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PCDHGB3 protocadherin gamma subfamily B, 3 [ Homo sapiens (human) ]

Gene ID: 56102, updated on 23-Nov-2021

Summary

Official Symbol
PCDHGB3provided by HGNC
Official Full Name
protocadherin gamma subfamily B, 3provided by HGNC
Primary source
HGNC:HGNC:8710
See related
Ensembl:ENSG00000262209 MIM:606301
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-B3
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

See PCDHGB3 in Genome Data Viewer
Location:
5q31.3
Exon count:
4
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (141370242..141512975)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140749809..140892542)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene solute carrier family 25 member 2 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 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 A, 6 Neighboring gene protocadherin gamma subfamily A, 7 Neighboring gene protocadherin gamma subfamily B, 4 Neighboring gene protocadherin gamma subfamily A, 8 Neighboring gene protocadherin gamma subfamily B, 5 Neighboring gene protocadherin gamma subfamily A, 9 Neighboring gene protocadherin gamma subfamily B, 6 Neighboring gene protocadherin gamma subfamily A, 10 Neighboring gene protocadherin gamma subfamily A, 11 Neighboring gene protocadherin gamma subfamily B, 7 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 RNA, 7SL, cytoplasmic 68, pseudogene Neighboring gene protocadherin gamma subfamily C, 3 Neighboring gene protocadherin gamma subfamily C, 4 Neighboring gene protocadherin gamma subfamily C, 5 Neighboring gene Sharpr-MPRA regulatory region 13534 Neighboring gene diaphanous related formin 1 Neighboring gene Sharpr-MPRA regulatory region 13738

Genomic regions, transcripts, and products

Expression

  • 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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
PubMed 
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

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
    80461..223176
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_018924.5NP_061747.2  protocadherin gamma-B3 isoform 1 precursor

    See identical proteins and their annotated locations for NP_061747.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript, which includes the constant region exons, and encodes the longer isoform (1).
    Source sequence(s)
    AF152332, BC150172, KC877131
    Consensus CDS
    CCDS58980.1
    UniProtKB/Swiss-Prot
    Q9Y5G1
    Related
    ENSP00000461862.1, ENST00000576222.2
    Conserved Domains (4) summary
    cd11304
    Location:247343
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:32112
    Cadherin_2; Cadherin-like
    pfam15974
    Location:808902
    Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region
    pfam16492
    Location:687769
    Cadherin_C_2; Cadherin cytoplasmic C-terminal
  2. NM_032097.3NP_115268.2  protocadherin gamma-B3 isoform 2 precursor

    See identical proteins and their annotated locations for NP_115268.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks the constant region exons and contains an alternate 3' coding region compared to variant 1. The encoded isoform (2) has a shorter, distinct C-terminus than isoform 1.
    Source sequence(s)
    AF152519, BC150172, KC877131
    Consensus CDS
    CCDS75334.1
    UniProtKB/Swiss-Prot
    Q9Y5G1
    Related
    ENSP00000483339.1, ENST00000618934.1
    Conserved Domains (3) summary
    cd11304
    Location:247343
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:32112
    Cadherin_2; Cadherin-like
    pfam16492
    Location:687768
    Cadherin_C_2; Cadherin cytoplasmic C-terminal

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    141370242..141512975
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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