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PCDHB6 Gene

protein-coding   GIFtS: 43
GCID: GC05P140529

Protocadherin Beta 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)
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Aliases
Protocadherin Beta 61 2
PCDH-beta-62 3
PCDH-BETA62
Protocadherin Beta-62

External Ids:    HGNC: 86911   Entrez Gene: 561302   Ensembl: ENSG000001132117   OMIM: 6063325   UniProtKB: Q9Y5E33   

Export aliases for PCDHB6 gene to outside databases

Previous GC identifers: GC05P140346 GC05P141112 GC05P140512 GC05P140558 GC05P140510 GC05P135674


(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 PCDHB6 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 PCDHB6 Gene:
PCDHB6 (protocadherin beta 6) is a protein-coding gene. Diseases associated with PCDHB6 include neuronitis. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHB16.

UniProtKB/Swiss-Prot: PCDB6_HUMAN, Q9Y5E3
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:
NC_000005.10  NC_018916.2  NT_029289.12  
Regulatory elements:
   Regulatory transcription factor binding sites in the PCDHB6 gene promoter:
         AhR   ATF-2   HTF   Lmo2   Nkx2-5   PPAR-alpha   Sox9   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPCDHB6 promoter sequence
   Search Chromatin IP Primers for PCDHB6

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PCDHB6


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

PCDHB6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHB6 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P140529:  view genomic region     (about GC identifiers)

Start:
140,529,683 bp from pter      End:
140,532,868 bp from pter
Size:
3,186 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, 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., 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: PCDB6_HUMAN, Q9Y5E3 (See protein sequence)
Recommended Name: Protocadherin beta-6 precursor  
Size: 794 amino acids; 87350 Da
Secondary accessions: B2R8R9

Explore the universe of human proteins at neXtProt for PCDHB6: NX_Q9Y5E3

Explore proteomics data for PCDHB6 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn46, Asn183, Asn416, Asn565
  • Modification sites at PhosphoSitePlus

  • See PCDHB6 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_061762.1  
    ENSEMBL proteins: 
     ENSP00000231136   ENSP00000438466  

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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 Q9Y5E3

    ProtoNet protein and cluster: Q9Y5E3

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCDB6_HUMAN, Q9Y5E3
    Similarity: Contains 6 cadherin domains


    PCDHB6 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,
    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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PCDB6_HUMAN, Q9Y5E3
    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--
         
    PCDHB6 for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for PCDHB6
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    hsa-miR-181c hsa-miR-181a hsa-miR-543 hsa-miR-181d hsa-miR-181b hsa-miR-4262
    SwitchGear 3'UTR luciferase reporter plasmidPCDHB6 3' UTR sequence
    Inhib. RNA
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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
    PCDB6_HUMAN, Q9Y5E3: Cell membrane; Single-pass type I membrane protein (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    extracellular2
    cytosol1
    nucleus1
    peroxisome1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane ----
    GO:0005887integral component of plasma membrane TAS10380929
    GO:0016020membrane ----
    GO:0016021integral component of membrane NAS11322959

    PCDHB6 for ontologies           About GeneDecksing


    (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 PCDHB6
    Interactions:

        Search GeneGlobe Interaction Network for PCDHB6

    Gene Ontology (GO): Selected biological process terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007155cell adhesion TAS10380929
    GO:0007156homophilic cell adhesion IEA--
    GO:0007268synaptic transmission TAS12231349
    GO:0007399nervous system development TAS10380929
    GO:0007416synapse assembly TAS12231349

    PCDHB6 for ontologies           About GeneDecksing



    (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 PCDHB6 (PCDB6)

    1 HMDB Compound for PCDHB6    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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for PCDHB6 gene: 
    NM_018939.2  

    Unigene Cluster for PCDHB6:

    Protocadherin beta 6
    Hs.283085  [show with all ESTs]
    Unigene Representative Sequence: NM_018939
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000231136(uc003lir.3) ENST00000543635
    miRNA
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    6 qRT-PCR Assays for microRNAs that regulate PCDHB6:
    hsa-miR-181c hsa-miR-181a hsa-miR-543 hsa-miR-181d hsa-miR-181b hsa-miR-4262
    SwitchGear 3'UTR luciferase reporter plasmidPCDHB6 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for PCDHB6
    Predesigned siRNA for gene silencing in human, mouse, rat PCDHB6
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      QuantiTect SYBR Green Assays in human, mouse, rat PCDHB6
      QuantiFast Probe-based Assays in human, mouse, rat PCDHB6

    Additional mRNA sequence: 

    AF152499.1 AF217752.1 AK299661.1 AK313482.1 

    1 DOTS entry:

    DT.91762325 

    Selected AceView cDNA sequences (see all 50):

    AL117449 BX116605 AF217752 AA290901 NM_015669 AF152499 AF134474 NM_018939 
    AF217753 AF152498 C02372 BV198369 AI470093 BX090111 BV198368 AU131635 
    BV198681 AA481828 AA679116 BV198370 AA283794 AI681523 BC001186 AU279941 

    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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    PCDHB6 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ATGGTCTTTT
    PCDHB6 Expression
    About this image

    PCDHB6 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PCDHB6 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.283085
        Custom PCR Arrays for PCDHB6
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHB6

    (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 PCDHB6 gene from Selected species (see all 6)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pcdhb131 , 5 protocadherin beta 131, 5 79.91(n)1
    77.81(a)1
      18 (19.49 cM)5
    938841  NM_053138.21  NP_444368.11 
     374425175 


    ENSEMBL Gene Tree for PCDHB6 (if available)
    TreeFam Gene Tree for PCDHB6 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PCDHB6 gene
    PCDHB162  PCDHB22  PCDHAC22  PCDHB72  PCDHB152  PCDHGA102  PCDHGA122  PCDHGB22  
    PCDHGA92  PCDHGA82  PCDHGB32  PCDHGB62  PCDHGA52  PCDHB52  PCDHB132  PCDHGA42  
    PCDHGA72  PCDHB42  PCDHB112  ENSG000002556222  PCDHB142  PCDHB122  PCDHB82  PCDHGB12  
    PCDHGB42  PCDHGA22  PCDHGA62  PCDHB32  PCDHGA112  PCDHGC42  PCDHGC52  PCDHGA12  
    PCDHB102  PCDHB12  PCDHGA32  PCDHGB72  
    Selected SIMAP similar genes for PCDHB6 using alignment to 2 protein entries:     PCDB6_HUMAN (see all proteins) (see all similar genes):
    ME4    PCDHB17    PCDHB16    PCDHB5    PCDHB15    ME1
    PCDHB11    PCDHB3    PCDHB4    PCDHB13    PCDHB8    PCDHB14
    PCDHB2    DKFZp586I1919    PCDHB9    PCDHB12    PCDHB18    PCDHB10

    PCDHB6 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), 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 PCDHB6 (see all 251)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1469376301,2
    Cuntested1140532190(+) GAAACC/TCCCAC 2 T syn10--------
    rs1510318651,2
    --140527894(+) GATATA/CTTTTT 1 -- us2k10--------
    rs1909195581,2
    --140527928(+) CTTTCC/TATATA 1 -- us2k10--------
    rs737935981,2
    C,F--140528006(+) AATTTG/TCTCTG 1 -- us2k13Minor allele frequency- T:0.10WA CSA 122
    rs176290111,2
    C,F,H--140528013(+) TCTGAC/TGTAAA 1 -- us2k1 tfbs317Minor allele frequency- T:0.05NA NS EA 1846
    rs1821779591,2
    --140528030(+) ATTCAA/GCAACC 1 -- us2k10--------
    rs1397131851,2
    C--140528043(+) TATTCA/GAGGAT 1 -- us2k10--------
    rs1497973491,2
    --140528060(+) TGGTGC/TTTCAG 1 -- us2k10--------
    rs170969161,2
    C,F--140528140(+) AAGAAG/CGAAGC 1 -- us2k1 trp34Minor allele frequency- C:0.06NA CSA 144
    rs1872952861,2
    --140528196(+) TGACAA/CCAGTC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for PCDHB6 (140529683 - 140532868 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for PCDHB6 (see all 12):    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv1045e199CNV Deletion23128226
    nsv5029CNV Insertion18451855
    nsv10755CNV Loss18304495
    dgv6349n71CNV Loss21882294
    dgv6348n71CNV Loss21882294
    nsv522785CNV Loss19592680
    dgv6350n71CNV Loss21882294
    nsv428127CNV Loss18775914
    esv25821CNV Loss19812545
    nsv471634CNV Gain+Loss15918152

    Site Specific Mutation Identification with 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.)
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    OMIM gene information: 606332    OMIM disorders: --

    1 disease for PCDHB6:    
    About MalaCards
    neuronitis


    PCDHB6 for disorders           About GeneDecksing


    Export disorders for PCDHB6 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 PCDHB6 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with PCDHB6)
        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. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. Protocadherins. (PubMed id 12231349)1 Frank M. and Kemler R. (Curr. Opin. Cell Biol. 2002)
    5. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1 Wu Q.... Maniatis T. (Genome Res. 2001)
    6. 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)
    7. 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)
    8. Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. (PubMed id 10817752)1 Yagi T. and Takeichi M. (amp 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: 56130 HGNC: 8691 AceView: PCDHB5andPCDHB6 Ensembl:ENSG00000113211 euGenes: HUgn56130
    ECgene: PCDHB6 H-InvDB: PCDHB6

    (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 PCDHB6 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 PCDHB6 gene:
    Search GeneIP for patents involving PCDHB6

    GeneCards and IP:
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