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PCDH1 protocadherin 1 [ Homo sapiens (human) ]

Gene ID: 5097, updated on 1-Jun-2020

Summary

Official Symbol
PCDH1provided by HGNC
Official Full Name
protocadherin 1provided by HGNC
Primary source
HGNC:HGNC:8655
See related
Ensembl:ENSG00000156453 MIM:603626
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
PC42; PCDH42
Summary
This gene belongs to the protocadherin subfamily within the cadherin superfamily. The encoded protein is a membrane protein found at cell-cell boundaries. It is involved in neural cell adhesion, suggesting a possible role in neuronal development. The protein includes an extracelllular region, containing 7 cadherin-like domains, a transmembrane region and a C-terminal cytoplasmic region. Cells expressing the protein showed cell aggregation activity. Alternative splicing occurs in this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in brain (RPKM 10.0), colon (RPKM 8.9) and 22 other tissues See more
Orthologs

Genomic context

See PCDH1 in Genome Data Viewer
Location:
5q31.3
Exon count:
9
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (141850393..141878410, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (141232655..141258361, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 9103 Neighboring gene uncharacterized LOC107986454 Neighboring gene glycine cleavage system protein H (aminomethyl carrier) pseudogene Neighboring gene DAP3 binding cell death enhancer 1 Neighboring gene protocadherin 12

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

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide meta-analysis identifies two novel loci associated with high myopia in the Han Chinese population.
NHGRI GWA Catalog
Common genetic variation and antidepressant efficacy in major depressive disorder: a meta-analysis of three genome-wide pharmacogenetic studies.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ53887, MGC45991

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 
cell-cell signaling TAS
Traceable Author Statement
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
cell junction IDA
Inferred from Direct Assay
more info
 
cell-cell junction TAS
Traceable Author Statement
more info
PubMed 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
plasma membrane TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
protocadherin-1
Names
cadherin-like 1
cadherin-like protein 1
protocadherin 42

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.

mRNA and Protein(s)

  1. NM_001278613.2NP_001265542.1  protocadherin-1 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has an alternate 5' exon and lacks two 3' exons. Its transcription extends past a splice site that is used in variant 2, resulting in a novel 3' coding region and 3' UTR compared to variant 2. It encodes isoform 3 which is shorter and has a distinct C-terminus, compared to isoform 2.
    Source sequence(s)
    AK300564, AK304231, BC035812, HO663512
    UniProtKB/Swiss-Prot
    Q08174
    UniProtKB/TrEMBL
    B4DUA8, B4E2D8
    Related
    ENST00000357517.6
    Conserved Domains (3) summary
    cd11304
    Location:528624
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:8311042
    Protocadherin; Protocadherin
    cl09101
    Location:76154
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  2. NM_001278615.1NP_001265544.1  protocadherin-1 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two 5' and 3' exons, respectively. It has an alternate 5' exon and its transcription extends past a splice site that is used in variant 2, resulting in a novel 3' coding region and 3' UTR compared to variant 2. It encodes isoform 4 which has a shorter N-terminus and a shorter and distinct C-terminus, compared to isoform 2.
    Source sequence(s)
    AK308338, BC035812
    UniProtKB/Swiss-Prot
    Q08174
    Related
    ENST00000511044.1
    Conserved Domains (2) summary
    cd11304
    Location:133229
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:436647
    Protocadherin; Protocadherin
  3. NM_002587.5NP_002578.2  protocadherin-1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_002578.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks two exons and its transcription extends past a splice site that is used in variant 2, resulting in a novel 3' coding region and 3' UTR compared to variant 2. It encodes isoform 1 which is shorter and has a distinct C-terminus, compared to isoform 2.
    Source sequence(s)
    AK289512, AK304231, BC035812
    Consensus CDS
    CCDS43375.1
    UniProtKB/Swiss-Prot
    Q08174
    UniProtKB/TrEMBL
    A8K0E7, B4E2D8
    Related
    ENSP00000378043.3, ENST00000394536.4
    Conserved Domains (3) summary
    cd11304
    Location:512608
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:8151026
    Protocadherin; Protocadherin
    cl09101
    Location:60138
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  4. NM_032420.5NP_115796.2  protocadherin-1 isoform 2 precursor

    See identical proteins and their annotated locations for NP_115796.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (2).
    Source sequence(s)
    AC094107, AK304231, BC035812, BM680840, DA096772, L11369
    Consensus CDS
    CCDS4267.1
    UniProtKB/Swiss-Prot
    Q08174
    UniProtKB/TrEMBL
    B4E2D8
    Related
    ENSP00000287008.3, ENST00000287008.7
    Conserved Domains (3) summary
    cd11304
    Location:512608
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:8151026
    Protocadherin; Protocadherin
    cl09101
    Location:60138
    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
    141850393..141878410 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005268452.3XP_005268509.2  protocadherin-1 isoform X1

    Conserved Domains (3) summary
    cd11304
    Location:528624
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:8311042
    Protocadherin
    cl09101
    Location:76154
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  2. XM_005268455.3XP_005268512.1  protocadherin-1 isoform X3

    Conserved Domains (2) summary
    cd11304
    Location:133229
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:436647
    Protocadherin; Protocadherin
  3. XM_017009517.2XP_016865006.1  protocadherin-1 isoform X3

    Conserved Domains (2) summary
    cd11304
    Location:133229
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:436647
    Protocadherin; Protocadherin
  4. XM_005268454.5XP_005268511.2  protocadherin-1 isoform X2

    Conserved Domains (3) summary
    cd11304
    Location:528624
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:8311042
    Protocadherin
    cl09101
    Location:76154
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  5. XM_017009518.1XP_016865007.1  protocadherin-1 isoform X4

    Conserved Domains (2) summary
    cd11304
    Location:133229
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:436647
    Protocadherin; Protocadherin
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