Format

Send to:

Choose Destination

PCDHGC3 protocadherin gamma subfamily C, 3 [ Homo sapiens (human) ]

Gene ID: 5098, updated on 2-Oct-2018

Summary

Official Symbol
PCDHGC3provided by HGNC
Official Full Name
protocadherin gamma subfamily C, 3provided by HGNC
Primary source
HGNC:HGNC:8716
See related
Ensembl:ENSG00000240184 MIM:603627; Vega:OTTHUMG00000129613
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
PC43; PCDH2; PCDH-GAMMA-C3
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 PCDHGC3 in Genome Data Viewer
Location:
5q31.3
Exon count:
4
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (141476002..141512977)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140855569..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 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, 4 Neighboring gene protocadherin gamma subfamily C, 5 Neighboring gene diaphanous related formin 1 Neighboring gene uncharacterized LOC100505658 Neighboring gene ribosomal protein S27a pseudogene 10

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules NAS
Non-traceable Author Statement
more info
PubMed 
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 
membrane NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
protocadherin gamma-C3
Names
cadherin-like 2
protocadherin 43
protocadherin-2

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
    186199..223176
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_002588.3NP_002579.2  protocadherin gamma-C3 isoform 1 precursor

    See identical proteins and their annotated locations for NP_002579.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) includes the constant region exons and encodes the longest isoform (1).
    Source sequence(s)
    BC006439, BC019299, BC063437
    Consensus CDS
    CCDS4261.1
    UniProtKB/Swiss-Prot
    Q9UN70
    UniProtKB/TrEMBL
    Q9BR81
    Related
    ENSP00000312070.3, OTTHUMP00000160013, ENST00000308177.4, OTTHUMT00000251808
    Conserved Domains (4) summary
    cd11304
    Location:249348
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:33114
    Cadherin_2; Cadherin-like
    pfam15974
    Location:813907
    Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region
    pfam16492
    Location:689770
    Cadherin_C_2; Cadherin cytoplasmic C-terminal
  2. NM_032402.1NP_115778.1  protocadherin gamma-C3 isoform 2 precursor

    See identical proteins and their annotated locations for NP_115778.1

    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)
    AF152524, BC006439, L11371
    Consensus CDS
    CCDS75348.1
    UniProtKB/Swiss-Prot
    Q9UN70
    UniProtKB/TrEMBL
    Q9BR81
    Related
    ENSP00000481219.1, OTTHUMP00000275906, ENST00000611950.1, OTTHUMT00000476717
    Conserved Domains (3) summary
    cd11304
    Location:249348
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:33114
    Cadherin_2; Cadherin-like
    pfam16492
    Location:689775
    Cadherin_C_2; Cadherin cytoplasmic C-terminal
  3. NM_032403.2NP_115779.1  protocadherin gamma-C3 isoform 3

    See identical proteins and their annotated locations for NP_115779.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) utilizes an alternative splice donor site that truncates exon 1. This shortest isoform (3) contains no cadherin domains and lacks a signal sequence and transmembrane region. The functional significance of this isoform is unknown but the transcript is well represented in the EST database.
    Source sequence(s)
    BC006439, BC063437
    Consensus CDS
    CCDS75347.1
    UniProtKB/TrEMBL
    Q9BR81
    Related
    ENSP00000483383.1, OTTHUMP00000275881, ENST00000617641.4, OTTHUMT00000476716
    Conserved Domains (1) summary
    pfam15974
    Location:13107
    Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region

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.p12 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p12 Primary Assembly

    Range
    141476002..141512977
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Support Center