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    PCDHGB5 protocadherin gamma subfamily B, 5 [ Homo sapiens (human) ]

    Gene ID: 56101, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PCDHGB5provided by HGNC
    Official Full Name
    protocadherin gamma subfamily B, 5provided by HGNC
    Primary source
    HGNC:HGNC:8712
    See related
    Ensembl:ENSG00000276547 MIM:606302; AllianceGenome:HGNC:8712
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PCDH-GAMMA-B5
    Summary
    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]
    Orthologs
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    Genomic context

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    See PCDHGB5 in Genome Data Viewer
    Location:
    5q31.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (141397947..141512975)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (141923583..142038959)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140777514..140892542)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23291 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23293 Neighboring gene solute carrier family 25 member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23294 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:140713237-140713466 Neighboring gene protocadherin gamma subfamily A, 1 Neighboring gene TATA-box binding protein associated factor 7 Neighboring gene protocadherin gamma cluster Neighboring gene protocadherin gamma subfamily A, 2 Neighboring gene protocadherin gamma subfamily A, 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:140745768-140745946 Neighboring gene protocadherin gamma subfamily B, 1 Neighboring gene protocadherin gamma subfamily A, 4 Neighboring gene protocadherin gamma subfamily B, 2 Neighboring gene protocadherin gamma subfamily A, 5 Neighboring gene protocadherin gamma subfamily B, 3 Neighboring gene protocadherin gamma subfamily A, 6 Neighboring gene protocadherin gamma subfamily A, 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23295 Neighboring gene protocadherin gamma subfamily B, 4 Neighboring gene protocadherin gamma subfamily A, 8 Neighboring gene protocadherin gamma subfamily A, 9 Neighboring gene protocadherin gamma subfamily B, 6 Neighboring gene protocadherin gamma subfamily A, 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23296 Neighboring gene protocadherin gamma subfamily A, 11 Neighboring gene protocadherin gamma subfamily B, 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140821493-140821993 Neighboring gene protocadherin gamma subfamily B, 8 pseudogene Neighboring gene protocadherin gamma subfamily A, 12 Neighboring gene protocadherin gamma subfamily B, 9 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23297 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140855840-140856383 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:140864468-140864695 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23298 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16454 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23299 Neighboring gene RNA, 7SL, cytoplasmic 68, pseudogene Neighboring gene protocadherin gamma subfamily C, 3 Neighboring gene protocadherin gamma subfamily C, 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23301 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140888408-140888908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23303 Neighboring gene protocadherin gamma subfamily C, 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140893101-140893726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140893727-140894352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140894353-140894978 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140895605-140896230 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140896231-140896856 Neighboring gene uncharacterized LOC124901091 Neighboring gene Sharpr-MPRA regulatory region 13534 Neighboring gene diaphanous related formin 1 Neighboring gene MPRA-validated peak5501 silencer Neighboring gene Sharpr-MPRA regulatory region 13738 Neighboring gene DIAPH1 antisense RNA 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members. Nollet F, et al. J Mol Biol, 2000 Jun 9. PMID 10835267
    2. Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. Yagi T, et al. Genes Dev, 2000 May 15. PMID 10817752
    3. PTPRA Phosphatase Regulates GDNF-Dependent RET Signaling and Inhibits the RET Mutant MEN2A Oncogenic Potential. Yadav L, et al. iScience, 2020 Feb 21. PMID 32062451, Free PMC Article
    4. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. Wu Q, et al. Genome Res, 2001 Mar. PMID 11230163, Free PMC Article
    5. A striking organization of a large family of human neural cadherin-like cell adhesion genes. Wu Q, et al. Cell, 1999 Jun 11. PMID 10380929

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    protocadherin gamma-B5

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_000012.2 

      Range
      108325..223176
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_018925.3 → NP_061748.1  protocadherin gamma-B5 isoform 1 precursor

      See identical proteins and their annotated locations for NP_061748.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) includes the constant region exons and encodes the longest isoform (1).
      Source sequence(s)
      AC005618, AC008781
      Consensus CDS
      CCDS75339.1
      UniProtKB/Swiss-Prot
      Q52LK8, Q9Y5C6, Q9Y5G0
      Related
      ENSP00000478258.1, ENST00000617380.2
      Conserved Domains (4) summary
      cd11304
      Location:246 → 339
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:32 → 112
      Cadherin_2; Cadherin-like
      pfam15974
      Location:800 → 896
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region
      pfam16492
      Location:683 → 764
      Cadherin_C_2; Cadherin cytoplasmic C-terminal

    2. NM_032099.1 → NP_115270.1  protocadherin gamma-B5 isoform 2 precursor

      See identical proteins and their annotated locations for NP_115270.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) utilizes the large, first exon then continues into the downstream intron 1 sequence before terminating. This one-exon transcript encodes the shorter isoform (2).
      Source sequence(s)
      AF152521
      Consensus CDS
      CCDS75340.1
      UniProtKB/Swiss-Prot
      Q9Y5G0
      Related
      ENSP00000484888.1, ENST00000621169.1
      Conserved Domains (3) summary
      cd11304
      Location:246 → 339
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:32 → 112
      Cadherin_2; Cadherin-like
      pfam16492
      Location:683 → 764
      Cadherin_C_2; Cadherin cytoplasmic C-terminal

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      141397947..141512975
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      141923583..142038959
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y5G0.1 GenPept UniProtKB/Swiss-Prot:Q9Y5G0

    Gene LinkOut

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