NM_001003894 BX279566 NM_170723 NM_001003895 NM_004680 AF080597 AF000981 AA292905 
BC033041 BI459455 BU569556 AA401738 

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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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CDY1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: ACTAGAATTG
CDY1 Expression
About this image

CDY1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

CDY1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.159281

UniProtKB/Swiss-Prot: CDY1_HUMAN, Q9Y6F8
Tissue specificity: Testis-specific. Detected in spermatids (at protein level)

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In Situ
Assay Products:
 

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

Orthologs for CDY1 gene from Selected species (see all 11)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
dog
(Canis familiaris)
Mammalia --
Uncharacterized protein
60(a)
1 → many
35(4844693-5075064)
chicken
(Gallus gallus)
Aves --
Uncharacterized protein
60(a)
1 → many
2(65668286-65773998)
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
59(a)
1 → many
GL343209.1(12187-102820)
zebrafish
(Danio rerio)
Actinopterygii cdyl6
chromodomain protein, Y-like
44(a)
1 → many
2(24186724-24241358) ENSDARG00000038985
fruit fly
(Drosophila melanogaster)
Insecta CG36806
--
9(a)
1 → many
3L(20802769-20806432)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DCI1(YOR180C)4 Peroxisomal protein; identification as a delta(3,5)-delta(2,4)-dienoyl-CoA more   --   15(675167-674352) 854352  NP_014823.1 


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

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for CDY1 gene
CDY1B1 2  CDY2A1 2  CDY2B1 2  ECI22  CDYL22  AUH2  ECHDC32  ECHS12  
ECHDC22  CDYL2  ECH12  
6 SIMAP similar genes for CDY1 using alignment to 1 protein entry:     CDY1_HUMAN:
CDY2A    CDY2B    CDYL    CDYL2    CBX5    ECI2

CDY1 for paralogs           About GeneDecksing


Selected Pseudogenes.org Pseudogenes for CDY1 (see all 17)
PGOHUM00000233699 PGOHUM00000233765 PGOHUM00000233770 PGOHUM00000233814 PGOHUM00000233832


(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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Structural Variations
     Database of Genomic Variants (DGV) 7 variations for CDY1:    About this table    
Variant IDTypeSubtypePubMed ID
essv10843CNV CNV17122850
nsv442826CNV CNV18776908
nsv442824CNV CNV18776908
nsv515229CNV Complex21397061
nsv469828CNV Complex16826518
nsv515231CNV Complex21397061
dgv2510e1CNV Complex17122850

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(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.)
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OMIM gene information: 400016    OMIM disorders: --

4 diseases for CDY1:    
About MalaCards
y chromosome infertility    gonadoblastoma    azoospermia    infertility

2 diseases from the University of Copenhagen DISEASES database for CDY1:
Azoospermia     Gonadoblastoma

CDY1 for disorders           About GeneDecksing

GeneTests: CDY1
GeneReviews: CDY1
Genetic Association Database (GAD): CDY1
Human Genome Epidemiology (HuGE) Navigator: CDY1 (4 documents)

Export disorders for CDY1 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)
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PubMed articles for CDY1 gene, integrated from 10 sources (see all 23):
(articles sorted by number of sources associating them with CDY1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Functional coherence of the human Y chromosome. (PubMed id 9381176)1, 2, 3 Lahn B.T. and Page D.C. (Science 1997)
  2. Features of constitutive gr/gr deletion in a Japanese population. (PubMed id 20663794)1, 4 Sin H.S....Namiki M. (Hum. Reprod. 2010)
  3. Differential effect of specific gr/gr deletion subtypes on spermatogenesis in the Chinese Han population. (PubMed id 20039973)1, 4 Yang Y....Zhang S. (Int. J. Androl. 2010)
  4. Do we need to search for gr/gr deletions in infertile men in a clinical setting? (PubMed id 18326516)1, 4 Stouffs K....Lissens W. (Hum. Reprod. 2008)
  5. Previously uncharacterized histone acetyltransferases implicated in mammalian spermatogenesis. (PubMed id 12072557)1, 2 Lahn B.T....Page D.C. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  6. Retroposition of autosomal mRNA yielded testis-specific gene family on human Y chromosome. (PubMed id 10192397)1, 2 Lahn B.T. and Page D.C. (Nat. Genet. 1999)
  7. Specificity of the chromodomain Y chromosome family of chromodomains for lysine-methylated ARK(S/T) motifs. (PubMed id 18450745)2, 9 Fischle W....Khorasanizadeh S. (J. Biol. Chem. 2008)
  8. CDY1 and BOULE transcripts assessed in the same biopsy as predictive markers for successful testicular sperm retrieval. (PubMed id 21474125)1 Kleiman S.E....Yogev L. (Fertil. Steril. 2011)
  9. Crystal structures of human CDY proteins reveal a crotonase-like fold. (PubMed id 19507244)2 Wu H.... Plotnikov A.N. (Proteins 2009)
  10. Partial AZFc deletions and duplications: clinical correlates in the Italian population. (PubMed id 18807255)1 Giachini C....Krausz C. (Hum. Genet. 2008)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Disorders
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)
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Entrez Gene: 9085 HGNC: 1809 AceView: CDY1.1 Ensembl:ENSG00000172288 euGenes: HUgn9085
ECgene: CDY1 H-InvDB: CDY1

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for CDY1 Pharmacogenomics, SNPs, Pathways
GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=CDY1[genesymbol]

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for CDY1 gene:
Search GeneIP for patents involving CDY1

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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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