CDY1B Gene
protein-coding GIFtS: 44
GCID: GC0YM026191
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chromodomain protein, Y-linked, 1B
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Aliases
for CDY1B gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| 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 | | |
Export aliases for CDY1B gene to outside databasesPrevious GC identifers: GC0YM024530 GC0YU900278 GC0YM024600 |
Summaries
for CDY1B gene(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 CDY1B:
This gene encodes a protein containing a chromodomain and a histone acetyltransferase catalytic domain. Chromodomainproteins are components of heterochromatin-like complexes and can act as gene repressors. This protein is localized tothe nucleus of late spermatids where histone hyperacetylation takes place. Histone hyperacetylation is thought tofacilitate the transition in which protamines replace histones as the major DNA-packaging protein. The humanchromosome Y has two identical copies of this gene within a palindromic region; this record represents the morecentromeric copy. Chromosome Y also contains a pair of closely related genes in another more telomeric palindrome aswell as several related pseudogenes. Two protein isoforms are encoded by transcript variants of this gene. Additionaltranscript variants have been described, but their full-length nature has not been determined. (provided by RefSeq,Jul 2008)
UniProtKB/Swiss-Prot: CDY1_HUMAN, Q9Y6F8Function: Has histone acetyltransferase activity, with a preference for histone H4
|
Genomic Views
for CDY1B 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 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000024.9 NT_011903.12
Regulatory elements:
 SABiosciences 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
Search SABiosciences Chromatin IP Primers for CDY1B
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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: Yq11.223CDY1B Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome Y GeneLoc Exon Structure GeneLoc location for GC0YM026191: view genomic region
(about GC identifiers)
Start:
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26,191,376 bp from pter |
End:
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26,194,166 bp from pter |
Size:
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2,791 bases |
Orientation:
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minus strand |
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Proteins
for CDY1B gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
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
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
|
UniProtKB/Swiss-Prot: CDY1_HUMAN, Q9Y6F8 (See
protein sequence)Recommended Name: Testis-specific chromodomain protein Y 1 Size: 540 amino acids; 60473 Da
Subcellular location: Nucleus (By similarity)
1 PDB 3D structure from  and Proteopedia  for CDY1B:2FBM (3D)
Secondary accessions: A2RUK1 O14600Alternative splicing: 2 isoforms: Q9Y6F8-1 Q9Y6F8-2 Explore the universe of human proteins at neXtProt for CDY1B: NX_Q9Y6F8
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q9Y6F8
4/9 DME Specific Peptides for CDY1B (Q9Y6F8) (see all 9)
CDY1B Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins (2 alternative transcripts):
NP_001003894.1 NP_001003895.1
ENSEMBL proteins: ENSP00000303178 ENSP00000371844
Human Recombinant Protein Products for CDY1B:
Gene Ontology (GO): 1 cellular component term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005634 | nucleus |
IEA | -- |
CDY1B for ontologies About GeneDecksing
CDY1B Antibody Products:
Assay Products for CDY1B: |
Protein
Domains /
Families
for CDY1B gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
CDY1B for domains About GeneDecksing
5/6 InterPro domains/families (see all 6):Graphical View of Domain Structure for InterPro Entry Q9Y6F8ProtoNet protein and cluster: Q9Y6F8 1 Blocks protein family: IPB000953 Chromo domain
UniProtKB/Swiss-Prot: CDY1_HUMAN, Q9Y6F8Similarity: Contains 1 chromo domain |
Function
for CDY1B gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
inGenious Targeting Laboratory,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase,
shRNA from
OriGene,
Sirion Biotech,
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,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
Sirion Biotech,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Molecular Function:
UniProtKB/Swiss-Prot Summary: CDY1_HUMAN, Q9Y6F8Function: Has histone acetyltransferase activity, with a preference for histone H4Catalytic activity: Acetyl-CoA + [histone] = CoA + acetyl-[histone] Enzyme Number (IUBMB): EC 2.3.1.481 2
Gene Ontology (GO): 1 molecular function term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0004402 | histone acetyltransferase activity |
IEA | -- |
CDY1B for ontologies About GeneDecksing
Phenotypes:
1 GenomeRNAi human phenotype for CDY1B:
Animal Models:
Clone
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OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for CDY1B (see all 2)
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In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CDY1B |
|
Pathways & Interactions
for CDY1B gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
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 Mar 2013 via
Entrez Gene).
About This Section
|
Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CDY1B
STRING Interaction
Network Preview (showing 2 interactants - click image to see more details)
5/15 Interacting proteins for CDY1B (Q9Y6F83 ENSP000003031784) via UniProtKB, MINT, STRING, and/or I2D (see all 15)About this table
Gene Ontology (GO): 1 biological process term (GO ID links to tree view): About this table
CDY1B for ontologies About GeneDecksing
|
Drugs & Compounds
for CDY1B gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for CDY1B
Search CenterWatch for drugs/clinical trials and news about CDY1B / CDY1
|
Transcripts
for CDY1B gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 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,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
Sirion Biotech,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
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_0010038952 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000306882(uc004fvz.3) ENST00000382407(uc004fwa.3)
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for CDY1B (see all 2)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for CDY1B (see all 2)
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector (see all 2): CDY1B (NM_001003895) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for CDY1B | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CDY1B |
Additional cDNA sequence: AK292318.1 BC132929.1 4 DOTS entries: DT.92059991 DT.120654013 DT.105323 DT.120653220
GeneLoc Exon Structure
|
Expression
for CDY1B gene
(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
| CDY1B expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --
About this image
See CDY1B Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for CDY1B
SOURCE GeneReport for Unigene cluster: Hs.562095
UniProtKB/Swiss-Prot: CDY1_HUMAN, Q9Y6F8Tissue specificity: Testis-specific. Detected in spermatids (at protein level)
SABiosciences Custom PCR Arrays for CDY1B
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for CDY1B
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse / rat CDY1B | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat CDY1B | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CDY1B | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CDY1B |
Orthologs
for CDY1B gene
(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 last universal common ancestor (LUCA).
Orthologs for CDY1B gene from 8/23 species (see all 23) About this table
ENSEMBL Gene Tree for CDY1B (if available)
TreeFam Gene Tree for CDY1B (if available) |
Paralogs
for CDY1B gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for CDY1B gene
- CDY11 2 CDY2A1 2 CDY2B1 2 ECI22 CDYL2 CDYL22
6 SIMAP similar genes for CDY1B using alignment to 1 protein entry: CDY1_HUMAN:CDY2A CDY2B CDYL CDYL2 CBX5 ECI2
CDY1B for paralogs About GeneDecksing
|
Genomic Variants
for CDY1B gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, 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
|
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 5 variations for CDY1B
5 CNVs: 38828 38830 4185 33193 2291 | SABiosciences Cancer Mutation PCR Assays |
|
Disorders
/ Diseases
for CDY1B gene
(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.)
About This Section
|
CDY1B for disorders About GeneDecksing
3  diseases for CDY1B: About MalaCardsgonadoblastoma azoospermia infertility
1 disease from the University of Copenhagen DISEASES database for CDY1B:Azoospermia Export disorders for CDY1B gene to outside databases
|
Publications
for CDY1B gene (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 CDY1B gene, integrated from 9 sources (see all 16):
(articles sorted by number of sources associating them with CDY1B) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- 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)
- Functional coherence of the human Y chromosome. (PubMed id 9381176)1, 2, 3 Lahn B.T. and Page D.C. (1997)
- 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)
- Previously uncharacterized histone acetyltransferases implicated in mammalian spermatogenesis. (PubMed id 12072557)1, 2 Lahn B.T....Page D.C. (2002)
- Crystal structures of human CDY proteins reveal a crotonase-like fold. (PubMed id 19507244)2 Wu H.... Plotnikov A.N. (2009)
- 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. (2003)
- The CDY-related gene family: coordinated evolution in copy number, expression profile and protein sequence. (PubMed id 12837688)1 Dorus S.... Lahn B.T. (2003)
- 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)
- 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)
- Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
|
External Searches for CDY1B gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
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Genome Databases showing CDY1B gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing CDY1B gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing CDY1B gene(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
|
| Name | Description |
| PharmGKB entry for CDY1B | Pharmacogenomics, SNPs, Pathways | | GeneReviews | http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CDY1 |
|
| | |
About This Section
| 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
|
Products
for CDY1B gene(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, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, 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)
About This Section
|
 | |
 | |
 |
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| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CDY1B |
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