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

PCDHB10 Gene

protein-coding   GIFtS: 45
GCID: GC05P140688

protocadherin beta 10
 Explore 1 disease affiliated with
PCDHB10 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for PCDHB10    

Aliases
for PCDHB10 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Protocadherin Beta 101 2
PCDH-Beta-101
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


Summaries
for PCDHB10 gene

(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 PCDHB10:
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)

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


Genomic Views
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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000005.9  NC_018916.1  NT_029289.11  
Regulatory elements:
   SABiosciences 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 plasmid: PCDHB10 promoter sequence
   Search SABiosciences Chromatin IP Primers for PCDHB10

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 GC05P140688:  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

Proteins
for PCDHB10 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: PCDBA_HUMAN, Q9UN67 (See protein sequence)
Recommended Name: Protocadherin beta-10 precursor  
Size: 800 amino acids; 87621 Da
Subcellular location: Cell membrane; Single-pass type I membrane protein (By similarity)
Secondary accessions: Q96T99

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

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9UN67

    • PCDHB10 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_061753.1  
    ENSEMBL proteins: 
     ENSP00000239446  

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    Browse Proteins at Uscn

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane IEA--
    GO:0016021integral to membrane NAS11322959


    PCDHB10 for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for PCDHB10 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    PCDHB10 for domains           About GeneDecksing

    4 InterPro domains/families:
     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 family: IPB002126 Cadherin

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


    Function
    for PCDHB10 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         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

    miRNA
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    1 QIAGEN miScript miRNA Assays for microRNA that regulate PCDHB10:
    hsa-miR-664
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    Inhib. RNA
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    Gene Editing
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    Clone
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    In Situ Assay
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    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--


    PCDHB10 for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-out Pcdhb18tm1Lex for PCDHB10
         1 MGI phenotypic allele for Pcdhb18 (no phenotypes)

    PCDHB10 for phenotypes           About GeneDecksing


    Pathways & Interactions
    for PCDHB10 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PCDHB10

    Gene Ontology (GO): 4 biological process terms (GO ID links to tree view):    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


    PCDHB10 for ontologies           About GeneDecksing



    Drugs & Compounds
    for PCDHB10 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 PCDHB10

    1 HMDB Compound for PCDHB10    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--
    Search CenterWatch for drugs/clinical trials and news about PCDHB10 / PCDBA 

    Transcripts
    for PCDHB10 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    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, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    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 QIAGEN miScript miRNA Assays for microRNA that regulate PCDHB10:
    hsa-miR-664
    SwitchGear 3'UTR luciferase reporter plasmid: PCDHB10 3' UTR sequence
    Inhib. RNA
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    Clone
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    Primer
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    Additional cDNA 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:

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

    GeneLoc Exon Structure


    Expression
    for PCDHB10 gene

    (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

    PCDHB10 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CTACTTTTAC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    PCDHB10 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    PureStem™ progenitor EN13 (Embryonic Progenitor Cell)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See PCDHB10 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PCDHB10

    SOURCE GeneReport for Unigene cluster: Hs.657953
        SABiosciences Custom PCR Arrays for PCDHB10
    Primer
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    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHB10

    Orthologs
    for PCDHB10 gene

    (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 PCDHB10 gene from 3/9 species (see all 9)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves PCDHB46
    --
    (see all 5)    		 Uncharacterized protein
    (see all 5)    		 48(a)
    48(a)
    (see all 5)    		 many ↔ many
    many ↔ many
    (see all 5)    		 Un(25949097-25951430)
    13(562057-583011)
    lizard
    (Anolis carolinensis)    		 Reptilia D0IQ25_ANOCA6
    		 Protocadherin alpha c1 unspliced isoform
    		 37(a)
    		 possible ortholog
    		 4(77250923-77253391)
    zebrafish
    (Danio rerio)    		 Actinopterygii pcdh2g206
    pcdh1g96
    (see all 44)    		 protocadherin 1 gamma 9
    (see all 44)    		 44(a)
    44(a)
    (see all 44)    		 many ↔ many
    many ↔ many
    (see all 44)    		 14(2970284-2971751)
    10(21767295-21770275)


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

    Paralogs
    for PCDHB10 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PCDHB10 gene
    PCDHAC12  PCDHB162  PCDHB22  PCDHAC22  PCDHB72  PCDHB152  PCDHGA102  PCDHGA122  
    PCDHGB22  PCDHGA82  PCDHGA92  PCDHGB32  PCDHGC32  PCDHGB62  PCDHA62  PCDHGA52  
    PCDHA82  PCDHA132  PCDHB52  PCDHB132  PCDHA32  PCDHGA42  PCDHGA72  PCDHA42  
    PCDHB42  PCDHB112  PCDHA22  ENSG000002556222  PCDHB142  PCDHB122  PCDHA122  PCDHB82  
    PCDHA52  PCDHGB12  PCDHGB42  PCDHA12  PCDHGA22  PCDHA112  PCDHA72  PCDHGA112  
    PCDHGA62  PCDHB32  PCDHB62  PCDHGC52  PCDHGC42  PCDHA102  PCDHA92  PCDHGA12  
    PCDHB12  PCDHGA32  PCDHGB72  
    18/66 SIMAP similar genes for PCDHB10 using alignment to 1 protein entry:     PCDBA_HUMAN(see all similar genes):
    PCDHB9    PCDHB11    DKFZp586I1919    PCDHB12    PCDHB14    PCDHB15
    PCDHB16    PCDHB18    PCDHB2    PCDHB13    PCDHB3    PCDHB4
    PCDHB7    PCDHB8    PCDHB5    PCDHB6    PCDHB17    PCDHB1

    PCDHB10 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for PCDHB10
    PGOHUM00000235781


    Genomic Variants
    for PCDHB10 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/164 NCBI SNPs in PCDHB10 are shown (see all 164)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 5 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs37336891,2
    		C,F,H,--140572156(-) CCTTTG/ATCTTG 2 /Q /* stg1 ese36Minor allele frequency- A:0.01NS EA NA 672
    rs1415252921,2
    		C,F,--140572185(+) CTTTTT/CTGGGG 2 /F syn12Minor allele frequency- C:0.01NA EU 5781
    rs2003357541,2
    		--140572186(+) TTTTTG/TGGGGA 2 G W mis10--------
    rs178445511,2
    		C,--140572236(+) ACTGAA/GGAAAC 2 E syn1 ese30--------
    rs1383411321,2
    		C,F,--140572248(+) GAGAAA/GGGATC 2 K syn12Minor allele frequency- G:0.01NA EU 4513
    rs1488678031,2
    		C,F,--140572299(+) GGGGAG/ACTGGC 2 /E syn12Minor allele frequency- A:0.00NA EU 3743
    rs2020012001,2
    		--140572308(+) GCTGCA/CAGGGG 2 A syn10--------
    rs1496482411,2
    		C,F,--140572456(+) TAATGG/TATGAT 2 D Y mis12Minor allele frequency- T:0.00NA EU 4291
    rs1381843331,2
    		C--140572469(+) CTTTCA/CGATTT 2 Q P mis11Minor allele frequency- C:0.00NA 3364
    rs1438821121,2
    		C,F,--140572475(+) GATTTA/CCCGGG 2 Y S mis12Minor allele frequency- C:0.00NA EU 4789

    HapMap Linkage Disequilibrium report for PCDHB10 (140571942 - 140575215 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 4 variations for PCDHB10
         4 CNVs: 0714 3578 36352 36351

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PCDHB10
    DNA2.0 Custom Variant and Variant Library Synthesis for PCDHB10

    Disorders / Diseases
    for PCDHB10 gene

    (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.)
    About This Section
    PCDHB10 for disorders           About GeneDecksing

    OMIM gene information: 606336    OMIM disorders: --

    1 disease for PCDHB10:    About MalaCards
    neuronitis


    Export disorders for PCDHB10 gene to outside databases

    Publications
    for PCDHB10 gene

    (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 PCDHB10 gene, integrated from 9 sources (see all 15):
    (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. (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. (2004)
    3. Signal peptide prediction based on analysis of experimentally verified cleavage sites. (PubMed id 15340161)1, 2 Zhang Z. and Henzel W.J. (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. (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. (2001)
    6. Identification of novel ATP13A2 interactors and their role in a-synuclein misfolding and toxicity. (PubMed id 22645275)1 Usenovic M....Krainc D. (2012)
    7. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (2004)
    8. Protocadherins. (PubMed id 12231349)1 Frank M. and Kemler R. (2002)
    9. 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. (2002)
    10. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1 Wu Q.... Maniatis T. (2001)

    External Searches for PCDHB10 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
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    Genome Databases showing PCDHB10 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 56126 HGNC: 8681 AceView: PCDHB10 Ensembl:ENSG00000120324 euGenes: HUgn56126
    ECgene: PCDHB10 H-InvDB: PCDHB10

    Other Databases showing PCDHB10 gene

    (According to HUGE)
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    Specialized Databases showing PCDHB10 gene

    (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 PCDHB10 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
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    		Patent Information for PCDHB10 gene:
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