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PCDHB3 Gene

protein-coding   GIFtS: 45
GCID: GC05P140480

Protocadherin Beta 3
  See related diseases
at
MalaCards
 

Aliases
for PCDHB3 gene

(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 31 2
PCDH-BETA32
Protocadherin Beta-32
PCDH-beta-33

External Ids:    HGNC: 86881   Entrez Gene: 561322   Ensembl: ENSG000001132057   OMIM: 6063295   UniProtKB: Q9Y5E63   

Export aliases for PCDHB3 gene to outside databases

Previous GC identifers: GC05P140296 GC05P141063 GC05P140463 GC05P140508 GC05P140460 GC05P135624


Summaries
for PCDHB3 gene

(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 PCDHB3 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 PCDHB3 Gene:
PCDHB3 (protocadherin beta 3) is a protein-coding gene. Diseases associated with PCDHB3 include neuronitis, and endotheliitis. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHB16.

UniProtKB/Swiss-Prot: PCDB3_HUMAN, Q9Y5E6
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 PCDHB3 Gene


Genomic Views
for PCDHB3 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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TryGeneCards Plus		 Regulatory elements:
   Regulatory transcription factor binding sites in the PCDHB3 gene promoter:
         Pax-3   AML1a   ATF-2   Sox9   CUTL1   c-Jun   Tal-1beta   C/EBPalpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: PCDHB3 promoter sequence
   Search Chromatin IP Primers for PCDHB3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PCDHB3


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

PCDHB3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHB3 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P140480:  view genomic region     (about GC identifiers)

Start:
 140,480,234 bp from pter      End:
 140,483,406 bp from pter
Size:
 3,173 bases      Orientation:
 plus strand

Proteins
for PCDHB3 gene

(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, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: PCDB3_HUMAN, Q9Y5E6 (See protein sequence)
Recommended Name: Protocadherin beta-3 precursor  
Size: 796 amino acids; 86773 Da
Secondary accessions: B2R8P2

Explore the universe of human proteins at neXtProt for PCDHB3: NX_Q9Y5E6

Explore proteomics data for PCDHB3 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn169, Asn418, Asn436, Asn567
  • Modification sites at PhosphoSitePlus

    • See PCDHB3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_061760.1  
    ENSEMBL proteins: 
     ENSP00000231130  

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    Domains /
    Families
    for PCDHB3 gene

    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    TryGeneCards Plus    		 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 Q9Y5E6

    ProtoNet protein and cluster: Q9Y5E6

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCDB3_HUMAN, Q9Y5E6
    Similarity: Contains 6 cadherin domains


    PCDHB3 for domains           About GeneDecksing


    Function
    for PCDHB3 gene

    (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: PCDB3_HUMAN, Q9Y5E6
    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--
         
    PCDHB3 for ontologies           About GeneDecksing


    Animal Models:
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    miRNA
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    1 qRT-PCR Assays for microRNA that regulate PCDHB3:
    hsa-miR-4272
    SwitchGear 3'UTR luciferase reporter plasmid: PCDHB3 3' UTR sequence
    Inhib. RNA
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    Gene Editing
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    Localization
    for PCDHB3 gene

    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
    About This Section

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    Subcellular locations from UniProtKB/Swiss-Prot
    PCDB3_HUMAN, Q9Y5E6: Cell membrane; Single-pass type I membrane protein (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    extracellular2
    cytosol1
    endoplasmic reticulum1
    golgi apparatus1
    lysosome1
    mitochondrion1
    peroxisome1

    Gene Ontology (GO): 3 cellular component terms:    About this table

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

    PCDHB3 for ontologies           About GeneDecksing


    Pathways & Interactions
    for PCDHB3 gene

    (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 PCDHB3
    Interactions:

        Search GeneGlobe Interaction Network for PCDHB3

    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

    PCDHB3 for ontologies           About GeneDecksing



    Drugs & Compounds
    for PCDHB3 gene

    (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 PCDHB3 (PCDB3)

    1 HMDB Compound for PCDHB3    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--



    Transcripts
    for PCDHB3 gene

    (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,
    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 PCDHB3 gene: 
    NM_018937.3  

    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000231130(uc003lio.3)
    miRNA
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    1 qRT-PCR Assays for microRNA that regulate PCDHB3:
    hsa-miR-4272
    SwitchGear 3'UTR luciferase reporter plasmid: PCDHB3 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat PCDHB3
      QuantiFast Probe-based Assays in human, mouse, rat PCDHB3

    10 AceView cDNA sequences:

    AF152496 AF217755 BF477839 NM_018937 AW452497 BF477537 AW302546 BV198750 
    AI905980 BQ306284 

    GeneLoc Exon Structure


    Expression
    for PCDHB3 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™, 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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    PCDHB3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ATGACTGAGG
    PCDHB3 Expression
    About this image


    PCDHB3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Eye (Sensory Organs)
             Retina
    PCDHB3 Protein expression data from MOPED1, PaxDb2 and MaxQB3:     About this image

    PCDHB3 Protein Expression
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    In Situ
    Assay Products:     
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    Orthologs
    for PCDHB3 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)
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    This gene was present in the common ancestor of chordates.

    Orthologs for PCDHB3 gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia Pcdhb31 , 5 protocadherin beta 31, 5 80.28(n)1
    78.87(a)1    		   18 (19.46 cM)5
    938741  NM_053128.21  NP_444358.21 
     373007995 
    chicken
    (Gallus gallus)    		 Aves LOC1008575441 protocadherin beta-4-like 58.8(n)
    50.85(a)    		   100857544  XM_004944735.1  XP_004944792.1 
    zebrafish
    (Danio rerio)    		 Actinopterygii pcdh2g171 protocadherin 2 gamma 17 52.45(n)
    47.19(a)    		   554064  NM_001024189.1  NP_001019360.1 


    ENSEMBL Gene Tree for PCDHB3 (if available)
    TreeFam Gene Tree for PCDHB3 (if available)

    Paralogs
    for PCDHB3 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PCDHB3 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  PCDHGA112  PCDHB62  PCDHGC42  PCDHGC52  PCDHGA12  
    PCDHB102  PCDHB12  PCDHGA32  PCDHGB72  
    Selected SIMAP similar genes for PCDHB3 using alignment to 2 protein entries:     PCDB3_HUMAN (see all proteins) (see all similar genes):
    ME1    PCDHB16    PCDHB11    PCDHB13    PCDHB14    PCDHB15
    PCDHB2    PCDHB8    DKFZp586I1919    ME4    PCDHB18    PCDHB4
    PCDHB6    PCDHB5    PCDHB10    PCDHB12    PCDHB17    PCDHB7

    PCDHB3 for paralogs           About GeneDecksing



    Genomic Variants
    for PCDHB3 gene

    (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 PCDHB3 (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
    ----------
    rs1866866391,2
    		--140478260(+) ATATTG/TAAATA 1 -- us2k10--------
    rs1896065841,2
    		--140478392(+) TTGTCA/GCTTTC 1 -- us2k10--------
    rs1481906211,2
    		C--140478806(+) CAAATA/GATAGC 1 -- us2k10--------
    rs1833325481,2
    		--140478981(+) AACAAA/CCTTGC 1 -- us2k10--------
    rs1877065211,2
    		--140478991(+) CAATGA/GCTTCC 1 -- us2k10--------
    rs1442713531,2
    		C--140479009(+) CTTAG-/AATAATAA 1 -- us2k10--------
    rs361135381,2
    		C--140479016(+) AATAATAA/-AATCC 2 -- us2k1 cds11Minor allele frequency- -:0.50NA 2
    rs318511,2
    		C,F,A,H--140479105(-) TGAAGG/TACAGT 1 -- us2k1 tfbs322Minor allele frequency- T:0.46MN NS EA NA WA CSA 2420
    rs131836111,2
    		C,F,A,H--140479121(+) TATCTA/CTTAAT 1 -- us2k1 tfbs37Minor allele frequency- C:0.04NS EA NA 612
    rs1160211301,2
    		C,F--140479219(+) TGCACC/GTTGGG 1 -- us2k11Minor allele frequency- G:0.02NA 120

    HapMap Linkage Disequilibrium report for PCDHB3 (140480234 - 140483406 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for PCDHB3:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv6348n71CNV Loss21882294
    nsv522785CNV Loss19592680
    nsv428127CNV Loss18775914
    nsv882971CNV Loss21882294
    nsv516514CNV Gain19592680
    dgv1857e1CNV Complex17122850

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    Disorders / Diseases
    for PCDHB3 gene

    (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.)
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    OMIM gene information: 606329    OMIM disorders: --

    2 diseases for PCDHB3:    
    About MalaCards
    neuronitis    endotheliitis


    PCDHB3 for disorders           About GeneDecksing

    Genetic Association Database (GAD): PCDHB3

    Export disorders for PCDHB3 gene to outside databases

    Publications
    for PCDHB3 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

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    PubMed articles for PCDHB3 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with PCDHB3)    		    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. 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)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
    5. Protocadherins. (PubMed id 12231349)1 Frank M. and Kemler R. (Curr. Opin. Cell Biol. 2002)
    6. 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)
    7. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1 Wu Q.... Maniatis T. (Genome Res. 2001)
    8. 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)
    9. 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)
    10. Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. (PubMed id 10817752)1 Yagi T. and Takeichi M. (amp 2000)

    External Searches for PCDHB3 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
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    Genome Databases showing PCDHB3 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 56132 HGNC: 8688 AceView: PCDHB3 Ensembl:ENSG00000113205 euGenes: HUgn56132
    ECgene: PCDHB3 H-InvDB: PCDHB3

    Other Databases showing PCDHB3 gene

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    Specialized Databases showing PCDHB3 gene

    (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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    PharmGKB entry for PCDHB3 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
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    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    TryGeneCards Plus    		Patent Information for PCDHB3 gene:
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