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PCDHB10 Gene

protein-coding   GIFtS: 44
GCID: GC05P141363

Protocadherin Beta 10

  Search for PCDHB10
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 101 2
PCDH-beta-102 3
PCHB102 5
PCDH-BETA102
Protocadherin Beta-102

External Ids:    HGNC: 86811   Entrez Gene: 561262   Ensembl: ENSG000001203247   OMIM: 6063365   UniProtKB: Q9UN673   

Export aliases for PCDHB10 gene to outside databases

Previous GC identifers: GC05P140388 GC05P141154 GC05P140555 GC05P140600 GC05P140552 GC05P140572 GC05P135717 GC05P140574 GC05P140577 GC05P140688 GC05P141281


(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 PCDHB10 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 PCDHB10 Gene:
PCDHB10 (protocadherin beta 10) 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: PCDBA_HUMAN, Q9UN67
Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance
of specific neuronal connections in the brain

Gene Wiki entry for PCDHB10 Gene


(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 PCDHB10 gene promoter:
         AhR   Egr-1   Pax-2   Pax-2a   LCR-F1   Arnt   AREB6   NF-AT1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPCDHB10 promoter sequence
   Search Chromatin IP Primers for PCDHB10

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PCDHB10


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

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

PCDHB10 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHB10 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P141363:  view genomic region     (about GC identifiers)

Start:
140,571,942 bp from pter      End:
140,575,215 bp from pter
Size:
3,274 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: PCDBA_HUMAN, Q9UN67 (See protein sequence)
Recommended Name: Protocadherin beta-10 precursor  
Size: 800 amino acids; 87621 Da
Secondary accessions: Q96T99

Explore the universe of human proteins at neXtProt for PCDHB10: NX_Q9UN67

Explore proteomics data for PCDHB10 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn169, Asn181, Asn418, Asn436, Asn567

  • See PCDHB10 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_061753.1  
    ENSEMBL proteins: 
     ENSP00000239446  

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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 Q9UN67

    ProtoNet protein and cluster: Q9UN67

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCDBA_HUMAN, Q9UN67
    Similarity: Contains 6 cadherin domains


    Find genes that share domains with PCDHB10           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: PCDBA_HUMAN, Q9UN67
    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 PCDHB10           About GenesLikeMe


    Phenotypes:
         1 MGI phenotypic allele for Pcdhb18 (no phenotypes)

    Find genes that share phenotypes with PCDHB10           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Pcdhb18tm1Lex for PCDHB10

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for PCDHB10
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    miRNA
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    miRTarBase miRNAs that target PCDHB10:
    hsa-mir-335-5p (MIRT016983)

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    1 qRT-PCR Assays for microRNA that regulate PCDHB10:
    hsa-miR-664
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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
    PCDBA_HUMAN, Q9UN67: Cell membrane; Single-pass type I membrane protein (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    endoplasmic reticulum1
    extracellular1
    golgi apparatus1
    lysosome1

    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 NAS11322959

    Find genes that share ontologies with PCDHB10           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 PCDHB10
    Interactions:

        Search GeneGlobe Interaction Network for PCDHB10

    Gene Ontology (GO): 4 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007156homophilic cell adhesion IEA--
    GO:0007268synaptic transmission TAS12231349
    GO:0007416synapse assembly TAS12231349
    GO:0016339calcium-dependent cell-cell adhesion NAS11322959

    Find genes that share ontologies with PCDHB10           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 PCDHB10 (PCDBA)

    1 HMDB Compound for PCDHB10    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 PCDHB10 gene: 
    NM_018930.3  

    Unigene Cluster for PCDHB10:

    Protocadherin beta 10
    Hs.657953  [show with all ESTs]
    Unigene Representative Sequence: AY358720
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000239446(uc003lix.3)
    miRNA
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    1 qRT-PCR Assays for microRNA that regulate PCDHB10:
    hsa-miR-664
    SwitchGear 3'UTR luciferase reporter plasmidPCDHB10 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat PCDHB10
      QuantiFast Probe-based Assays in human, mouse, rat PCDHB10

    Additional mRNA sequence: 

    AF131761.1 AF152489.1 AF217748.1 AK056391.1 AK315583.1 AY358720.1 BC031837.1 

    5 DOTS entries:

    DT.75135517  DT.100680537  DT.100690065  DT.120879824  DT.308530 

    17 AceView cDNA sequences:

    AF131761 BC031837 AF152489 NM_018930 AY358720 BX451672 BX462013 AF217748 
    BG819161 AK056391 BI850895 AI983573 D61772 T80549 BX462012 H17394 
    BG105493 

    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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    PCDHB10 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTACTTTTAC
    PCDHB10 Expression
    About this image

    PCDHB10 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PCDHB10 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.657953
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    In Situ
    Assay Products:
     

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

    Orthologs for PCDHB10 gene from Selected species (see all 5)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pcdhb185 protocadherin beta 18   --   18 (19.50 cM) 37489465 


    ENSEMBL Gene Tree for PCDHB10 (if available)
    TreeFam Gene Tree for PCDHB10 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PCDHB10 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  PCDHB62  PCDHGC42  PCDHGC52  
    PCDHGA12  PCDHB12  PCDHGB72  PCDHGA32  
    Selected SIMAP similar genes for PCDHB10 using alignment to 1 protein entry:     PCDBA_HUMAN(see all similar genes):
    PCDHB9    PCDHB11    DKFZp586I1919    PCDHB14    PCDHB15    PCDHB16
    PCDHB18    PCDHB2    PCDHB13    PCDHB3    PCDHB4    PCDHB7
    PCDHB8    PCDHB5    PCDHB6    PCDHB12    PCDHB17    PCDHB1

    Find genes that share paralogs with PCDHB10           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for PCDHB10
    PGOHUM00000235781


    (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 PCDHB10 (see all 238)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs582441821,2
    C--135719230(+) GCCGA-/GGCCGA
            
    CTTGC
    2 C L fra12Minor allele frequency- GGCCGA:0.25NA 4
    rs1505249141,2
    C--140571661(+) AGGTG-/GACA  
            
    GAGTT
    1 -- us2k10--------
    rs1872067401,2
    --140571763(+) TCAACA/GTTAAT 1 -- us2k10--------
    rs131685931,2
    C,F,H--140571807(+) TTTAAA/GTGAGG 1 -- us2k17Minor allele frequency- G:0.01NS EA NA 424
    rs1159789561,2
    F--140571906(+) AGAGAC/TGGTTT 1 -- us2k11Minor allele frequency- T:0.03WA 118
    rs1929558761,2
    --140571911(+) CGGTTC/TGGGAA 1 -- us2k10--------
    rs1447202181,2
    --140571933(+) ATGCTA/GTGCAA 1 -- us2k10--------
    rs1846076781,2
    --140571954(+) AAGGAA/GGACAC 1 -- ut510--------
    rs1895825231,2
    --140572002(+) AGATTG/TGGAAA 1 -- ut510--------
    rs2012476431,2
    C,F--140572102(+) CCAACT/CAGGAA 1 -- ut511Minor allele frequency- C:0.01EU 1323

    HapMap Linkage Disequilibrium report for PCDHB10 (140571942 - 140575215 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for PCDHB10 (see all 16):    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv1005e201CNV Deletion23290073
    esv2730844CNV Deletion23290073
    esv2730846CNV Deletion23290073
    esv2664767CNV Deletion23128226
    esv2730845CNV Deletion23290073
    nsv5031CNV Insertion18451855
    dgv6349n71CNV Loss21882294
    dgv6348n71CNV Loss21882294
    nsv428127CNV Loss18775914
    dgv6350n71CNV Loss21882294

    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: 606336    OMIM disorders: --


    Find genes that share disorders with PCDHB10           About GenesLikeMe


    Export disorders for PCDHB10 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 PCDHB10 gene, integrated from 10 sources (see all 16):
    (articles sorted by number of sources associating them with PCDHB10)
        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 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. (Genome Res. 2004)
    3. Signal peptide prediction based on analysis of experimentally verified cleavage sites. (PubMed id 15340161)1, 2 Zhang Z. and Henzel W.J. (Protein Sci. 2004)
    4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (Genome Res. 2003)
    5. 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)
    6. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (Nat. Cell Biol. 2012)
    7. Identification of novel ATP13A2 interactors and their role in I+-synuclein misfolding and toxicity. (PubMed id 22645275)1 Usenovic M....Krainc D. (Hum. Mol. Genet. 2012)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
    9. Protocadherins. (PubMed id 12231349)1 Frank M. and Kemler R. (Curr. Opin. Cell Biol. 2002)
    10. 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)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
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    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: 56126 HGNC: 8681 AceView: PCDHB10 Ensembl:ENSG00000120324 euGenes: HUgn56126
    ECgene: PCDHB10 H-InvDB: PCDHB10

    (According to HUGE)
    About This Section

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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 PCDHB10 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 PCDHB10 gene:
    Search GeneIP for patents involving PCDHB10

    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)
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