Human Gene PKP3 (uc001lpc.3)
  Description: Homo sapiens plakophilin 3 (PKP3), mRNA.
RefSeq Summary (NM_007183): This gene encodes a member of the arm-repeat (armadillo) and plakophilin gene families. Plakophilin proteins contain numerous armadillo repeats, localize to cell desmosomes and nuclei, and participate in linking cadherins to intermediate filaments in the cytoskeleton. This protein may act in cellular desmosome-dependent adhesion and signaling pathways. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2014].
Transcript (Including UTRs)
   Position: hg19 chr11:394,217-404,908 Size: 10,692 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr11:394,293-404,569 Size: 10,277 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:394,217-404,908)mRNA (may differ from genome)Protein (797 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PKP3_HUMAN
DESCRIPTION: RecName: Full=Plakophilin-3;
FUNCTION: May play a role in junctional plaques.
SUBCELLULAR LOCATION: Nucleus. Cell junction, desmosome. Note=Nuclear and associated with desmosomes.
TISSUE SPECIFICITY: Found in desmosomes of most simple and stratified epithelia. Not found in foreskin fibroblasts and various sarcoma-derived cell lines. Beside dendritic reticular cells of lymphatic follicles not found in non-epithelial desmosome-bearing tissues.
SIMILARITY: Belongs to the beta-catenin family.
SIMILARITY: Contains 8 ARM repeats.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PKP3
CDC HuGE Published Literature: PKP3

-  MalaCards Disease Associations
  MalaCards Gene Search: PKP3
Diseases sorted by gene-association score: uterine body mixed cancer (11), uterine corpus cancer (5), irritant dermatitis (5)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 135.98 RPKM in Esophagus - Mucosa
Total median expression: 580.69 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -29.0076-0.382 Picture PostScript Text
3' UTR -150.80339-0.445 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011989 - ARM-like
IPR016024 - ARM-type_fold
IPR000225 - Armadillo

Pfam Domains:
PF00514 - Armadillo/beta-catenin-like repeat

SCOP Domains:
48371 - ARM repeat

ModBase Predicted Comparative 3D Structure on Q9Y446
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0019899 enzyme binding
GO:0045294 alpha-catenin binding
GO:0050839 cell adhesion molecule binding
GO:0098641 cadherin binding involved in cell-cell adhesion
GO:0003723 RNA binding
GO:0045182 translation regulator activity

Biological Process:
GO:0002159 desmosome assembly
GO:0007155 cell adhesion
GO:0010628 positive regulation of gene expression
GO:0031424 keratinization
GO:0070268 cornification
GO:0072659 protein localization to plasma membrane
GO:0098609 cell-cell adhesion
GO:1902373 negative regulation of mRNA catabolic process
GO:0006417 regulation of translation

Cellular Component:
GO:0001533 cornified envelope
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0005913 cell-cell adherens junction
GO:0030054 cell junction
GO:0030057 desmosome
GO:1990124 messenger ribonucleoprotein complex


-  Descriptions from all associated GenBank mRNAs
  FN421477 - Homo sapiens partial mRNA for plakophilin 3b (PKP3 gene), splice variant B, cell line HaCaT.
BC000081 - Homo sapiens plakophilin 3, mRNA (cDNA clone MGC:3235 IMAGE:3504300), complete cds.
AK025067 - Homo sapiens cDNA: FLJ21414 fis, clone COL04025, highly similar to HSZ98265 Homo sapiens mRNA for plakophilin 3.
AK223511 - Homo sapiens mRNA for plakophilin 3 variant, clone: FCC122A01.
Z98265 - Homo sapiens mRNA for plakophilin 3.
AF053719 - Homo sapiens plakophilin-3 protein mRNA, complete cds.
JD221217 - Sequence 202241 from Patent EP1572962.
JD457278 - Sequence 438302 from Patent EP1572962.
JD075764 - Sequence 56788 from Patent EP1572962.
JD409642 - Sequence 390666 from Patent EP1572962.
JD222513 - Sequence 203537 from Patent EP1572962.
DQ894875 - Synthetic construct Homo sapiens clone IMAGE:100009335; FLH180803.01L; RZPDo839G03133D plakophilin 3 (PKP3) gene, encodes complete protein.
DQ891692 - Synthetic construct clone IMAGE:100004322; FLH180807.01X; RZPDo839G03134D plakophilin 3 (PKP3) gene, encodes complete protein.
CU674026 - Synthetic construct Homo sapiens gateway clone IMAGE:100020547 5' read PKP3 mRNA.
KJ898373 - Synthetic construct Homo sapiens clone ccsbBroadEn_07767 PKP3 gene, encodes complete protein.
JD122465 - Sequence 103489 from Patent EP1572962.
JD110538 - Sequence 91562 from Patent EP1572962.
JD174054 - Sequence 155078 from Patent EP1572962.
JD273691 - Sequence 254715 from Patent EP1572962.
JD204285 - Sequence 185309 from Patent EP1572962.
JD054125 - Sequence 35149 from Patent EP1572962.
JD346221 - Sequence 327245 from Patent EP1572962.
JD053250 - Sequence 34274 from Patent EP1572962.
JD092669 - Sequence 73693 from Patent EP1572962.
JD276859 - Sequence 257883 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9Y446 (Reactome details) participates in the following event(s):

R-HSA-6809393 Keratin filaments bind cell-cell adhesion complexes
R-HSA-6814695 PERP binds desmosomes
R-HSA-8942224 Filaggrin binds Keratin tonofilament:Desmosome
R-HSA-6805567 Keratinization
R-HSA-6809371 Formation of the cornified envelope
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: NM_007183, NP_009114, PKP3_HUMAN, Q53EX8, Q9Y446
UCSC ID: uc001lpc.3
RefSeq Accession: NM_007183
Protein: Q9Y446 (aka PKP3_HUMAN)
CCDS: CCDS7695.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_007183.2
exon count: 13CDS single in 3' UTR: no RNA size: 2845
ORF size: 2394CDS single in intron: no Alignment % ID: 99.96
txCdsPredict score: 4514.00frame shift in genome: no % Coverage: 98.73
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 112# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.