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PCDHGB5 Gene

protein-coding   GIFtS: 36
GCID: GC05P141386

Protocadherin Gamma Subfamily B, 5

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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, 51 2
PCDH-GAMMA-B52
Protocadherin Gamma-B52
PCDH-gamma-B53

External Ids:    HGNC: 87121   Entrez Gene: 561012   OMIM: 6063025   UniProtKB: Q9Y5G03   

Export aliases for PCDHGB5 gene to outside databases

Previous GC identifers: GC05P140594 GC05P141311 GC05P140713 GC05P140771 GC05P140792 GC05P140731 GC05P140808 GC05P140828 GC05P140845 GC05P140870 GC05P140877 GC05P140897 GC05P140930 GC05P140952 GC05P140973 GC05P140995 GC05P141025 GC05P141043 GC05P141070 GC05P141090 GC05P141109 GC05P141151 GC05P141168 GC05P141204 GC05P141244 GC05P141327


(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 PCDHGB5 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 PCDHGB5 Gene:
PCDHGB5 (protocadherin gamma subfamily B, 5) is a protein-coding gene. GO annotations related to this gene include calcium ion binding.

UniProtKB/Swiss-Prot: PCDGH_HUMAN, Q9Y5G0
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 PCDHGB5 gene promoter:
         p300   Pax-2   FOXD3   Pax-2a   FOXL1   Max   Egr-2   COMP1   c-Myc   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PCDHGB5


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

Entrez Gene cytogenetic band: 5q31   HGNC cytogenetic band: 5q31

PCDHGB5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHGB5 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P141386:  view genomic region     (about GC identifiers)

Start:
140,777,695 bp from pter      End:
140,892,546 bp from pter
Size:
114,852 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: PCDGH_HUMAN, Q9Y5G0 (See protein sequence)
Recommended Name: Protocadherin gamma-B5 precursor  
Size: 923 amino acids; 99875 Da
Secondary accessions: Q52LK8 Q9Y5C6
Alternative splicing: 2 isoforms:  Q9Y5G0-1   Q9Y5G0-2   

Explore the universe of human proteins at neXtProt for PCDHGB5: NX_Q9Y5G0

Explore proteomics data for PCDHGB5 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn415, Asn541
  • Modification sites at PhosphoSitePlus

  • See PCDHGB5 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_061748.1  NP_115270.1  

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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 Q9Y5G0

    ProtoNet protein and cluster: Q9Y5G0

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCDGH_HUMAN, Q9Y5G0
    Similarity: Contains 6 cadherin domains


    Find genes that share domains with PCDHGB5           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: PCDGH_HUMAN, Q9Y5G0
    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): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0005509calcium ion binding IEA--
         
    Find genes that share ontologies with PCDHGB5           About GenesLikeMe


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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
    PCDGH_HUMAN, Q9Y5G0: Cell membrane; Single-pass type I membrane protein (By similarity)

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--
    GO:0005886plasma membrane IEA--
    GO:0016021integral component of membrane IEA--
    GO:0070062extracellular vesicular exosome IDA19199708

    Find genes that share ontologies with PCDHGB5           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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    Interactions:

        Search GeneGlobe Interaction Network for PCDHGB5

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007156homophilic cell adhesion IEA--
    GO:0008150biological_process ND--

    Find genes that share ontologies with PCDHGB5           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
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      Browse compounds at ApexBio 

    Browse Tocris compounds for PCDHGB5 (PCDGH)

    1 HMDB Compound for PCDHGB5    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 PCDHGB5 gene (2 alternative transcripts): 
    NM_018925.2  NM_032099.1  

    miRNA
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    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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    Selected AceView cDNA sequences (see all 737):

    AF152521 BQ716279 NM_018929 NM_032403 AF152526 BG055977 CA442860 AW089227 
    AF152505 NM_018923 BC004321 BQ689381 BC006439 BG740932 BF513666 BM702196 
    BM821512 CA388789 BG912888 BM694643 BF511055 AB000896 AF152318 CA390638 

    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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    PCDHGB5 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    PCDHGB5 Expression
    About this image

    PCDHGB5 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PCDHGB5 Protein Expression
        Custom PCR Arrays for PCDHGB5
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    In Situ
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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 PCDHGB5 gene from Selected species (see all 5)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pcdhgb51 , 5 protocadherin gamma subfamily B, 51, 5 83.19(n)1
    84.8(a)1
      18 (19.59 cM)5
    937021  NM_033577.11  NP_291055.11 
     377311545 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PCDHGB5 gene
    Selected SIMAP similar genes for PCDHGB5 using alignment to 1 protein entry:     PCDGH_HUMAN(see all similar genes):
    PCDHGB4    PCDHGB6    PCDHGB7    PCDHGB1    PCDHGB2    PCDHGC3
    PCDHGB3    PCDHGA1    PCDHGA11    PCDHGA8    PCDHGA9    PCDHGA12
    PCDHGA2    PCDHGA4    PCDHGA5    PCDHGA3    PCDHGA10    PCDHGA6

    Find genes that share paralogs with PCDHGB5           About GenesLikeMe



    (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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    1 SNPs for PCDHGB5    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs68674601,2,4
    ----see VAR_0485712 mis40--------

    HapMap Linkage Disequilibrium report for PCDHGB5 (140777695 - 140892546 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for PCDHGB5 (see all 13):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2730847CNV Deletion23290073
    esv267823CNV Insertion20981092
    nsv462470CNV Loss19166990
    nsv327707CNV Loss16902084
    dgv6351n71CNV Loss21882294
    nsv882990CNV Loss21882294
    dgv6352n71CNV Loss21882294
    nsv518799CNV Loss19592680
    dgv6353n71CNV Loss21882294
    nsv519627CNV Loss19592680

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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: 606302    OMIM disorders: --


    Find genes that share disorders with PCDHGB5           About GenesLikeMe

    Genetic Association Database (GAD): PCDHGB5

    Export disorders for PCDHGB5 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 PCDHGB5 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with PCDHGB5)
        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. Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT). (PubMed id 19199708)1 Gonzalez-Begne M....Yates J.R. (J. Proteome Res. 2009)
    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: 56101 HGNC: 8712 AceView: PCDHGC3 euGenes: HUgn56101 ECgene: PCDHGB5
    H-InvDB: PCDHGB5

    (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 PCDHGB5 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 PCDHGB5 gene:
    Search GeneIP for patents involving PCDHGB5

    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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