Pkp2 (plakophilin 2) - Rat Genome Database
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Gene: Pkp2 (plakophilin 2) Rattus norvegicus
Analyze
Symbol: Pkp2
Name: plakophilin 2
RGD ID: 1306533
Description: Predicted to have several functions, including alpha-catenin binding activity; intermediate filament binding activity; and protein kinase C binding activity. Involved in several processes, including cell-cell junction organization; lipid homeostasis; and regulation of bicellular tight junction assembly. Localizes to adherens junction and intercalated disc. Human ortholog(s) of this gene implicated in arrhythmogenic right ventricular cardiomyopathy and arrhythmogenic right ventricular dysplasia 9. Orthologous to human PKP2 (plakophilin 2); PARTICIPATES IN arrhythmogenic right ventricular cardiomyopathy pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; all-trans-retinoic acid.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC287925; plakophilin-2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21184,661,783 - 84,727,730 (-)NCBI
Rnor_6.01188,912,163 - 88,972,213 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01191,966,047 - 92,031,277 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41186,553,493 - 86,584,425 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11186,497,846 - 86,625,018 (+)NCBI
Celera1183,407,295 - 83,471,505 (-)NCBICelera
Cytogenetic Map11q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
4-hydroxyphenyl retinamide  (ISO)
all-trans-retinoic acid  (EXP,ISO)
amphetamine  (EXP)
arsenite(3-)  (ISO)
benzo[a]pyrene  (EXP,ISO)
bisphenol A  (EXP)
bisphenol F  (ISO)
butan-1-ol  (ISO)
calcitriol  (ISO)
capecitabine  (ISO)
carbon nanotube  (ISO)
carmustine  (EXP)
cisplatin  (ISO)
cocaine  (EXP)
cyclosporin A  (ISO)
cytarabine  (ISO)
dextran sulfate  (ISO)
diethylstilbestrol  (EXP,ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxifluridine  (ISO)
doxorubicin  (ISO)
ethanol  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (EXP)
genistein  (ISO)
glafenine  (EXP)
glycidol  (EXP)
hydroquinone  (ISO)
kainic acid  (ISO)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
mercury dibromide  (ISO)
methamphetamine  (EXP)
methotrexate  (EXP)
methylmercury chloride  (ISO)
mifepristone  (EXP)
p-chloromercuribenzoic acid  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
pentachlorophenol  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
SCH 23390  (EXP)
sodium dichromate  (EXP)
sunitinib  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
tioguanine  (EXP)
trichloroethene  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9864371   PMID:10852826   PMID:12477932   PMID:15479741   PMID:16917092   PMID:17535849   PMID:17980246   PMID:18474624   PMID:20859650   PMID:21296051   PMID:21617128   PMID:22274697  
PMID:22781308   PMID:22889254   PMID:23136403   PMID:23863954   PMID:25225333   PMID:25468996   PMID:26858265  


Genomics

Comparative Map Data
Pkp2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21184,661,783 - 84,727,730 (-)NCBI
Rnor_6.01188,912,163 - 88,972,213 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01191,966,047 - 92,031,277 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41186,553,493 - 86,584,425 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11186,497,846 - 86,625,018 (+)NCBI
Celera1183,407,295 - 83,471,505 (-)NCBICelera
Cytogenetic Map11q23NCBI
PKP2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1232,790,755 - 32,896,777 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1232,790,745 - 32,896,840 (-)EnsemblGRCh38hg38GRCh38
GRCh381232,790,755 - 32,896,777 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371232,943,689 - 33,049,711 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361232,834,947 - 32,941,047 (-)NCBINCBI36hg18NCBI36
Build 341232,834,953 - 32,940,993NCBI
Celera1212,764,378 - 12,870,162 (-)NCBI
Cytogenetic Map12p11.21NCBI
HuRef1232,696,154 - 32,802,035 (-)NCBIHuRef
CHM1_11232,910,199 - 33,015,916 (-)NCBICHM1_1
Pkp2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391616,031,209 - 16,090,576 (+)NCBIGRCm39mm39
GRCm39 Ensembl1616,031,182 - 16,090,576 (+)Ensembl
GRCm381616,213,345 - 16,272,712 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1616,213,318 - 16,272,712 (+)EnsemblGRCm38mm10GRCm38
MGSCv371616,213,438 - 16,272,805 (+)NCBIGRCm37mm9NCBIm37
MGSCv361616,126,923 - 16,186,290 (+)NCBImm8
Celera1616,784,266 - 16,843,631 (+)NCBICelera
Cytogenetic Map16A2NCBI
Pkp2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555052,878,081 - 2,958,404 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555052,878,001 - 2,959,299 (+)NCBIChiLan1.0ChiLan1.0
PKP2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11255,925,514 - 56,030,996 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1255,925,174 - 56,030,998 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01253,322,227 - 53,428,747 (+)NCBIMhudiblu_PPA_v0panPan3
PKP2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2716,023,224 - 16,109,603 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12716,023,186 - 16,109,978 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Pkp2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366073,458,406 - 3,530,066 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PKP2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl541,424,845 - 41,508,868 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1541,424,687 - 41,509,590 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2544,676,288 - 44,708,684 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PKP2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11132,225,743 - 32,333,951 (-)NCBI
ChlSab1.1 Ensembl1132,225,600 - 32,333,615 (-)Ensembl
Pkp2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247783,261,446 - 3,344,204 (+)NCBI

Position Markers
RH127356  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01188,949,309 - 88,949,515NCBIRnor6.0
Rnor_5.01192,008,373 - 92,008,579UniSTSRnor5.0
Celera1183,448,227 - 83,448,433UniSTS
Cytogenetic Map6q31UniSTS
Cytogenetic Map11q23UniSTS
AI556444  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01188,912,180 - 88,912,391NCBIRnor6.0
Rnor_5.01191,966,064 - 91,966,275UniSTSRnor5.0
RGSC_v3.41186,584,197 - 86,584,408UniSTSRGSC3.4
Celera1183,407,312 - 83,407,523UniSTS
Cytogenetic Map11q23UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111901627290463843Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115785881090463843Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115994302390463843Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116449467190463843Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116964970890463843Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:44
Count of miRNA genes:43
Interacting mature miRNAs:44
Transcripts:ENSRNOT00000002498
Prediction methods:Miranda, Rnahybrid
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.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: NM_001100499   ⟹   NP_001093969
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21184,661,783 - 84,727,730 (-)NCBI
Rnor_6.01188,912,163 - 88,972,213 (-)NCBI
Rnor_5.01191,966,047 - 92,031,277 (-)NCBI
RGSC_v3.41186,553,493 - 86,584,425 (+)RGD
Celera1183,407,295 - 83,471,505 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001093969 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH92602 (Get FASTA)   NCBI Sequence Viewer  
  EDL77846 (Get FASTA)   NCBI Sequence Viewer  
  EDL77847 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001093969   ⟸   NM_001100499
- Sequence:


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306533 AgrOrtholog
Gene3D-CATH 1.25.10.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7305258 IMAGE-MGC_LOAD
InterPro ARM-like UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/TrEMBL
  Armadillo UniProtKB/TrEMBL
  Plakophilin/d_Catenin UniProtKB/TrEMBL
MGC_CLONE MGC:109189 IMAGE-MGC_LOAD
NCBI Gene 287925 ENTREZGENE
PANTHER PTHR10372 UniProtKB/TrEMBL
Pfam Arm UniProtKB/TrEMBL
PhenoGen Pkp2 PhenoGen
SMART ARM UniProtKB/TrEMBL
Superfamily-SCOP SSF48371 UniProtKB/TrEMBL
UniProt Q562C0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Pkp2  plakophilin 2  Pkp2_predicted  plakophilin 2 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Pkp2_predicted  plakophilin 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED