Prkcd (protein kinase C, delta) - Rat Genome Database

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Gene: Prkcd (protein kinase C, delta) Rattus norvegicus
Analyze
Symbol: Prkcd
Name: protein kinase C, delta
RGD ID: 67383
Description: Exhibits TIR domain binding activity; calcium-independent protein kinase C activity; and protein kinase binding activity. Involved in several processes, including D-aspartate import across plasma membrane; cellular response to glucose starvation; and positive regulation of glucose import. Localizes to several cellular components, including mitochondrion; nucleus; and postsynaptic cytosol. Used to study brain ischemia and hypertension. Biomarker of hyperinsulinism; hypertension; muscular disease; obesity; and restrictive cardiomyopathy. Human ortholog(s) of this gene implicated in autoimmune lymphoproliferative syndrome type 3 and fatty liver disease. Orthologous to human PRKCD (protein kinase C delta); PARTICIPATES IN the extracellular signal-regulated Raf/Mek/Erk signaling pathway; vascular endothelial growth factor signaling pathway; ceramide signaling pathway; INTERACTS WITH (+)-pilocarpine; (R)-mevalonic acid; (S)-amphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: nPKC-delta; Pkcd; protein kinase C delta type
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2165,769,226 - 5,807,214 (-)NCBI
Rnor_6.0 Ensembl166,655,120 - 6,675,746 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0166,655,131 - 6,675,746 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0166,588,990 - 6,608,725 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4165,954,218 - 5,975,743 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1165,954,214 - 5,975,741 (-)NCBI
Celera169,398,816 - 9,419,806 (+)NCBICelera
Cytogenetic Map16p16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
(R)-mevalonic acid  (EXP)
(S)-amphetamine  (EXP)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
1-(5-isoquinolinesulfonyl)-2-methylpiperazine  (EXP)
1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-butoxyethanol  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
5-(2-methylpiperazine-1-sulfonyl)isoquinoline  (EXP)
5-aza-2'-deoxycytidine  (ISO)
6-formylpterin  (ISO)
6-propyl-2-thiouracil  (EXP)
8-OH-DPAT  (ISO)
acetaldehyde  (ISO)
acetamide  (EXP)
acetylsalicylic acid  (ISO)
acrolein  (EXP,ISO)
actinomycin D  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (ISO)
allyl alcohol  (EXP)
alpha-Zearalanol  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
Anacardic acid  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
apocynin  (EXP,ISO)
aripiprazole  (ISO)
arjunolic acid  (EXP)
arsenite(3-)  (ISO)
arsenous acid  (EXP,ISO)
benzo[a]pyrene  (EXP,ISO)
bisdemethoxycurcumin  (ISO)
bisoprolol  (EXP)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
bortezomib  (ISO)
brimonidine tartrate  (EXP)
bromocriptine  (EXP)
butorphanol  (ISO)
butylated hydroxyanisole  (ISO)
butyric acid  (EXP)
cadmium atom  (EXP)
cadmium dichloride  (ISO)
Calcimycin  (ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
capsaicin  (ISO)
captan  (ISO)
carbon nanotube  (ISO)
carvedilol  (EXP)
chloroprene  (EXP)
chlorpyrifos  (EXP)
chromium(6+)  (ISO)
ciglitazone  (ISO)
cisplatin  (EXP,ISO)
citalopram  (ISO)
cobalt dichloride  (EXP)
cocaine  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
crotonaldehyde  (ISO)
curcumin  (EXP,ISO)
cycloheximide  (EXP)
D-glucose  (EXP,ISO)
D-mannitol  (ISO)
daidzein  (ISO)
daunorubicin  (ISO)
demethoxycurcumin  (ISO)
desferrioxamine B  (ISO)
diarsenic trioxide  (EXP,ISO)
diazinon  (EXP)
dibenziodolium  (EXP,ISO)
dibutyl phthalate  (EXP,ISO)
dieldrin  (EXP,ISO)
diethyl maleate  (EXP)
dioxygen  (ISO)
disodium selenite  (ISO)
divanadium pentaoxide  (EXP,ISO)
dopamine  (ISO)
doxorubicin  (EXP,ISO)
emodin  (EXP,ISO)
endosulfan  (EXP)
entinostat  (ISO)
ethanol  (EXP,ISO)
etoposide  (ISO)
fenamidone  (ISO)
folic acid  (ISO)
folpet  (ISO)
fomepizole  (EXP)
genistein  (ISO)
ginsenoside Re  (ISO)
glucose  (EXP,ISO)
glutathione  (ISO)
heptachlor  (EXP)
hexadecanoic acid  (ISO)
histamine  (ISO)
hydrogen peroxide  (EXP,ISO)
irinotecan  (ISO)
isoprenaline  (EXP)
isorhamnetin  (ISO)
lead(0)  (EXP)
lead(2+)  (EXP)
lipopolysaccharide  (ISO)
lovastatin  (EXP)
LY294002  (ISO)
magnesium atom  (ISO)
manganese atom  (EXP,ISO)
manganese(0)  (EXP,ISO)
manganese(II) chloride  (EXP,ISO)
methamphetamine  (ISO)
methotrexate  (ISO)
methyl beta-cyclodextrin  (ISO)
mitomycin C  (ISO)
morphine  (ISO)
motexafin gadolinium  (ISO)
myo-inositol hexakisphosphate  (ISO)
N-[2-[4-(2-methoxyphenyl)-1-piperazinyl]ethyl]-N-(2-pyridinyl)cyclohexanecarboxamide  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
naringin  (EXP)
nickel dichloride  (EXP)
nicotine  (ISO)
nitric oxide  (EXP)
oroxylin A  (ISO)
oxidopamine  (EXP,ISO)
ozone  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
phencyclidine  (ISO)
phenylephrine  (EXP)
phorbol 12,13-dibutanoate  (ISO)
phorbol 13-acetate 12-myristate  (EXP,ISO)
picrotoxin  (EXP)
progesterone  (EXP,ISO)
propofol  (EXP)
propranolol  (EXP)
puerarin  (ISO)
quercetin  (ISO)
reactive oxygen species  (EXP,ISO)
rotenone  (EXP)
rottlerin  (EXP,ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (EXP,ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
sirolimus  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium dichromate  (ISO)
staurosporine  (EXP,ISO)
streptozocin  (EXP)
tamibarotene  (ISO)
tamoxifen  (ISO)
taurine  (EXP)
testosterone  (ISO)
tetraphene  (ISO)
thapsigargin  (ISO)
thiram  (ISO)
titanium dioxide  (ISO)
toluene  (EXP)
tributylstannane  (ISO)
trichloroethene  (ISO)
trimethyltin  (ISO)
triptonide  (ISO)
tungsten  (ISO)
tyrphostin AG 1478  (ISO)
U-73122  (ISO)
U50488  (ISO)
urethane  (ISO)
ursodeoxycholic acid  (ISO)
valproic acid  (ISO)
vanadium atom  (ISO)
vanadium(0)  (ISO)
vincaleukoblastine  (ISO)
vinclozolin  (EXP)
vincristine  (ISO)
wortmannin  (ISO)
Yessotoxin  (ISO)
zinc acetate  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of protein kinase activity  (IEA,ISO)
aging  (IEP)
apoptotic process  (IEA,IMP,ISO,ISS)
B cell proliferation  (IEA,ISO)
cell chemotaxis  (IEA,ISO)
cellular response to angiotensin  (IEA,ISO,ISS)
cellular response to glucose starvation  (IEP)
cellular response to hydrogen peroxide  (IEA,ISO)
cellular response to hydroperoxide  (IEA,ISO)
cellular response to insulin stimulus  (IEP)
cellular response to oxidative stress  (IDA)
cellular response to UV  (IEA,ISO,ISS)
cellular senescence  (IEA,ISO)
collagen metabolic process  (IMP)
D-aspartate import across plasma membrane  (IMP)
defense response to bacterium  (IEA,ISO,ISS)
histone phosphorylation  (IEA,ISO)
immunoglobulin mediated immune response  (IEA,ISO)
intracellular signal transduction  (IBA,IDA,IEA)
negative regulation of actin filament polymerization  (IEA,ISO,ISS)
negative regulation of filopodium assembly  (IEA,ISO,ISS)
negative regulation of glial cell apoptotic process  (IEA,ISO,ISS)
negative regulation of insulin receptor signaling pathway  (IEA,ISO)
negative regulation of MAP kinase activity  (IEA,ISO)
negative regulation of peptidyl-tyrosine phosphorylation  (IEA,ISO)
negative regulation of platelet aggregation  (IEA,ISO,ISS)
neutrophil activation  (IEA,ISO)
peptidyl-serine phosphorylation  (IBA,IEA,ISO,ISS)
peptidyl-threonine phosphorylation  (IEA,ISO)
peptidyl-tyrosine phosphorylation  (IEA)
positive regulation of apoptotic process  (IMP)
positive regulation of apoptotic signaling pathway  (IEA,ISO)
positive regulation of ceramide biosynthetic process  (IEA,ISO)
positive regulation of endodeoxyribonuclease activity  (IEA,ISO)
positive regulation of glucose import  (IMP)
positive regulation of glucosylceramide catabolic process  (IEA,ISO)
positive regulation of MAP kinase activity  (IMP)
positive regulation of MAPK cascade  (IMP)
positive regulation of phospholipid scramblase activity  (IEA,ISO)
positive regulation of protein dephosphorylation  (IEA,ISO)
positive regulation of protein import into nucleus  (IEA,ISO)
positive regulation of response to DNA damage stimulus  (IEA,ISO)
positive regulation of sphingomyelin catabolic process  (IEA,ISO)
positive regulation of superoxide anion generation  (IEA,ISO,ISS)
protein autophosphorylation  (IDA)
protein phosphorylation  (IDA,IEA,ISO)
regulation of actin cytoskeleton organization  (ISO)
regulation of ceramide biosynthetic process  (ISO,ISS)
regulation of phosphorylation  (IDA)
response to amino acid  (IEP)
response to drug  (IEP)
response to ethanol  (IEP)
response to glucose  (IEP)
response to heat  (IEP)
response to hydrogen peroxide  (IEP)
response to hypoxia  (IEP)
response to mechanical stimulus  (IEP)
response to organic cyclic compound  (IEP)
response to organonitrogen compound  (IEP)
response to oxidative stress  (IMP)
termination of signal transduction  (IEA,ISO)

Cellular Component
cell-cell junction  (IEA,ISO)
cytoplasm  (IDA,IEA,ISO)
cytosol  (IDA,IEA,ISO)
endolysosome  (IEA,ISO,ISS)
endoplasmic reticulum  (IEA,ISO,ISS)
membrane  (IDA,ISO)
mitochondrion  (IDA)
nuclear matrix  (IEA,ISO)
nucleus  (IDA,ISO)
perinuclear region of cytoplasm  (IEA)
plasma membrane  (IDA,IEA,ISO)
postsynaptic cytosol  (IDA)

References

References - curated
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Additional References at PubMed
PMID:3691811   PMID:9447980   PMID:9677322   PMID:9687370   PMID:10431815   PMID:10446219   PMID:10617144   PMID:10708593   PMID:10713049   PMID:10721703   PMID:10770950   PMID:10882525  
PMID:11118818   PMID:11738801   PMID:11744693   PMID:11916978   PMID:11950946   PMID:11976687   PMID:11998977   PMID:12167703   PMID:12391145   PMID:12456804   PMID:12477932   PMID:12510148  
PMID:12566450   PMID:12606313   PMID:12619877   PMID:12700627   PMID:12809676   PMID:12826681   PMID:12878476   PMID:12893264   PMID:12904329   PMID:13679307   PMID:14555230   PMID:14561782  
PMID:14583092   PMID:14715667   PMID:15105418   PMID:15210825   PMID:15217780   PMID:15282327   PMID:15339931   PMID:15476586   PMID:15576445   PMID:15632189   PMID:15716854   PMID:15731106  
PMID:15769752   PMID:15774464   PMID:15817708   PMID:15838306   PMID:15935342   PMID:15961393   PMID:15963450   PMID:15978696   PMID:15991247   PMID:16118209   PMID:16361258   PMID:16361709  
PMID:16367743   PMID:16396499   PMID:16611985   PMID:16648180   PMID:16781675   PMID:16940418   PMID:16962999   PMID:16987961   PMID:17109817   PMID:17293847   PMID:17306383   PMID:17316401  
PMID:17531159   PMID:17569658   PMID:17728398   PMID:17825316   PMID:17901241   PMID:17938203   PMID:17959830   PMID:17978575   PMID:17989210   PMID:18097471   PMID:18158336   PMID:18180404  
PMID:18182053   PMID:18195168   PMID:18273864   PMID:18285345   PMID:18285462   PMID:18323529   PMID:18335519   PMID:18387943   PMID:18388183   PMID:18497307   PMID:18550549   PMID:18556656  
PMID:18583709   PMID:18668351   PMID:18725417   PMID:18836180   PMID:18991865   PMID:19056867   PMID:19057126   PMID:19059439   PMID:19063870   PMID:19246637   PMID:19249914   PMID:19279008  
PMID:19279011   PMID:19339511   PMID:19356729   PMID:19366211   PMID:19497417   PMID:19540196   PMID:19632305   PMID:19646462   PMID:19752773   PMID:19782747   PMID:19801500   PMID:19808702  
PMID:19820255   PMID:19837873   PMID:19837952   PMID:19879903   PMID:19900507   PMID:19914792   PMID:19914793   PMID:19965374   PMID:20395372   PMID:20578995   PMID:20610768   PMID:20686066  
PMID:20691763   PMID:20817341   PMID:20853175   PMID:21117027   PMID:21119009   PMID:21132404   PMID:21172324   PMID:21338602   PMID:21406958   PMID:21625957   PMID:21704002   PMID:21766206  
PMID:21789211   PMID:21865164   PMID:21984583   PMID:22259083   PMID:22265677   PMID:22282354   PMID:22371141   PMID:22499584   PMID:22554282   PMID:22577133   PMID:22648735   PMID:22684549  
PMID:22798525   PMID:22871113   PMID:22885697   PMID:22972957   PMID:23010893   PMID:23022406   PMID:23063429   PMID:23104422   PMID:23144458   PMID:23376485   PMID:23727579   PMID:23827392  
PMID:23932656   PMID:24008408   PMID:24018979   PMID:24107416   PMID:24211111   PMID:24519937   PMID:24840386   PMID:24909118   PMID:24914766   PMID:25489059   PMID:25659900   PMID:25707622  
PMID:25755284   PMID:26199377   PMID:26519110   PMID:26546672   PMID:27190303   PMID:27379421   PMID:27606614   PMID:28428613   PMID:28795305   PMID:29313986   PMID:29435096   PMID:29617417  
PMID:29705702   PMID:30641088   PMID:31257458   PMID:31908004   PMID:32291286  


Genomics

Comparative Map Data
Prkcd
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2165,769,226 - 5,807,214 (-)NCBI
Rnor_6.0 Ensembl166,655,120 - 6,675,746 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0166,655,131 - 6,675,746 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0166,588,990 - 6,608,725 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4165,954,218 - 5,975,743 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1165,954,214 - 5,975,741 (-)NCBI
Celera169,398,816 - 9,419,806 (+)NCBICelera
Cytogenetic Map16p16NCBI
PRKCD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl353,156,009 - 53,192,717 (+)EnsemblGRCh38hg38GRCh38
GRCh38353,161,209 - 53,192,717 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37353,195,225 - 53,226,733 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36353,170,263 - 53,201,773 (+)NCBINCBI36hg18NCBI36
Build 34353,170,262 - 53,201,771NCBI
Celera353,162,239 - 53,193,756 (+)NCBI
Cytogenetic Map3p21.1NCBI
HuRef353,210,511 - 53,276,026 (+)NCBIHuRef
CHM1_1353,146,796 - 53,178,291 (+)NCBICHM1_1
Prkcd
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391430,317,310 - 30,348,637 (-)NCBIGRCm39mm39
GRCm39 Ensembl1430,317,311 - 30,348,167 (-)Ensembl
GRCm381430,595,353 - 30,626,414 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1430,595,354 - 30,626,210 (-)EnsemblGRCm38mm10GRCm38
MGSCv371431,408,555 - 31,423,498 (-)NCBIGRCm37mm9NCBIm37
MGSCv361429,424,378 - 29,447,560 (-)NCBImm8
Celera1426,853,019 - 26,867,962 (-)NCBICelera
Cytogenetic Map14BNCBI
cM Map1418.82NCBI
Prkcd
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554303,124,738 - 3,153,274 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554303,125,066 - 3,151,857 (+)NCBIChiLan1.0ChiLan1.0
PRKCD
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1354,330,328 - 54,357,910 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl354,330,328 - 54,357,910 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0353,104,137 - 53,135,588 (+)NCBIMhudiblu_PPA_v0panPan3
PRKCD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12036,723,491 - 36,751,982 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2036,723,809 - 36,752,191 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2036,660,459 - 36,673,894 (-)NCBI
ROS_Cfam_1.02037,001,697 - 37,030,998 (-)NCBI
UMICH_Zoey_3.12036,438,983 - 36,452,419 (-)NCBI
UNSW_CanFamBas_1.02036,800,686 - 36,814,133 (-)NCBI
UU_Cfam_GSD_1.02037,015,742 - 37,029,186 (-)NCBI
Prkcd
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118170,754,028 - 170,788,044 (+)NCBI
SpeTri2.0NW_0049364733,892,625 - 3,923,467 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRKCD
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1335,290,264 - 35,323,356 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11335,290,835 - 35,323,245 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21338,361,707 - 38,390,508 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PRKCD
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12214,561,401 - 14,592,877 (+)NCBI
ChlSab1.1 Ensembl2214,565,282 - 14,592,873 (+)Ensembl
Vero_WHO_p1.0NW_023666041152,302,998 - 152,334,406 (-)NCBI
Prkcd
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248224,035,819 - 4,062,907 (-)NCBI

Position Markers
D16Mgh7  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2165,769,407 - 5,769,550 (+)MAPPER
Rnor_6.0166,655,313 - 6,655,455NCBIRnor6.0
Rnor_5.0166,589,172 - 6,589,314UniSTSRnor5.0
RGSC_v3.4165,954,398 - 5,954,541RGDRGSC3.4
RGSC_v3.4165,954,399 - 5,954,541UniSTSRGSC3.4
RGSC_v3.1165,954,396 - 5,954,539RGD
Celera169,419,482 - 9,419,624UniSTS
Cytogenetic Map16p16UniSTS
D16Arb4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2165,769,278 - 5,769,666 (+)MAPPER
Rnor_6.0166,655,184 - 6,655,571NCBIRnor6.0
Rnor_5.0166,589,043 - 6,589,430UniSTSRnor5.0
RGSC_v3.4165,954,270 - 5,954,657UniSTSRGSC3.4
RGSC_v3.1165,954,266 - 5,954,655RGD
Celera169,419,366 - 9,419,753UniSTS
SHRSP x BN Map161.1599UniSTS
SHRSP x BN Map161.1599RGD
FHH x ACI Map165.3399RGD
Cytogenetic Map16p16UniSTS
AI044238  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2165,769,531 - 5,769,780 (+)MAPPER
Rnor_6.0166,655,437 - 6,655,685NCBIRnor6.0
Rnor_5.0166,589,296 - 6,589,544UniSTSRnor5.0
RGSC_v3.4165,954,523 - 5,954,771UniSTSRGSC3.4
Celera169,419,252 - 9,419,500UniSTS
RH 3.4 Map1631.5UniSTS
Cytogenetic Map16p16UniSTS
UniSTS:224276  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2165,769,421 - 5,769,611 (+)MAPPER
Rnor_6.0166,655,327 - 6,655,516NCBIRnor6.0
Rnor_5.0166,589,186 - 6,589,375UniSTSRnor5.0
RGSC_v3.4165,954,413 - 5,954,602UniSTSRGSC3.4
Celera169,419,421 - 9,419,610UniSTS
Cytogenetic Map16p16UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16110660736Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16124228366Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16127556253Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16127556253Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16127556253Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16131816439Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16133160624Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16134465490Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16141240937Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16141240937Rat
631561Hcuc2Hepatic copper content QTL 22.8hepatic copper amount (VT:0003065)liver total copper weight (CMO:0001507)16141240957Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)1624459345244593Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)16109005486162972Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16134074146340741Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)16155018749247447Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)16155018763210301Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16155018763210301Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)16155018763210301Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)16155018763210301Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16172829746728297Rat
2301406Kidm39Kidney mass QTL 390.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)16329668817464293Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16413635523105837Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16413635545905331Rat
737825Alc13Alcohol consumption QTL 134.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16501380218360147Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16501380245905331Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16501380245905331Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16501380245905331Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16501380250013802Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16501380250169318Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16501380252144919Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16501380264012784Rat
61372Bp40Blood pressure QTL 402.2blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)16509870419398181Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:459
Count of miRNA genes:255
Interacting mature miRNAs:306
Transcripts:ENSRNOT00000025858, ENSRNOT00000067639
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


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 39 35 19 19 19 46 35 41 11
Low 4 22 22 22 8 11 28 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_133307 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF219629 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ230615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ230616 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ230617 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ230618 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ230619 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ230620 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ230621 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ230622 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ230623 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ230624 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ230625 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ230626 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ230627 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ230628 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ230629 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ230630 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ230631 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ230632 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ230633 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC076505 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235241 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M18330 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000025858   ⟹   ENSRNOP00000025858
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl166,655,120 - 6,675,746 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000067639   ⟹   ENSRNOP00000061108
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl166,655,662 - 6,669,045 (-)Ensembl
RefSeq Acc Id: NM_133307   ⟹   NP_579841
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,769,226 - 5,807,214 (-)NCBI
Rnor_6.0166,655,131 - 6,675,746 (-)NCBI
Rnor_5.0166,588,990 - 6,608,725 (-)NCBI
RGSC_v3.4165,954,218 - 5,975,743 (-)RGD
Celera169,398,816 - 9,419,806 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_579841   ⟸   NM_133307
- Sequence:
RefSeq Acc Id: ENSRNOP00000061108   ⟸   ENSRNOT00000067639
RefSeq Acc Id: ENSRNOP00000025858   ⟸   ENSRNOT00000025858
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 (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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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
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 (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 (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
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:67383 AgrOrtholog
BIND 134041
Ensembl Genes ENSRNOG00000016346 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000025858 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000061108 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025858 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000067639 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.150 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7099952 IMAGE-MGC_LOAD
InterPro AGC-kinase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C2_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DAG/PE-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kinase-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PE/DAG-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PKC_delta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pkinase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Prot_kin_PKC_delta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Prot_kinase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Protein_kinase_ATP_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ser/Thr_kinase_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:170538 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91512 IMAGE-MGC_LOAD
NCBI Gene 170538 ENTREZGENE
Pfam C1_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pkinase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pkinase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Prkcd PhenoGen
PIRSF PKC_delta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Protein_kin_C_delta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS DAGPEDOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE AGC_KINASE_CTER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_ATP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_ST UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PS50004 UniProtKB/Swiss-Prot
  ZF_DAG_PE_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_DAG_PE_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART S_TK_X UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  S_TKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00109 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A140UHX0_RAT UniProtKB/TrEMBL
  D4A0U0_RAT UniProtKB/TrEMBL
  KPCD_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q6DG48 UniProtKB/Swiss-Prot
  Q9JK29 UniProtKB/Swiss-Prot
  Q9JL03 UniProtKB/Swiss-Prot
  Z4YNR1 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Prkcd  protein kinase C, delta      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization translocates from cytosol into the nucleus upon treatment with etoposide; Intralipid + heparin (IH) induces translocation from the cytosolic to membrane fraction 729633
gene_cellular_localization translocates from cytosol into the nucleus upon treatment with etoposide; Intralipid + heparin (IH) induces translocation from the cytosolic to membrane fraction 729667
gene_expression expressed in pancreatic acini 631304
gene_function binds phorbol esters 61695
gene_function binds phorbol esters 628336
gene_pathway activation by the digitalis drug ouabain is linked to Na+/K+-ATPase through Src/EGFR, and is required for the activation of ERK1/2 631304
gene_process involved in proheparin-binding EGF-like growth factor (HBEGF) ectodomain shedding upon TPA stimulation 61695
gene_process involved in proheparin-binding EGF-like growth factor (HBEGF) ectodomain shedding upon TPA stimulation 628336
gene_regulation maximal activation requires phosphatidylserine and diacylglycerol 61695
gene_regulation maximal activation requires phosphatidylserine and diacylglycerol 628336
gene_regulation tyrosine phosphorylation results in increased instability leading to degradation 631304
gene_regulation administration of the digitalis drug ouabain with intact cardiac myocytes causes rapid translocation/activation from the soluble to the particulate pools of enzymes 631304
gene_regulation protein is tyrosine phosphorylated by activated Cholecystokinin A receptor (Cckar) in pancreatic acinar cells 631304