Human Gene PKP1 (ENST00000367324.8_5) from GENCODE V47lift37
  Description: plakophilin 1, transcript variant 1a (from RefSeq NM_001005337.3)
Gencode Transcript: ENST00000367324.8_5
Gencode Gene: ENSG00000081277.13_7
Transcript (Including UTRs)
   Position: hg19 chr1:201,252,634-201,302,117 Size: 49,484 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg19 chr1:201,252,831-201,297,964 Size: 45,134 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:201,252,634-201,302,117)mRNA (may differ from genome)Protein (726 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PKP1_HUMAN
DESCRIPTION: RecName: Full=Plakophilin-1; AltName: Full=Band 6 protein; Short=B6P;
FUNCTION: Seems to play a role in junctional plaques. Contributes to epidermal morphogenesis.
SUBCELLULAR LOCATION: Isoform 1: Nucleus. Cell junction, desmosome.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Isoform 2 is widely expressed. Isoform 1 is expressed in stratified squamous, complex, glandular duct and bladder epithelia.
DISEASE: Defects in PKP1 are the cause of ectodermal dysplasia- skin fragility syndrome (EDSFS) [MIM:604536]; also known as McGrath syndrome. Ectodermal dysplasia defines a heterogeneous group of disorders due to abnormal development of two or more ectodermal structures. EDSFS is characterized by features of both cutaneous fragility and congenital ectodermal dysplasia affecting abnormalities in other epithelia or tissues. Desmosomes in the skin are small and poorly formed with widening of keratinocyte intercellular spaces and perturbed desmosome/keratin intermediate filament interactions.
SIMILARITY: Belongs to the beta-catenin family.
SIMILARITY: Contains 9 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


-  MalaCards Disease Associations
  MalaCards Gene Search: PKP1
Diseases sorted by gene-association score: ectodermal dysplasia/skin fragility syndrome* (1415), pkp1-related ectodermal dysplasia/skin fragility syndrome* (100), ectodermal dysplasia (36)
* = Manually curated disease association

-  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: 469.64 RPKM in Skin - Sun Exposed (Lower leg)
Total median expression: 1257.11 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 -72.30197-0.367 Picture PostScript Text
3' UTR -1160.102948-0.394 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
48431 - Lipovitellin-phosvitin complex, superhelical domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1XM9 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q13835
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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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004871 signal transducer activity
GO:0005515 protein binding
GO:0005521 lamin binding
GO:0019215 intermediate filament binding
GO:0030280 structural constituent of epidermis

Biological Process:
GO:0007155 cell adhesion
GO:0007165 signal transduction
GO:0007275 multicellular organism development
GO:0010628 positive regulation of gene expression
GO:0031424 keratinization
GO:0043312 neutrophil degranulation
GO:0045110 intermediate filament bundle assembly
GO:0070268 cornification
GO:0098609 cell-cell adhesion
GO:1902373 negative regulation of mRNA catabolic process

Cellular Component:
GO:0001533 cornified envelope
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005882 intermediate filament
GO:0005886 plasma membrane
GO:0030054 cell junction
GO:0030057 desmosome
GO:0043231 intracellular membrane-bounded organelle
GO:0101003 ficolin-1-rich granule membrane
GO:1990124 messenger ribonucleoprotein complex


-  Descriptions from all associated GenBank mRNAs
  Z34974 - H.sapiens mRNA for plakophilin (partial).
AK315291 - Homo sapiens cDNA, FLJ96309.
JD230163 - Sequence 211187 from Patent EP1572962.
X79293 - H.sapiens band-6-protein mRNA.
JD323768 - Sequence 304792 from Patent EP1572962.
JD169066 - Sequence 150090 from Patent EP1572962.
JD040988 - Sequence 22012 from Patent EP1572962.
BC115702 - Homo sapiens plakophilin 1 (ectodermal dysplasia/skin fragility syndrome), mRNA (cDNA clone IMAGE:40082608), complete cds.
BC114571 - Homo sapiens plakophilin 1 (ectodermal dysplasia/skin fragility syndrome), mRNA (cDNA clone MGC:138829 IMAGE:40082609), complete cds.
AK316131 - Homo sapiens cDNA, FLJ79030 complete cds, highly similar to Plakophilin-1.
AK299473 - Homo sapiens cDNA FLJ56941 complete cds, highly similar to Plakophilin-1.
JD499328 - Sequence 480352 from Patent EP1572962.
JD219155 - Sequence 200179 from Patent EP1572962.
AK123555 - Homo sapiens cDNA FLJ41561 fis, clone CTONG1000288.
BC040253 - Homo sapiens, clone IMAGE:4754288, mRNA.

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

Protein Q13835 (Reactome details) participates in the following event(s):

R-HSA-201595 Caspase-mediated cleavage of plakophilin-1
R-HSA-6800426 Exocytosis of ficolin-rich granule membrane proteins
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-351906 Apoptotic cleavage of cell adhesion proteins
R-HSA-6798695 Neutrophil degranulation
R-HSA-111465 Apoptotic cleavage of cellular proteins
R-HSA-168249 Innate Immune System
R-HSA-6805567 Keratinization
R-HSA-6809371 Formation of the cornified envelope
R-HSA-75153 Apoptotic execution phase
R-HSA-168256 Immune System
R-HSA-1266738 Developmental Biology
R-HSA-109581 Apoptosis
R-HSA-5357801 Programmed Cell Death

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000367324.1, ENST00000367324.2, ENST00000367324.3, ENST00000367324.4, ENST00000367324.5, ENST00000367324.6, ENST00000367324.7, NM_001005337, O00645, PKP1_HUMAN, Q13835, Q14CA0, Q15152, uc318fvd.1, uc318fvd.2
UCSC ID: ENST00000367324.8_5
RefSeq Accession: NM_001005337.3
Protein: Q13835 (aka PKP1_HUMAN)

-  Gene Model Information
  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.