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PCDHGB2 Gene

protein-coding   GIFtS: 39
GCID: GC05P141378

Protocadherin Gamma Subfamily B, 2

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(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 Gamma Subfamily B, 21 2
PCDH-GAMMA-B22
Protocadherin Gamma-B22
PCDH-gamma-B23

External Ids:    HGNC: 87091   Entrez Gene: 561032   Ensembl: ENSG000002539107   OMIM: 6063005   UniProtKB: Q9Y5G23   

Export aliases for PCDHGB2 gene to outside databases

Previous GC identifers: GC05P140556 GC05P141305 GC05P140710 GC05P140769 GC05P140790 GC05P140728 GC05P140814 GC05P140822 GC05P140837 GC05P140864 GC05P140890 GC05P140912 GC05P140924 GC05P140946 GC05P140967 GC05P140989 GC05P141019 GC05P141038 GC05P141082 GC05P135884 GC05P141104 GC05P141142 GC05P141181 GC05P141212 GC05P141251 GC05P141291


(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 PCDHGB2 Gene:
This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on
chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism
may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3
subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more
distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed
by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes
the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region
exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a
critical role in the establishment and function of specific cell-cell connections in the brain. Alternative
splicing has been described for the gamma cluster genes. (provided by RefSeq, Jul 2008)

GeneCards Summary for PCDHGB2 Gene:
PCDHGB2 (protocadherin gamma subfamily B, 2) 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: PCDGE_HUMAN, Q9Y5G2
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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the PCDHGB2 gene promoter:
         SRF   Max1   SRF (504 AA)   LCR-F1   YY1   E47   Hand1   STAT3   ZID   Ik-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for PCDHGB2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PCDHGB2


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

PCDHGB2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHGB2 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P141378:  view genomic region     (about GC identifiers)

Start:
140,739,703 bp from pter      End:
140,892,546 bp from pter
Size:
152,844 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: PCDGE_HUMAN, Q9Y5G2 (See protein sequence)
Recommended Name: Protocadherin gamma-B2 precursor  
Size: 931 amino acids; 100875 Da
Secondary accessions: Q3MIJ3 Q9UN65
Alternative splicing: 2 isoforms:  Q9Y5G2-1   Q9Y5G2-2   

Explore the universe of human proteins at neXtProt for PCDHGB2: NX_Q9Y5G2

Explore proteomics data for PCDHGB2 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn419, Asn545
  • Modification sites at PhosphoSitePlus

  • See PCDHGB2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_061746.1  NP_115267.1  

    ENSEMBL proteins: 
     ENSP00000429018  

    PCDHGB2 Human Recombinant Protein Products:

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    antibodies-online proteins for PCDHGB2 (4 products) 

     
    antibodies-online peptides for PCDHGB2

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    antibodies-online antibodies for PCDHGB2 (63 products) 

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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 Q9Y5G2

    ProtoNet protein and cluster: Q9Y5G2

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCDGE_HUMAN, Q9Y5G2
    Similarity: Contains 6 cadherin domains


    Find genes that share domains with PCDHGB2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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: PCDGE_HUMAN, Q9Y5G2
    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 PCDHGB2           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for PCDHGB2:
     Increased gamma-H2AX phosphory 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for PCDHGB2

    miRNA
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    miRTarBase miRNAs that target PCDHGB2:
    hsa-mir-125a-5p (MIRT045714), hsa-mir-125b-5p (MIRT045936)

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    Selected qRT-PCR Assays for microRNAs that regulate PCDHGB2 (see all 29):
    hsa-miR-1226 hsa-miR-448 hsa-miR-4272 hsa-miR-765 hsa-miR-624* hsa-miR-650 hsa-miR-3150a-3p hsa-miR-548a-3p
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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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
    PCDGE_HUMAN, Q9Y5G2: Cell membrane; Single-pass type I membrane protein (By similarity)

    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 IEA--

    Find genes that share ontologies with PCDHGB2           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 PCDHGB2
    Interactions:

        Search GeneGlobe Interaction Network for PCDHGB2

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007156homophilic cell adhesion IEA--

    Find genes that share ontologies with PCDHGB2           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 PCDHGB2 (PCDGE)

    1 HMDB Compound for PCDHGB2    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 PCDHGB2 gene (2 alternative transcripts): 
    NM_018923.2  NM_032096.1  

    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000522605(uc003ljs.2)
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate PCDHGB2 (see all 29):
    hsa-miR-1226 hsa-miR-448 hsa-miR-4272 hsa-miR-765 hsa-miR-624* hsa-miR-650 hsa-miR-3150a-3p hsa-miR-548a-3p
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    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat PCDHGB2
      QuantiFast Probe-based Assays in human, mouse, rat PCDHGB2

    Selected AceView cDNA sequences (see all 737):

    BQ055812 BX346373 AF152512 AW002439 AF152332 AF152323 BU155361 CB305621 
    BU145848 CA449241 NM_032091 NM_018915 BF924785 N54122 AA999664 AF152510 
    AW571846 BQ899198 NM_018926 NM_032402 CA397152 NM_018920 F04936 NM_032090 

    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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    PCDHGB2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    PCDHGB2 Expression
    About this image

    PCDHGB2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PCDHGB2 Protein Expression
        Custom PCR Arrays for PCDHGB2
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHGB2

    (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 PCDHGB2 gene from Selected species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pcdhgb21 , 5 protocadherin gamma subfamily B, 21, 5 82.73(n)1
    82.8(a)1
      18 (19.55 cM)5
    937001  NM_033575.31  NP_291053.11 
     376898595 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    (see all 21)
    Uncharacterized protein
    (see all 21)
    52(a)
    51(a)
    (see all 21)
    many ↔ many
    many ↔ many
    (see all 21)
    4(76789872-76792178)
    4(76659821-76662238)


    ENSEMBL Gene Tree for PCDHGB2 (if available)
    TreeFam Gene Tree for PCDHGB2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PCDHGB2 gene
    PCDHB162  PCDHB22  PCDHAC22  PCDHB72  PCDHB152  PCDHGA102  PCDHGA122  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  
    PCDHB102  PCDHB12  PCDHGA32  PCDHGB72  
    Selected SIMAP similar genes for PCDHGB2 using alignment to 1 protein entry:     PCDGE_HUMAN(see all similar genes):
    PCDHGB1    PCDHGB4    PCDHGB3    PCDHGB5    PCDHGB6    PCDHGB7
    PCDHGC3    PCDHGA3    PCDHGA12    PCDHGA6    PCDHGA11    PCDHGA2
    PCDHGA4    PCDHGA5    PCDHGA7    PCDHGA8    PCDHGA9    PCDHGA1

    Find genes that share paralogs with PCDHGB2           About GenesLikeMe


    2 Pseudogenes.org Pseudogenes for PCDHGB2
    PGOHUM00000257130 PGOHUM00000235797


    (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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    3 SNPs for PCDHGB2    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs131718591,2,4
    ----see VAR_0610712 mis40--------
    rs577356331,2,4
    ----see VAR_0610722 mis40--------
    rs170972311,2,4
    ----see VAR_0485682 mis40--------

    HapMap Linkage Disequilibrium report for PCDHGB2 (140739703 - 140892546 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for PCDHGB2 (see all 15):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2730847CNV Deletion23290073
    esv267823CNV Insertion20981092
    nsv823280CNV Loss20364138
    nsv462470CNV Loss19166990
    nsv327707CNV Loss16902084
    dgv6351n71CNV Loss21882294
    nsv882990CNV Loss21882294
    dgv6352n71CNV Loss21882294
    nsv518799CNV Loss19592680
    dgv6353n71CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing PCDHGB2
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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: 606300    OMIM disorders: --


    Find genes that share disorders with PCDHGB2           About GenesLikeMe

    Genetic Association Database (GAD): PCDHGB2

    Export disorders for PCDHGB2 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 PCDHGB2 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with PCDHGB2)
        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. Bcl2-associated athanogene 3 interactome analysis reveals a new role in modulating proteasome activity. (PubMed id 23824909)1 Chen Y....Ge F. (amp 2013)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    4. 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)
    5. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1 Wu Q.... Maniatis T. (Genome Res. 2001)
    6. 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)
    7. 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)
    8. Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. (PubMed id 10817752)1 Yagi T. and Takeichi M. (amp 2000)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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)
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    Entrez Gene: 56103 HGNC: 8709 AceView: PCDHGC3 Ensembl:ENSG00000253910 euGenes: HUgn56103
    ECgene: PCDHGB2 H-InvDB: PCDHGB2

    (According to HUGE)
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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 PCDHGB2 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 PCDHGB2 gene:
    Search GeneIP for patents involving PCDHGB2

    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, eBioscience, antibodies-online, 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 genOway)
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