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

PCDH8 Gene

protein-coding   GIFtS: 54
GCID: GC13M053418

protocadherin 8

 Explore 7 diseases affiliated with
PCDH8 via our new
 Human Malady Compendium 
Biological research products
for PCDH8
    

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

Aliases
Protocadherin 81 2
ARCADLIN1 2
PAPC1 2
Protocadherin-81
Arcadlin3

External Ids:    HGNC: 86601   Entrez Gene: 51002   Ensembl: ENSG000001360997   OMIM: 6035805   UniProtKB: O952063   

Export aliases for PCDH8 gene to outside databases

Previous GC identifers: GC13M051385 GC13M047413 GC13M052354 GC13M051216 GC13M052316 GC13M034132


(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 PCDH8:
This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The gene encodes an
integral membrane protein that is thought to function in cell adhesion in a CNS-specific manner. Unlike classical
cadherins, which are generally encoded by 15-17 exons, this gene includes only 3 exons. Notable is the large first
exon encoding the extracellular region, including 6 cadherin domains and a transmembrane region. Alternative splicing
yields isoforms with unique cytoplasmic tails. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: PCDH8_HUMAN, O95206
Function: Calcium-dependent cell-adhesion protein (By similarity). May play a role in activity-induced synaptic
reorganization underlying long term memory (By similarity). Could be involved in CDH2 internalization through
TAOK2/p38 MAPK pathway. In hippocampal neurons, may play a role in the down-regulation of dendritic spines, maybe
through its action on CDH2 endocytosis (By similarity)

Gene Wiki entry for PCDH8


(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_000013.10  NC_018924.1  NT_024524.14  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PCDH8 gene promoter:
         AP-1   ATF-2   NRSF form 1   Sox9   NRSF form 2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPCDH8 promoter sequence
   Search SABiosciences Chromatin IP Primers for PCDH8

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDH8


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

Entrez Gene cytogenetic band: 13q21.1   Ensembl cytogenetic band:  13q14.3   HGNC cytogenetic band: 13q21.1

PCDH8 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDH8 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13M053418:  view genomic region     (about GC identifiers)

Start:
53,418,109 bp from pter      End:
53,422,775 bp from pter
Size:
4,667 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: PCDH8_HUMAN, O95206 (See protein sequence)
Recommended Name: Protocadherin-8 precursor  
Size: 1070 amino acids; 113019 Da
Subunit: The N-terminal extracellular domain forms homophilic interactions; these interactions activate p38 MAPK via
TAOK2 and trigger endocytosis (By similarity). Interacts with CDH2; this interaction may lead to CDH2
cointernalization (By similarity). Interacts with CDH11 (By similarity). Interacts with TAOK2 (By similarity)
Subcellular location: Cell membrane; Single-pass type I membrane protein (By similarity). Cell projection, dendrite (By
similarity). Cell junction, synapse, presynaptic cell membrane. Cell junction, synapse, postsynaptic cell membrane.
Note=Also expressed in neuronal cell bodies (By similarity). Localized to excitatory, but not with inhibitory,
synapses (By similarity)
Secondary accessions: B4DMV7 Q5TAN1 Q5TAN2 Q8IYE9 Q96SF1
Alternative splicing: 3 isoforms:  O95206-1   O95206-2   O95206-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for PCDH8: NX_O95206

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_O95206

  • PCDH8 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_002581.2  NP_116567.1  

    ENSEMBL proteins: 
     ENSP00000367177   ENSP00000341350  

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    Uscn Proteins for PCDH8

    Gene Ontology (GO): 5/6 cellular component terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane TAS9787079
    GO:0005887integral to plasma membrane TAS9787079
    GO:0030054cell junction IEA--
    GO:0030425dendrite IEA--
    GO:0042734presynaptic membrane IEA--


    PCDH8 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

    PCDH8 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR015919 Cadherin-like
     IPR013164 Cadherin_N
     IPR020894 Cadherin_CS
     IPR002126 Cadherin

    Graphical View of Domain Structure for InterPro Entry O95206

    ProtoNet protein and cluster: O95206

    UniProtKB/Swiss-Prot: PCDH8_HUMAN, O95206
    Similarity: Contains 6 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: PCDH8_HUMAN, O95206
    Function: Calcium-dependent cell-adhesion protein (By similarity). May play a role in activity-induced synaptic
    reorganization underlying long term memory (By similarity). Could be involved in CDH2 internalization through
    TAOK2/p38 MAPK pathway. In hippocampal neurons, may play a role in the down-regulation of dendritic spines, maybe
    through its action on CDH2 endocytosis (By similarity)

         Genatlas biochemistry entry for PCDH8:
    BH protocadherin 8,cadherin-related neuronal receptor,predominantly expressed in brain,localizing to synaptic junctions
    and putatively involved in specific neuronal connections and signal transduction,cadherin superfamily of calcium
    dependent cell-cell adhesion glycoproteins

    miRNA
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--


    PCDH8 for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-out Pcdh8tm1Emdr for PCDH8
         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Pcdh8):
     normal 

    PCDH8 for phenotypes           About GeneDecksing


    (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 PCDH8

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    2 Interacting proteins for PCDH8 (O952062, 3 ENSP000003671774) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    BTRCQ9Y2972, 3, ENSP000003592064MINT-8249729 I2D: score=2 STRING: ENSP00000359206
    UBQLN4Q9NRR52, 3, ENSP000003572924MINT-2861586 I2D: score=3 STRING: ENSP00000357292
    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:0001756somitogenesis IEA--
    GO:0007156homophilic cell adhesion IEA--
    GO:0007267cell-cell signaling TAS9787079
    GO:0007268synaptic transmission IEA--
    GO:0016331morphogenesis of embryonic epithelium IEA--


    PCDH8 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
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    Browse Tocris compounds for PCDH8

    1 HMDB Compound for PCDH8    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--
    Search CenterWatch for drugs/clinical trials and news about PCDH8 

    (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, 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 PCDH8 gene (2 alternative transcripts): 
    NM_002590.3  NM_032949.2  

    Unigene Cluster for PCDH8:

    Protocadherin 8
    Hs.19492  [show with all ESTs]
    Unigene Representative Sequence: NM_002590
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000377942(uc001vhi.3 uc001vhj.3) ENST00000338862

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    hsa-miR-323-3p hsa-miR-448 hsa-miR-300 hsa-miR-429 hsa-miR-1271 hsa-let-7a-2* hsa-miR-371-5p hsa-miR-410
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    Additional cDNA sequence: 

    AF061573.2 AK293747.1 AY013873.1 BC036025.1 

    2 DOTS entries:

    DT.305773  DT.95159950 

    16 AceView cDNA sequences:

    AY013873 NM_002590 CA397561 BC036025 AF061573 NM_032949 BI755978 BI546620 
    BI457955 BI550551 BI553836 R05468 BI669686 AA780138 H29216 AW135620 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for PCDH8    About this scheme

    ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3a · 3b · 3c
    SP1:                    -                           
    SP2:              -     -                           
    SP3:                                                


    ECgene alternative splicing isoforms for PCDH8

    (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

    PCDH8 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TGTTTGAAGA

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

    About this image

    PCDH8 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)
    LimbZeugopodMesenchymal Condensate CellsBone, Cartilage
    LimbZeugopodPrechondrocytic Mesenchymal CellsBone, Cartilage
    BrainBlood Brain BarrierEndothelial CellsBlood Brain Barrier, Endothelium
    EyeInner Nuclear LayernGnG Amacrine CellsAmacrine, Retina
    Yolk SacDefinitive Yolk SacDefinitive Hematopoietic Stem CellsBlood
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See PCDH8 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PCDH8

    SOURCE GeneReport for Unigene cluster: Hs.19492
        SABiosciences Expression via Pathway-Focused PCR Arrays including PCDH8: 
              Notch Signaling Targets in human mouse rat
              Synaptic Plasticity in human mouse rat

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    In Situ
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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 animals.

    Orthologs for PCDH8 gene from 4/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves PCDH81 protocadherin 8 71.72(n)
    68.69(a)
      428065  NM_001098609.1  NP_001092079.1 
    African clawed frog
    (Xenopus laevis)
    Amphibia MGC525532 similar to protocadherin 18 70.56(n)    BC047955.1 
    zebrafish
    (Danio rerio)
    Actinopterygii pcdh82 protocadherin 8 74.27(n)   30456  AF042191.1 
    worm
    (Caenorhabditis elegans)
    Secernentea cdh-106
    CaDHerin family member (cdh-10)
    7(a)
    1 → many
    IV(2436514-2463368)


    ENSEMBL Gene Tree for PCDH8 (if available)
    TreeFam Gene Tree for PCDH8 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PCDH8 gene
    PCDH172  PCDH72  PCDH11X2  PCDH202  PCDH12  PCDH102  PCDH11Y2  PCDH122  
    PCDH182  PCDH92  PCDH192  
    18/38 SIMAP similar genes for PCDH8 using alignment to 1 protein entry:     PCDH8_HUMAN(see all similar genes):
    PCDHGA3    PCDH10    PCDH12    PCDHB17    PCDHB7    PCDHGA12
    PCDHAC2    PCDHA10    PCDHA8    PCDHAC1    PCDHB16    PCDHB3
    PCDH18    PCDHA3    PCDHGC4    PCDH17    PCDHA5    PCDHA7

    PCDH8 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for PCDH8
    PGOHUM00000248601


    (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

    10/130 NCBI SNPs in PCDH8 are shown (see all 130    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1999062931,2
    Cother53418722(+) TTCTTC/TGGGGA 4 P syn11Minor allele frequency- T:0.00EU 1321
    rs1856704971,2
    --53417629(+) ACAGAA/CTGTAG 2 -- ds50010--------
    rs1916173941,2
    --53417631(+) AGAATA/GTAGTG 2 -- ds50010--------
    rs1473053751,2
    --53417752(+) GAGGAA/GGAGGT 2 -- ds50010--------
    rs1170526151,2
    --53417947(+) TAATAC/ATTGGG 2 -- ds50011Minor allele frequency- A:0.01NA 120
    rs1816126051,2
    --53418158(+) GACACA/GGTTTA 2 -- ut310--------
    rs1872995351,2
    --53418379(+) AAAATA/GTAACA 2 -- ut310--------
    rs2005582901,2
    --53418656(+) TTCTCA/GGAGTG 2 -- ut310--------
    rs2000128301,2
    --53418682(+) AAGACA/GTGCAG 2 -- ut310--------
    rs796803501,2
    C,F,--53418731(+) GACAGG/ATACCT 4 /Y syn12Minor allele frequency- A:0.00WA NA 4662

    HapMap Linkage Disequilibrium report for PCDH8 (53418109 - 53422775 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for PCDH8
         1 CNV: 66444

    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

    PCDH8 for disorders           About GeneDecksing

    OMIM gene information: 603580    OMIM disorders: --

    7 diseases for PCDH8:    About MalaCards
    bacteriuria    pyelonephritis    cystitis    breast cancer
    ataxia    schizophrenia    neuronitis


    Export disorders for PCDH8 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 PCDH8 gene, integrated from 9 sources (see all 27):
    (articles sorted by number of sources associating them with PCDH8)
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    1. Characterization of two novel protocadherins (PCDH8 and PCDH9) localized on human chromosome 13 and mouse chromosome 14. (PubMed id 9787079)1, 2, 3, 9 Strehl S.... Lalande M. (1998)
    2. Screening the human protocadherin 8 (PCDH8) gene in schizophrenia. (PubMed id 12884975)1, 2, 9 Bray N.J.... Owen M.J. (2002)
    3. 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)
    4. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1, 2 Wu Q.... Maniatis T. (2001)
    5. High-resolution analysis of DNA replication domain or ganization across an R/G-band boundary. (PubMed id 9315676)1, 3 Strehl S....Lalande M. (1997)
    6. PCDH8, the human homolog of PAPC, is a candidate tumor suppressor of breast cancer. (PubMed id 18408767)1, 9 Yu J.S....Parsons R. (2008)
    7. Arcadlin is a neural activity-regulated cadherin involved in long term potentiation. (PubMed id 10383464)1, 9 Yamagata K....Worley P.F. (1999)
    8. A genome-wide association study of host genetic determ inants of the antibody response to Anthrax Vaccine Adsorbed. (PubMed id 22658931)1 Pajewski N.M....Kaslow R.A. (2012)
    9. Genome-wide association studies identify CHRNA5/3 and HTR4 in the development of airflow obstruction. (PubMed id 22837378)1 Wilk J.B....Stricker B.H. (2012)
    10. A directed protein interaction network for investigat ing intracellular signal transduction. (PubMed id 21900206)1 Vinayagam A....Wanker E.E. (2011)

    (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: 5100 HGNC: 8660 AceView: PCDH8 Ensembl:ENSG00000136099 euGenes: HUgn5100
    ECgene: PCDH8 H-InvDB: PCDH8

    (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 PCDH8 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for PCDH8 gene:
    Search GeneIP for patents involving PCDH8

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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