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

PCDHB13 Gene

protein-coding   GIFtS: 44
GCID: GC05P141285

Protocadherin Beta 13

  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 131 2
PCDH-BETA132
Protocadherin Beta-132
PCDH-beta-133

External Ids:    HGNC: 86841   Entrez Gene: 561232   Ensembl: ENSG000001873727   OMIM: 6063395   UniProtKB: Q9Y5F03   

Export aliases for PCDHB13 gene to outside databases

Previous GC identifers: GC05P140409 GC05P141176 GC05P140576 GC05P140623 GC05P140624 GC05P140573 GC05P140657 GC05P140662 GC05P135738 GC05P140668 GC05P140673 GC05P140678 GC05P140684 GC05P140694


(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 PCDHB13 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 PCDHB13 Gene: 
PCDHB13 (protocadherin beta 13) is a protein-coding gene. Diseases associated with PCDHB13 include neuronitis. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHAC1.

UniProtKB/Swiss-Prot: PCDBD_HUMAN, Q9Y5F0
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 PCDHB13 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 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 PCDHB13 gene promoter:
         AhR   GR   GR-beta   LUN-1   E47   Arnt   HEN1   PPAR-alpha   GR-alpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPCDHB13 promoter sequence
   Search SABiosciences Chromatin IP Primers for PCDHB13

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDHB13


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

PCDHB13 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHB13 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P141285:  view genomic region     (about GC identifiers)

Start:
140,593,509 bp from pter      End:
140,596,993 bp from pter
Size:
3,485 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: PCDBD_HUMAN, Q9Y5F0 (See protein sequence)
Recommended Name: Protocadherin beta-13 precursor  
Size: 798 amino acids; 87552 Da
Subcellular location: Cell membrane; Single-pass type I membrane protein (By similarity)

Explore the universe of human proteins at neXtProt for PCDHB13: NX_Q9Y5F0

Explore proteomics data for PCDHB13 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9Y5F0

  • PCDHB13 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    PCDHB13 Protein Expression
    REFSEQ proteins: NP_061756.1  
    ENSEMBL proteins: 
     ENSP00000345491  

    Human Recombinant Protein Products for PCDHB13: 
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    Novus Biologicals PCDHB13 Protein
    Novus Biologicals PCDHB13 Lysates
    Browse Sino Biological Recombinant Proteins
    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 NAS11322959

    PCDHB13 for ontologies           About GeneDecksing



    PCDHB13 Antibody Products: 
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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 Q9Y5F0

    ProtoNet protein and cluster: Q9Y5F0

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCDBD_HUMAN, Q9Y5F0
    Similarity: Contains 6 cadherin domains


    PCDHB13 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: PCDBD_HUMAN, Q9Y5F0
    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--
         
    PCDHB13 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for PCDHB13:
     G0/1 arrest  Increased G1 DNA content 

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for PCDHB13 
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    miRNA
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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 PCDHB13

    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

    PCDHB13 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 PCDHB13 (PCDBD)

    1 HMDB Compound for PCDHB13    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--

    Search CenterWatch for drugs/clinical trials and news about PCDHB13 / PCDBD

    (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 PCDHB13 gene: 
    NM_018933.3  

    Unigene Cluster for PCDHB13:

    Protocadherin beta 13
    Hs.283803  [show with all ESTs]
    Unigene Representative Sequence: AF217745
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000341948(uc003lja.1)
    miRNA
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    Inhib. RNA
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    Primer
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PCDHB13

    Additional mRNA sequence: 

    AF152492.1 AF217745.1 AK021915.1 AK292821.1 AK296151.1 AY358427.1 BC033068.1 BC051348.1 
    BC071934.1 

    2 DOTS entries:

    DT.95210419  DT.97834597 

    24/30 AceView cDNA sequences (see all 30):

    AF217745 BC071934 AF152492 BC033068 BU552555 AA489646 NM_018933 BG697250 
    BQ927385 BE856564 AY358427 BC051348 AI363933 BX117042 AK021915 BM921141 
    AA489751 AU119840 BQ958557 BM047725 BE677909 BQ887350 BM046493 BM048171 

    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

    PCDHB13 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    PCDHB13 Expression
    About this image


    See PCDHB13 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PCDHB13

    SOURCE GeneReport for Unigene cluster: Hs.283803
        SABiosciences Custom PCR Arrays for PCDHB13
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PCDHB13
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHB13

    (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
      --

    ENSEMBL Gene Tree for PCDHB13 (if available)
    TreeFam Gene Tree for PCDHB13 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PCDHB13 gene
    PCDHAC12  PCDHB162  PCDHB22  PCDHAC22  PCDHB72  PCDHB152  PCDHGA102  PCDHGB22  
    PCDHGA122  PCDHGA92  PCDHGA82  PCDHGC32  PCDHGA52  PCDHA82  PCDHB52  PCDHGA42  
    PCDHGA72  PCDHB42  PCDHB112  PCDHA22  ENSG000002556222  PCDHB142  PCDHB122  PCDHB82  
    PCDHGB12  PCDHGB42  PCDHA52  PCDHGA22  PCDHGA62  PCDHB32  PCDHGA112  PCDHB62  
    PCDHGC42  PCDHGC52  PCDHGA12  PCDHB102  PCDHB12  PCDHGB72  PCDHGA32  
    18/65 SIMAP similar genes for PCDHB13 using alignment to 1 protein entry:     PCDBD_HUMAN(see all similar genes):
    PCDHB8    PCDHB16    PCDHB3    PCDHB11    PCDHB12    PCDHB15
    PCDHB18    PCDHB6    DKFZp586I1919    PCDHB14    PCDHB2    PCDHB10
    PCDHB17    PCDHB4    PCDHB5    PCDHB9    PCDHB7    PCDHB1

    PCDHB13 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

    10/214 SNPs in PCDHB13 are shown (see all 214)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1381684451,2
    C,Funtested1140596039(+) GGAAAA/G/TAAATA 2 K E mis12NA EU 5873
    rs1132298951,2
    F--140592310(+) CCACTG/CAAATA 1 -- us2k11Minor allele frequency- C:0.50CSA 2
    rs113432611,2
    C--140592402(+) ATTAA-/ATAATG 1 -- us2k10--------
    rs77074611,2
    C,F,H--140592408(+) aataaT/Cgttaa 1 -- us2k19Minor allele frequency- C:0.09NS NA CSA WA 1180
    rs1835559961,2
    --140592627(+) ATTATA/TCTCCT 1 -- us2k10--------
    rs1460706841,2
    C--140592812(+) TGGAC-/ATAACC 1 -- us2k10--------
    rs1890174221,2
    --140592850(+) TATTCG/TTCTAC 1 -- us2k10--------
    rs732736841,2
    C,F--140593071(+) CTTATC/ACTCAC 1 -- us2k11Minor allele frequency- A:0.50WA 2
    rs595609721,2
    C,F--140593187(+) TGTTGT/CCCATG 1 -- us2k13Minor allele frequency- C:0.11WA NA 122
    rs1480664621,2
    --140593201(+) ACTACA/TATTAT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for PCDHB13 (140593509 - 140596993 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/13 variations for PCDHB13 (see all 13):    About this table     
    Variant IDTypeSubtypePubMed ID
    dgv1005e201CNV Deletion23290073
    dgv6349n71CNV Loss21882294
    dgv6348n71CNV Loss21882294
    dgv6350n71CNV Loss21882294
    nsv428127CNV Loss18775914
    nsv823278CNV Gain20364138
    nsv823266CNV Gain20364138
    nsv823277CNV Gain20364138
    nsv10757CNV Gain18304495
    esv26005CNV Gain19812545

    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing PCDHB13
    DNA2.0 Custom Variant and Variant Library Synthesis for PCDHB13

    (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: 606339    OMIM disorders: --

    2 diseases for PCDHB13:    About MalaCards
    neuronitis    


    PCDHB13 for disorders           About GeneDecksing


    Export disorders for PCDHB13 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 PCDHB13 gene, integrated from 9 sources (see all 11):
    (articles sorted by number of sources associating them with PCDHB13)
        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. 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)
    4. 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)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (2004)
    6. Protocadherins. (PubMed id 12231349)1 Frank M. and Kemler R. (2002)
    7. 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)
    8. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1 Wu Q.... Maniatis T. (2001)
    9. 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)
    10. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PubMed id 10716726)1 Wu Q. and Maniatis T. (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: 56123 HGNC: 8684 AceView: PCDHB13 Ensembl:ENSG00000187372 euGenes: HUgn56123
    ECgene: PCDHB13 H-InvDB: PCDHB13

    (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 PCDHB13 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 PCDHB13 gene:
    Search GeneIP for patents involving PCDHB13

    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)
    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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    (GIFtS: 73)
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    Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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