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

PCDHB6 Gene

protein-coding   GIFtS: 42
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)
About This Section

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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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 PCDHAC1.

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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000005.9  NC_018916.2  NT_029289.11  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for PCDHB6

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 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: PCDB6_HUMAN, Q9Y5E3 (See protein sequence)
Recommended Name: Protocadherin beta-6 precursor  
Size: 794 amino acids; 87350 Da
Subcellular location: Cell membrane; Single-pass type I membrane protein (By similarity)

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

Explore proteomics data for PCDHB6 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9Y5E3

  • PCDHB6 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    PCDHB6 Protein Expression
    REFSEQ proteins: NP_061762.1  
    ENSEMBL proteins: 
     ENSP00000231136   ENSP00000438466  

    Human Recombinant Protein Products for PCDHB6: 
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    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

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

    PCDHB6 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 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,
    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: 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 (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--
         
    PCDHB6 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 PCDHB6

    Gene Ontology (GO): 5/6 biological process terms (GO ID links to tree view) (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 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 PCDHB6 (PCDB6)

    1 HMDB Compound for PCDHB6    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--

    Search CenterWatch for drugs/clinical trials and news about PCDHB6 / PCDB6

    (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 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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    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
    Products:
         
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    Additional mRNA sequence: 

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

    1 DOTS entry:

    DT.91762325 

    24/50 AceView cDNA sequences (see all 50):

    AF134474 NM_018939 NM_015669 AL117449 AF217752 AF152498 AF152499 AF217753 
    BX116605 AA290901 BX090111 BV198369 AU127985 CD679133 AA283794 AI681523 
    C02372 BC001186 BV198368 AI470093 AU131635 AI201698 BV198681 BV198370 

    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

    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


    See PCDHB6 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PCDHB6

    SOURCE GeneReport for Unigene cluster: Hs.283085
        SABiosciences 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)
    About This Section

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

    Orthologs for PCDHB6 gene from 1/7 species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pcdhb131 , 5 protocadherin beta 131, 5 80.2(n)1
    78.18(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)
    About This Section
    Paralogs for PCDHB6 gene
    PCDHAC12  PCDHB162  PCDHB22  PCDHAC22  PCDHB72  PCDHB152  PCDHGA102  PCDHGA122  
    PCDHGB22  PCDHGA92  PCDHGA82  PCDHGC32  PCDHGA52  PCDHA82  PCDHB52  PCDHB132  
    PCDHGA42  PCDHGA72  PCDHB42  PCDHB112  PCDHA22  ENSG000002556222  PCDHB142  PCDHB122  
    PCDHB82  PCDHGB12  PCDHGB42  PCDHA52  PCDHGA22  PCDHGA62  PCDHB32  PCDHGA112  
    PCDHGC42  PCDHGC52  PCDHGA12  PCDHB102  PCDHB12  PCDHGB72  PCDHGA32  
    18/72 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    PCDHB12
    ME1    PCDHB11    PCDHB3    PCDHB4    PCDHB13    PCDHB8
    PCDHB14    PCDHB2    DKFZp586I1919    PCDHB9    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) 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

    10/249 SNPs in PCDHB6 are shown (see all 249)    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) 10/12 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

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    (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: 606332    OMIM disorders: --

    2 diseases 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)
    About This Section

    PubMed articles for PCDHB6 gene integrated from 9 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. (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. (2001)
    3. Protocadherins. (PubMed id 12231349)1 Frank M. and Kemler R. (2002)
    4. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1 Wu Q.... Maniatis T. (2001)
    5. 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)
    6. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PubMed id 10716726)1 Wu Q. and Maniatis T. (2000)
    7. 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: 56130 HGNC: 8691 AceView: PCDHB5andPCDHB6 Ensembl:ENSG00000113211 euGenes: HUgn56130
    ECgene: PCDHB6 H-InvDB: PCDHB6

    (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 PCDHB6 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 PCDHB6 gene:
    Search GeneIP for patents involving PCDHB6

    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
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    About This Section

     
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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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