Prkca (protein kinase C, alpha) - Rat Genome Database

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Gene: Prkca (protein kinase C, alpha) Rattus norvegicus
Analyze
Symbol: Prkca
Name: protein kinase C, alpha
RGD ID: 3395
Description: Enables calcium-dependent protein kinase C activity. Involved in several processes, including positive regulation of ERK1 and ERK2 cascade; protein phosphorylation; and regulation of vesicle-mediated transport. Located in several cellular components, including membrane raft; mitochondrion; and perinuclear region of cytoplasm. Part of protein-containing complex. Used to study hypertension. Biomarker of brain ischemia; congestive heart failure; and ischemia. Human ortholog(s) of this gene implicated in dilated cardiomyopathy; high grade glioma (multiple); large cell carcinoma; and reproductive organ cancer (multiple). Orthologous to human PRKCA (protein kinase C alpha); PARTICIPATES IN eicosanoid signaling pathway; endothelin signaling pathway; Fc epsilon receptor mediated signaling pathway; INTERACTS WITH (S)-nicotine; 1-(5-isoquinolinesulfonyl)-2-methylpiperazine; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: PKC-A; PKC-alpha; Pkca; protein kinase C alpha type
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
mRatBN7.21092,889,390 - 93,288,013 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1092,894,012 - 93,288,012 (-)Ensembl
Rnor_6.01096,186,509 - 96,585,168 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1096,191,133 - 96,584,947 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01095,919,013 - 96,311,328 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41097,367,196 - 97,638,910 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11097,382,023 - 97,632,491 (-)NCBI
Celera1091,557,626 - 91,951,823 (-)NCBICelera
RH 3.4 Map101035.79RGD
Cytogenetic Map10q32.1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(5Z,8Z,11Z,13E)-15-HETE  (ISO)
(9R)-9-[(dimethylamino)methyl]-6,7,10,11-tetrahydro-9H,18H-5,21:12,17-dimethenodibenzo[e,k]pyrrolo[3,4-h][1,4,13]oxadiazacyclohexadecine-18,20-dione  (ISO)
(S)-naringenin  (ISO)
(S)-nicotine  (EXP,ISO)
1,2-dimethylhydrazine  (ISO)
1-(5-isoquinolinesulfonyl)-2-methylpiperazine  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 17-glucosiduronic acid  (EXP)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2,6-di-tert-butyl-4-methylphenol  (ISO)
2-methylcholine  (ISO)
3,3',4,4'-tetrachlorobiphenyl  (EXP)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (ISO)
3alpha-hydroxy-5beta-pregnan-20-one  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-(2-methylpiperazine-1-sulfonyl)isoquinoline  (EXP)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (EXP)
8-Br-cAMP  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (EXP,ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (EXP,ISO)
atorvastatin calcium  (EXP)
ATP  (ISO)
atrazine  (ISO)
baicalein  (ISO)
beauvericin  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
berberine  (EXP)
bisoprolol  (EXP)
bisphenol A  (EXP,ISO)
brimonidine tartrate  (EXP)
bryostatin 1  (ISO)
butan-1-ol  (EXP)
cadmium atom  (EXP)
cadmium dichloride  (EXP)
calcium atom  (EXP)
calcium(0)  (EXP)
cannabidiol  (ISO)
cannabigerol  (ISO)
capsaicin  (EXP,ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carvedilol  (EXP)
celecoxib  (ISO)
chelerythrine  (EXP)
chlorpyrifos  (EXP)
cisplatin  (ISO)
clobetasol  (ISO)
cobalt dichloride  (EXP,ISO)
cocaine  (EXP,ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
corticosterone  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
curcumin  (ISO)
D-gluconic acid  (EXP)
D-glucose  (EXP,ISO)
daidzein  (EXP)
dapagliflozin  (EXP)
deoxycholic acid  (EXP)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (EXP,ISO)
dibutyl phthalate  (ISO)
dichloroacetic acid  (ISO)
diclofenac  (ISO)
dicrotophos  (ISO)
diethylstilbestrol  (ISO)
dihydroartemisinin  (ISO)
dimethylarsinic acid  (EXP)
dimethylarsinous acid  (ISO)
disodium selenite  (EXP)
dizocilpine maleate  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
emodin  (EXP)
enalapril  (EXP)
enniatin  (ISO)
entinostat  (ISO)
ethanol  (EXP,ISO)
ethylene glycol bis(2-aminoethyl)tetraacetic acid  (ISO)
Evodiamine  (ISO)
fluticasone  (ISO)
folic acid  (ISO)
folpet  (ISO)
fructose  (EXP)
gallic acid  (ISO)
genistein  (EXP,ISO)
glucose  (EXP,ISO)
glyphosate  (EXP)
Goe 6976  (EXP,ISO)
heptachlor  (EXP)
hydrogen peroxide  (EXP,ISO)
imidaprilat  (ISO)
irinotecan  (ISO)
isophthalic acid  (ISO)
isoprenaline  (EXP)
ivermectin  (ISO)
lead diacetate  (EXP,ISO)
lead(0)  (EXP)
lead(2+)  (EXP)
leflunomide  (ISO)
leptomycin B  (ISO)
linsidomine  (EXP)
lipopolysaccharide  (ISO)
lithium atom  (ISO)
lithium hydride  (ISO)
luteolin  (ISO)
manganese atom  (EXP)
manganese(0)  (EXP)
manganese(II) chloride  (EXP)
mercury atom  (EXP)
mercury(0)  (EXP)
metformin  (ISO)
methamphetamine  (ISO)
methapyrilene  (ISO)
methotrexate  (ISO)
methoxychlor  (EXP)
methylarsonic acid  (EXP)
methylseleninic acid  (ISO)
methyltestosterone  (ISO)
Mezerein  (ISO)
mianserin  (ISO)
mifepristone  (ISO)
miltefosine  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
morphine  (ISO)
mycophenolic acid  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
nickel atom  (ISO)
nickel dichloride  (ISO)
nicotine  (EXP,ISO)
nitric oxide  (EXP)
o-cresol  (EXP)
obeticholic acid  (ISO)
ochratoxin A  (EXP)
p-cresol  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
paricalcitol  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
permethrin  (EXP)
phenethyl isothiocyanate  (ISO)
phenobarbital  (ISO)
phenylephrine  (EXP,ISO)
phenylmercury acetate  (ISO)
phorbol 12,13-dibutanoate  (EXP,ISO)
phorbol 13-acetate 12-myristate  (EXP,ISO)
pioglitazone  (ISO)
piperine  (ISO)
pirinixic acid  (EXP,ISO)
procyanidin B2  (EXP)
progesterone  (ISO)
propranolol  (EXP)
quercetin  (ISO)
reactive oxygen species  (EXP)
resveratrol  (ISO)
riddelliine  (EXP)
ritonavir  (ISO)
Ro 31-8220  (ISO)
rotenone  (EXP)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (EXP)
S-nitroso-N-acetyl-D-penicillamine  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sirolimus  (ISO)
sodium arsenite  (ISO)
sodium chloride  (ISO)
sorafenib  (ISO)
staurosporine  (EXP,ISO)
streptozocin  (EXP)
SU6656  (ISO)
sulforaphane  (ISO)
superoxide  (ISO)
tamoxifen  (ISO)
taurine  (EXP)
temozolomide  (ISO)
tert-butyl hydroperoxide  (EXP,ISO)
testosterone  (ISO)
testosterone enanthate  (EXP)
testosterone undecanoate  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP)
tetrahydropalmatine  (ISO)
thapsigargin  (ISO)
theophylline  (ISO)
thioacetamide  (EXP)
thiram  (ISO)
titanium dioxide  (ISO)
tributylstannane  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
trimethylarsine oxide  (EXP)
Triptolide  (EXP)
tunicamycin  (ISO)
tyrphostin AG 1478  (ISO)
U-73122  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vanadium atom  (ISO)
vanadium(0)  (ISO)
vitamin D  (ISO)
vorinostat  (ISO)
zinc atom  (ISO)
zinc dichloride  (EXP)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
aging  (IEP)
angiogenesis  (IEA)
cell adhesion  (IEA)
cellular calcium ion homeostasis  (ISO)
cellular response to carbohydrate stimulus  (ISO)
central nervous system neuron axonogenesis  (IMP)
chondrocyte differentiation  (ISO)
desmosome assembly  (IEA,ISO)
establishment of protein localization  (TAS)
histone H3-T6 phosphorylation  (IEA,ISO)
induction of positive chemotaxis  (ISO)
intracellular signal transduction  (IBA,IDA,IEA)
intrinsic apoptotic signaling pathway  (ISO)
learning or memory  (IMP)
negative regulation of anion channel activity  (ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of glial cell apoptotic process  (IEA,ISO,ISS)
negative regulation of glucose import  (ISO)
negative regulation of heart contraction  (IMP)
negative regulation of insulin receptor signaling pathway  (ISO)
negative regulation of MAPK cascade  (ISO)
negative regulation of protein kinase activity  (ISO)
negative regulation of protein phosphorylation  (ISO)
negative regulation of translation  (IMP)
neutrophil chemotaxis  (ISO)
peptidyl-serine autophosphorylation  (ISO)
peptidyl-serine phosphorylation  (IBA,IDA)
peptidyl-threonine phosphorylation  (IDA,IMP)
positive regulation of angiogenesis  (IEA,ISO,ISS)
positive regulation of blood vessel endothelial cell migration  (IEA,ISO)
positive regulation of bone resorption  (ISO)
positive regulation of cardiac muscle hypertrophy  (IDA)
positive regulation of cell adhesion  (IEA,ISO,ISS)
positive regulation of cell migration  (ISO,ISS)
positive regulation of dense core granule biogenesis  (ISO,ISS)
positive regulation of endothelial cell migration  (ISO,ISS)
positive regulation of endothelial cell proliferation  (IEA,ISO,ISS)
positive regulation of ERK1 and ERK2 cascade  (IMP)
positive regulation of exocytosis  (IMP)
positive regulation of inflammatory response  (ISO)
positive regulation of lipopolysaccharide-mediated signaling pathway  (IEA,ISO,ISS)
positive regulation of macrophage differentiation  (ISO,ISS)
positive regulation of mitotic cell cycle  (IEA,ISO,ISS)
positive regulation of protein phosphorylation  (ISO)
positive regulation of smooth muscle cell proliferation  (IMP)
positive regulation of synapse assembly  (IMP)
presynaptic modulation of chemical synaptic transmission  (ISO)
protein autophosphorylation  (IDA)
protein phosphorylation  (IDA,IEA,ISO)
regulation of muscle contraction  (ISO)
regulation of peptidyl-tyrosine phosphorylation  (ISO)
regulation of platelet aggregation  (IEA,ISO,ISS)
regulation of receptor-mediated endocytosis  (IMP)
regulation of response to osmotic stress  (ISO)
regulation of synaptic vesicle exocytosis  (ISO)
regulation of the force of heart contraction  (ISO)
response to antibiotic  (IEP)
response to corticosterone  (IEP)
response to estradiol  (IMP)
response to ethanol  (IMP)
response to interleukin-1  (IEA,ISO)
response to mechanical stimulus  (IEP)
response to organic cyclic compound  (IEP)
response to peptide hormone  (IEP)
response to reactive oxygen species  (IMP)
response to toxic substance  (IEP)

Cellular Component

References

References - curated
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Additional References at PubMed
PMID:2023931   PMID:3045562   PMID:3666147   PMID:7520444   PMID:7539802   PMID:7741753   PMID:7828597   PMID:7929424   PMID:8083223   PMID:8631738   PMID:8947489   PMID:9447980  
PMID:9508782   PMID:9535877   PMID:9830023   PMID:9927633   PMID:10365161   PMID:10407019   PMID:10617144   PMID:10722046   PMID:10770950   PMID:10813773   PMID:10848585   PMID:10871288  
PMID:10879655   PMID:10882525   PMID:11118818   PMID:11123317   PMID:11278415   PMID:11306676   PMID:11738801   PMID:11795668   PMID:11850425   PMID:11906323   PMID:11909826   PMID:11916978  
PMID:11923480   PMID:11940581   PMID:11952172   PMID:11981754   PMID:12079385   PMID:12112001   PMID:12115694   PMID:12198656   PMID:12391145   PMID:12426311   PMID:12477932   PMID:12525479  
PMID:12551925   PMID:12562894   PMID:12612139   PMID:12618484   PMID:12637266   PMID:12637991   PMID:12647293   PMID:12700627   PMID:12700701   PMID:12724315   PMID:12785016   PMID:12826667  
PMID:12928424   PMID:12967633   PMID:12970181   PMID:12970360   PMID:14602083   PMID:14613966   PMID:14638691   PMID:14681019   PMID:14698304   PMID:14717343   PMID:14966518   PMID:15100355  
PMID:15149857   PMID:15157674   PMID:15182202   PMID:15187091   PMID:15262987   PMID:15271671   PMID:15383279   PMID:15388777   PMID:15456937   PMID:15557340   PMID:15574738   PMID:15590069  
PMID:15632189   PMID:15632699   PMID:15748507   PMID:15763930   PMID:15784685   PMID:15830100   PMID:15833739   PMID:15838306   PMID:16014375   PMID:16099831   PMID:16114872   PMID:16131649  
PMID:16155104   PMID:16205321   PMID:16342423   PMID:16407557   PMID:16476439   PMID:16585392   PMID:16630892   PMID:16648180   PMID:16814779   PMID:16870611   PMID:16900949   PMID:17109817  
PMID:17178122   PMID:17208995   PMID:17209006   PMID:17252537   PMID:17267947   PMID:17363267   PMID:17392515   PMID:17487264   PMID:17531159   PMID:17558679   PMID:17591920   PMID:17644814  
PMID:17728398   PMID:17786270   PMID:17893151   PMID:17956267   PMID:17959934   PMID:17983652   PMID:17989210   PMID:18265009   PMID:18304574   PMID:18315563   PMID:18323529   PMID:18346469  
PMID:18474624   PMID:18523655   PMID:18550542   PMID:18556656   PMID:18668351   PMID:18778746   PMID:19005059   PMID:19056867   PMID:19057126   PMID:19080278   PMID:19147982   PMID:19166962  
PMID:19249914   PMID:19281832   PMID:19321046   PMID:19339511   PMID:19373133   PMID:19420114   PMID:19429666   PMID:19519660   PMID:19544110   PMID:19581409   PMID:19586612   PMID:19592485  
PMID:19672103   PMID:19693770   PMID:19723805   PMID:19806888   PMID:19826069   PMID:19843630   PMID:20011604   PMID:20053794   PMID:20170615   PMID:20177957   PMID:20181831   PMID:20228790  
PMID:20448043   PMID:20629316   PMID:20673182   PMID:20807573   PMID:20833797   PMID:20973479   PMID:21097843   PMID:21172324   PMID:21180072   PMID:21281821   PMID:21465534   PMID:21528054  
PMID:21658591   PMID:21718540   PMID:21929289   PMID:22097723   PMID:22203737   PMID:22393054   PMID:22472890   PMID:22527640   PMID:22531886   PMID:22713544   PMID:22801596   PMID:22855535  
PMID:22872317   PMID:23099255   PMID:23152155   PMID:23295407   PMID:23374940   PMID:23508961   PMID:23585120   PMID:23686852   PMID:23824537   PMID:23863479   PMID:23874859   PMID:23882690  
PMID:23900841   PMID:23990668   PMID:24008114   PMID:24151077   PMID:24297175   PMID:24305805   PMID:24349196   PMID:24355769   PMID:24876385   PMID:24914766   PMID:24992834   PMID:25150189  
PMID:25231108   PMID:25300290   PMID:25332685   PMID:25489662   PMID:26078455   PMID:26199377   PMID:26206583   PMID:26333598   PMID:26505750   PMID:26591616   PMID:26660275   PMID:26713421  
PMID:26830133   PMID:26854722   PMID:27353086   PMID:27624386   PMID:27837432   PMID:28154205   PMID:28423323   PMID:28485503   PMID:29561757   PMID:29642029   PMID:29845266   PMID:30053369  
PMID:30230261   PMID:30790506   PMID:31366607   PMID:31578312   PMID:32084499   PMID:32244197   PMID:32645222   PMID:33250241   PMID:33673008  


Genomics

Candidate Gene Status
Prkca is a candidate Gene for QTL Eau3
Prkca is a candidate Gene for QTL Pia10
Prkca is a candidate Gene for QTL Cia5
Comparative Map Data
Prkca
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21092,889,390 - 93,288,013 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1092,894,012 - 93,288,012 (-)Ensembl
Rnor_6.01096,186,509 - 96,585,168 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1096,191,133 - 96,584,947 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01095,919,013 - 96,311,328 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41097,367,196 - 97,638,910 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11097,382,023 - 97,632,491 (-)NCBI
Celera1091,557,626 - 91,951,823 (-)NCBICelera
RH 3.4 Map101035.79RGD
Cytogenetic Map10q32.1NCBI
PRKCA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1766,302,613 - 66,810,743 (+)EnsemblGRCh38hg38GRCh38
GRCh381766,302,613 - 66,810,743 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371764,298,731 - 64,806,861 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361761,729,388 - 62,237,324 (+)NCBINCBI36hg18NCBI36
Build 341761,729,387 - 62,237,324NCBI
Celera1760,870,958 - 61,379,534 (+)NCBI
Cytogenetic Map17q24.2NCBI
HuRef1759,689,927 - 60,196,110 (+)NCBIHuRef
CHM1_11764,362,982 - 64,870,449 (+)NCBICHM1_1
Prkca
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911107,824,213 - 108,237,360 (-)NCBIGRCm39mm39
GRCm39 Ensembl11107,824,213 - 108,234,754 (-)Ensembl
GRCm3811107,933,387 - 108,343,888 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11107,933,387 - 108,343,928 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711107,794,701 - 108,205,202 (-)NCBIGRCm37mm9NCBIm37
MGSCv3611107,754,338 - 108,160,018 (-)NCBImm8
Celera11119,670,475 - 120,082,817 (-)NCBICelera
Cytogenetic Map11E1NCBI
cM Map1170.8NCBI
Prkca
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554785,686,640 - 6,083,967 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554785,686,639 - 6,090,356 (+)NCBIChiLan1.0ChiLan1.0
PRKCA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11765,454,911 - 65,954,610 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1765,454,907 - 65,947,903 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01760,246,485 - 60,747,158 (+)NCBIMhudiblu_PPA_v0panPan3
PRKCA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1913,638,106 - 13,879,571 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl913,644,010 - 13,967,630 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha914,532,025 - 14,927,673 (-)NCBI
ROS_Cfam_1.0915,300,837 - 15,695,928 (-)NCBI
UMICH_Zoey_3.1914,247,910 - 14,642,594 (-)NCBI
UNSW_CanFamBas_1.0912,891,369 - 13,286,136 (+)NCBI
UU_Cfam_GSD_1.0912,891,959 - 13,287,663 (+)NCBI
Prkca
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560212,615,841 - 12,962,986 (+)NCBI
SpeTri2.0NW_0049365416,231,604 - 6,488,201 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRKCA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1212,882,064 - 13,263,554 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11212,882,287 - 13,268,647 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21213,197,691 - 13,602,529 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PRKCA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11654,638,548 - 55,144,372 (-)NCBI
ChlSab1.1 Ensembl1654,642,729 - 54,948,256 (-)Ensembl
Vero_WHO_p1.0NW_02366607725,683,064 - 26,190,115 (-)NCBI
Prkca
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248701,589,775 - 2,023,160 (-)NCBI

Position Markers
D10Rat53  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21093,184,764 - 93,184,904 (+)MAPPERmRatBN7.2
Rnor_6.01096,482,302 - 96,482,441NCBIRnor6.0
Rnor_5.01096,209,202 - 96,209,341UniSTSRnor5.0
Celera1091,849,622 - 91,849,761UniSTS
RH 3.4 Map101036.2RGD
RH 3.4 Map101036.2UniSTS
RH 2.0 Map101145.8RGD
FHH x ACI Map1076.87RGD
Cytogenetic Map10q32.1UniSTS
D10Rat189  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21093,223,816 - 93,224,011 (+)MAPPERmRatBN7.2
Rnor_6.01096,520,816 - 96,521,010NCBIRnor6.0
Rnor_5.01096,247,437 - 96,247,631UniSTSRnor5.0
Celera1091,888,082 - 91,888,276UniSTS
RH 2.0 Map101138.3RGD
FHH x ACI Map1076.87RGD
Cytogenetic Map10q32.1UniSTS
D10Rat139  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera1091,706,718 - 91,707,295UniSTS
RH 2.0 Map101130.4RGD
SHRSP x BN Map1073.35RGD
Cytogenetic Map10q32.1UniSTS
D10Chm19  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21092,997,482 - 92,997,642 (+)MAPPERmRatBN7.2
Rnor_6.01096,295,049 - 96,295,208NCBIRnor6.0
Rnor_5.01096,022,399 - 96,022,558UniSTSRnor5.0
RGSC_v3.41097,470,298 - 97,470,457UniSTSRGSC3.4
Celera1091,660,804 - 91,660,963UniSTS
Cytogenetic Map10q32.1UniSTS
D10Chm12  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21092,981,530 - 92,981,737 (+)MAPPERmRatBN7.2
Rnor_6.01096,279,083 - 96,279,287NCBIRnor6.0
Rnor_5.01096,006,498 - 96,006,702UniSTSRnor5.0
RGSC_v3.41097,454,479 - 97,454,683UniSTSRGSC3.4
Celera1091,644,856 - 91,645,060UniSTS
Cytogenetic Map10q32.1UniSTS
RH94851  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21092,894,507 - 92,894,747 (+)MAPPERmRatBN7.2
Rnor_6.01096,191,629 - 96,191,868NCBIRnor6.0
Rnor_5.01095,919,509 - 95,919,748UniSTSRnor5.0
RGSC_v3.41097,367,692 - 97,367,931UniSTSRGSC3.4
Celera1091,558,122 - 91,558,361UniSTS
RH 3.4 Map101035.79UniSTS
Cytogenetic Map10q32.1UniSTS
Prkca  
Rat AssemblyChrPosition (strand)SourceJBrowse
RGSC_v3.41097,368,649 - 97,368,778UniSTSRGSC3.4
RGSC_v3.41097,368,649 - 97,368,881UniSTSRGSC3.4
Celera1091,559,079 - 91,559,208UniSTS
Celera1091,559,079 - 91,559,311UniSTS
RH94850  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21092,894,869 - 92,895,073 (+)MAPPERmRatBN7.2
Rnor_6.01096,191,991 - 96,192,194NCBIRnor6.0
Rnor_5.01095,919,871 - 95,920,074UniSTSRnor5.0
RGSC_v3.41097,368,054 - 97,368,257UniSTSRGSC3.4
Celera1091,558,484 - 91,558,687UniSTS
Cytogenetic Map10q32.1UniSTS
RH137792  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21093,238,639 - 93,238,779 (+)MAPPERmRatBN7.2
Rnor_6.01096,535,775 - 96,535,914NCBIRnor6.0
Rnor_5.01096,261,992 - 96,262,131UniSTSRnor5.0
Celera1091,902,756 - 91,902,895UniSTS
Cytogenetic Map10q32.1UniSTS
fk85g05.x1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01657,183,630 - 57,183,785UniSTSRnor5.0
Rnor_5.01096,021,469 - 96,022,449UniSTSRnor5.0
RGSC_v3.41657,645,822 - 57,645,977UniSTSRGSC3.4
RGSC_v3.41097,469,368 - 97,470,348UniSTSRGSC3.4
Celera1651,895,620 - 51,895,775UniSTS
Celera1091,659,874 - 91,660,854UniSTS
Cytogenetic Map16q12.1UniSTS
Cytogenetic Map10q32.1UniSTS
Prkca  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01095,920,466 - 95,920,698UniSTSRnor5.0
RGSC_v3.41097,368,649 - 97,368,881UniSTSRGSC3.4
Celera1091,559,079 - 91,559,311UniSTS
Cytogenetic Map10q32.1UniSTS
Prkca  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01095,920,466 - 95,920,595UniSTSRnor5.0
RGSC_v3.41097,368,649 - 97,368,778UniSTSRGSC3.4
Celera1091,559,079 - 91,559,208UniSTS
Cytogenetic Map10q32.1UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105177461295600334Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106134527698211570Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)106134527699703528Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)106134527699703528Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106674365598003205Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068383129107211142Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068420376107211142Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1069738412107211142Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1069738412107211142Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1069738412107211142Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070199100107211142Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072224939107211142Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1072224939107211142Rat
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107255241693995749Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107437208494965338Rat
10450495Bp383Blood pressure QTL 3830.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107624608594965338Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1076246085107211142Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076452683107211142Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1076748906107211142Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)107877551698279596Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1080515287101325465Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1081285008107211142Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1082685200107211142Rat
12880055Am11Aortic mass QTL 110.004aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)108400727295933025Rat
2301398Kidm38Kidney mass QTL 380.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)108400727295933025Rat
2306792Ean4Experimental allergic neuritis QTL 44nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)108402232193995963Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1085565469103884409Rat
631538Oia5Oil induced arthritis QTL 5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087055121107211142Rat
2313856Bp342Blood pressure QTL 3424.40.0001life span trait (VT:0005372)age at time of death (CMO:0001193)108730761796121100Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087307617107211142Rat
634320Niddm49Non-insulin dependent diabetes mellitus QTL 494.41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1088539139107211142Rat
12880395Cm109Cardiac mass QTL 1090.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1090404397107211142Rat
12880396Am13Aortic mass QTL 130.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1090404397107211142Rat
12880398Kidm67Kidney mass QTL 670.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1090404397107211142Rat
12880384Cm107Cardiac mass QTL 1070.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)90404397107211142Rat
12880385Cm108Cardiac mass QTL 1080.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)90404397107211142Rat
1579915Bp280Blood pressure QTL 2800.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090404397107211142Rat
1300137Bp186Blood pressure QTL 1863.57arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1090627439107057807Rat
724530Bp149Blood pressure QTL 1490.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090627439107211142Rat
1558652Bw57Body weight QTL 574.20.0008body mass (VT:0001259)body weight (CMO:0000012)1090910316107211142Rat
61436Cia5Collagen induced arthritis QTL 54.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1091228102104060283Rat
70168Eae12Experimental allergic encephalomyelitis QTL 120.0009nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1092238497101012337Rat
1354641Bvd2Brain ventricular dilatation QTL 26.360.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)1093223816107057807Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:822
Count of miRNA genes:230
Interacting mature miRNAs:255
Transcripts:ENSRNOT00000004699, ENSRNOT00000055073
Prediction methods:Microtar, Miranda
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 26 15 8 18 8 8 10 52 26 16 9 8
Low 17 42 33 1 33 1 22 9 23 2
Below cutoff 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004699   ⟹   ENSRNOP00000004699
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1092,894,264 - 93,287,756 (-)Ensembl
Rnor_6.0 Ensembl1096,191,385 - 96,584,896 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000055073   ⟹   ENSRNOP00000051949
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1092,894,012 - 93,287,807 (-)Ensembl
Rnor_6.0 Ensembl1096,191,133 - 96,584,947 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100596   ⟹   ENSRNOP00000079110
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1092,895,139 - 93,287,807 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112512   ⟹   ENSRNOP00000083509
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1092,894,264 - 93,135,944 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115522   ⟹   ENSRNOP00000091320
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1092,894,264 - 93,288,012 (-)Ensembl
RefSeq Acc Id: NM_001105713   ⟹   NP_001099183
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21092,894,012 - 93,287,807 (-)NCBI
Rnor_6.01096,191,133 - 96,584,947 (-)NCBI
Rnor_5.01095,919,013 - 96,311,328 (-)NCBI
RGSC_v3.41097,367,196 - 97,638,910 (-)RGD
Celera1091,557,626 - 91,951,823 (-)RGD
Sequence:
RefSeq Acc Id: XM_017597006   ⟹   XP_017452495
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21092,889,390 - 93,287,801 (-)NCBI
Rnor_6.01096,186,509 - 96,585,168 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597007   ⟹   XP_017452496
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21092,894,267 - 93,287,801 (-)NCBI
Rnor_6.01096,186,509 - 96,585,160 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039085211   ⟹   XP_038941139
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21092,889,390 - 93,288,013 (-)NCBI
RefSeq Acc Id: XM_039085212   ⟹   XP_038941140
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21092,889,390 - 93,213,292 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001099183   ⟸   NM_001105713
- Sequence:
RefSeq Acc Id: XP_017452495   ⟸   XM_017597006
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017452496   ⟸   XM_017597007
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000051949   ⟸   ENSRNOT00000055073
RefSeq Acc Id: ENSRNOP00000004699   ⟸   ENSRNOT00000004699
RefSeq Acc Id: XP_038941139   ⟸   XM_039085211
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038941140   ⟸   XM_039085212
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000091320   ⟸   ENSRNOT00000115522
RefSeq Acc Id: ENSRNOP00000083509   ⟸   ENSRNOT00000112512
RefSeq Acc Id: ENSRNOP00000079110   ⟸   ENSRNOT00000100596
Transcriptome

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

Promoters
RGD ID:13697861
Promoter ID:EPDNEW_R8378
Type:initiation region
Name:Prkca_1
Description:protein kinase C, alpha
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_6.01096,584,907 - 96,584,967EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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
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-Lx/CubMcwi (2019)
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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
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 (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
BXH2/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (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: 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)
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)
DA/OlaHsd (2019)
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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/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
F344/NCrl (2019)
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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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: 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)
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
LEXF10A/StmMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
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)
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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
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)
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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/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)
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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/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)
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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 (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)
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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 (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)
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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)