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PCDHAC1 protocadherin alpha subfamily C, 1 [ Homo sapiens (human) ]

Gene ID: 56135, updated on 1-Jun-2020

Summary

Official Symbol
PCDHAC1provided by HGNC
Official Full Name
protocadherin alpha subfamily C, 1provided by HGNC
Primary source
HGNC:HGNC:8676
See related
Ensembl:ENSG00000248383 MIM:606320
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-ALPHA-C1
Summary
This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]
Orthologs

Genomic context

See PCDHAC1 in Genome Data Viewer
Location:
5q31.3
Exon count:
4
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (140926299..141012347)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140306302..140391929)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene protocadherin alpha 1 Neighboring gene protocadherin alpha cluster, complex locus Neighboring gene protocadherin alpha 2 Neighboring gene protocadherin alpha 3 Neighboring gene protocadherin alpha 4 Neighboring gene protocadherin alpha 5 Neighboring gene protocadherin alpha 6 Neighboring gene uncharacterized LOC112267934 Neighboring gene protocadherin alpha 7 Neighboring gene protocadherin alpha 8 Neighboring gene protocadherin alpha 9 Neighboring gene protocadherin alpha 10 Neighboring gene protocadherin alpha 14 pseudogene Neighboring gene protocadherin alpha 11 Neighboring gene protocadherin alpha 12 Neighboring gene protocadherin alpha 13 Neighboring gene protocadherin alpha subfamily C, 2 Neighboring gene protocadherin alpha constant Neighboring gene uncharacterized LOC101926905 Neighboring gene protocadherin beta 1 Neighboring gene protocadherin beta cluster Neighboring gene protocadherin beta 2

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

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
NHGRI GWA Catalog

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
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
 
nervous system development TAS
Traceable Author Statement
more info
PubMed 
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_000016.2 

    Range
    192591..278218
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
  2. NG_050672.1 RefSeqGene

    Range
    5001..90628
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_018898.5NP_061721.2  protocadherin alpha-C1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_061721.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) includes the constant region exons and encodes the longest isoform (1).
    Source sequence(s)
    AC010223
    Consensus CDS
    CCDS4241.1
    UniProtKB/Swiss-Prot
    Q9H158
    Related
    ENSP00000253807.2, ENST00000253807.2
    Conserved Domains (3) summary
    cd11304
    Location:449551
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:21103
    Cadherin_2; Cadherin-like
    pfam15974
    Location:812955
    Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region
  2. NM_031882.3NP_114088.2  protocadherin alpha-C1 isoform 2 precursor

    See identical proteins and their annotated locations for NP_114088.2

    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 a shorter isoform (2), compared to isoform 1. This short variant is represented based on data in PMID:10380929.
    Source sequence(s)
    AA601497, AC010223, BC136785, HY126945
    UniProtKB/TrEMBL
    B2RNA7
    Related
    ENSP00000386356.3, ENST00000409700.4
    Conserved Domains (2) summary
    cd11304
    Location:449551
    Cadherin_repeat; Cadherin tandem repeat domain
    cl09101
    Location:21103
    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 Updated Annotation Release 109.

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
    140926299..141012347
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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