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PCDHB8 Gene

protein-coding   GIFtS: 41
GCID: GC05P140557

Protocadherin Beta 8

  Search for PCDHB8
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Protocadherin Beta 81 2     Protocadherin Beta-82
PCDH-beta-82 3     protocadherin-3i2
PCDH3I2 3     Protocadherin-3I3
PCDH-BETA82     

External Ids:    HGNC: 86931   Entrez Gene: 561282   Ensembl: ENSG000001203227   OMIM: 6063345   UniProtKB: Q9UN663   

Export aliases for PCDHB8 gene to outside databases

Previous GC identifers: GC05P140373 GC05P141140 GC05P140541 GC05P140585 GC05P140537 GC05P135702


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for PCDHB8 Gene:
This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked
on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and
T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6
extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The
extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the
alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common
3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins.
Their specific functions are unknown but they most likely play a critical role in the establishment and function
of specific cell-cell neural connections. (provided by RefSeq, Jul 2008)

GeneCards Summary for PCDHB8 Gene:
PCDHB8 (protocadherin beta 8) is a protein-coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHB16.

UniProtKB/Swiss-Prot: PCDB8_HUMAN, Q9UN66
Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance
of specific neuronal connections in the brain




(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000005.9  NC_018916.2  NT_029289.12  
Regulatory elements:
   Regulatory transcription factor binding sites in the PCDHB8 gene promoter:
         AhR   Egr-1   LCR-F1   Arnt   AREB6   PPAR-alpha   POU2F1   POU2F1a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPCDHB8 promoter sequence
   Search Chromatin IP Primers for PCDHB8

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PCDHB8


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

Entrez Gene cytogenetic band: 5q31   Ensembl cytogenetic band:  5q31.3   HGNC cytogenetic band: 5q31

PCDHB8 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHB8 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P140557:  view genomic region     (about GC identifiers)

Start:
140,557,371 bp from pter      End:
140,560,081 bp from pter
Size:
2,711 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: PCDB8_HUMAN, Q9UN66 (See protein sequence)
Recommended Name: Protocadherin beta-8 precursor  
Size: 801 amino acids; 87639 Da
Secondary accessions: B9EGV1

Explore the universe of human proteins at neXtProt for PCDHB8: NX_Q9UN66

Explore proteomics data for PCDHB8 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn419, Asn437, Asn568

  • See PCDHB8 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_061993.2  
    ENSEMBL proteins: 
     ENSP00000239444  

    PCDHB8 Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    PCDHC: Cadherins / Protocadherins : Clustered

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

    Graphical View of Domain Structure for InterPro Entry Q9UN66

    ProtoNet protein and cluster: Q9UN66

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCDB8_HUMAN, Q9UN66
    Similarity: Contains 6 cadherin domains


    Find genes that share domains with PCDHB8           About GenesLikeMe


    (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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PCDB8_HUMAN, Q9UN66
    Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance
    of specific neuronal connections in the brain

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--
         
    Find genes that share ontologies with PCDHB8           About GenesLikeMe


    Phenotypes:
         1 MGI phenotypic allele for Pcdhb16 (no phenotypes)

    Find genes that share phenotypes with PCDHB8           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Pcdhb16tm1Lex for PCDHB8

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for PCDHB8
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    miRNA
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    hsa-mir-181a-5p (MIRT025076), hsa-mir-26b-5p (MIRT028811)

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    PCDB8_HUMAN, Q9UN66: Cell membrane; Single-pass type I membrane protein (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane IEA--
    GO:0016020membrane ----
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with PCDHB8           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PCDHB8
    Interactions:

        Search GeneGlobe Interaction Network for PCDHB8

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007156homophilic cell adhesion IEA--

    Find genes that share ontologies with PCDHB8           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for PCDHB8 (PCDB8)

    1 HMDB Compound for PCDHB8    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--



    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for PCDHB8 gene: 
    NM_019120.3  

    Unigene Cluster for PCDHB8:

    Protocadherin beta 8
    Hs.287793  [show with all ESTs]
    Unigene Representative Sequence: NM_019120
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000239444(uc011dai.2)
    miRNA
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      QuantiTect SYBR Green Assays in human, mouse, rat PCDHB8
      QuantiFast Probe-based Assays in human, mouse, rat PCDHB8

    Additional mRNA sequence: 

    AF152501.2 BC136801.1 

    3 DOTS entries:

    DT.91762334  DT.95210419  DT.97834597 

    3 AceView cDNA sequences:

    NM_019120 AF152501 AW675244 

    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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    PCDHB8 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    PCDHB8 Expression
    About this image

    PCDHB8 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PCDHB8 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.287793
        Custom PCR Arrays for PCDHB8
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHB8

    (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)
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    This gene was present in the common ancestor of human and mouse.

    Orthologs for PCDHB8 gene from Selected species (see all 6)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pcdhb161 , 5 protocadherin beta 161, 5 79.61(n)1
    75.03(a)1
      18 (19.50 cM)5
    938871  NM_053141.31  NP_444371.31 
     374777685 


    ENSEMBL Gene Tree for PCDHB8 (if available)
    TreeFam Gene Tree for PCDHB8 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PCDHB8 gene
    PCDHB162  PCDHB22  PCDHAC22  PCDHB72  PCDHB152  PCDHGA102  PCDHGA122  PCDHGB22  
    PCDHGA92  PCDHGA82  PCDHGB32  PCDHGB62  PCDHGA52  PCDHB52  PCDHB132  PCDHGA42  
    PCDHGA72  PCDHB42  PCDHB112  ENSG000002556222  PCDHB142  PCDHB122  PCDHGB12  PCDHGB42  
    PCDHGA22  PCDHGA62  PCDHB32  PCDHGA112  PCDHB62  PCDHGC42  PCDHGC52  PCDHGA12  
    PCDHB102  PCDHB12  PCDHGB72  PCDHGA32  
    Selected SIMAP similar genes for PCDHB8 using alignment to 1 protein entry:     PCDB8_HUMAN(see all similar genes):
    PCDHB13    PCDHB11    PCDHB15    PCDHB16    PCDHB3    PCDHB14
    PCDHB6    DKFZp586I1919    PCDHB17    PCDHB18    PCDHB2    PCDHB4
    PCDHB10    PCDHB5    PCDHB9    PCDHB12    PCDHB7    PCDHB1

    Find genes that share paralogs with PCDHB8           About GenesLikeMe



    (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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for PCDHB8 (see all 108)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1838265371,2
    --140556559(+) ATTGCA/TGGTTA 1 -- us2k10--------
    rs1866001431,2
    --140556618(+) CTTTTG/TAAAAT 1 -- us2k10--------
    rs1382449531,2
    --140556733(+) CCAGCC/TTTTCC 1 -- us2k10--------
    rs1412902501,2
    --140556739(+) TTTCCC/TTGTTT 1 -- us2k10--------
    rs791438601,2
    F--140556799(+) TACTAT/GTCTAC 1 -- us2k11Minor allele frequency- G:0.03WA 118
    rs1925803181,2
    --140556988(+) TATTAC/TTATCC 1 -- us2k10--------
    rs1495124291,2
    C--140557076(+) GGTTCA/G/TTGGAA 1 -- us2k10--------
    rs170969501,2
    C,F,H--140557122(+) ACTACT/AATTAT 1 -- us2k111Minor allele frequency- A:0.13NA NS EA WA 770
    rs18120541,2
    C,F,O--140557254(-) ATCGCC/TGGACG 1 -- us2k12Minor allele frequency- T:0.00MN NA 186
    rs20171241,2
    C,F,O,A,H--140557337(-) TGTGGG/AATGAT 1 -- us2k116Minor allele frequency- A:0.09NS MN NA EA CSA WA 972

    HapMap Linkage Disequilibrium report for PCDHB8 (140557371 - 140560081 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for PCDHB8 (see all 21):    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv1005e201CNV Deletion23290073
    esv2664767CNV Deletion23128226
    esv2730842CNV Deletion23290073
    nsv471439CNV Duplication19718026
    nsv509092CNV Insertion20534489
    nsv5031CNV Insertion18451855
    dgv6349n71CNV Loss21882294
    dgv6348n71CNV Loss21882294
    nsv428127CNV Loss18775914
    dgv6350n71CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing PCDHB8
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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.)
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    OMIM gene information: 606334    OMIM disorders: --


    Find genes that share disorders with PCDHB8           About GenesLikeMe


    Export disorders for PCDHB8 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 PCDHB8 gene, integrated from 10 sources (see all 11):
    (articles sorted by number of sources associating them with PCDHB8)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A striking organization of a large family of human neural cadherin- like cell adhesion genes. (PubMed id 10380929)1, 2, 3 Wu Q. and Maniatis T. (Cell 1999)
    2. The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number. (PubMed id 11322959)1, 2 Vanhalst K.... van Roy F. (FEBS Lett. 2001)
    3. A whole genome screen for HIV restriction factors. (PubMed id 22082156)1 Liu L....McKnight A. (Retrovirology 2011)
    4. Hsp90 cochaperone Aha1 downregulation rescues misfolding of CFTR in cystic fibrosis. (PubMed id 17110338)1 Wang X....Balch W.E. (Cell 2006)
    5. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
    6. 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. (Genome Res. 2004)
    7. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    8. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1 Wu Q.... Maniatis T. (Genome Res. 2001)
    9. Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members. (PubMed id 10835267)1 Nollet F....van Roy F. (J. Mol. Biol. 2000)
    10. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PubMed id 10716726)1 Wu Q. and Maniatis T. (Proc. Natl. Acad. Sci. U.S.A. 2000)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    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)
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    Entrez Gene: 56128 HGNC: 8693 AceView: PCDHB8 Ensembl:ENSG00000120322 euGenes: HUgn56128
    ECgene: PCDHB8 H-InvDB: PCDHB8

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for PCDHB8 Pharmacogenomics, SNPs, Pathways

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

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    Patent Information for PCDHB8 gene:
    Search GeneIP for patents involving PCDHB8

    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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

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      eBioscience FlowRNA Probe Sets
           
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