Pkp1 plakophilin 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Pkp1provided by RGD
Official Full Name: plakophilin 1provided by RGD
Primary source: RGD:1307472
See related: EnsemblRapid:ENSRNOG00000010076 AllianceGenome:RGD:1307472
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 DNA binding activity; cadherin binding activity; and lamin binding activity. Predicted to be involved in several processes, including intermediate filament bundle assembly; positive regulation of cell-cell adhesion; and positive regulation of macromolecule biosynthetic process. Predicted to be located in desmosome; nucleus; and perinuclear region of cytoplasm. Predicted to be active in several cellular components, including adherens junction; cornified envelope; and nucleus. Human ortholog(s) of this gene implicated in ectodermal dysplasia. Orthologous to human PKP1 (plakophilin 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Lung (RPKM 25.0), Thymus (RPKM 23.5) and 6 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 13q13

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (49861340..49909162, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (47309607..47357432, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (52705174..52753089, complement)

Chromosome 13 - NC_086031.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables cadherin binding	IBA Inferred from Biological aspect of Ancestor more info
enables lamin binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in ameloblast differentiation	IEA Inferred from Electronic Annotation more info
involved_in biological_process	ND No biological Data available more info
involved_in cell-cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in desmosome assembly	IEA Inferred from Electronic Annotation more info
involved_in desmosome maintenance	IEA Inferred from Electronic Annotation more info
involved_in intermediate filament bundle assembly	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of mRNA catabolic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cap-dependent translational initiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cap-dependent translational initiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell-cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell-cell adhesion	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of keratinocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein localization to plasma membrane	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in transepithelial water transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cornified envelope	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in desmosome	ISO Inferred from Sequence Orthology more info
located_in nuclear stress granule	IEA Inferred from Electronic Annotation more info
located_in nuclear stress granule	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	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

General protein information

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Preferred Names: plakophilin-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_001394216.2 → NP_001381145.1 plakophilin-1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000013

UniProtKB/TrEMBL

A6ICH3, D3ZY51

Related

ENSRNOP00000013532.5, ENSRNOT00000013531.7

Conserved Domains (3) summary

smart00185
Location:277 → 317

ARM; Armadillo/beta-catenin-like repeats

sd00043
Location:240 → 273

ARM; armadillo repeat [structural motif]

pfam00514
Location:516 → 557

Arm; Armadillo/beta-catenin-like repeat

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086031.1 Reference GRCr8

Range

49861340..49909162 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001107181.1: Suppressed sequence

Description

NM_001107181.1: This RefSeq was removed because it is a nonsense-mediated mRNA decay (NMD) candidate.