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CDY1B Gene

protein-coding   GIFtS: 40
GCID: GC0YM026191

Chromodomain Protein, Y-Linked, 1B

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(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, 1B1 2     Testis-Specific Chromodomain Protein On Y, Centromeric2
EC 2.3.1.483 8     Testis-Specific Chromodomain Protein Y 12
CDY2     CDY1A3
Chromodomain Protein, Y Chromosome, 1, Centromeric2     

External Ids:    HGNC: 239201   Entrez Gene: 2531752   Ensembl: ENSG000001723527   UniProtKB: Q9Y6F83   

Export aliases for CDY1B gene to outside databases

Previous GC identifers: GC0YM024530 GC0YU900278 GC0YM024600


(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 CDY1B 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 centromeric 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 CDY1B Gene:
CDY1B (chromodomain protein, Y-linked, 1B) is a protein-coding gene. GO annotations related to this gene include histone acetyltransferase activity. 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




(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 at NCBI GenBank:
NC_000024.9  NT_011903.12  
Regulatory elements:
   Regulatory transcription factor binding sites in the CDY1B gene promoter:
         Bach1   POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   POU3F2   RORalpha2   AREB6   Max   PPAR-gamma1   PPAR-gamma2   c-Myc   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CDY1B


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

Entrez Gene cytogenetic band: Yq11.223   Ensembl cytogenetic band:  Yq11.223   HGNC cytogenetic band: Yq11.223

CDY1B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CDY1B gene location

GeneLoc information about chromosome Y         GeneLoc Exon Structure

GeneLoc location for GC0YM026191:  view genomic region     (about GC identifiers)

Start:
26,191,376 bp from pter      End:
26,194,166 bp from pter
Size:
2,791 bases      Orientation:
minus 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, Cloud-Clone Corp., and/or eBioscience,
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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 CDY1B:
2FBM (3D)    
Secondary accessions: A2RUK1 O14600
Alternative splicing: 2 isoforms:  Q9Y6F8-1   Q9Y6F8-2   

Explore the universe of human proteins at neXtProt for CDY1B: NX_Q9Y6F8

Explore proteomics data for CDY1B at MOPED

Selected DME Specific Peptides for CDY1B (Q9Y6F8) (see all 9)
 KALVRCN  KGLVSQVF  YLVRWKGYD  DDTWEPEQHL 


See CDY1B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_001003894.1  NP_001003895.1  

ENSEMBL proteins: 
 ENSP00000303178   ENSP00000371844  

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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


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(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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, 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]

     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 IEA--
GO:0035064methylated histone residue binding IDA18450745
     
Find genes that share ontologies with CDY1B           About GenesLikeMe


Phenotypes:
     1 GenomeRNAi human phenotype for CDY1B:
 Increased gamma-H2AX phosphory 

Animal Models:
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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 IDA18450745

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(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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Interactions:

    Search GeneGlobe Interaction Network for CDY1B

STRING Interaction Network Preview (showing 5 interactants - click image to see 16)

Selected Interacting proteins for CDY1B (Q9Y6F83 ENSP000003031784) via UniProtKB, MINT, STRING, and/or I2D (see all 29)
InteractantInteraction Details
GeneCardExternal ID(s)
HIST1H4AP628053, ENSP000003529804I2D: score=1 STRING: ENSP00000352980
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 TAS9381176
GO:0008152metabolic process ----

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(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
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for CDY1B (CDY1)



(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,
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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for CDY1B gene (2 alternative transcripts): 
NM_001003894.1  NM_001003895.1  

Unigene Cluster for CDY1B:

Chromodomain protein, Y-linked, 1B
Hs.562095  [show with all ESTs]
Unigene Representative Sequence: NM_001003895
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000306882(uc004fvz.3) ENST00000382407(uc004fwa.3)
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Additional mRNA sequence: 

AK292318.1 BC132929.1 

4 DOTS entries:

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

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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CDY1B expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
CDY1B Expression
About this image

CDY1B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

CDY1B Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.562095

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 CDY1B 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 CDY1B (if available)
TreeFam Gene Tree for CDY1B (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for CDY1B gene
CDY11 2  CDY2A1 2  CDY2B1 2  ECI22  CDYL22  AUH2  ECHDC32  ECHS12  
ECHDC22  CDYL2  ECH12  
6 SIMAP similar genes for CDY1B using alignment to 1 protein entry:     CDY1_HUMAN:
CDY2A    CDY2B    CDYL    CDYL2    CBX5    ECI2

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(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 CDY1B:    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, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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1 disease from the University of Copenhagen DISEASES database for CDY1B:
Azoospermia

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Export disorders for CDY1B 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 CDY1B gene, integrated from 10 sources (see all 18):
(articles sorted by number of sources associating them with CDY1B)
    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. (Nat. Genet. 1999)
  2. Functional coherence of the human Y chromosome. (PubMed id 9381176)1, 2, 3 Lahn B.T. and Page D.C. (Science 1997)
  3. Specificity of the chromodomain Y chromosome family of chromodomains for lysine-methylated ARK(S/T) motifs. (PubMed id 18450745)1, 2 Fischle W....Khorasanizadeh S. (J. Biol. Chem. 2008)
  4. 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. (Genome Res. 2004)
  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. Why do cellular proteins linked to K63-polyubiquitin chains not associate with proteasomes? (PubMed id 23314748)1 Nathan J.A....Goldberg A.L. (EMBO J. 2013)
  7. Crystal structures of human CDY proteins reveal a crotonase-like fold. (PubMed id 19507244)2 Wu H.... Plotnikov A.N. (Proteins 2009)
  8. 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. (Nature 2003)
  9. The CDY-related gene family: coordinated evolution in copy number, expression profile and protein sequence. (PubMed id 12837688)1 Dorus S.... Lahn B.T. (Hum. Mol. Genet. 2003)
  10. Members of the CDY family have different expression patterns: CDY1 transcripts have the best correlation with complete spermatogenesis. (PubMed id 14569460)1 Kleiman S.E....Yavetz H. (Hum. Genet. 2003)

(in PubMed, OMIM, and NCBI Bookshelf)
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 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)
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Entrez Gene: 253175 HGNC: 23920 Ensembl:ENSG00000172352 euGenes: HUgn253175 ECgene: CDY1B
H-InvDB: CDY1B

(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 CDY1B Pharmacogenomics, SNPs, Pathways
GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=CDY1[genesymbol]

(Patent information from GeneIP,
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Patent Information for CDY1B gene:
Search GeneIP for patents involving CDY1B

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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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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 Block miRNA regulation of human, mouse, rat CDY1B using miScript Target Protectors SeqTarget long-range PCR primers for resequencing CDY1B
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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 , 21 Aug 2014 , 8 Sep 2014

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