Prkaca (protein kinase cAMP-activated catalytic subunit alpha) - Rat Genome Database

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Gene: Prkaca (protein kinase cAMP-activated catalytic subunit alpha) Rattus norvegicus
Analyze
Symbol: Prkaca
Name: protein kinase cAMP-activated catalytic subunit alpha
RGD ID: 3389
Description: Enables cAMP-dependent protein kinase activity; protein kinase binding activity; and small GTPase binding activity. Involved in several processes, including circadian sleep/wake cycle, REM sleep; regulation of glutamatergic synaptic transmission; and spontaneous exocytosis of neurotransmitter. Located in several cellular components, including Golgi apparatus; perinuclear region of cytoplasm; and presynapse. Part of cAMP-dependent protein kinase complex. Biomarker of brain ischemia. Human ortholog(s) of this gene implicated in adrenal cortical adenoma; congestive heart failure; and primary pigmented nodular adrenocortical disease. Orthologous to human PRKACA (protein kinase cAMP-activated catalytic subunit alpha); PARTICIPATES IN acebutolol pharmacodynamics pathway; adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway; amiodarone pharmacodynamics pathway; INTERACTS WITH (+)-schisandrin B; 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 1,2-dimethylhydrazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: cAMP-dependent protein kinase catalytic subunit alpha; cAMP-dependent protein kinase catalytic subunit C alpha; Cs-PKA; PKA C-alpha; PKCA1; protein kinase A; protein kinase, cAMP-dependent, alpha catalytic subunit; protein kinase, cAMP-dependent, catalytic, alpha
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
mRatBN7.21924,155,081 - 24,178,430 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1924,155,090 - 24,178,430 (-)Ensembl
Rnor_6.01925,095,089 - 25,118,869 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1925,095,089 - 25,118,860 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01936,073,104 - 36,096,884 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41925,840,795 - 25,864,786 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11925,845,620 - 25,861,927 (-)NCBI
Celera1923,703,180 - 23,726,723 (-)NCBICelera
Cytogenetic Map19q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP,ISO)
1,2-dimethylhydrazine  (EXP)
14-Deoxy-11,12-didehydroandrographolide  (ISO)
17alpha-ethynylestradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-tert-butylhydroquinone  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
ammonium chloride  (EXP)
antimycin A  (ISO)
aristolochic acid  (ISO)
arsenite(3-)  (ISO)
asbestos  (ISO)
atorvastatin calcium  (EXP)
atrazine  (EXP)
BAPTA  (EXP)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bucladesine  (EXP)
buprenorphine  (EXP)
buspirone  (EXP)
cadmium atom  (EXP)
cadmium dichloride  (EXP,ISO)
caffeine  (EXP,ISO)
cannabidiol  (EXP)
capsaicin  (ISO)
captopril  (EXP)
chaetocin  (EXP)
chlorpyrifos  (ISO)
cisplatin  (ISO)
clenbuterol  (EXP)
clozapine  (EXP)
cobalt dichloride  (ISO)
cocaine  (EXP)
colforsin daropate hydrochloride  (EXP,ISO)
daidzein  (ISO)
daidzein 7-O-beta-D-glucoside  (ISO)
Deguelin  (ISO)
dexamethasone  (ISO)
dicrotophos  (ISO)
dobutamine  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
fluoranthene  (ISO)
formaldehyde  (ISO)
genistein  (ISO)
genistein 7-O-beta-D-glucoside  (ISO)
glycitein  (ISO)
glycitin  (ISO)
glyphosate  (ISO)
haloperidol  (EXP)
hydrogen peroxide  (ISO)
hydrogen sulfide  (ISO)
hydroxysafflor yellow A  (EXP)
ivermectin  (ISO)
KT 5720  (EXP)
lead diacetate  (EXP)
lead(0)  (EXP)
lead(2+)  (EXP)
Licarin A  (ISO)
maneb  (EXP)
manganese atom  (EXP)
manganese(0)  (EXP)
manganese(II) chloride  (EXP)
mercury dibromide  (ISO)
methylmercury chloride  (EXP)
mono(2-ethylhexyl) phthalate  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
nefazodone  (EXP)
Nor-9-carboxy-delta9-THC  (ISO)
ochratoxin A  (ISO)
oxidopamine  (EXP)
oxycodone  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
perfluorooctanoic acid  (EXP)
permethrin  (EXP)
phenethyl caffeate  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (EXP)
pregabalin  (EXP)
prostaglandin E2  (ISO)
Pyridostigmine bromide  (EXP)
pyrimidifen  (ISO)
quercetin  (EXP)
reserpine  (ISO)
resveratrol  (ISO)
rotenone  (EXP,ISO)
SB 431542  (ISO)
serpentine asbestos  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
streptozocin  (ISO)
sulindac  (EXP)
sulindac sulfide  (ISO)
sunitinib  (ISO)
tamibarotene  (ISO)
taurine  (EXP)
taurolithocholic acid  (EXP)
tebufenpyrad  (ISO)
telmisartan  (EXP)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
theophylline  (ISO)
thioacetamide  (EXP)
trichloroethene  (EXP)
triclosan  (EXP)
Triptolide  (EXP)
Tylophorine  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
vanadium atom  (ISO)
vanadium(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
acebutolol pharmacodynamics pathway  (ISO)
adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway  (ISO)
amiodarone pharmacodynamics pathway  (ISO)
amlodipine pharmacodynamics pathway  (ISO)
apoptotic cell death pathway  (IEA)
atenolol pharmacodynamics pathway  (ISO)
betaxolol pharmacodynamics pathway  (ISO)
bile acid transport pathway  (IEA)
bisoprolol pharmacodynamics pathway  (ISO)
bupranolol drug pathway  (ISO)
bupranolol pharmacodynamics pathway  (ISO)
calcium/calcium-mediated signaling pathway  (IEA)
carvedilol pharmacodynamics pathway  (ISO)
chemokine mediated signaling pathway  (IEA)
dilated cardiomyopathy pathway  (IEA)
diltiazem pharmacodynamics pathway  (ISO)
disopyramide pharmacodynamics pathway  (ISO)
dobutamine pharmacodynamics pathway  (ISO)
dopamine signaling pathway  (ISO)
eicosanoid signaling pathway  (ISO)
Entamoebiasis pathway  (IEA)
esmolol pharmacodynamics pathway  (ISO)
flecainde pharmacodynamics pathway  (ISO)
fosphenytoin pharmacodynamics pathway  (ISO)
glutamate signaling pathway  (IEA)
gonadotropin-releasing hormone signaling pathway  (IEA)
granulocyte-macrophage colony-stimulating factor signaling pathway  (ISO)
Hedgehog signaling pathway  (IEA,ISO)
ibutilide pharmacodynamics pathway  (ISO)
insulin signaling pathway  (IEA)
interleukin-3 signaling pathway  (ISO)
isoprenaline pharmacodynamics pathway  (ISO)
isradipine pharmacodynamics pathway  (ISO)
levobunolol pharmacodynamics pathway  (ISO)
lidocaine pharmacodynamics pathway  (ISO)
long term potentiation  (IEA)
metoprolol pharmacodynamics pathway  (ISO)
mexiletine pharmacodynamics pathway  (ISO)
mitogen activated protein kinase signaling pathway  (IEA)
nadolol pharmacodynamics pathway  (ISO)
nebivolol pharmacodynamics pathway  (ISO)
nifedipine pharmacodynamics pathway  (ISO)
nimodipine pharmacodynamics pathway  (ISO)
nisoldipine pharmacodynamics pathway  (ISO)
nitrendipine pharmacodynamics pathway  (ISO)
penbutolol pharmacodynamics pathway  (ISO)
phenytoin pharmacodynamics pathway  (ISO)
phosphatidylinositol 3-kinase-Akt signaling pathway  (ISO)
pindolol pharmacodynamics pathway  (ISO)
prion disease pathway  (IEA)
procainamide pharmacodynamics pathway  (ISO)
propranolol pharmacodynamics pathway  (ISO)
protein kinase A (PKA) signaling pathway  (ISO)
quinidine pharmacodynamics pathway  (ISO)
sotalol pharmacodynamics pathway  (ISO)
syndecan signaling pathway  (ISO)
timolol pharmacodynamics pathway  (ISO)
vascular endothelial growth factor signaling pathway  (ISO)
vasopressin signaling pathway via receptor type 2  (IEA)
verapamil pharmacodynamics pathway  (ISO)
Wnt signaling pathway  (IEA)

References

References - curated
1. Daniel PB, etal., Annu Rev Nutr 1998;18:353-83.
2. Datta S and Desarnaud F, J Neurosci. 2010 Sep 15;30(37):12263-73. doi: 10.1523/JNEUROSCI.1563-10.2010.
3. Dwivedi Y, etal., J Pharmacol Exp Ther. 2002 Apr;301(1):197-209.
4. Fang X, etal., Proc Natl Acad Sci U S A. 2000 Oct 24;97(22):11960-5.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. GOA data from the GO Consortium
7. Han Y, etal., Biol Reprod. 2013 Mar 7;88(3):57. doi: 10.1095/biolreprod.112.105106. Print 2013 Mar.
8. Jeske NA, etal., Pain. 2008 Sep 15;138(3):604-16. Epub 2008 Apr 1.
9. KEGG
10. Kiryu S, etal., Brain Res Mol Brain Res. 1995 Mar;29(1):147-56.
11. Kovo M, etal., Reproduction. 2006 Jul;132(1):33-43.
12. Manni S, etal., J Biol Chem. 2008 Aug 29;283(35):24145-54. Epub 2008 Jun 12.
13. Marx SO, etal., Cell. 2000 May 12;101(4):365-76.
14. Maximov A, etal., J Cell Biol. 2007 Jan 1;176(1):113-24. Epub 2006 Dec 26.
15. MGD data from the GO Consortium
16. Nagakura A, etal., Neuroscience. 2002;113(3):519-28.
17. NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. Obara Y, etal., J Cell Sci. 2004 Dec 1;117(Pt 25):6085-94. Epub 2004 Nov 16.
19. OMIM Disease Annotation Pipeline
20. Pipeline to import KEGG annotations from KEGG into RGD
21. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
22. Pipeline to import SMPDB annotations from SMPDB into RGD
23. RGD automated data pipeline
24. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
25. RGD automated import pipeline for gene-chemical interactions
26. Sato Y, etal., Science. 2014 May 23;344(6186):917-20. doi: 10.1126/science.1252328.
27. Schmidtmann A, etal., FEBS J. 2005 Dec;272(23):6087-97.
28. Shao XM, etal., J Physiol. 2003 Mar 1;547(Pt 2):543-53. Epub 2003 Jan 24.
29. Su W and Liu X, J Mol Endocrinol. 2013 Apr 12;50(3):305-18. doi: 10.1530/JME-13-0011. Print 2013 Jun.
30. Tasken K and Aandahl EM, Physiol Rev. 2004 Jan;84(1):137-67.
31. Widen C, etal., Biochem J. 2003 Jul 1;373(Pt 1):211-20.
32. Wiemann S, etal., Biochim Biophys Acta 1991 Jun 13;1089(2):254-6.
33. Yao L, etal., Cell. 2002 Jun 14;109(6):733-43.
34. Yao L, etal., Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):14379-84. Epub 2003 Nov 6.
35. Yasuda H, etal., Nat Neurosci. 2003 Jan;6(1):15-6.
36. Yger M and Girault JA, Front Behav Neurosci. 2011 Sep 8;5:56. doi: 10.3389/fnbeh.2011.00056. eCollection 2011.
Additional References at PubMed
PMID:1862342   PMID:6281762   PMID:7905001   PMID:8200992   PMID:8598227   PMID:8647104   PMID:8794865   PMID:9218452   PMID:9413984   PMID:9521123   PMID:9688563   PMID:10805756  
PMID:10906071   PMID:10970852   PMID:11029056   PMID:11590243   PMID:11739747   PMID:11799117   PMID:12004056   PMID:12167631   PMID:12200423   PMID:12475942   PMID:12477932   PMID:12628924  
PMID:12931191   PMID:14514679   PMID:15375008   PMID:15465019   PMID:15499025   PMID:15533936   PMID:15539636   PMID:15557275   PMID:15569306   PMID:15574738   PMID:15590926   PMID:15634677  
PMID:15692043   PMID:15760935   PMID:15905176   PMID:16004991   PMID:16088955   PMID:16123333   PMID:16129693   PMID:16481613   PMID:16519540   PMID:16531999   PMID:16538385   PMID:16554304  
PMID:16782699   PMID:16793902   PMID:16901946   PMID:16916513   PMID:17001449   PMID:17043310   PMID:17120015   PMID:17166179   PMID:17296605   PMID:17373911   PMID:17392500   PMID:17565987  
PMID:17594903   PMID:17693412   PMID:17855365   PMID:17895835   PMID:17901878   PMID:17911601   PMID:17938178   PMID:17942071   PMID:17960568   PMID:17964599   PMID:17978575   PMID:18191828  
PMID:18202122   PMID:18239846   PMID:18385332   PMID:18430554   PMID:18450967   PMID:18467524   PMID:18551621   PMID:18631385   PMID:19056373   PMID:19104749   PMID:19197368   PMID:19223768  
PMID:19233842   PMID:19377265   PMID:19387418   PMID:19418263   PMID:19447092   PMID:19501060   PMID:19560455   PMID:19601643   PMID:19723499   PMID:19842549   PMID:19949837   PMID:20007468  
PMID:20026202   PMID:20107112   PMID:20147366   PMID:20457802   PMID:20554643   PMID:20610540   PMID:20640531   PMID:20838877   PMID:21085490   PMID:21357689   PMID:21399614   PMID:21423175  
PMID:21438013   PMID:21438014   PMID:21526220   PMID:21572420   PMID:21613513   PMID:21630459   PMID:21718540   PMID:21723926   PMID:21807900   PMID:21808064   PMID:21812984   PMID:21957496  
PMID:22007132   PMID:22076955   PMID:22354948   PMID:22357862   PMID:22389500   PMID:22402347   PMID:22527640   PMID:22674394   PMID:22797923   PMID:22871113   PMID:23193054   PMID:23376485  
PMID:23533145   PMID:23933165   PMID:24006303   PMID:24125809   PMID:24277933   PMID:24349260   PMID:24431445   PMID:24469067   PMID:24585759   PMID:24733293   PMID:24859650   PMID:24904057  
PMID:24912137   PMID:25073061   PMID:25793374   PMID:25802336   PMID:25932647   PMID:26225746   PMID:26258546   PMID:26403276   PMID:26462734   PMID:26475678   PMID:26537248   PMID:26767953  
PMID:27097102   PMID:27105888   PMID:27206677   PMID:27245613   PMID:28077322   PMID:28222740   PMID:28337441   PMID:28463107   PMID:28656205   PMID:28717010   PMID:29473541   PMID:29476059  
PMID:30026308   PMID:30053369  


Genomics

Comparative Map Data
Prkaca
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21924,155,081 - 24,178,430 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1924,155,090 - 24,178,430 (-)Ensembl
Rnor_6.01925,095,089 - 25,118,869 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1925,095,089 - 25,118,860 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01936,073,104 - 36,096,884 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41925,840,795 - 25,864,786 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11925,845,620 - 25,861,927 (-)NCBI
Celera1923,703,180 - 23,726,723 (-)NCBICelera
Cytogenetic Map19q11NCBI
PRKACA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1914,091,688 - 14,118,084 (-)EnsemblGRCh38hg38GRCh38
GRCh381914,091,688 - 14,117,762 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371914,202,500 - 14,228,574 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361914,063,500 - 14,089,559 (-)NCBINCBI36hg18NCBI36
Build 341914,063,508 - 14,085,992NCBI
Celera1914,096,777 - 14,122,833 (-)NCBI
Cytogenetic Map19p13.12NCBI
HuRef1913,774,379 - 13,800,126 (-)NCBIHuRef
CHM1_11914,202,926 - 14,228,985 (-)NCBICHM1_1
Prkaca
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39884,699,607 - 84,723,073 (+)NCBIGRCm39mm39
GRCm39 Ensembl884,699,622 - 84,723,072 (+)Ensembl
GRCm38883,972,978 - 83,996,444 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl883,972,993 - 83,996,443 (+)EnsemblGRCm38mm10GRCm38
MGSCv37886,496,877 - 86,520,344 (+)NCBIGRCm37mm9NCBIm37
MGSCv36886,863,093 - 86,886,544 (+)NCBImm8
Celera888,266,474 - 88,289,645 (+)NCBICelera
Cytogenetic Map8C2NCBI
Prkaca
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541532,793,718 - 32,812,930 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541532,794,172 - 32,807,944 (-)NCBIChiLan1.0ChiLan1.0
PRKACA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11914,385,183 - 14,406,205 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1914,385,191 - 14,406,205 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01913,657,344 - 13,683,864 (-)NCBIMhudiblu_PPA_v0panPan3
PRKACA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12048,416,730 - 48,425,237 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2048,409,045 - 48,426,669 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2048,283,546 - 48,299,768 (+)NCBI
ROS_Cfam_1.02048,926,811 - 48,944,065 (+)NCBI
UMICH_Zoey_3.12048,138,017 - 48,154,228 (+)NCBI
UNSW_CanFamBas_1.02048,564,570 - 48,580,793 (+)NCBI
UU_Cfam_GSD_1.02048,807,387 - 48,823,603 (+)NCBI
Prkaca
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118207,588,938 - 207,605,559 (+)NCBI
SpeTri2.0NW_0049366592,750,015 - 2,765,914 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRKACA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl265,074,870 - 65,095,553 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1265,074,876 - 65,095,564 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2265,350,544 - 65,371,236 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PRKACA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1612,743,752 - 12,759,155 (-)NCBI
Vero_WHO_p1.0NW_0236660746,888,080 - 6,914,845 (+)NCBI
Prkaca
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249011,319,426 - 1,336,848 (-)NCBI

Position Markers
RH128078  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21924,155,247 - 24,155,471 (-)MAPPERmRatBN7.2
Rnor_6.01925,118,479 - 25,118,702NCBIRnor6.0
Rnor_5.01936,096,494 - 36,096,717UniSTSRnor5.0
RGSC_v3.41925,840,962 - 25,841,185UniSTSRGSC3.4
Celera1923,703,347 - 23,703,570UniSTS
Cytogenetic Map19q11UniSTS
RH94810  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21924,155,451 - 24,155,566 (-)MAPPERmRatBN7.2
Rnor_6.01925,118,384 - 25,118,498NCBIRnor6.0
Rnor_5.01936,096,399 - 36,096,513UniSTSRnor5.0
RGSC_v3.41925,841,166 - 25,841,280UniSTSRGSC3.4
Celera1923,703,551 - 23,703,665UniSTS
Cytogenetic Map19q11UniSTS
PMC18620P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21924,174,399 - 24,174,661 (-)MAPPERmRatBN7.2
Rnor_6.01925,098,864 - 25,099,125NCBIRnor6.0
Rnor_5.01936,076,879 - 36,077,140UniSTSRnor5.0
RGSC_v3.41925,860,749 - 25,861,010UniSTSRGSC3.4
Celera1923,722,943 - 23,723,204UniSTS
Cytogenetic Map19q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124688055Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127355345Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19128982497Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19128982497Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131963836Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19136824771Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)191392640130303727Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)191511459834521833Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:590
Count of miRNA genes:230
Interacting mature miRNAs:278
Transcripts:ENSRNOT00000007281, ENSRNOT00000041717
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 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000041717   ⟹   ENSRNOP00000044732
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1924,155,090 - 24,178,430 (-)Ensembl
Rnor_6.0 Ensembl1925,095,089 - 25,118,860 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000095425   ⟹   ENSRNOP00000082120
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1924,155,090 - 24,173,242 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103388   ⟹   ENSRNOP00000076567
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1924,155,090 - 24,171,305 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107553   ⟹   ENSRNOP00000079272
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1924,155,090 - 24,172,860 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000109274   ⟹   ENSRNOP00000086764
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1924,155,090 - 24,174,427 (-)Ensembl
RefSeq Acc Id: NM_001100922   ⟹   NP_001094392
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21924,155,081 - 24,178,430 (-)NCBI
Rnor_6.01925,095,089 - 25,118,869 (+)NCBI
Rnor_5.01936,073,104 - 36,096,884 (+)NCBI
RGSC_v3.41925,840,795 - 25,864,786 (-)RGD
Celera1923,703,180 - 23,726,723 (-)RGD
Sequence:
RefSeq Acc Id: XM_006255219   ⟹   XP_006255281
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21924,155,081 - 24,174,663 (-)NCBI
Rnor_6.01925,099,001 - 25,117,832 (+)NCBI
Rnor_5.01936,073,104 - 36,096,884 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601184   ⟹   XP_017456673
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21924,155,081 - 24,175,513 (-)NCBI
Rnor_6.01925,097,867 - 25,117,832 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001094392   ⟸   NM_001100922
- UniProtKB: A1L1M0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255281   ⟸   XM_006255219
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017456673   ⟸   XM_017601184
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000044732   ⟸   ENSRNOT00000041717
RefSeq Acc Id: ENSRNOP00000082120   ⟸   ENSRNOT00000095425
RefSeq Acc Id: ENSRNOP00000086764   ⟸   ENSRNOT00000109274
RefSeq Acc Id: ENSRNOP00000076567   ⟸   ENSRNOT00000103388
RefSeq Acc Id: ENSRNOP00000079272   ⟸   ENSRNOT00000107553
Transcriptome

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

Promoters
RGD ID:13701007
Promoter ID:EPDNEW_R11531
Type:initiation region
Name:Prkaca_1
Description:protein kinase cAMP-activated catalytic subunit alpha
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01925,095,020 - 25,095,080EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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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:3389 AgrOrtholog
Ensembl Genes ENSRNOG00000005257 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000044732 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041717 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7314651 IMAGE-MGC_LOAD
InterPro AGC-kinase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kinase-like_dom_sf 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
  STKc_PKA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25636 UniProtKB/TrEMBL
MGC_CLONE MGC:156823 IMAGE-MGC_LOAD
NCBI Gene 25636 ENTREZGENE
Pfam Pkinase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Prkaca PhenoGen
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
SMART S_TK_X UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  S_TKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A1L1M0 ENTREZGENE, UniProtKB/TrEMBL
  KAPCA_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q6UA68 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-03 Prkaca  protein kinase cAMP-activated catalytic subunit alpha  Prkaca  protein kinase, cAMP-dependent, alpha catalytic subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-30 Prkaca  protein kinase, cAMP-dependent, alpha catalytic subunit  Prkaca  protein kinase, cAMP-dependent, catalytic, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Prkaca  protein kinase, cAMP-dependent, catalytic, alpha       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function phosphorylates serine and threonine contained within the motif RRX 724621