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

PCDHGB6 Gene

protein-coding   GIFtS: 35
GCID: GC05P141333

Protocadherin Gamma Subfamily B, 6

  See related disease
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
Protocadherin Gamma Subfamily B, 61 2
PCDH-GAMMA-B62
Protocadherin Gamma-B62
PCDH-gamma-B63

External Ids:    HGNC: 87131   Entrez Gene: 561002   Ensembl: ENSG000002533057   OMIM: 6063035   UniProtKB: Q9Y5F93   

Export aliases for PCDHGB6 gene to outside databases

Previous GC identifers: GC05P140589 GC05P141314 GC05P140714 GC05P140772 GC05P140793 GC05P140732 GC05P140809 GC05P140830 GC05P140847 GC05P140872 GC05P140879 GC05P140899 GC05P140933 GC05P140955 GC05P140976 GC05P141000 GC05P141027 GC05P141046 GC05P141073 GC05P135932 GC05P141111 GC05P141153 GC05P141170 GC05P141206 GC05P141246


(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 PCDHGB6 Gene:
This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on
chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism
may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3
subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more
distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed
by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes
the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region
exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a
critical role in the establishment and function of specific cell-cell connections in the brain. Alternative
splicing has been described for the gamma cluster genes. (provided by RefSeq, Jul 2008)

GeneCards Summary for PCDHGB6 Gene: 
PCDHGB6 (protocadherin gamma subfamily B, 6) is a protein-coding gene. Diseases associated with PCDHGB6 include neuronitis. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDH7.

UniProtKB/Swiss-Prot: PCDGI_HUMAN, Q9Y5F9
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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PCDHGB6 gene promoter:
         p300   FOXD3   Nkx2-5   c-Ets-1   Max   CREB   Egr-2   COMP1   deltaCREB   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for PCDHGB6

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDHGB6


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

PCDHGB6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHGB6 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P141333:  view genomic region     (about GC identifiers)

Start:
140,787,770 bp from pter      End:
140,892,546 bp from pter
Size:
104,777 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: PCDGI_HUMAN, Q9Y5F9 (See protein sequence)
Recommended Name: Protocadherin gamma-B6 precursor  
Size: 930 amino acids; 101043 Da
Subcellular location: Cell membrane; Single-pass type I membrane protein (By similarity)
Secondary accessions: Q9Y5C5
Alternative splicing: 2 isoforms:  Q9Y5F9-1   Q9Y5F9-2   

Explore the universe of human proteins at neXtProt for PCDHGB6: NX_Q9Y5F9

Explore proteomics data for PCDHGB6 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9Y5F9

  • PCDHGB6 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    PCDHGB6 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_061749.1  NP_115271.1  

    ENSEMBL proteins: 
     ENSP00000428603  

    Human Recombinant Protein Products for PCDHGB6: 
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    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

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

    PCDHGB6 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    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 Q9Y5F9

    ProtoNet protein and cluster: Q9Y5F9

    UniProtKB/Swiss-Prot: PCDGI_HUMAN, Q9Y5F9
    Similarity: Contains 6 cadherin domains


    PCDHGB6 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: PCDGI_HUMAN, Q9Y5F9
    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 (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--
         
    PCDHGB6 for ontologies           About GeneDecksing


    Animal Models:
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    (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 PCDHGB6

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

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

    PCDHGB6 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 PCDHGB6 (PCDGI)

    1 HMDB Compound for PCDHGB6    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--

    Search CenterWatch for drugs/clinical trials and news about PCDHGB6 / PCDGI

    (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 PCDHGB6 gene (2 alternative transcripts): 
    NM_018926.2  NM_032100.1  

    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000520790(uc003lkj.2)
    miRNA
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    hsa-miR-1226 hsa-miR-448 hsa-miR-4272 hsa-miR-765 hsa-miR-624* hsa-miR-650 hsa-miR-3150a-3p hsa-miR-548a-3p
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    Inhib. RNA
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    24/737 AceView cDNA sequences (see all 737):

    NM_018920 AF152339 NM_018926 AF152338 AF152510 CF126043 AF152335 CA449241 
    AF152321 AF152511 T05153 BF924785 AF152330 AF152323 BU145848 CB305621 
    BX346373 NM_032406 BM664891 BU155361 BQ055812 AA999664 AF152324 BQ318895 

    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

    PCDHGB6 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    PCDHGB6 Expression
    About this image


    See PCDHGB6 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PCDHGB6
        SABiosciences Custom PCR Arrays for PCDHGB6
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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHGB6

    (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 PCDHGB6 gene from 3/8 species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pcdhgb61 , 5 protocadherin gamma subfamily B, 61, 5 82.37(n)1
    83.23(a)1
      18 (19.61 cM)5
    937031  NM_033578.31  NP_291056.11 
     377420945 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    (see all 25)
    --
    53(a)
    52(a)
    (see all 25)
    many ↔ many
    many ↔ many
    (see all 25)
    4(76789872-76792178)
    AAWZ02040178(21-2546)
    zebrafish
    (Danio rerio)
    Actinopterygii pcdh1g96
    zgc:1937516
    (see all 24)
    zgc:193751
    (see all 24)
    43(a)
    43(a)
    (see all 24)
    many ↔ many
    many ↔ many
    (see all 24)
    10(21767295-21770275)
    14(2919875-2922280)


    ENSEMBL Gene Tree for PCDHGB6 (if available)
    TreeFam Gene Tree for PCDHGB6 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PCDHGB6 gene
    PCDH72  PCDH202  PCDH12  PCDHA122  PCDH11Y2  PCDH122  PCDHA112  PCDHA12  
    PCDH182  PCDH92  PCDH192  PCDH82  PCDH172  PCDHGB32  PCDHA72  PCDH11X2  
    PCDHA62  PCDH102  PCDHA102  PCDHA132  PCDHA92  PCDHA32  PCDHA42  
    18/60 SIMAP similar genes for PCDHGB6 using alignment to 1 protein entry:     PCDGI_HUMAN(see all similar genes):
    PCDHGB7    PCDHGB5    PCDHGB4    PCDHGB2    PCDHGB1    PCDHGB3
    PCDHGA11    PCDHGA12    PCDHGA1    PCDHGA5    PCDHGA6    PCDHGA9
    PCDHGA10    PCDHGA2    PCDHGA3    PCDHGA4    PCDHGA8    PCDHB17

    PCDHGB6 for paralogs           About GeneDecksing



    (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

    3 SNPs in PCDHGB6 are shown    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0485724
    ----see VAR_0485722 S A mis40--------
    VAR_0218834
    ----see VAR_0218832 P S mis40--------
    VAR_0218844
    ----see VAR_0218842 A T mis40--------

    HapMap Linkage Disequilibrium report for PCDHGB6 (140787770 - 140892546 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/11 variations for PCDHGB6 (see all 11):    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2730847CNV Deletion23290073
    nsv462470CNV Loss19166990
    nsv327707CNV Loss16902084
    dgv6351n71CNV Loss21882294
    nsv882990CNV Loss21882294
    dgv6352n71CNV Loss21882294
    nsv518799CNV Loss19592680
    nsv519627CNV Loss19592680
    esv25744CNV Gain19812545
    nsv882987CNV Gain21882294

    SABiosciences Cancer Mutation PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing PCDHGB6
    DNA2.0 Custom Variant and Variant Library Synthesis for PCDHGB6

    (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: 606303    OMIM disorders: --

    2 diseases for PCDHGB6:    About MalaCards
    neuronitis    


    PCDHGB6 for disorders           About GeneDecksing

    Genetic Association Database (GAD): PCDHGB6

    Export disorders for PCDHGB6 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 PCDHGB6 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with PCDHGB6)
        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. (1999)
    2. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1 Wu Q.... Maniatis T. (2001)
    3. 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. (2000)
    4. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PubMed id 10716726)1 Wu Q. and Maniatis T. (2000)
    5. Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. (PubMed id 10817752)1 Yagi T. and Takeichi M. (2000)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 56100 HGNC: 8713 AceView: PCDHGC3 Ensembl:ENSG00000253305 euGenes: HUgn56100
    ECgene: PCDHGB6 H-InvDB: PCDHGB6

    (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 PCDHGB6 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 PCDHGB6 gene:
    Search GeneIP for patents involving PCDHGB6

    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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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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