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

CDY1 Gene

protein-coding   GIFtS: 52
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)
About This Section

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

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 73), 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

Browse SwitchGear Promoter luciferase reporter plasmids
   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: Yq11.22

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 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: 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 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 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9Y6F8

  • 4/9 DME Specific Peptides for CDY1 (Q9Y6F8) (see all 9)
     KALVRCN  KGLVSQVF  YLVRWKGYD  DDTWEPEQHL 

    CDY1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    CDY1 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_004671.1  NP_733841.1  

    ENSEMBL proteins: 
     ENSP00000302968   ENSP00000354799  

    Human Recombinant Protein Products for CDY1: 
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    Cloud-Clone Corp. Proteins for CDY1 

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

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

    CDY1 for ontologies           About GeneDecksing



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    Cloud-Clone Corp. CLIAs for CDY1


    (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 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,
    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: 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): 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 ----
         
    CDY1 for ontologies           About GeneDecksing


    Animal Models:
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CDY1


    (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 CDY1

    5/15 Interacting proteins for CDY1 (Q9Y6F83) via UniProtKB, MINT, STRING, and/or I2D (see all 15)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4AP628053I2D: score=1 
    HIST1H4BP628053I2D: score=1 
    HIST1H4CP628053I2D: score=1 
    HIST1H4DP628053I2D: score=1 
    HIST1H4EP628053I2D: score=1 
    About this table

    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 ----

    CDY1 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 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--

    Search CenterWatch for drugs/clinical trials and news about 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,
    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 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)
    miRNA
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    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for CDY1
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    Clone
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    GenScript: all cDNA clones in your preferred vector (see all 2): CDY1 (NM_004680)
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    Primer
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CDY1

    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_004680 BX279566 NM_170723 AF000981 NM_001003894 AF080597 NM_001003895 BI459455 
    AA292905 BU569556 BC033041 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™, 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 <intensity>2/3
    CGAP TAG: ACTAGAATTG
    CDY1 Expression
    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, Q9Y6F8
    Tissue specificity: Testis-specific. Detected in spermatids (at protein level)

        SABiosciences Custom PCR Arrays for CDY1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CDY1

    (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 CDY1 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 --
    --
    59(a)
    1 → many
    2(65668286-65773998)
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    58(a)
    1 → many
    GL343209.1(12187-102820)
    zebrafish
    (Danio rerio)
    Actinopterygii cdyl6
    chromodomain protein, Y-like
    42(a)
    1 → many
    2(24187298-24239708)
    fruit fly
    (Drosophila melanogaster)
    Insecta CG138906
    --
    25(a)
    1 → many
    3L(851346-852673)
    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 
            Species with no ortholog for CDY1

    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)
    About This Section
    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


    5/17 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) 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
         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

    SABiosciences Cancer Mutation PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing CDY1
    DNA2.0 Custom Variant and Variant Library Synthesis for CDY1

    (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: 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)
    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

    1. Functional coherence of the human Y chromosome. (PubMed id 9381176)1, 2, 3 Lahn B.T. and Page D.C. (1997)
    2. Features of constitutive gr/gr deletion in a Japanese population. (PubMed id 20663794)1, 4 Sin H.S....Namiki M. (2010)
    3. Differential effect of specific gr/gr deletion subtyp es on spermatogenesis in the Chinese Han population. (PubMed id 20039973)1, 4 Yang Y....Zhang S. (2009)
    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. (2008)
    5. Previously uncharacterized histone acetyltransferases implicated in mammalian spermatogenesis. (PubMed id 12072557)1, 2 Lahn B.T....Page D.C. (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. (1999)
    7. 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)
    8. Crystal structures of human CDY proteins reveal a crotonase-like fold. (PubMed id 19507244)2 Wu H.... Plotnikov A.N. (2009)
    9. Partial AZFc deletions and duplications: clinical correlates in the Italian population. (PubMed id 18807255)1 Giachini C....Krausz C. (2008)
    10. 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)

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

    (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 CDY1 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CDY1

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    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



    (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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     EMD Millipore Custom Antibody & Bulk Services
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     Regulatory tfbs in CDY1 promoter
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     Browse Sino Biological Proteins and Antibodies
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     Proteins for CDY1
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     inGenious Targeting Laboratory - Custom generated mouse model solutions for CDY1
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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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