CDY1 Gene
protein-coding GIFtS: 52
GCID: GC0YP027768
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chromodomain protein, Y-linked, 1(Previous names: chromodomain protein, Y chromosome, 1 )
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Aliases
for CDY1 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, 11 2 | | CDY2 5 | | CDY1A1 2 3 | | Testis-Specific Chromodomain Protein On Y2 | | Chromodomain Protein, Y Chromosome, 11 2 | | Testis-Specific Chromodomain Protein Y 12 | | EC 2.3.1.483 8 | | |
Export aliases for CDY1 gene to outside databasesPrevious GC identifers: GC0YP026933 GC0YM025438 GC0YM025036 GC0YP026106 GC0YP026177 GC0YM018183 |
Summaries
for CDY1 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 CDY1:
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 moretelomeric 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
Gene Wiki entry for CDY1
|
Genomic Views
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 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 CDY1 gene promoter:
GR GR-beta GR-alpha
Other transcription factors
Search SABiosciences Chromatin IP Primers for CDY1
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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: Yq11.22CDY1 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 GC0YP027768: view genomic region
(about GC identifiers)
Start:
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27,768,264 bp from pter |
End:
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27,771,049 bp from pter |
Size:
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2,786 bases |
Orientation:
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plus strand |
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Proteins
for CDY1 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 CDY1:2FBM (3D)
Secondary accessions: A2RUK1 O14600Alternative splicing: 2 isoforms: Q9Y6F8-1 Q9Y6F8-2 Explore the universe of human proteins at neXtProt for CDY1: NX_Q9Y6F8
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q9Y6F8
4/9 DME Specific Peptides for CDY1 (Q9Y6F8) (see all 9)
CDY1 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins (2 alternative transcripts):
NP_004671.1 NP_733841.1
ENSEMBL proteins: ENSP00000302968 ENSP00000354799
Human Recombinant Protein Products for CDY1:
Gene Ontology (GO): 1 cellular component term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
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| GO:0005634 | nucleus |
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CDY1 for ontologies About GeneDecksing
CDY1 Antibody Products:
Assay Products for CDY1: |
Protein
Domains /
Families
for CDY1 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
CDY1 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 CDY1 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] Genatlas biochemistry entry for CDY1:DNA binding protein with a chromatin organization modifier (chromo) domain,involved in compaction duringspermatogenesis,testis specific,CHD family,1,in a AZF deleted region
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 |
-- | -- |
CDY1 for ontologies About GeneDecksing
Animal Models:
Clone
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OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for CDY1 (see all 2)
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
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Synthesis Service for CDY1 | |  | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CDY1 |
In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CDY1 |
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Pathways & Interactions
for CDY1 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 CDY1
5/15 Interacting proteins for CDY1 (Q9Y6F83) 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 | GO ID | Qualified GO term | Evidence | PubMed IDs |
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| GO:0007283 | spermatogenesis |
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CDY1 for ontologies About GeneDecksing
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Drugs & Compounds
for CDY1 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 CDY1
2 HMDB Compounds for CDY1 About this table
Search CenterWatch for drugs/clinical trials and news about CDY1
|
Transcripts
for CDY1 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 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_0046802 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000306609(uc004fxf.3) ENST00000361963(uc004fxe.3)
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for CDY1 (see all 2)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for CDY1 (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): CDY1 (NM_004680) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for CDY1 | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CDY1 |
Additional cDNA 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: BX279566 AF080597 NM_001003895 AF000981 NM_170723 NM_001003894 NM_004680 BU569556 AA292905 BC033041 BI459455 AA401738
GeneLoc Exon Structure
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Expression
for CDY1 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
| CDY1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: ACTAGAATTG
About this image
See CDY1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for CDY1
SOURCE GeneReport for Unigene cluster: Hs.159281
UniProtKB/Swiss-Prot: CDY1_HUMAN, Q9Y6F8Tissue specificity: Testis-specific. Detected in spermatids (at protein level)
SABiosciences Custom PCR Arrays for CDY1
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for CDY1
Browse OriGene validated miRNA SYBR primer pairs
| | | Search SABiosciences RT2 qPCR
Primer Assays in human, mouse, rat CDY1 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat CDY1 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CDY1 | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CDY1 |
Orthologs
for CDY1 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 CDY1 gene from 8/23 species (see all 23) About this table
ENSEMBL Gene Tree for CDY1 (if available)
TreeFam Gene Tree for CDY1 (if available) |
Paralogs
for CDY1 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for CDY1 gene
- CDY1B1 2 CDY2A1 2 CDY2B1 2 ECI22 CDYL2 CDYL22
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
5/17 Pseudogenes.org Pseudogenes for CDY1 (see all 17)
PGOHUM00000233699 PGOHUM00000233765 PGOHUM00000233770 PGOHUM00000233814 PGOHUM00000233832
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Genomic Variants
for CDY1 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 CDY1
5 CNVs: 38828 38830 4185 33193 2291 | SABiosciences Cancer Mutation PCR Assays |
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Disorders
/ Diseases
for CDY1 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
|
CDY1 for disorders About GeneDecksing
OMIM gene information: 400016
OMIM disorders: --
4  diseases for CDY1: About MalaCardsy chromosome infertility gonadoblastoma infertility azoospermia
2 diseases from the University of Copenhagen DISEASES database for CDY1:Azoospermia Gonadoblastoma GeneTests: CDY1
Y Chromosome Infertility
Human Genome Epidemiology (HuGE) Navigator: CDY1 (4 documents)
Export disorders for CDY1 gene to outside databases
|
Publications
for CDY1 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 CDY1 gene, integrated from 9 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 |
- Functional coherence of the human Y chromosome. (PubMed id 9381176)1, 2, 3 Lahn B.T. and Page D.C. (1997)
- Previously uncharacterized histone acetyltransferases implicated in mammalian spermatogenesis. (PubMed id 12072557)1, 2 Lahn B.T....Page D.C. (2002)
- 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. (1999)
- CDY1 and BOULE transcripts assessed in the same biops y as predictive markers for successful testicular sperm retrieval. (PubMed id 21474125)1 Kleiman S.E....Yogev L. (2011)
- Features of constitutive gr/gr deletion in a Japanese population. (PubMed id 20663794)1 Sin H.S....Namiki M. (2010)
- Crystal structures of human CDY proteins reveal a crotonase-like fold. (PubMed id 19507244)2 Wu H.... Plotnikov A.N. (2009)
- Differential effect of specific gr/gr deletion subtyp es on spermatogenesis in the Chinese Han population. (PubMed id 20039973)1 Yang Y....Zhang S. (2009)
- Do we need to search for gr/gr deletions in infertile men in a clinical setting? (PubMed id 18326516)1 Stouffs K....Lissens W. (2008)
- Partial AZFc deletions and duplications: clinical correlates in the Italian population. (PubMed id 18807255)1 Giachini C....Krausz C. (2008)
- The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
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External Searches for CDY1 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
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Genome Databases showing CDY1 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing CDY1 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing CDY1 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 CDY1 | Pharmacogenomics, SNPs, Pathways | | GeneReviews | http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CDY1 |
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About This Section
| 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
|
Products
for CDY1 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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| | | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat CDY1 | | | Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing CDY1 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CDY1 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat CDY1 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CDY1 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat CDY1 |
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 | | | CDY1 Proteins, Antibodies, CLIAs, and ELISAs |
| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CDY1 |
|  |  |  |  | | | | Search ThermoFisher Antibodies for CDY1 |
| | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CDY1 |
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