Pkp4 (plakophilin 4) - Rat Genome Database

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Gene: Pkp4 (plakophilin 4) Rattus norvegicus
Analyze
Symbol: Pkp4
Name: plakophilin 4
RGD ID: 1307840
Description: Predicted to enable cadherin binding activity. Predicted to be involved in several processes, including cell-cell junction assembly; positive regulation of GTPase activity; and positive regulation of cytokinesis. Predicted to be located in several cellular components, including desmosome; postsynaptic density; and spindle. Predicted to be active in several cellular components, including adherens junction; nucleus; and plasma membrane. Predicted to colocalize with cell-cell contact zone and midbody. Orthologous to human PKP4 (plakophilin 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC295625; plakophilin-4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2343,632,364 - 43,835,834 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl343,631,880 - 43,835,474 (+)Ensembl
Rnor_6.0345,211,097 - 45,414,524 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl345,277,348 - 45,414,613 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0350,328,374 - 50,531,152 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4340,859,032 - 41,062,477 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1340,785,055 - 40,958,851 (+)NCBI
Celera341,682,689 - 41,884,590 (+)NCBICelera
Cytogenetic Map3q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:8937994   PMID:17114649   PMID:17115030   PMID:22965878  


Genomics

Comparative Map Data
Pkp4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2343,632,364 - 43,835,834 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl343,631,880 - 43,835,474 (+)Ensembl
Rnor_6.0345,211,097 - 45,414,524 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl345,277,348 - 45,414,613 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0350,328,374 - 50,531,152 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4340,859,032 - 41,062,477 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1340,785,055 - 40,958,851 (+)NCBI
Celera341,682,689 - 41,884,590 (+)NCBICelera
Cytogenetic Map3q21NCBI
PKP4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2158,456,952 - 158,682,879 (+)EnsemblGRCh38hg38GRCh38
GRCh382158,456,952 - 158,681,429 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372159,313,464 - 159,537,941 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362159,021,722 - 159,246,187 (+)NCBINCBI36hg18NCBI36
Build 342159,138,983 - 159,363,445NCBI
Celera2152,930,251 - 153,154,736 (+)NCBI
Cytogenetic Map2q24.1NCBI
HuRef2151,277,855 - 151,426,157 (+)NCBIHuRef
CHM1_12159,319,662 - 159,544,088 (+)NCBICHM1_1
Pkp4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39258,991,123 - 59,185,549 (+)NCBIGRCm39mm39
GRCm39 Ensembl258,991,194 - 59,185,552 (+)Ensembl
GRCm38259,160,850 - 59,355,205 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl259,160,850 - 59,355,208 (+)EnsemblGRCm38mm10GRCm38
MGSCv37258,998,907 - 59,193,262 (+)NCBIGRCm37mm9NCBIm37
MGSCv36258,961,859 - 59,156,042 (+)NCBImm8
Celera260,907,299 - 61,046,531 (+)NCBICelera
Cytogenetic Map2C1.1NCBI
Pkp4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544914,833,945 - 15,051,007 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544914,835,423 - 15,050,237 (-)NCBIChiLan1.0ChiLan1.0
PKP4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B162,965,884 - 163,192,565 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B162,986,256 - 163,192,565 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B45,726,315 - 45,953,602 (+)NCBIMhudiblu_PPA_v0panPan3
PKP4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1364,342,715 - 4,575,672 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl364,342,688 - 4,575,016 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha364,483,224 - 4,715,761 (+)NCBI
ROS_Cfam_1.0364,465,991 - 4,698,991 (+)NCBI
UMICH_Zoey_3.1364,466,783 - 4,706,254 (+)NCBI
UNSW_CanFamBas_1.0364,526,814 - 4,759,926 (+)NCBI
UU_Cfam_GSD_1.0364,569,772 - 4,802,204 (+)NCBI
Pkp4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303121,497,043 - 121,739,971 (+)NCBI
SpeTri2.0NW_00493646919,877,749 - 20,120,677 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PKP4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1565,430,309 - 65,680,889 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11565,431,173 - 65,680,891 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21572,627,850 - 72,886,964 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PKP4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11043,859,446 - 44,089,751 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1043,930,975 - 44,091,291 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666040155,487,919 - 155,718,334 (-)NCBIVero_WHO_p1.0
Pkp4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247326,970,728 - 7,208,842 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D3Rat186  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2343,650,198 - 43,650,351 (+)MAPPERmRatBN7.2
Rnor_6.0345,228,240 - 45,228,392NCBIRnor6.0
Rnor_5.0350,344,849 - 50,345,001UniSTSRnor5.0
RGSC_v3.4340,876,100 - 40,876,252UniSTSRGSC3.4
RGSC_v3.4340,876,097 - 40,876,433RGDRGSC3.4
RGSC_v3.1340,772,472 - 40,772,624RGD
Celera341,700,202 - 41,700,354UniSTS
RH 3.4 Map3561.6RGD
RH 3.4 Map3561.6UniSTS
RH 2.0 Map3340.9RGD
SHRSP x BN Map331.7599RGD
Cytogenetic Map3q21UniSTS
D3Rat227  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2343,827,364 - 43,827,511 (+)MAPPERmRatBN7.2
Rnor_6.0345,406,058 - 45,406,204NCBIRnor6.0
Rnor_5.0350,522,686 - 50,522,832UniSTSRnor5.0
RGSC_v3.4341,054,013 - 41,054,159UniSTSRGSC3.4
RGSC_v3.4341,054,012 - 41,054,159RGDRGSC3.4
RGSC_v3.1340,950,385 - 40,950,531RGD
Celera341,876,124 - 41,876,270UniSTS
RH 3.4 Map3562.6RGD
RH 3.4 Map3562.6UniSTS
RH 2.0 Map3341.5RGD
SHRSP x BN Map330.1998RGD
Cytogenetic Map3q21UniSTS
D18Mco1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2183,287,248 - 3,287,445 (+)MAPPERmRatBN7.2
mRatBN7.2343,706,366 - 43,706,533 (+)MAPPERmRatBN7.2
Rnor_6.0183,524,613 - 3,524,807NCBIRnor6.0
Rnor_6.0345,284,413 - 45,284,579NCBIRnor6.0
Rnor_5.0183,534,088 - 3,534,282UniSTSRnor5.0
Rnor_5.0350,401,022 - 50,401,188UniSTSRnor5.0
RGSC_v3.4183,632,387 - 3,632,581UniSTSRGSC3.4
RGSC_v3.4340,932,267 - 40,932,433UniSTSRGSC3.4
RGSC_v3.1361,403,992 - 61,404,152RGD
Celera341,756,534 - 41,756,700UniSTS
Celera183,147,855 - 3,148,061UniSTS
Cytogenetic Map18p13UniSTS
Cytogenetic Map3q21UniSTS
RH133858  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2343,818,495 - 43,819,732 (+)MAPPERmRatBN7.2
Rnor_6.0345,397,189 - 45,398,425NCBIRnor6.0
Rnor_5.0350,513,817 - 50,515,053UniSTSRnor5.0
RGSC_v3.4341,045,144 - 41,046,380UniSTSRGSC3.4
Celera341,867,255 - 41,868,491UniSTS
RH 3.4 Map3560.2UniSTS
Cytogenetic Map3q21UniSTS
RH137757  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2343,749,849 - 43,750,016 (+)MAPPERmRatBN7.2
Rnor_6.0345,327,871 - 45,328,037NCBIRnor6.0
Rnor_5.0350,444,528 - 50,444,694UniSTSRnor5.0
RGSC_v3.4340,976,062 - 40,976,228UniSTSRGSC3.4
Celera341,799,531 - 41,799,697UniSTS
Cytogenetic Map3q21UniSTS
RH129057  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2343,835,668 - 43,835,830 (+)MAPPERmRatBN7.2
Rnor_6.0345,414,362 - 45,414,523NCBIRnor6.0
Rnor_5.0350,530,990 - 50,531,151UniSTSRnor5.0
RGSC_v3.4341,062,317 - 41,062,478UniSTSRGSC3.4
Celera341,884,428 - 41,884,589UniSTS
RH 3.4 Map3560.7UniSTS
Cytogenetic Map3q21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)31077870450302886Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31500542276927699Rat
631676Cm8Cardiac mass QTL 87.030.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)31695470861954708Rat
731172Bp151Blood pressure QTL 1510.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31831145447233430Rat
12879849Bw180Body weight QTL 1800.037body mass (VT:0001259)body weight (CMO:0000012)31831145447233430Rat
12879850Cm91Cardiac mass QTL 910.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)31831145447233430Rat
12879851Cm92Cardiac mass QTL 920.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)31831145447233430Rat
12879852Cm93Cardiac mass QTL 930.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)31831145447233430Rat
12879853Am5Aortic mass QTL 50.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)31831145447233430Rat
12879854Kidm63Kidney mass QTL 630.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)31831145447233430Rat
10450804Scl70Serum cholesterol level QTL 704.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
10450794Scl69Serum cholesterol level QTL 696.30.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
631832Sach1Saccharin preference QTL 12.70.02consumption behavior trait (VT:0002069)calculated saccharin drink intake volume (CMO:0001600)32749462144188411Rat
2313049Bss72Bone structure and strength QTL 722.60.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)32749462150302886Rat
2313076Bss74Bone structure and strength QTL 7420.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)32749462150302886Rat
2313079Bss73Bone structure and strength QTL 731.5tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)32749462150302886Rat
2313093Bmd77Bone mineral density QTL 772.20.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)32749462150302886Rat
2313101Bmd76Bone mineral density QTL 763.60.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)32749462150302886Rat
2302055Pia30Pristane induced arthritis QTL 303.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)32793691972936919Rat
9590286Uminl1Urine mineral level QTL 13.50.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)32824968773249687Rat
8694196Abfw2Abdominal fat weight QTL 216.580.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)32824968773249687Rat
8694386Bw159Body weight QTL 1594.520.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)32824968773249687Rat
8552950Pigfal12Plasma insulin-like growth factor 1 level QTL 127.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)32824968773249687Rat
9590136Scort3Serum corticosterone level QTL 323.370.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32824968773249687Rat
2303593Gluco46Glucose level QTL 463blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)32846857173468571Rat
1354590Despr11Despair related QTL 110.000031locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)32846857173468571Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)33035677398535386Rat
61356Bp37Blood pressure QTL 373blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)33068464275684642Rat
631647Bp122Blood pressure QTL 1226.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)33068464275684642Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
11565451Bw177Body weight QTL 1770.002body mass (VT:0001259)body weight (CMO:0000012)33142640370668733Rat
11565452Kidm57Kidney mass QTL 570.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)33142640370668733Rat
12879866Cm94Cardiac mass QTL 940.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)33142640370668733Rat
12879867Cm95Cardiac mass QTL 950.047heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)33142640370668733Rat
12879868Am6Aortic mass QTL 60.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)33142640370668733Rat
2301400Cm68Cardiac mass QTL 680.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)33142640370668733Rat
1300169Bp177Blood pressure QTL 1772.96arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)33370334761017857Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)33370334778196190Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)333703347104104347Rat
10450852Stl33Serum triglyceride level QTL 333.40.05blood LDL triglyceride amount (VT:0010699)blood lipoprotein triglyceride level (CMO:0002685)33819223350749747Rat
10450816Scl75Serum cholesterol level QTL 754.40.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)33819223350749747Rat
10450813Scl74Serum cholesterol level QTL 745.80.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)33819223350749747Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
738019Anxrr10Anxiety related response QTL 103.9exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)33851780383517803Rat
4889975Bmd81Bone mineral density QTL 814.3tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)33871036550302886Rat
634317Bw117Body weight QTL 1173.58abdominal fat pad mass (VT:1000711)abdominal fat pad weight to body weight ratio (CMO:0000095)33945463753296578Rat
2302276Bw82Body weight QTL 824.32body mass (VT:0001259)body weight (CMO:0000012)33945463762951183Rat
1331777Bw24Body weight QTL 243.503body mass (VT:0001259)body weight (CMO:0000012)33945463789115240Rat
1331795Rf30Renal function QTL 303.708urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)33945463789115240Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)341874578104104347Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1300178Hrtrt4Heart rate QTL 43.74heart pumping trait (VT:2000009)heart rate (CMO:0000002)34382736490905114Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:96
Count of miRNA genes:44
Interacting mature miRNAs:48
Transcripts:ENSRNOT00000007531, ENSRNOT00000059246
Prediction methods: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.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 51 41 19 41 1 1 74 35 38 11 1
Low 6 7 10 3 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_003749475 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_003749476 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_003753725 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_003753726 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224440 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224441 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224442 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224443 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224444 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224445 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234216 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234217 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234218 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234220 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234221 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761868 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761869 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761870 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761871 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761872 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008775386 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008775387 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008775388 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008775389 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008775390 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592151 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592152 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602308 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602311 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106305 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106306 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106307 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106308 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106309 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106310 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106311 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106312 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106314 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106315 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106316 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106317 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106318 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106319 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106320 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106321 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106322 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106324 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106325 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473983 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000115 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000059246   ⟹   ENSRNOP00000056013
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl343,632,409 - 43,835,445 (+)Ensembl
Rnor_6.0 Ensembl345,277,348 - 45,414,613 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093790   ⟹   ENSRNOP00000081746
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl343,631,880 - 43,835,081 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000111282   ⟹   ENSRNOP00000080285
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl343,684,832 - 43,835,445 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000117979   ⟹   ENSRNOP00000087918
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl343,631,880 - 43,835,474 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000118961   ⟹   ENSRNOP00000086370
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl343,631,880 - 43,835,474 (+)Ensembl
RefSeq Acc Id: XM_003749476   ⟹   XP_003749524
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,699,306 - 43,835,453 (+)NCBI
Rnor_6.0345,211,099 - 45,414,524 (+)NCBI
Rnor_5.0350,328,374 - 50,531,152 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006234216   ⟹   XP_006234278
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,633,242 - 43,835,834 (+)NCBI
Rnor_6.0345,211,098 - 45,414,524 (+)NCBI
Rnor_5.0350,328,374 - 50,531,152 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017592152   ⟹   XP_017447641
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,699,306 - 43,835,081 (+)NCBI
Rnor_6.0345,211,098 - 45,414,524 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039106305   ⟹   XP_038962233
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,632,364 - 43,835,834 (+)NCBI
RefSeq Acc Id: XM_039106306   ⟹   XP_038962234
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,684,032 - 43,835,834 (+)NCBI
RefSeq Acc Id: XM_039106307   ⟹   XP_038962235
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,632,364 - 43,835,834 (+)NCBI
RefSeq Acc Id: XM_039106308   ⟹   XP_038962236
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,632,364 - 43,835,834 (+)NCBI
RefSeq Acc Id: XM_039106309   ⟹   XP_038962237
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,632,364 - 43,835,834 (+)NCBI
RefSeq Acc Id: XM_039106310   ⟹   XP_038962238
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,632,364 - 43,835,081 (+)NCBI
RefSeq Acc Id: XM_039106311   ⟹   XP_038962239
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,632,364 - 43,835,081 (+)NCBI
RefSeq Acc Id: XM_039106312   ⟹   XP_038962240
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,632,364 - 43,835,081 (+)NCBI
RefSeq Acc Id: XM_039106314   ⟹   XP_038962242
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,699,306 - 43,835,081 (+)NCBI
RefSeq Acc Id: XM_039106315   ⟹   XP_038962243
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,699,306 - 43,835,081 (+)NCBI
RefSeq Acc Id: XM_039106316   ⟹   XP_038962244
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,632,364 - 43,835,453 (+)NCBI
RefSeq Acc Id: XM_039106317   ⟹   XP_038962245
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,699,306 - 43,835,453 (+)NCBI
RefSeq Acc Id: XM_039106318   ⟹   XP_038962246
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,699,306 - 43,835,453 (+)NCBI
RefSeq Acc Id: XM_039106319   ⟹   XP_038962247
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,632,381 - 43,835,834 (+)NCBI
RefSeq Acc Id: XM_039106320   ⟹   XP_038962248
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,632,374 - 43,835,834 (+)NCBI
RefSeq Acc Id: XM_039106321   ⟹   XP_038962249
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,632,374 - 43,835,834 (+)NCBI
RefSeq Acc Id: XM_039106322   ⟹   XP_038962250
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,632,381 - 43,835,834 (+)NCBI
RefSeq Acc Id: XM_039106324   ⟹   XP_038962252
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,699,320 - 43,835,834 (+)NCBI
RefSeq Acc Id: XM_039106325   ⟹   XP_038962253
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2343,748,995 - 43,835,834 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_003749524   ⟸   XM_003749476
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_006234278   ⟸   XM_006234216
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017447641   ⟸   XM_017592152
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: ENSRNOP00000056013   ⟸   ENSRNOT00000059246
RefSeq Acc Id: XP_038962233   ⟸   XM_039106305
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038962235   ⟸   XM_039106307
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038962236   ⟸   XM_039106308
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038962237   ⟸   XM_039106309
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038962244   ⟸   XM_039106316
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038962238   ⟸   XM_039106310
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038962239   ⟸   XM_039106311
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038962240   ⟸   XM_039106312
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038962248   ⟸   XM_039106320
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038962249   ⟸   XM_039106321
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038962247   ⟸   XM_039106319
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038962250   ⟸   XM_039106322
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038962234   ⟸   XM_039106306
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038962245   ⟸   XM_039106317
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038962246   ⟸   XM_039106318
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038962242   ⟸   XM_039106314
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038962243   ⟸   XM_039106315
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038962252   ⟸   XM_039106324
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038962253   ⟸   XM_039106325
- Peptide Label: isoform X16
RefSeq Acc Id: ENSRNOP00000086370   ⟸   ENSRNOT00000118961
RefSeq Acc Id: ENSRNOP00000080285   ⟸   ENSRNOT00000111282
RefSeq Acc Id: ENSRNOP00000087918   ⟸   ENSRNOT00000117979
RefSeq Acc Id: ENSRNOP00000081746   ⟸   ENSRNOT00000093790

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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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)
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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
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/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
F344/NRrrc (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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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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)
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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
FHL/EurMcwi (MCW)
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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)
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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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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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/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (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
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (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
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (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
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (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
MNS/Gib (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
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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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)
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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)
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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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/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
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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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)
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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
SS/Jr (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
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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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)
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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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307840 AgrOrtholog
Ensembl Genes ENSRNOG00000005504 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000056013 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000059246 UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.10 UniProtKB/TrEMBL
InterPro ARM-like UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/TrEMBL
  Armadillo UniProtKB/TrEMBL
  Plakophilin-4 UniProtKB/TrEMBL
  Plakophilin/d_Catenin UniProtKB/TrEMBL
NCBI Gene 295625 ENTREZGENE
PANTHER PTHR10372 UniProtKB/TrEMBL
  PTHR10372:SF8 UniProtKB/TrEMBL
Pfam Arm UniProtKB/TrEMBL
PhenoGen Pkp4 PhenoGen
PROSITE ARM_REPEAT UniProtKB/TrEMBL
SMART ARM UniProtKB/TrEMBL
Superfamily-SCOP ARM-type_fold UniProtKB/TrEMBL
UniProt F1M2K6_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Pkp4  plakophilin 4   Pkp4_predicted  plakophilin 4 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Pkp4_predicted  plakophilin 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED