Pcdha4 protocadherin alpha 4 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Pcdha4provided by MGI
Official Full Name: protocadherin alpha 4provided by MGI
Primary source: MGI:MGI:1298406
See related: Ensembl:ENSMUSG00000104252 AllianceGenome:MGI:1298406
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Cnr1; Crnr1
Summary: Enables calcium ion binding activity and identical protein binding activity. Predicted to be involved in cell adhesion. Located in endoplasmic reticulum; membrane; and synapse. Is expressed in brain. Orthologous to human PCDHA4 (protocadherin alpha 4). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in CNS E18 (RPKM 20.9), cortex adult (RPKM 12.7) and 6 other tissues See more
Orthologs: human all
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Genomic context

Location:: 18 B2- B3; 18 19.46 cM

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	18	NC_000084.7 (37085742..37320710)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	18	NC_000084.6 (36952689..37187657)

Chromosome 18 - NC_000084.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Shedding of the Pcdhalpha extracellular domain and subsequent processing by gamma-secretase require endocytosis.
Title: Proteolytic processing of protocadherin proteins requires endocytosis.
show that protocadherins (Pcdhs) form a heteromeric signaling complex(es), consisting of multiple Pcdh isoforms, receptor tyrosine kinases, phosphatases, and cell adhesion molecules.
Title: Phosphorylation of protocadherin proteins by the receptor tyrosine kinase Ret.
CNR1 has a heterophilic, calcium-dependent cell adhesion activity with the beta1 integrin subfamily, suggesting the possibility of CNR-beta1 integrin association in synaptogenesis.
Title: Cadherin-related neuronal receptor 1 (CNR1) has cell adhesion activity with beta1 integrin mediated through the RGD site of CNR1.
This pattern of Pcdha4 expression suggests its involvement in the development of neocortical connectivity.
Title: CNR/Pcdhalpha family in subplate neurons, and developing cortical connectivity.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Pcdha4 (e-PCR), detects polymorphism
- UniSTS:164869

PMC312645P1 (e-PCR)
- UniSTS:272906

Pcdha4 (e-PCR), detects polymorphism
- UniSTS:265498

Pcdha4 (e-PCR), detects polymorphism
- UniSTS:265266

WI-19540 (e-PCR)
- UniSTS:63886

NoName (e-PCR)
- UniSTS:547524

Pcdha (e-PCR), detects polymorphism
- UniSTS:547524

RH65516 (e-PCR)
- UniSTS:66009

RH125196 (e-PCR)
- UniSTS:162018

PMC311048P1 (e-PCR)
- UniSTS:272867

PMC311048P2 (e-PCR)
- UniSTS:272868

PMC311048P3 (e-PCR)
- UniSTS:272869

NoName (e-PCR)
- UniSTS:224501

Readthrough Pcdha4b

Readthrough gene: Pcdha4b, Included gene: Pcdhga9

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IC Inferred by Curator more info	PubMed

Component	Evidence Code	Pubs
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in synapse	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: protocadherin alpha-4

Names: PCDH-alpha-4; cadherin-related neuronal receptor 1

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.

mRNA and Protein(s)

NM_007766.3 → NP_031792.1 protocadherin alpha-4 precursor

See identical proteins and their annotated locations for NP_031792.1

Status: VALIDATED

Source sequence(s)

AC020968, AC020972, AC020973

Consensus CDS

CCDS37776.1

UniProtKB/Swiss-Prot

O88689, Q3UEX3, Q6PAM9, Q8K487, Q8K489

Related

ENSMUSP00000141408.2, ENSMUST00000192512.6

Conserved Domains (3) summary

cd11304
Location:247 → 346

Cadherin_repeat; Cadherin tandem repeat domain

pfam08266
Location:30 → 111

Cadherin_2; Cadherin-like

pfam15974
Location:796 → 939

Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region