Camk2a (calcium/calmodulin-dependent protein kinase II alpha) - Rat Genome Database

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Gene: Camk2a (calcium/calmodulin-dependent protein kinase II alpha) Rattus norvegicus
Analyze
Symbol: Camk2a
Name: calcium/calmodulin-dependent protein kinase II alpha
RGD ID: 2261
Description: Exhibits GTPase activating protein binding activity and calmodulin-dependent protein kinase activity. Involved in several processes, including NMDA selective glutamate receptor signaling pathway; protein phosphorylation; and regulation of protein localization to cell periphery. Localizes to several cellular components, including dendrite cytoplasm; glutamatergic postsynaptic density; and region of cytosol. Biomarker of middle cerebral artery infarction and transient cerebral ischemia. Human ortholog(s) of this gene implicated in autosomal dominant mental retardation 53 and autosomal recessive non-syndromic intellectual disability. Orthologous to human CAMK2A (calcium/calmodulin dependent protein kinase II alpha); PARTICIPATES IN calcium/calmodulin dependent kinase 2 signaling pathway; fibroblast growth factor signaling pathway; transforming growth factor-beta Smad dependent signaling pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: alpha CaM kinase II; Ca2+/calmodulin-dependent protein kinase II alpha; calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha; calcium/calmodulin-dependent protein kinase II alpha subunit; calcium/calmodulin-dependent protein kinase II, alpha; calcium/calmodulin-dependent protein kinase type II alpha chain; calcium/calmodulin-dependent protein kinase type II subunit alpha; caM kinase II subunit alpha; caM-kinase II alpha chain; caMK-II subunit alpha; PK2CDD; PKCCD
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21854,378,642 - 54,441,120 (+)NCBI
Rnor_6.0 Ensembl1856,193,978 - 56,295,869 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01856,193,978 - 56,295,869 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01855,428,487 - 55,463,016 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01855,514,559 - 55,529,045 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41856,879,247 - 56,948,537 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11856,951,478 - 57,020,769 (+)NCBI
Celera1852,533,226 - 52,592,130 (+)NCBICelera
Cytogenetic Map18q12.1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (ISO)
17beta-estradiol  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
6-propyl-2-thiouracil  (EXP)
7-chlorokynurenic acid  (EXP)
acrylamide  (EXP,ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
azamethiphos  (EXP)
Bay-K-8644  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP,ISO)
cadmium atom  (EXP)
cadmium dichloride  (EXP)
capsaicin  (EXP)
chlorpyrifos  (EXP,ISO)
cisplatin  (EXP)
clozapine  (EXP,ISO)
cobalt dichloride  (ISO)
cocaine  (EXP,ISO)
copper atom  (EXP)
copper(0)  (EXP)
curcumin  (EXP,ISO)
cyclosporin A  (EXP)
cyfluthrin  (ISO)
cyhalothrin  (EXP)
cypermethrin  (ISO)
decabromodiphenyl ether  (EXP,ISO)
diarsenic trioxide  (ISO)
dieldrin  (EXP)
diethyl malate  (ISO)
diethylstilbestrol  (ISO)
dopamine  (EXP)
ethanol  (EXP,ISO)
ethylene glycol bis(2-aminoethyl)tetraacetic acid  (EXP)
flurotyl  (EXP)
FPL 64176  (EXP)
glyphosate  (ISO)
haloperidol  (EXP)
heptachlor  (EXP)
ibuprofen  (EXP)
ionomycin  (EXP)
KN-93  (EXP,ISO)
lead diacetate  (EXP,ISO)
lead(0)  (EXP)
lead(2+)  (EXP)
losartan  (ISO)
malathion  (EXP)
manganese atom  (EXP)
manganese(0)  (EXP)
memantine  (EXP)
methapyrilene  (ISO)
methimazole  (EXP)
monosodium L-glutamate  (EXP)
morphine  (ISO)
N-methyl-6-chloro-1-(3-methylphenyl)-2,3,4,5-tetrahydro-3-benzazepine-7,8-diol  (EXP)
N-nitrosodiethylamine  (ISO)
Nicardipine  (EXP)
nicotine  (ISO)
nifedipine  (EXP,ISO)
ochratoxin A  (EXP)
olanzapine  (EXP)
paclitaxel  (EXP)
paracetamol  (ISO)
PCB138  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
phencyclidine  (ISO)
phenylephrine  (EXP)
piperonyl butoxide  (ISO)
pirinixic acid  (ISO)
platycodin D  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
risperidone  (EXP)
rotenone  (ISO)
S-allylcysteine  (ISO)
SCH 23390  (EXP)
sirolimus  (EXP)
sodium arsenite  (EXP,ISO)
sodium benzoate  (EXP)
streptozocin  (EXP,ISO)
sulfur dioxide  (EXP)
titanium dioxide  (ISO)
trichostatin A  (EXP)
trifluoperazine  (EXP)
tris(2-chloroethyl) phosphate  (EXP)
U-73122  (EXP)
valproic acid  (EXP,ISO)
venlafaxine hydrochloride  (EXP)
verapamil  (EXP)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

References

References - curated
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3. Carlton SM Brain Res. 2002 Aug 30;947(2):252-9.
4. Chin D and Means AR, Biochemistry 2002 Nov 26;41(47):14001-9.
5. Cho KO, etal., Neuron 1992 Nov;9(5):929-42.
6. Coultrap SJ and Bayer KU, Trends Neurosci. 2012 Oct;35(10):607-18. doi: 10.1016/j.tins.2012.05.003. Epub 2012 Jun 19.
7. De Felice FG, etal., Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1971-6. doi: 10.1073/pnas.0809158106. Epub 2009 Feb 2.
8. Dhavan R, etal., J Neurosci. 2002 Sep 15;22(18):7879-91.
9. Dupuis JP, etal., EMBO J. 2014 Apr 16;33(8):842-61. doi: 10.1002/embj.201386356. Epub 2014 Mar 3.
10. Esteban JA, etal., Nat Neurosci. 2003 Feb;6(2):136-43.
11. Gardoni F, etal., J Biol Chem 2003 Nov 7;278(45):44745-52. Epub 2003 Aug 21.
12. Gardoni F, etal., J Biol Chem. 2001 Mar 9;276(10):7609-13. Epub 2000 Dec 4.
13. Gardoni F, etal., J Neurosci. 2001 Mar 1;21(5):1501-9.
14. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
15. Guo ML, etal., EMBO J. 2010 Jun 16;29(12):2070-81. doi: 10.1038/emboj.2010.93. Epub 2010 May 11.
16. House SJ, etal., Am J Physiol Cell Physiol. 2007 Jun;292(6):C2276-87. Epub 2007 Jan 31.
17. Jiang X, etal., Proc Natl Acad Sci U S A. 2008 Jan 8;105(1):341-6. Epub 2007 Dec 27.
18. Jones TL, etal., Anesth Analg. 2007 Dec;105(6):1650-6, table of contents.
19. Lisman J, etal., Nat Rev Neurosci. 2012 Feb 15;13(3):169-82. doi: 10.1038/nrn3192.
20. Lu W, etal., Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22266-71. doi: 10.1073/pnas.1016289107. Epub 2010 Dec 6.
21. Matsumoto S, etal., J Cereb Blood Flow Metab 2004 Jan;24(1):54-61.
22. Meng F and Zhang G, Neurosci Lett 2002 Nov 15;333(1):59-63.
23. Mengesdorf T, etal., Neurochem Res. 2002 Jun;27(6):477-84.
24. MGD data from the GO Consortium
25. NCBI rat LocusLink and RefSeq merged data July 26, 2002
26. Ochiishi T, etal., Brain Res. 1994 Oct 3;659(1-2):179-93.
27. Opazo P, etal., Neuron. 2010 Jul 29;67(2):239-52. doi: 10.1016/j.neuron.2010.06.007.
28. Petrini EM, etal., Nat Commun. 2014 Jun 4;5:3921. doi: 10.1038/ncomms4921.
29. Pipeline to import KEGG annotations from KEGG into RGD
30. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
31. Price TJ, etal., Neurosci Lett. 2005 Dec 2;389(2):94-8.
32. RGD automated data pipeline
33. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
34. RGD automated import pipeline for gene-chemical interactions
35. Robison AJ, etal., J Biol Chem. 2005 Oct 21;280(42):35329-36. Epub 2005 Aug 24.
36. Shen K and Meyer T, Science. 1999 Apr 2;284(5411):162-6.
37. Song B, etal., Neurosci Lett. 2003 Oct 9;349(3):183-6.
38. Swulius MT, etal., J Comp Neurol. 2010 Oct 15;518(20):4243-60. doi: 10.1002/cne.22451.
39. Szpirer C, etal., Mamm Genome 2000 Sep;11(9):729-35
40. Tao-Cheng JH, etal., Brain Cell Biol. 2006 Jun;35(2-3):117-24. doi: 10.1007/s11068-007-9012-5. Epub 2007 Sep 20.
41. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
42. Wang P, etal., Neurotoxicology. 2013 Jul;37:51-62. doi: 10.1016/j.neuro.2013.03.007. Epub 2013 Apr 1.
43. Wang YJ, etal., Brain Res. 2005 Jan 7;1031(1):101-8. doi: 10.1016/j.brainres.2004.10.061.
44. Xue J, etal., Brain Res Dev Brain Res 2002 Sep 20;138(1):61-70.
45. Yamamoto H Tanpakushitsu Kakusan Koso 2002 Mar;47(3):241-7.
46. Zhang Y, etal., Int J Mol Med. 2018 Apr;41(4):2070-2078. doi: 10.3892/ijmm.2018.3422. Epub 2018 Jan 25.
47. Zhu JJ, etal., Cell. 2002 Aug 23;110(4):443-55.
Additional References at PubMed
PMID:1328883   PMID:2153289   PMID:2842767   PMID:2856087   PMID:3037704   PMID:3475713   PMID:8280084   PMID:8598227   PMID:10347170   PMID:11036263   PMID:11160423   PMID:11264466  
PMID:11403681   PMID:11427314   PMID:12218415   PMID:12218416   PMID:12629219   PMID:12660151   PMID:12823475   PMID:12873384   PMID:12873385   PMID:12896970   PMID:12954639   PMID:14499348  
PMID:15044062   PMID:15292517   PMID:15312654   PMID:15375008   PMID:15383398   PMID:15494036   PMID:15574738   PMID:15607978   PMID:15649892   PMID:15659234   PMID:15664178   PMID:15673434  
PMID:15714506   PMID:15775983   PMID:15964981   PMID:15994560   PMID:16214364   PMID:16277604   PMID:16436603   PMID:16501029   PMID:16627565   PMID:16632208   PMID:16648177   PMID:16709720  
PMID:16710293   PMID:16843447   PMID:16872923   PMID:17052756   PMID:17114649   PMID:17212683   PMID:17332063   PMID:17404223   PMID:17442679   PMID:17494705   PMID:17570344   PMID:17610578  
PMID:17652761   PMID:17660813   PMID:17898207   PMID:17948240   PMID:18046020   PMID:18053645   PMID:18094239   PMID:18271754   PMID:18278040   PMID:18305102   PMID:18305109   PMID:18408996  
PMID:18436302   PMID:18480293   PMID:18562151   PMID:18617607   PMID:18697934   PMID:19046383   PMID:19047462   PMID:19121366   PMID:19135986   PMID:19172997   PMID:19182667   PMID:19200342  
PMID:19217373   PMID:19235894   PMID:19292454   PMID:19332038   PMID:19409102   PMID:19555740   PMID:19591836   PMID:19638347   PMID:19735285   PMID:19735700   PMID:19858198   PMID:19860859  
PMID:19882720   PMID:19934217   PMID:20008273   PMID:20023119   PMID:20060004   PMID:20060891   PMID:20124353   PMID:20127074   PMID:20424167   PMID:20459031   PMID:20551968   PMID:20584908  
PMID:20643921   PMID:20654708   PMID:20660727   PMID:20668654   PMID:20807573   PMID:21041242   PMID:21059908   PMID:21143596   PMID:21491127   PMID:21593322   PMID:21610080   PMID:21630459  
PMID:21697368   PMID:21869818   PMID:21884935   PMID:21925648   PMID:21933187   PMID:22227452   PMID:22294157   PMID:22609102   PMID:22627922   PMID:22764246   PMID:22796763   PMID:22815963  
PMID:22871113   PMID:22906554   PMID:22929440   PMID:22952977   PMID:22960015   PMID:22965911   PMID:23051746   PMID:23160045   PMID:23267764   PMID:23297306   PMID:23408944   PMID:23426668  
PMID:23549416   PMID:23576750   PMID:23584669   PMID:23602566   PMID:23602989   PMID:23643989   PMID:23645665   PMID:23651084   PMID:23749614   PMID:23825405   PMID:23953174   PMID:23976956  
PMID:24032403   PMID:24560900   PMID:24755854   PMID:24872564   PMID:25034033   PMID:25054156   PMID:25067828   PMID:25073061   PMID:25266254   PMID:25297099   PMID:25457025   PMID:25515219  
PMID:25568108   PMID:25644714   PMID:25682687   PMID:25701274   PMID:25944900   PMID:26086939   PMID:26110816   PMID:26174594   PMID:26291163   PMID:26742808   PMID:26779588   PMID:26809094  
PMID:26821292   PMID:27477489   PMID:27611779   PMID:28130356   PMID:28230177   PMID:28236215   PMID:28536695   PMID:28553222   PMID:28573136   PMID:28638088   PMID:28717010   PMID:28730575  
PMID:28754591   PMID:28865231   PMID:28940879   PMID:28957669   PMID:29100089   PMID:29184507   PMID:29273596   PMID:29279520   PMID:29476059   PMID:29604406   PMID:29806529   PMID:30053369  
PMID:30142538   PMID:30177751   PMID:30299584   PMID:30520144   PMID:30526621   PMID:30919283   PMID:31100477   PMID:31935048   PMID:32005763   PMID:32238193   PMID:32303334   PMID:32716967  


Genomics

Comparative Map Data
Camk2a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21854,378,642 - 54,441,120 (+)NCBI
Rnor_6.0 Ensembl1856,193,978 - 56,295,869 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01856,193,978 - 56,295,869 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01855,428,487 - 55,463,016 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01855,514,559 - 55,529,045 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41856,879,247 - 56,948,537 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11856,951,478 - 57,020,769 (+)NCBI
Celera1852,533,226 - 52,592,130 (+)NCBICelera
Cytogenetic Map18q12.1NCBI
CAMK2A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5150,219,491 - 150,290,291 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl5150,219,491 - 150,290,093 (-)EnsemblGRCh38hg38GRCh38
GRCh385150,219,491 - 150,290,130 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh375149,599,054 - 149,669,693 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365149,579,248 - 149,649,529 (-)NCBINCBI36hg18NCBI36
Build 345149,579,247 - 149,649,529NCBI
Celera5145,680,447 - 145,750,799 (-)NCBI
Cytogenetic Map5q32NCBI
HuRef5144,747,170 - 144,817,356 (-)NCBIHuRef
CHM1_15149,031,647 - 149,101,993 (-)NCBICHM1_1
Camk2a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391861,058,379 - 61,121,224 (+)NCBIGRCm39mm39
GRCm39 Ensembl1861,058,690 - 61,121,224 (+)Ensembl
GRCm381860,925,307 - 60,988,152 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1860,925,618 - 60,988,152 (+)EnsemblGRCm38mm10GRCm38
MGSCv371861,085,286 - 61,147,806 (+)NCBIGRCm37mm9NCBIm37
MGSCv361861,051,001 - 61,113,513 (+)NCBImm8
Celera1862,212,530 - 62,274,768 (+)NCBICelera
Cytogenetic Map18E1NCBI
cM Map1834.41NCBI
Camk2a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554154,247,014 - 4,307,458 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554154,247,307 - 4,307,402 (+)NCBIChiLan1.0ChiLan1.0
CAMK2A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15151,649,062 - 151,719,373 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5151,649,062 - 151,719,373 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05145,644,164 - 145,714,143 (-)NCBIMhudiblu_PPA_v0panPan3
CAMK2A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1458,800,818 - 58,865,830 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl458,800,813 - 58,865,830 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha458,567,052 - 58,631,982 (+)NCBI
ROS_Cfam_1.0459,281,664 - 59,346,612 (+)NCBI
UMICH_Zoey_3.1459,070,398 - 59,135,346 (+)NCBI
UNSW_CanFamBas_1.0459,184,686 - 59,249,804 (+)NCBI
UU_Cfam_GSD_1.0459,715,947 - 59,780,872 (+)NCBI
Camk2a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213143,064,159 - 143,126,577 (+)NCBI
SpeTri2.0NW_0049365044,636,863 - 4,700,887 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CAMK2A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2151,248,356 - 151,308,658 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12151,248,356 - 151,353,907 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22158,335,771 - 158,396,987 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CAMK2A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12352,829,438 - 52,899,428 (-)NCBI
ChlSab1.1 Ensembl2352,829,350 - 52,899,375 (-)Ensembl
Vero_WHO_p1.0NW_02366603424,817,181 - 24,887,318 (+)NCBI
Camk2a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247749,526,323 - 9,585,647 (-)NCBI

Position Markers
D18Got54  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21854,401,652 - 54,401,849 (+)MAPPER
Rnor_6.01856,216,839 - 56,217,035NCBIRnor6.0
Rnor_5.01855,451,263 - 55,451,459UniSTSRnor5.0
Celera1852,556,111 - 52,556,307UniSTS
RH 3.4 Map18530.2RGD
RH 3.4 Map18530.2UniSTS
RH 2.0 Map18383.9RGD
Cytogenetic Map18q11UniSTS
RH143135  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21854,424,382 - 54,424,523 (+)MAPPER
Rnor_6.01856,282,221 - 56,282,361NCBIRnor6.0
Rnor_5.01855,515,397 - 55,515,537UniSTSRnor5.0
RGSC_v3.41856,934,889 - 56,935,029UniSTSRGSC3.4
Celera1852,578,482 - 52,578,622UniSTS
Cytogenetic Map18q11UniSTS
BF399379  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21854,403,634 - 54,403,764 (+)MAPPER
Rnor_6.01856,218,821 - 56,218,950NCBIRnor6.0
Rnor_5.01855,453,245 - 55,453,374UniSTSRnor5.0
Celera1852,558,093 - 52,558,222UniSTS
RH 3.4 Map18534.5UniSTS
Cytogenetic Map18q11UniSTS
RH137986  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21854,424,283 - 54,424,453 (+)MAPPER
Rnor_6.01856,282,122 - 56,282,291NCBIRnor6.0
Rnor_5.01855,515,298 - 55,515,467UniSTSRnor5.0
RGSC_v3.41856,934,790 - 56,934,959UniSTSRGSC3.4
Celera1852,578,383 - 52,578,552UniSTS
RH 3.4 Map18530.3UniSTS
Cytogenetic Map18q11UniSTS
RH138447  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21854,424,381 - 54,424,523 (+)MAPPER
Rnor_6.01856,282,220 - 56,282,361NCBIRnor6.0
Rnor_5.01855,515,396 - 55,515,537UniSTSRnor5.0
RGSC_v3.41856,934,888 - 56,935,029UniSTSRGSC3.4
Celera1852,578,481 - 52,578,622UniSTS
RH 3.4 Map18530.3UniSTS
Cytogenetic Map18q11UniSTS
BE119266  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21854,423,405 - 54,423,556 (+)MAPPER
Rnor_6.01856,281,244 - 56,281,394NCBIRnor6.0
Rnor_5.01855,514,420 - 55,514,570UniSTSRnor5.0
RGSC_v3.41856,933,193 - 56,933,343UniSTSRGSC3.4
Celera1852,577,505 - 52,577,655UniSTS
RH 3.4 Map18530.1UniSTS
Cytogenetic Map18q11UniSTS
UniSTS:225275  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21854,440,499 - 54,440,654 (+)MAPPER
Rnor_6.01856,298,335 - 56,298,489NCBIRnor6.0
Rnor_5.01855,531,511 - 55,531,665UniSTSRnor5.0
RGSC_v3.41856,951,003 - 56,951,157UniSTSRGSC3.4
Celera1852,594,596 - 52,594,750UniSTS
Cytogenetic Map18q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18440751362570466Rat
2313082Bss85Bone structure and strength QTL 850.80.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)181467885259678852Rat
1358358Sradr6Stress Responsive Adrenal Weight QTL 62.49adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)181553942761499684Rat
6903359Bp355Blood pressure QTL 3553.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181553967161985648Rat
2293708Bss46Bone structure and strength QTL 468.80.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)181569587268524999Rat
1578661Bss20Bone structure and strength QTL 203.7femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)181569587287080053Rat
1578667Bss21Bone structure and strength QTL 213.5femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)181569587287080053Rat
1358193Emca2Estrogen-induced mammary cancer QTL 21.6mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)181903103068436105Rat
1600373Mamtr6Mammary tumor resistance QTL 6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)182028575887080053Rat
7387267Uae42Urinary albumin excretion QTL 420.61urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)142163949166639491Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182260373687074531Rat
6903353Bp353Blood pressure QTL 3532.8arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182260476461985648Rat
1331733Bp233Blood pressure QTL 2333.97196arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182596102681761656Rat
2300157Bmd66Bone mineral density QTL 6613.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)183053361475533614Rat
2300177Bmd65Bone mineral density QTL 6519.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)183053361475533614Rat
2293704Bss35Bone structure and strength QTL 354.590.0002femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)183053361475533614Rat
9590318Scort22Serum corticosterone level QTL 227.640.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)183136134176361341Rat
1331754Bp230Blood pressure QTL 2304.61609arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183136134176361341Rat
9589816Gluco68Glucose level QTL 687.250.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)183136134176361341Rat
8694378Bw157Body weight QTL 1573.590.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)183136134176361341Rat
738005Anxrr11Anxiety related response QTL 113.4exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)183160842476608424Rat
61383Bp47Blood pressure QTL 4717.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)183172837362570429Rat
1331776Bp225Blood pressure QTL 2252.829arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)183267035261985812Rat
1331774Bp226Blood pressure QTL 2264.41065arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183267035261985812Rat
1331742Bp228Blood pressure QTL 2283.88752arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183267035261985812Rat
1331798Bp224Blood pressure QTL 2243.53873arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183267035261985812Rat
1331727Bp237Blood pressure QTL 2373.053arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183267035263897621Rat
61429Cia17Collagen induced arthritis QTL 174.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)183267035273016546Rat
2303120Mamtr8Mammary tumor resistance QTL 80.001mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)183267035287080053Rat
6903347Bp350Blood pressure QTL 3504.4arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183267047361985648Rat
631274Sprol1Serum protein level QTL 15.3blood total protein amount (VT:0005567)serum total protein level (CMO:0000661)183270402280696226Rat
631518Bw11Body weight QTL 112.8body mass (VT:0001259)body weight (CMO:0000012)183822191983221919Rat
61367Iddm4Insulin dependent diabetes mellitus QTL 42.330.0074blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)184037576985375769Rat
6893683Bw110Body weight QTL 1102.70.002body mass (VT:0001259)body weight (CMO:0000012)184500219488201929Rat
1598826Anxrr20Anxiety related response QTL 203.04body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)184631947688201929Rat
1331806Bp229Blood pressure QTL 2294.36484arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)184824887759473805Rat
1331736Bp227Blood pressure QTL 2272.791arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)184824887761985812Rat
1331780Bp238Blood pressure QTL 2383.269arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)184824887761985812Rat
6903345Bp349Blood pressure QTL 3493.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)184824904861985648Rat
6903349Bp351Blood pressure QTL 3513.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)184824904861985648Rat
6903351Bp352Blood pressure QTL 3523.3arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)184824904861985648Rat
61360EaeyExperimental allergic encephalomyelitis QTL y3nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis duration (CMO:0001424)184851929962570427Rat
9589041Epfw12Epididymal fat weight QTL 1217.080.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)184913092088201929Rat
8694432Bw165Body weight QTL 1653.810.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)184913092088201929Rat
8694366Abfw8Abdominal fat weight QTL 86.380.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)184913092088201929Rat
2303571Bw92Body weight QTL 923body mass (VT:0001259)body weight (CMO:0000012)185137581688201929Rat
2303584Gluco55Glucose level QTL 552blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)185137581688201929Rat
7411719Strs5Sensitivity to stroke QTL 59.4cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)185160903267502266Rat
2293658Bmd23Bone mineral density QTL 237.30.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)185303349468524999Rat
738008Hcar14Hepatocarcinoma resistance QTL 144.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion number (CMO:0001462)185303349487080053Rat
1331730Scl27Serum cholesterol level QTL 273.826blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)185386125261985812Rat
1331752Bw27Body weight QTL 272.963body mass (VT:0001259)body weight (CMO:0000012)185386125267502266Rat
1359020Ppulsi2Prepulse inhibition QTL 22.71prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)185386125277151443Rat
1600375Mcs22Mammary carcinoma susceptibility QTL 223.3mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)185410837568819562Rat
631509Sald2Serum aldosterone level QTL 22.9blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)185410837571692768Rat
2301417Bp319Blood pressure QTL 3190.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)185410837579575348Rat
12880368Bw187Body weight QTL 1870.045body mass (VT:0001259)body weight (CMO:0000012)185410837579575348Rat
12904067Cm122Cardiac mass QTL 1220.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)185410837579575348Rat
12904069Cm123Cardiac mass QTL 1230.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)185410837579575348Rat
12904070Cm124Cardiac mass QTL 1240.01heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)185410837579575348Rat
12904071Am18Aortic mass QTL 180.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)185410837579575348Rat
12904073Kidm71Kidney mass QTL 710.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)185410837579575348Rat
1300125Rf26Renal function QTL 263.2urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)185410847467502122Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:179
Count of miRNA genes:118
Interacting mature miRNAs:133
Transcripts:ENSRNOT00000041533
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 7
Medium 27 8 11 57 8
Low 3 16 14 5 19 5 10 8 38 11
Below cutoff 41 35 35 25 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000041533   ⟹   ENSRNOP00000041940
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1856,193,978 - 56,295,869 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080177   ⟹   ENSRNOP00000069249
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1856,194,019 - 56,295,594 (+)Ensembl
RefSeq Acc Id: NM_012920   ⟹   NP_037052
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21854,378,784 - 54,438,030 (+)NCBI
Rnor_6.01856,193,978 - 56,295,869 (+)NCBI
Rnor_5.01855,428,487 - 55,463,016 (+)NCBI
Rnor_5.01855,514,559 - 55,529,045 (+)NCBI
RGSC_v3.41856,879,247 - 56,948,537 (+)RGD
Celera1852,533,226 - 52,592,130 (+)RGD
Sequence:
RefSeq Acc Id: XM_039096592   ⟹   XP_038952520
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21854,378,642 - 54,441,120 (+)NCBI
RefSeq Acc Id: XM_039096593   ⟹   XP_038952521
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21854,378,642 - 54,437,755 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_037052   ⟸   NM_012920
- UniProtKB: P11275 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000069249   ⟸   ENSRNOT00000080177
RefSeq Acc Id: ENSRNOP00000041940   ⟸   ENSRNOT00000041533
RefSeq Acc Id: XP_038952520   ⟸   XM_039096592
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038952521   ⟸   XM_039096593
- Peptide Label: isoform X2
Protein Domains
Protein kinase

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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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
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/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
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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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 (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2261 AgrOrtholog
Ensembl Genes ENSRNOG00000018712 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000041940 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069249 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041533 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000080177 UniProtKB/TrEMBL
InterPro Ca/CaM-dep_prot_kinase-assoc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kinase-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NTF2-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
KEGG Report rno:25400 UniProtKB/Swiss-Prot
NCBI Gene 25400 ENTREZGENE
Pfam CaMKII_AD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pkinase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Camk2a PhenoGen
PROSITE PROTEIN_KINASE_ATP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_ST UniProtKB/Swiss-Prot
SMART S_TKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54427 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC228753
UniProt A0A0G2JUV8_RAT UniProtKB/TrEMBL
  F1LZG4_RAT UniProtKB/TrEMBL
  KCC2A_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q924T0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-11-11 Camk2a  calcium/calmodulin-dependent protein kinase II alpha  Camk2a  calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-24 Camk2a  calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha  Camk2a  calcium/calmodulin-dependent protein kinase II, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Camk2a  calcium/calmodulin-dependent protein kinase II, alpha    calcium/calmodulin-dependent protein kinase II alpha subunit  Name updated 1299863 APPROVED
2002-11-06 Camk2a  calcium/calmodulin-dependent protein kinase II alpha subunit    Ca2+/calmodulin-dependent protein kinase II alpha  Name updated 625702 APPROVED
2002-06-10 Camk2a  Ca2+/calmodulin-dependent protein kinase II alpha      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expression in hippocampal cells strongly induced upon ischemic insult 634689
gene_expression expressed at high levels in neurons 1299829
gene_function kinase subunit 634689
gene_function phosphorylates N-methyl-D-aspartate receptor subunit 2B on serine 634689
gene_function autophosphorylates on threonine (T286) 1299829
gene_physical_interaction binds to and is activated by calcium/calmodulin 1299829
gene_process may play a role in the development of the retina 634688
gene_process may regulate channel properties of N-methyl-D-aspartate receptor subunit 2B during ischemia via phosphorylation 634689
gene_process transduces cellular signals corresponding to fluctuations in intracellular calcium levels in conjuction with calmodulin 1299829
gene_process important in learning and memory 1299829
gene_regulation activity is regulated by calcium/calmodulin binding and autophosphorylation 1299829