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PCDHGC4 protocadherin gamma subfamily C, 4 [ Homo sapiens (human) ]

Gene ID: 56098, updated on 17-Jun-2019

Summary

Official Symbol
PCDHGC4provided by HGNC
Official Full Name
protocadherin gamma subfamily C, 4provided by HGNC
Primary source
HGNC:HGNC:8717
See related
Ensembl:ENSG00000242419 MIM:606305
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-C4
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

Genomic context

See PCDHGC4 in Genome Data Viewer
Location:
5q31.3
Exon count:
4
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (141485174..141512979)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140864741..140892546)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene protocadherin gamma subfamily A, 1 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 B, 3 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 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, 5 Neighboring gene diaphanous related formin 1 Neighboring gene Sharpr-MPRA regulatory region 13738 Neighboring gene uncharacterized LOC100505658

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

Clone Names

  • MGC24978, MGC119489

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
homophilic cell adhesion via plasma membrane adhesion molecules IEA
Inferred from Electronic Annotation
more info
 
synapse organization IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

NCBI Reference Sequences (RefSeq)

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
    195371..223176
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
  2. NG_050746.1 RefSeqGene

    Range
    5001..32806
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_018928.2NP_061751.1  protocadherin gamma-C4 isoform 1 precursor

    See identical proteins and their annotated locations for NP_061751.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) includes the constant region exons and encodes the longest isoform (1).
    Source sequence(s)
    AF152338
    Consensus CDS
    CCDS4262.1
    UniProtKB/Swiss-Prot
    Q9Y5F7
    Related
    ENSP00000306918.1, ENST00000306593.1
    Conserved Domains (3) summary
    cd11304
    Location:246346
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam15974
    Location:817911
    Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region
    cl09101
    Location:30111
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  2. NM_032406.1NP_115782.1  protocadherin gamma-C4 isoform 2 precursor

    See identical proteins and their annotated locations for NP_115782.1

    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)
    AF152525
    Consensus CDS
    CCDS75349.1
    UniProtKB/Swiss-Prot
    Q9Y5F7
    Related
    ENSP00000483845.1, ENST00000617094.1
    Conserved Domains (2) summary
    cd11304
    Location:246346
    Cadherin_repeat; Cadherin tandem repeat domain
    cl09101
    Location:30111
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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
    141485174..141512979
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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