Pcdha9 protocadherin alpha 9 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Pcdha9provided by MGI
Official Full Name: protocadherin alpha 9provided by MGI
Primary source: MGI:MGI:2447322
See related: Ensembl:ENSMUSG00000103770 AllianceGenome:MGI:2447322
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
Summary: Predicted to enable calcium ion binding activity. Acts upstream of or within aorta development; aortic valve development; and gene expression. Located in membrane. Is active in cell-cell contact zone. Is expressed in brain and gut. Orthologous to human PCDHA10 (protocadherin alpha 10). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in CNS E18 (RPKM 19.3), cortex adult (RPKM 12.0) and 7 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 (37130933..37320710)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	18	NC_000084.6 (36997880..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?

PCDHA9 as a candidate gene for amyotrophic lateral sclerosis.
Title: PCDHA9 as a candidate gene for amyotrophic lateral sclerosis.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Chemically induced (ENU) (1) 1 citation
Endonuclease-mediated (2) 1 citation

General gene information

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Markers

PMC312645P1 (e-PCR)
- UniSTS:272906

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

NoName (e-PCR)
- UniSTS:547524

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

RH65516 (e-PCR)
- UniSTS:66009

PMC311048P1 (e-PCR)
- UniSTS:272867

PMC311048P2 (e-PCR)
- UniSTS:272868

PMC311048P3 (e-PCR)
- UniSTS:272869

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables molecular_function	ND No biological Data available more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within aorta development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within aortic valve development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within aortic valve development	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within apoptotic process	ISA Inferred from Sequence Alignment more info	PubMed
acts_upstream_of_or_within apoptotic process	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within cardiac left ventricle formation	ISO Inferred from Sequence Orthology more info	PubMed
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cell migration	ISA Inferred from Sequence Alignment more info	PubMed
acts_upstream_of_or_within cell migration	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within cell population proliferation	ISA Inferred from Sequence Alignment more info	PubMed
acts_upstream_of_or_within cell population proliferation	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart development	ISS Inferred from Sequence or Structural Similarity more info	PubMed
acts_upstream_of_or_within heart valve development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in cell-cell contact zone	IDA Inferred from Direct Assay more info	PubMed
is_active_in cell-cell contact zone	ISS Inferred from Sequence or Structural Similarity 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

General protein information

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Preferred Names: protocadherin alpha-9

Names: PCDH-alpha-9

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_138661.1 → NP_619602.1 protocadherin alpha-9 precursor

See identical proteins and their annotated locations for NP_619602.1

Status: VALIDATED

Source sequence(s)

AY013767

Consensus CDS

CCDS37777.1

UniProtKB/Swiss-Prot

Q91Y11

UniProtKB/TrEMBL

O88195

Related

ENSMUSP00000111323.4, ENSMUST00000115659.6

Conserved Domains (3) summary

cd11304
Location:276 → 376

Cadherin_repeat; Cadherin tandem repeat domain

pfam08266
Location:60 → 141

Cadherin_2; Cadherin-like

pfam15974
Location:828 → 971

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