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

CDH9 Gene

protein-coding   GIFtS: 59
GCID: GC05M026916

cadherin 9, type 2 (T1-cadherin)

 Explore 2 diseases affiliated with
CDH9 via our new
 Human Malady Compendium 
Biological research products
for CDH9
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Cadherin 9, Type 2 (T1-Cadherin)1 2
T1-Cadherin1
Cadherin-91

External Ids:    HGNC: 17681   Entrez Gene: 10072   Ensembl: ENSG000001131007   OMIM: 6099745   UniProtKB: Q9ULB43   

Export aliases for CDH9 gene to outside databases

Previous GC identifers: GC05M026567 GC05M027314 GC05M026880 GC05M026926


(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 CDH9:
This gene encodes a type II classical cadherin from the cadherin superfamily, integral membrane proteins that mediate
calcium-dependent cell-cell adhesion. Mature cadherin proteins are composed of a large N-terminal extracellular
domain, a single membrane-spanning domain, and a small, highly conserved C-terminal cytoplasmic domain. The
extracellular domain consists of 5 subdomains, each containing a cadherin motif, and appears to determine the
specificity of the protein's homophilic cell adhesion activity. Type II (atypical) cadherins are defined based on
their lack of a HAV cell adhesion recognition sequence specific to type I cadherins. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: CADH9_HUMAN, Q9ULB4
Function: Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a
homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types

Gene Wiki entry for CDH9


(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_000005.9  NC_018916.1  NT_006576.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CDH9 gene promoter:
         HFH-3   LHX3b/Lhx3b   FOXF2   CUTL1   C/EBPalpha   POU2F1   POU2F1a   FOXJ2 (long isoform)   LHX3a/Lhx3a   FOXJ2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCDH9 promoter sequence
   Search SABiosciences Chromatin IP Primers for CDH9

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CDH9


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

Entrez Gene cytogenetic band: 5p14   Ensembl cytogenetic band:  5p14.1   HGNC cytogenetic band: 5p14

CDH9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CDH9 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05M026916:  view genomic region     (about GC identifiers)

Start:
26,880,709 bp from pter      End:
27,121,257 bp from pter
Size:
240,549 bases      Orientation:
minus strand

(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: CADH9_HUMAN, Q9ULB4 (See protein sequence)
Recommended Name: Cadherin-9 precursor  
Size: 789 amino acids; 88689 Da
Subcellular location: Cell membrane; Single-pass type I membrane protein (Potential)
Secondary accessions: Q3B7I5

Explore the universe of human proteins at neXtProt for CDH9: NX_Q9ULB4

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9ULB4

  • CDH9 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_057363.3  
    ENSEMBL proteins: 
     ENSP00000231021   ENSP00000426239   ENSP00000422538  
    Reactome Protein details: Q9ULB4
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    Uscn Proteins for CDH9

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane TAS--
    GO:0016021integral to membrane NAS--


    CDH9 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    CDH9 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR000233 Cadherin_cytoplasmic-dom
     IPR015919 Cadherin-like
     IPR020894 Cadherin_CS
     IPR002126 Cadherin

    Graphical View of Domain Structure for InterPro Entry Q9ULB4

    ProtoNet protein and cluster: Q9ULB4

    2 Blocks protein families:
    IPB000233 Cadherin cytoplasmic region
    IPB002126 Cadherin


    UniProtKB/Swiss-Prot: CADH9_HUMAN, Q9ULB4
    Domain: Three calcium ions are usually bound at the interface of each cadherin domain and rigidify the connections,
    imparting a strong curvature to the full-length ectodomain (By similarity)
    Similarity: Contains 5 cadherin domains


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: CADH9_HUMAN, Q9ULB4
    Function: Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a
    homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types

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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0005509calcium ion binding IEA--


    CDH9 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for CDH9:
     Increased homologous recombina 


    (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

    Unified GeneCards pathways - 5/7 super-pathways (see all 7About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Cell-cell junction organization
    Cell-cell junction organization1.00
    Adherens junctions interactions0.51
    Cell junction organization0.69
    Cell-Cell communication0.45
    2Rho Family GTPases
    Rho Family GTPases1.00
    ILK Signaling0.45
    3WNT Signaling
    WNT Signaling1.00
    4S-1P Stimulated Signaling
    S-1P Stimulated Signaling1.00
    5Presenilin-Mediated Signaling
    Presenilin-Mediated Signaling1.00

    Pathway sources
    See GeneCards unified pathways
    Show all pathways

    5/7 Downloadable PowerPoint Slides of QIAGEN Pathway Central Maps for CDH9 (see all 7)
        S-1P Stimulated Signaling
    ILK Signaling
    GSK3 Signaling
    G12-G13 in Cellular Signaling
    Presenilin-Mediated Signaling

    4        Reactome Pathways for CDH9
        Adherens junctions interactions
    Cell junction organization
    Cell-Cell communication
    Cell-cell junction organization



    CDH9 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CDH9

    STRING Interaction Network Preview (showing 5 interactants - click image to see 18)

    5/18 Interacting proteins for CDH9 (Q9ULB43 ENSP000002310214) via UniProtKB, MINT, STRING, and/or I2D (see all 18)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CDH15P552913, ENSP000002897464I2D: score=1 STRING: ENSP00000289746
    CDH18Q136343, ENSP000002741704I2D: score=1 STRING: ENSP00000274170
    CDH10Q9Y6N83, ENSP000002644634I2D: score=1 STRING: ENSP00000264463
    CDH6P552853, ENSP000002650714I2D: score=1 STRING: ENSP00000265071
    CDH7Q9ULB53, ENSP000003191664I2D: score=1 STRING: ENSP00000319166
    About this table

    Gene Ontology (GO): 5 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007156homophilic cell adhesion NAS--
    GO:0016337cell-cell adhesion NAS10861224
    GO:0034329cell junction assembly TAS--
    GO:0034332adherens junction organization TAS--
    GO:0045216cell-cell junction organization TAS--


    CDH9 for ontologies           About GeneDecksing



    (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 Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for CDH9

    1 HMDB Compound for CDH9    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--
    Search CenterWatch for drugs/clinical trials and news about CDH9 / CADH9 

    (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,
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    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 CDH9 gene: 
    NM_016279.3  

    Unigene Cluster for CDH9:

    Cadherin 9, type 2 (T1-cadherin)
    Hs.272212  [show with all ESTs]
    Unigene Representative Sequence: NM_016279
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000231021(uc003jgs.1) ENST00000505020(uc011cnv.1) ENST00000505045(uc010iug.3)
    ENST00000513289 ENST00000511822

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    Additional cDNA sequence: 

    AB035302.1 AK294183.1 AK307779.1 AK308697.1 BC107594.1 BC109384.1 BC113745.1 

    3 DOTS entries:

    DT.92037336  DT.100644350  DT.120863625 

    6 AceView cDNA sequences:

    NM_016279 AB035302 BE465213 BX281047 BP349505 BP349846 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for CDH9    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13
    SP1:              -                                                                           
    SP2:                                                                                          


    ECgene alternative splicing isoforms for CDH9

    (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

    CDH9 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CAATCCTGCA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    CDH9 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    5 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    Spinal CordSpinal Ventral ColumnsVentral Spinal Cord Progenitor CellsMotor Neurons
    BrainMedulla OblongataBrain
    BrainStriatumBrain
    Neural TubeMetencephalonNeural Tube
    Spinal CordSpinal Ventral ColumnsSpinal Cord
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See CDH9 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CDH9

    SOURCE GeneReport for Unigene cluster: Hs.272212
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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)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for CDH9 gene from 3/12 species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves CDH91 cadherin 9, type 2 (T1-cadherin) 79.26(n)
    83.65(a)
      428487  XM_001231540.2  XP_001231541.2 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    --
    86(a)
    80(a)
    1 ↔ many
    1 ↔ many
    GL343195.1(2892242-2910417)
    GL343195.1(2802712-2885824)
    zebrafish
    (Danio rerio)
    Actinopterygii CABZ01067945.16
    cdh106
    (see all 3)
    cadherin 10, type 2 (T2-cadherin)
    (see all 3)
    65(a)
    62(a)
    (see all 3)
    many ↔ many
    many ↔ many
    (see all 3)
    12(41246225-41349008)
    2(28604768-28649116)


    ENSEMBL Gene Tree for CDH9 (if available)
    TreeFam Gene Tree for CDH9 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CDH9 gene
    CDH42  CDH182  DSG42  CDH32  CDH102  CDH112  CDH12  CDH62  
    DSC22  CDH82  CDH202  CDH222  DSC12  CDH192  DSG12  CDH72  
    DSG22  CDH122  CDH262  DSC32  CDH22  CDH242  CDH152  CDH52  
    DSG32  
    18 SIMAP similar genes for CDH9 using alignment to 4 protein entries:     CADH9_HUMAN (see all proteins):
    CDH6    CDH11    CDH7    CDH19    CDH18    Nbla04261
    CDH8    CDH22    CDH10    CDH20    CDH12    CDH24
    CDH2    CDH5    CDH4    CDH3    CDH1    CDH15

    CDH9 for paralogs           About GeneDecksing



    (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

    10/3006 NCBI SNPs in CDH9 are shown (see all 3006    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1423995221,2
    --26880268(+) TGTGAG/TTTCTC 1 -- ds50010--------
    rs1142742601,2
    --26880347(+) TCTCAA/GATATA 1 -- ds50011Minor allele frequency- G:0.01NA 120
    rs623463751,2
    C,F,--26880365(+) AGTTGA/GTCCAT 1 -- ds50014Minor allele frequency- G:0.19WA NA 242
    rs1828872251,2
    --26880377(+) GTAAAG/TACTTG 1 -- ds50010--------
    rs105396611,2
    C,--26880414(+) ACAAC-/TATATAT 1 -- ds50010--------
    rs64523661,2
    C,A--26880423(+) tatatA/Gtgtat 1 -- ds50010--------
    rs64523671,2
    C,A--26880425(+) tatatA/Gtatat 1 -- ds50010--------
    rs1463509331,2
    --26880465(+) CATACC/TCTATT 1 -- ds50010--------
    rs38285811,2
    C,F,H,--26880525(+) TGAAAC/TGGAAA 1 -- ds500115Minor allele frequency- T:0.09NS EA NA WA 2094
    rs1886723561,2
    --26880545(+) TTGTAC/TCAAAG 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for CDH9 (26880709 - 27121257 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for CDH9
         1 CNV: 3549

    SABiosciences Cancer Mutation PCR Assays
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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.)
    About This Section

    CDH9 for disorders           About GeneDecksing

    OMIM gene information: 609974    OMIM disorders: --

    2 diseases for CDH9:    About MalaCards
    autism spectrum disorder    anorexia nervosa

    2 diseases from the University of Copenhagen DISEASES database for CDH9:
    Benign epilepsy with centrotemporal spikes     Autistic disorder
    Human Genome Epidemiology (HuGE) Navigator: CDH9 (2 documents)

    Export disorders for CDH9 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 CDH9 gene, integrated from 9 sources (see all 16):
    (articles sorted by number of sources associating them with CDH9)
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    1. Identification of three human type-II classic cadherins and frequent heterophilic interactions between different subclasses of type-II classic cadherins. (PubMed id 10861224)1, 2, 9 Shimoyama Y.... Natori M. (2000)
    2. 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)
    3. Diversity of the cadherin family: evidence for eight new cadherins in nervous tissue. (PubMed id 2059658)1, 3 Suzuki S....Tanihara H. (1991)
    4. Cadherin-9 is a novel cell surface marker for the heterogeneous pool of renal fibroblasts. (PubMed id 17668045)1, 9 Thedieck C....Klein G. (2007)
    5. Genome-wide association study of prognosis in advanced non-small cell lung cancer patients receiving platinum-based chemotherapy. (PubMed id 22872573)1 Hu L....Shen H. (2012)
    6. Analysis of four genes involved in the neurodevelopmen t shows association of rs4307059 polymorphism in the cadherin 9/10 region with c ompleted suicide. (PubMed id 22846907)1 Chojnicka I....Pl/oski R. (2012)
    7. Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. (PubMed id 22589738)1 Fox C.S....Borecki I.B. (2012)
    8. A genome-wide association study on common SNPs and ra re CNVs in anorexia nervosa. (PubMed id 21079607)1 Wang K....Hakonarson H. (2010)
    9. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (2009)
    10. Common genetic variants on 5p14.1 associate with autism spectrum disorders. (PubMed id 19404256)1 Wang K....Hakonarson H. (2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 1007 HGNC: 1768 AceView: CDH9 Ensembl:ENSG00000113100 euGenes: HUgn1007
    ECgene: CDH9 H-InvDB: CDH9

    (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 CDH9 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CDH9 gene:
    Search GeneIP for patents involving CDH9

    GeneCards and IP:
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