Prkcg (protein kinase C, gamma) - Rat Genome Database

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Gene: Prkcg (protein kinase C, gamma) Rattus norvegicus
Analyze
Symbol: Prkcg
Name: protein kinase C, gamma
RGD ID: 3397
Description: Enables calcium-dependent protein kinase C activity. Involved in several processes, including long-term synaptic potentiation; protein autophosphorylation; and response to psychosocial stress. Located in several cellular components, including perinuclear region of cytoplasm; postsynaptic cytosol; and synaptic membrane. Human ortholog(s) of this gene implicated in spinocerebellar ataxia type 14. Orthologous to human PRKCG (protein kinase C gamma); PARTICIPATES IN eicosanoid signaling pathway; endothelin signaling pathway; insulin signaling pathway; INTERACTS WITH (+)-pilocarpine; (S)-alpha-methyl-4-carboxyphenylglycine; 2-amino-5-phosphonopentanoic acid.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: MGC105487; PKC; PKC-gamma; PKCI; Prkc; Prkcc; protein kinase C gamma type; Protein kinase C type I (gamma type); Protein kinase C, type I (gamma type); RATPKCI
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
mRatBN7.2165,832,851 - 65,860,676 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl165,832,855 - 65,859,384 (-)Ensembl
Rnor_6.0164,407,098 - 64,433,698 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl164,407,114 - 64,433,636 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0163,399,153 - 63,425,645 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4164,145,749 - 64,172,712 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1164,223,859 - 64,250,823 (-)NCBI
Celera163,557,681 - 63,584,062 (-)NCBICelera
Cytogenetic Map1q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP,ISO)
(S)-alpha-methyl-4-carboxyphenylglycine  (EXP)
(S)-naringenin  (ISO)
1,2-dimethylhydrazine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-amino-5-phosphonopentanoic acid  (EXP)
2-methoxyethanol  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (ISO)
aflatoxin B1  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
benzo[a]pyrene  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP)
bryostatin 1  (ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
celecoxib  (ISO)
cobalt dichloride  (EXP)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
Cuprizon  (EXP)
cyclophosphamide  (EXP)
daidzein  (EXP)
deoxynivalenol  (ISO)
dimethylarsinic acid  (EXP)
dizocilpine maleate  (EXP,ISO)
endosulfan  (EXP)
ethanol  (EXP,ISO)
fenamidone  (ISO)
fluoxetine  (EXP)
hydrogen peroxide  (ISO)
ketamine  (EXP)
lead diacetate  (EXP)
lead(0)  (EXP)
lead(2+)  (EXP)
lidocaine  (EXP)
lithium atom  (ISO)
lithium hydride  (ISO)
memantine  (EXP)
mercury atom  (EXP)
mercury(0)  (EXP)
methoxyacetic acid  (EXP)
Mezerein  (ISO)
morphine  (EXP,ISO)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
ozone  (EXP)
paraquat  (EXP)
PCB138  (EXP)
perfluorooctane-1-sulfonic acid  (EXP)
phencyclidine  (EXP)
phorbol 13-acetate 12-myristate  (EXP,ISO)
pioglitazone  (ISO)
quercetin  (ISO)
Rebamipide  (EXP)
remifentanil  (EXP)
resveratrol  (EXP)
Ro 31-8220  (ISO)
S-nitroso-N-acetyl-D-penicillamine  (ISO)
sirolimus  (ISO)
sodium arsenite  (ISO)
thiram  (ISO)
triclosan  (ISO)
trimethylarsine oxide  (EXP)
triptonide  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
1. Al-Maghtheh M, etal., Am J Hum Genet 1998 May;62(5):1248-52.
2. Angenstein F, etal., Neuroscience. 1999;93(4):1289-95. doi: 10.1016/s0306-4522(99)00315-2.
3. Boesch DM and Garvin JL, Am J Physiol Regul Integr Comp Physiol 2001 Sep;281(3):R861-7.
4. Chen DH, etal., Am J Hum Genet 2003 Apr;72(4):839-49. Epub 2003 Mar 17.
5. Chen KH, etal., J Biol Chem 1990 Nov 15;265(32):19961-5.
6. Colombo PJ and Gallagher M, Hippocampus 2002;12(2):285-9.
7. Correia SS, etal., J Biol Chem. 2003 Feb 21;278(8):6307-13. Epub 2002 Dec 5.
8. Crocenzi FA, etal., Hepatology. 2008 Dec;48(6):1885-95.
9. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
10. GOA data from the GO Consortium
11. Hamabe W, etal., J Pharmacol Exp Ther. 2005 Jun;313(3):1027-34. Epub 2005 Feb 10.
12. Knopf JL, etal., Cell 1986 Aug 15;46(4):491-502.
13. Kose A, etal., Brain Res. 1990 Jun 4;518(1-2):209-17.
14. Krugers HJ, etal., Hippocampus. 1997;7(4):427-36.
15. Kuroda S, etal., J Biol Chem 1996 Dec 6;271(49):31029-32.
16. Mahadev K and Vemuri MC, Arch Biochem Biophys. 1998 Aug 15;356(2):249-57.
17. Matsumoto S, etal., J Cereb Blood Flow Metab 2004 Jan;24(1):54-61.
18. MGD data from the GO Consortium
19. NCBI rat LocusLink and RefSeq merged data July 26, 2002
20. Newton AC Am J Physiol Endocrinol Metab. 2010 Mar;298(3):E395-402. Epub 2009 Nov 24.
21. OMIM Disease Annotation Pipeline
22. Pipeline to import KEGG annotations from KEGG into RGD
23. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
24. RGD automated data pipeline
25. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
26. RGD automated import pipeline for gene-chemical interactions
27. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
28. Tokunaga C, etal., Biochem Biophys Res Commun 1998 Mar 17;244(2):353-9.
29. Wen ZH, etal., Brain Res. 2003 Feb 14;963(1-2):1-7. doi: 10.1016/s0006-8993(02)03751-4.
30. Youngren JF Cell Mol Life Sci. 2007 Apr;64(7-8):873-91.
Additional References at PubMed
PMID:1321150   PMID:3111527   PMID:3387228   PMID:7929424   PMID:8548809   PMID:8631738   PMID:9271501   PMID:9323205   PMID:10365161   PMID:10407019   PMID:10617144   PMID:10722046  
PMID:10753752   PMID:10871288   PMID:10882525   PMID:11123317   PMID:11246146   PMID:11278415   PMID:11306676   PMID:11549583   PMID:11606660   PMID:12175859   PMID:12477932   PMID:12551925  
PMID:14613966   PMID:15006698   PMID:15763930   PMID:15808853   PMID:15830100   PMID:15878171   PMID:15880264   PMID:15985361   PMID:16043888   PMID:16079148   PMID:16084468   PMID:16236710  
PMID:16319314   PMID:16324113   PMID:16500613   PMID:16571747   PMID:16648180   PMID:16724110   PMID:16905533   PMID:17114649   PMID:17904530   PMID:18288091   PMID:18387748   PMID:18436224  
PMID:18456322   PMID:18473171   PMID:18617608   PMID:18621396   PMID:18685019   PMID:18761789   PMID:19057126   PMID:19358756   PMID:19432589   PMID:20052412   PMID:21155805   PMID:21424759  
PMID:21665998   PMID:21700703   PMID:22126757   PMID:22284620   PMID:22736542   PMID:22797923   PMID:22871113   PMID:23185022   PMID:23793062   PMID:23982492   PMID:24794094   PMID:24824652  
PMID:24914766   PMID:25009260   PMID:25529429   PMID:25961142   PMID:26199377   PMID:26546817   PMID:27296621   PMID:27848062   PMID:28587770   PMID:29121795   PMID:29247648   PMID:29476059  
PMID:29555470   PMID:30053369   PMID:30355630   PMID:31283971   PMID:32865105  


Genomics

Comparative Map Data
Prkcg
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2165,832,851 - 65,860,676 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl165,832,855 - 65,859,384 (-)Ensembl
Rnor_6.0164,407,098 - 64,433,698 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl164,407,114 - 64,433,636 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0163,399,153 - 63,425,645 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4164,145,749 - 64,172,712 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1164,223,859 - 64,250,823 (-)NCBI
Celera163,557,681 - 63,584,062 (-)NCBICelera
Cytogenetic Map1q12NCBI
PRKCG
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1953,879,190 - 53,907,652 (+)EnsemblGRCh38hg38GRCh38
GRCh381953,882,197 - 53,907,652 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371954,385,451 - 54,410,906 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361959,077,279 - 59,102,713 (+)NCBINCBI36hg18NCBI36
Build 341959,077,278 - 59,102,713NCBI
Celera1951,426,508 - 51,451,938 (+)NCBI
Cytogenetic Map19q13.42NCBI
HuRef1950,704,660 - 50,730,288 (+)NCBIHuRef
CHM1_11954,386,673 - 54,412,682 (+)NCBICHM1_1
Prkcg
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3973,351,982 - 3,379,615 (+)NCBIGRCm39mm39
GRCm39 Ensembl73,337,704 - 3,379,615 (+)Ensembl
GRCm3873,303,532 - 3,331,099 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl73,289,179 - 3,331,099 (+)EnsemblGRCm38mm10GRCm38
MGSCv3773,303,658 - 3,331,005 (+)NCBIGRCm37mm9NCBIm37
MGSCv3673,303,658 - 3,331,005 (+)NCBImm8
Celera73,254,377 - 3,281,532 (+)NCBICelera
Cytogenetic Map7A1NCBI
cM Map71.93NCBI
Prkcg
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955604262,071 - 279,259 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955604262,182 - 279,259 (-)NCBIChiLan1.0ChiLan1.0
PRKCG
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11959,671,762 - 59,696,728 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1959,672,097 - 59,695,977 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01950,823,372 - 50,849,003 (+)NCBIMhudiblu_PPA_v0panPan3
PRKCG
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11103,295,110 - 103,312,562 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1103,361,568 - 103,378,698 (-)NCBI
ROS_Cfam_1.01103,950,090 - 103,967,279 (-)NCBI
UMICH_Zoey_3.11103,582,545 - 103,599,712 (-)NCBI
UNSW_CanFamBas_1.01103,344,283 - 103,361,444 (-)NCBI
UU_Cfam_GSD_1.01104,063,257 - 104,080,431 (-)NCBI
Prkcg
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244093492,832,669 - 2,850,276 (-)NCBI
SpeTri2.0NW_00493699487,525 - 105,125 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRKCG
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl656,213,483 - 56,234,656 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1656,213,479 - 56,235,683 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2652,981,725 - 53,001,720 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PRKCG
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1646,574,560 - 46,600,329 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl646,575,439 - 46,600,364 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607326,653,473 - 26,678,402 (+)NCBIVero_WHO_p1.0
Prkcg
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248322,548,286 - 2,566,365 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D1Wox11  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2165,832,929 - 65,833,076 (+)MAPPERmRatBN7.2
Rnor_6.0164,407,177 - 64,407,321NCBIRnor6.0
Rnor_5.0163,399,232 - 63,399,376UniSTSRnor5.0
RGSC_v3.4164,145,811 - 64,145,956RGDRGSC3.4
RGSC_v3.4164,145,812 - 64,145,956UniSTSRGSC3.4
RGSC_v3.1164,223,922 - 64,224,067RGD
Celera163,557,744 - 63,557,888UniSTS
RH 3.4 Map1739.8UniSTS
RH 3.4 Map1739.8RGD
RH 2.0 Map1473.2RGD
Cytogenetic Map1q12UniSTS
D1Arb31  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2165,832,901 - 65,833,203 (+)MAPPERmRatBN7.2
Rnor_6.0164,407,149 - 64,407,448NCBIRnor6.0
Rnor_5.0163,399,204 - 63,399,503UniSTSRnor5.0
RGSC_v3.4164,145,784 - 64,146,083UniSTSRGSC3.4
RGSC_v3.1164,223,894 - 64,224,194RGD
Celera163,557,716 - 63,558,015UniSTS
Cytogenetic Map1q12UniSTS
D1Mco31  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2165,832,927 - 65,833,076 (+)MAPPERmRatBN7.2
Rnor_6.0164,407,175 - 64,407,321NCBIRnor6.0
Rnor_5.0163,399,230 - 63,399,376UniSTSRnor5.0
RGSC_v3.4164,145,809 - 64,145,956RGDRGSC3.4
RGSC_v3.4164,145,810 - 64,145,956UniSTSRGSC3.4
RGSC_v3.1164,223,920 - 64,224,067RGD
Celera163,557,742 - 63,557,888UniSTS
Cytogenetic Map1q12UniSTS
Prkcc  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2165,833,755 - 65,834,159 (+)MAPPERmRatBN7.2
Rnor_6.0164,408,001 - 64,408,404NCBIRnor6.0
Rnor_5.0163,400,056 - 63,400,459UniSTSRnor5.0
RGSC_v3.4164,146,636 - 64,147,039UniSTSRGSC3.4
Celera163,558,568 - 63,558,971UniSTS
Cytogenetic Map1q12UniSTS
fc30h10.x1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2165,857,927 - 65,859,468 (+)MAPPERmRatBN7.2
mRatBN7.2165,857,947 - 65,859,468 (+)MAPPERmRatBN7.2
Rnor_6.0164,432,233 - 64,433,753NCBIRnor6.0
Rnor_6.0164,432,213 - 64,433,753NCBIRnor6.0
Rnor_5.0163,424,174 - 63,425,694UniSTSRnor5.0
Rnor_5.0163,424,154 - 63,425,694UniSTSRnor5.0
RGSC_v3.4164,171,289 - 64,172,829UniSTSRGSC3.4
RGSC_v3.4164,171,309 - 64,172,829UniSTSRGSC3.4
Celera163,582,659 - 63,584,179UniSTS
Celera163,582,639 - 63,584,179UniSTS
Cytogenetic Map1q12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11148131275088344Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11148131282174945Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
1357400Bw62Body weight QTL624.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)12234064767340647Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)12887978078430678Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13273727390665040Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
1354599Bw29Body weight QTL 293.460.001body mass (VT:0001259)body weight (CMO:0000012)13344984878449848Rat
1354643Foco2Food consumption QTL 27.170.0001eating behavior trait (VT:0001431)food intake rate (CMO:0000427)13344984878449848Rat
8552900Pigfal1Plasma insulin-like growth factor 1 level QTL 17.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
8552948Pigfal11Plasma insulin-like growth factor 1 level QTL 114.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
9589820Insglur3Insulin/glucose ratio QTL 310.750.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)13483685879836858Rat
1331732Srn4Serum renin concentration QTL 44.467renin activity (VT:0005581)plasma renin activity level (CMO:0000116)13523959878430678Rat
1331792Rf29Renal function QTL 294.589urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)13523959878430678Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143284731118944897Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14333300288333002Rat
1331778Rf28Renal function QTL 284.66urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)14580314078430678Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14936146582174945Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14939317294393172Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15386304190532583Rat
4889919Bss86Bone structure and strength QTL 864.1tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)15389511782174945Rat
4889929Bss87Bone structure and strength QTL 876.7tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)15389511782174945Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)15673266898773277Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)156949932101949932Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)157336763151090257Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)165789093115540829Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:510
Count of miRNA genes:223
Interacting mature miRNAs:258
Transcripts:ENSRNOT00000019825
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 2 54 3
Low 3 43 42 26 17 26 3 5 20 30 38 11 3
Below cutoff 15 15 15 5 6 5 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000080032   ⟹   ENSRNOP00000071203
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl165,832,855 - 65,859,384 (-)Ensembl
Rnor_6.0 Ensembl164,407,114 - 64,433,636 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104999   ⟹   ENSRNOP00000079620
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl165,832,855 - 65,859,384 (-)Ensembl
RefSeq Acc Id: NM_012628   ⟹   NP_036760
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,832,867 - 65,859,351 (-)NCBI
Rnor_6.0164,407,114 - 64,433,636 (-)NCBI
Rnor_5.0163,399,153 - 63,425,645 (-)NCBI
RGSC_v3.4164,145,749 - 64,172,712 (-)RGD
Celera163,557,681 - 63,584,062 (-)RGD
Sequence:
RefSeq Acc Id: XM_006228014   ⟹   XP_006228076
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,832,851 - 65,859,413 (-)NCBI
Rnor_6.0164,407,098 - 64,433,698 (-)NCBI
Rnor_5.0163,399,153 - 63,425,645 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039100669   ⟹   XP_038956597
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,832,851 - 65,859,070 (-)NCBI
RefSeq Acc Id: XM_039100699   ⟹   XP_038956627
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,832,851 - 65,859,060 (-)NCBI
RefSeq Acc Id: XM_039100736   ⟹   XP_038956664
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,832,851 - 65,860,676 (-)NCBI
RefSeq Acc Id: XM_039100756   ⟹   XP_038956684
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,832,851 - 65,850,706 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_036760   ⟸   NM_012628
- UniProtKB: P63319 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006228076   ⟸   XM_006228014
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000071203   ⟸   ENSRNOT00000080032
RefSeq Acc Id: XP_038956664   ⟸   XM_039100736
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038956597   ⟸   XM_039100669
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038956627   ⟸   XM_039100699
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038956684   ⟸   XM_039100756
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000079620   ⟸   ENSRNOT00000104999
Protein Domains
AGC-kinase C-terminal   C2   Protein kinase

Transcriptome

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

Promoters
RGD ID:13689666
Promoter ID:EPDNEW_R191
Type:single initiation site
Name:Prkcg_1
Description:protein kinase C, gamma
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_6.0164,433,688 - 64,433,748EPDNEW

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)
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
M520/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
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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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
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:3397 AgrOrtholog
Ensembl Genes ENSRNOG00000054371 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000071203 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000080032 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.150 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7319243 IMAGE-MGC_LOAD
InterPro AGC-kinase_C UniProtKB/Swiss-Prot
  C2_dom UniProtKB/Swiss-Prot
  C2_domain_sf UniProtKB/Swiss-Prot
  DAG/PE-bd UniProtKB/Swiss-Prot
  Kinase-like_dom_sf UniProtKB/Swiss-Prot
  PE/DAG-bd UniProtKB/Swiss-Prot
  Pkinase_C UniProtKB/Swiss-Prot
  Prot_kinase_dom UniProtKB/Swiss-Prot
  Protein_kinase_ATP_BS UniProtKB/Swiss-Prot
  Protein_kinase_C_a/b/g UniProtKB/Swiss-Prot
  Ser/Thr_kinase_AS UniProtKB/Swiss-Prot
KEGG Report rno:24681 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105487 IMAGE-MGC_LOAD
NCBI Gene 24681 ENTREZGENE
Pfam C1_1 UniProtKB/Swiss-Prot
  PF00168 UniProtKB/Swiss-Prot
  Pkinase UniProtKB/Swiss-Prot
  Pkinase_C UniProtKB/Swiss-Prot
PhenoGen Prkcg PhenoGen
PIRSF PKC_alpha UniProtKB/Swiss-Prot
PRINTS C2DOMAIN UniProtKB/Swiss-Prot
  DAGPEDOMAIN UniProtKB/Swiss-Prot
PROSITE AGC_KINASE_CTER UniProtKB/Swiss-Prot
  PROTEIN_KINASE_ATP UniProtKB/Swiss-Prot
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot
  PROTEIN_KINASE_ST UniProtKB/Swiss-Prot
  PS50004 UniProtKB/Swiss-Prot
  ZF_DAG_PE_1 UniProtKB/Swiss-Prot
  ZF_DAG_PE_2 UniProtKB/Swiss-Prot
SMART S_TK_X UniProtKB/Swiss-Prot
  S_TKc UniProtKB/Swiss-Prot
  SM00109 UniProtKB/Swiss-Prot
  SM00239 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49562 UniProtKB/Swiss-Prot
  SSF56112 UniProtKB/Swiss-Prot
TIGR TC231291
UniProt KPCG_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary P05697 UniProtKB/Swiss-Prot
  Q5FWS3 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-24 Prkcg  protein kinase C, gamma  Prkcc  protein kinase C, gamma  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Prkcc  protein kinase C, gamma  Prkcg  Protein kinase C, type I (gamma type)  Symbol and Name updated 629477 APPROVED
2002-06-10 Prkcg  Protein kinase C, type I (gamma type)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression highly expressed in cerebellum, hippocampus, amygdala, and cerebral cortex 633711
gene_transcript promoter region lacks TATA and CAAT boxes, contains AP2, Spl, and c-myc binding sites 633711