Pcdh15 protocadherin related 15 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Pcdh15provided by RGD
Full Name: protocadherin related 15provided by RGD
Primary source: RGD:1590969
See related: EnsemblRapid:ENSRNOG00000000606 AllianceGenome:RGD:1590969
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable calcium ion binding activity. Involved in response to calcium ion. Predicted to be located in several cellular components, including extracellular space; photoreceptor outer segment; and synapse. Predicted to be active in plasma membrane and stereocilium. Human ortholog(s) of this gene implicated in Usher syndrome type 1D; Usher syndrome type 1F; and autosomal recessive nonsyndromic deafness 23. Orthologous to human PCDH15 (protocadherin related 15). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Brain (RPKM 29.9), Spleen (RPKM 11.9) and 3 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 20p12-p11

Exon count:: 45

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (13996383..15495206, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (13997094..15496446, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (14952213..15334745, complement)

Chromosome 20 - NC_086038.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Since the rat is more advantageous for clinical and pharmacological studies than the mouse, the KCI rat strain may be a better disease model for Pcdh15-deficit USH1F and DFNB23.
Title: Characterization of the Kyoto circling (KCI) rat carrying a spontaneous nonsense mutation in the protocadherin 15 (Pcdh15) gene.

Submit: New GeneRIF Correction

General gene information

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Markers

D20Got15 (e-PCR)
- UniSTS:114986

RH144278 (e-PCR)
- UniSTS:233523

D20Got14 (e-PCR)
- UniSTS:114229

RH142552 (e-PCR)
- UniSTS:231799

AU048858 (e-PCR)
- UniSTS:145308

D20Rat60 (e-PCR), detects polymorphism
- UniSTS:227297

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within actin filament organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within adult locomotory behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within adult walking behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within auditory receptor cell stereocilium organization	ISO Inferred from Sequence Orthology more info
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within detection of mechanical stimulus involved in equilibrioception	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within detection of mechanical stimulus involved in sensory perception of sound	ISO Inferred from Sequence Orthology more info
involved_in equilibrioception	ISO Inferred from Sequence Orthology more info
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within inner ear auditory receptor cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inner ear development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inner ear receptor cell stereocilium organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within locomotory behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within morphogenesis of an epithelium	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within multicellular organism growth	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within non-motile cilium assembly	ISO Inferred from Sequence Orthology more info
involved_in photoreceptor cell maintenance	ISO Inferred from Sequence Orthology more info
involved_in response to calcium ion	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within righting reflex	ISO Inferred from Sequence Orthology more info
involved_in sensory perception of light stimulus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within sensory perception of sound	ISO Inferred from Sequence Orthology more info
involved_in sensory perception of sound	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within startle response	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within visual perception	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in extracellular space	ISO Inferred from Sequence Orthology more info
located_in photoreceptor outer segment	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in stereocilium	ISO Inferred from Sequence Orthology more info
located_in stereocilium	ISO Inferred from Sequence Orthology more info
located_in synapse	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: protocadherin-15

Names: protocadherin 15

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.