Pkp1 (plakophilin 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Pathways
Gene: Pkp1 (plakophilin 1) Rattus norvegicus
Analyze
Symbol: Pkp1
Name: plakophilin 1
RGD ID: 1307472
Description: Predicted to enable DNA binding activity; cadherin binding activity; and lamin binding activity. Predicted to be involved in several processes, including ameloblast differentiation; desmosome organization; and positive regulation of macromolecule biosynthetic process. Predicted to be located in desmosome; nuclear stress granule; 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); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC304822; plakophilin-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81349,861,340 - 49,909,162 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1349,861,340 - 49,909,162 (-)EnsemblGRCr8
mRatBN7.21347,309,607 - 47,357,432 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1347,309,614 - 47,357,465 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1349,917,668 - 49,965,528 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01351,205,725 - 51,253,592 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01348,468,998 - 48,517,003 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01352,705,174 - 52,753,089 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1352,705,174 - 52,752,997 (-)Ensemblrn6Rnor6.0
Rnor_5.01357,753,232 - 57,800,892 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41348,910,028 - 48,958,983 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1347,626,371 - 47,674,244 (-)NCBICelera
RGSC_v3.11348,924,070 - 48,973,030 (-)NCBI
Cytogenetic Map13q13NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Mutations in the plakophilin 1 gene result in ectodermal dysplasia/skin fragility syndrome. McGrath JA, etal., Nat Genet. 1997 Oct;17(2):240-4.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:10852826   PMID:18496566   PMID:23376485   PMID:25225333  


Genomics

Comparative Map Data
Pkp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81349,861,340 - 49,909,162 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1349,861,340 - 49,909,162 (-)EnsemblGRCr8
mRatBN7.21347,309,607 - 47,357,432 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1347,309,614 - 47,357,465 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1349,917,668 - 49,965,528 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01351,205,725 - 51,253,592 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01348,468,998 - 48,517,003 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01352,705,174 - 52,753,089 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1352,705,174 - 52,752,997 (-)Ensemblrn6Rnor6.0
Rnor_5.01357,753,232 - 57,800,892 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41348,910,028 - 48,958,983 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1347,626,371 - 47,674,244 (-)NCBICelera
RGSC_v3.11348,924,070 - 48,973,030 (-)NCBI
Cytogenetic Map13q13NCBI
PKP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381201,283,506 - 201,332,989 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1201,283,452 - 201,332,993 (+)Ensemblhg38GRCh38
GRCh371201,252,634 - 201,302,117 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361199,519,203 - 199,568,740 (+)NCBIBuild 36Build 36hg18NCBI36
Celera1174,376,403 - 174,425,974 (+)NCBICelera
Cytogenetic Map1q32.1NCBI
HuRef1172,418,808 - 172,468,387 (+)NCBIHuRef
CHM1_11202,674,744 - 202,724,331 (+)NCBICHM1_1
T2T-CHM13v2.01200,541,289 - 200,590,813 (+)NCBIT2T-CHM13v2.0
Pkp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391135,799,132 - 135,846,945 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1135,799,133 - 135,846,945 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381135,871,394 - 135,919,207 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1135,871,395 - 135,919,207 (-)Ensemblmm10GRCm38
MGSCv371137,767,972 - 137,815,601 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361137,687,806 - 137,735,435 (-)NCBIMGSCv36mm8
Celera1138,506,279 - 138,553,622 (-)NCBICelera
Cytogenetic Map1E4NCBI
cM Map159.35NCBI
Pkp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540637,419,856 - 37,465,655 (+)Ensembl
ChiLan1.0NW_00495540637,420,019 - 37,465,588 (+)NCBIChiLan1.0ChiLan1.0
PKP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2148,049,593 - 48,099,255 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1148,013,571 - 48,063,272 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01176,881,154 - 176,930,814 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11181,182,829 - 181,232,347 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1181,182,829 - 181,232,347 (+)EnsemblpanPan2panpan1.1
PKP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.171,921,143 - 1,966,910 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl71,921,143 - 1,967,703 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha71,602,267 - 1,648,044 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.071,559,536 - 1,605,354 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl71,559,536 - 1,605,354 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.171,547,384 - 1,593,191 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.071,655,145 - 1,700,910 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.071,679,800 - 1,725,628 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Pkp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934473,855,210 - 73,903,643 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365673,089,881 - 3,138,331 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365673,089,902 - 3,138,252 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PKP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1023,689,380 - 23,735,453 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11023,689,394 - 23,735,457 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21028,237,387 - 28,276,472 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PKP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12528,083,358 - 28,129,356 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2528,081,983 - 28,128,173 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605528,880,279 - 28,925,618 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pkp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248079,372,099 - 9,419,067 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248079,374,206 - 9,419,075 (-)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Pkp1
212 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:784
Count of miRNA genes:309
Interacting mature miRNAs:400
Transcripts:ENSRNOT00000013531
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134608804691088046Rat
10755495Bp387Blood pressure QTL 3873.78arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133466346187525369Rat
9589141Insul28Insulin level QTL 2810.820.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)13931346554313465Rat
6893344Cm79Cardiac mass QTL 791.50.04heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)134372077062022792Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)134619797684753113Rat
61391Bp5Blood pressure QTL 55.6arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)132230187567301875Rat
4889861Pur29Proteinuria QTL 2913.80.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)133741558480753406Rat
2317040Aia21Adjuvant induced arthritis QTL 212.75joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)13983154154831541Rat
631645Bp121Blood pressure QTL 1213.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131491565559915655Rat
2317046Aia8Adjuvant induced arthritis QTL 83.9700000286102295joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)13983154154831541Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134569998390699983Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133975454484754544Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
70170Eae14Experimental allergic encephalomyelitis QTL 140.0024nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)132320344868203448Rat
1331784Bp222Blood pressure QTL 2222.944arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131769443653050594Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133453521879535218Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)133843340883433408Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
4145117Mcs27Mammary carcinoma susceptibility QTL 270.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)134343790447841255Rat
1558644Cm45Cardiac mass QTL 453.60.002heart mass (VT:0007028)heart wet weight (CMO:0000069)132369296968692969Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133124133193395974Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
2303563Bw89Body weight QTL 896body mass (VT:0001259)body weight (CMO:0000012)133228447177284471Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
2301962Cm72Cardiac mass QTL 724.12heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)133124133158363171Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
12879477Bp401Blood pressure QTL 401arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133726209282262092Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133741558482415584Rat
6893338Cm76Cardiac mass QTL 7600.99heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)132369296968692969Rat
12879472Bp399Blood pressure QTL 399arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134522835847841255Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
9589164Gluco66Glucose level QTL 666.670.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)131515872260158722Rat
7411662Foco29Food consumption QTL 2920.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)13931346554313465Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 146 61 60 29 32 29 6 264 132 11 125 79 92 31 10 10

Sequence


Ensembl Acc Id: ENSRNOT00000013531   ⟹   ENSRNOP00000013532
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1349,861,340 - 49,909,162 (-)Ensembl
mRatBN7.2 Ensembl1347,309,614 - 47,357,465 (-)Ensembl
Rnor_6.0 Ensembl1352,705,174 - 52,752,997 (-)Ensembl
RefSeq Acc Id: NM_001394216   ⟹   NP_001381145
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81349,861,340 - 49,909,162 (-)NCBI
mRatBN7.21347,309,607 - 47,357,432 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001381145 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAP07495 (Get FASTA)   NCBI Sequence Viewer  
  CAP11463 (Get FASTA)   NCBI Sequence Viewer  
  CAR97077 (Get FASTA)   NCBI Sequence Viewer  
  CAT82305 (Get FASTA)   NCBI Sequence Viewer  
  EDM09674 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000013532
  ENSRNOP00000013532.5
Ensembl Acc Id: ENSRNOP00000013532   ⟸   ENSRNOT00000013531
RefSeq Acc Id: NP_001381145   ⟸   NM_001394216
- UniProtKB: D3ZY51 (UniProtKB/TrEMBL),   A6ICH3 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZY51-F1-model_v2 AlphaFold D3ZY51 1-605 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13698850
Promoter ID:EPDNEW_R9375
Type:initiation region
Name:Pkp1_1
Description:plakophilin 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01352,753,000 - 52,753,060EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307472 AgrOrtholog
BioCyc Gene G2FUF-18188 BioCyc
Ensembl Genes ENSRNOG00000010076 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013531 ENTREZGENE
  ENSRNOT00000013531.6 UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.10 UniProtKB/TrEMBL
InterPro ARM-like UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/TrEMBL
  Armadillo UniProtKB/TrEMBL
  Plakophilin/d_Catenin UniProtKB/TrEMBL
NCBI Gene 304822 ENTREZGENE
PANTHER PTHR10372 UniProtKB/TrEMBL
  PTHR10372:SF3 UniProtKB/TrEMBL
Pfam Arm UniProtKB/TrEMBL
PhenoGen Pkp1 PhenoGen
PROSITE ARM_REPEAT UniProtKB/TrEMBL
RatGTEx ENSRNOG00000010076 RatGTEx
SMART ARM UniProtKB/TrEMBL
Superfamily-SCOP ARM-type_fold UniProtKB/TrEMBL
UniProt A6ICH3 ENTREZGENE, UniProtKB/TrEMBL
  D3ZY51 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Pkp1  plakophilin 1   Pkp1_predicted  plakophilin 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Pkp1_predicted  plakophilin 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED