Calm2 (calmodulin 2) - Rat Genome Database

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Gene: Calm2 (calmodulin 2) Rattus norvegicus
Analyze
Symbol: Calm2
Name: calmodulin 2
RGD ID: 2258
Description: Exhibits several functions, including enzyme binding activity; ion channel binding activity; and nitric-oxide synthase regulator activity. Involved in several processes, including activation of adenylate cyclase activity; regulation of calcium ion transmembrane transporter activity; and regulation of vesicle-mediated transport. Localizes to several cellular components, including growth cone; myelin sheath; and nucleus. Colocalizes with mitochondrial membrane and synaptic vesicle membrane. Human ortholog(s) of this gene implicated in catecholaminergic polymorphic ventricular tachycardia 4; long QT syndrome 14; and long QT syndrome 15. Orthologous to several human genes including CALM1 (calmodulin 1); PARTICIPATES IN adenosine monophosphate-activated protein kinase (AMPK) signaling pathway; calcium/calcium-mediated signaling pathway; calcium/calmodulin dependent kinase 2 signaling pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-Tetrachlorodibenzofuran; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: calmodulin; calmodulin 2 (phosphorylase kinase delta); calmodulin 2 (phosphorylase kinase, delta); calmodulin-2; caM; Cam2; Camb; CaMII
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Calm-ps1   Calm-ps2  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.267,091,624 - 7,104,284 (+)NCBI
Rnor_6.0 Ensembl1565,506,874 - 65,507,968 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0611,067,675 - 11,080,078 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0621,052,945 - 21,068,133 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4664,161,641 - 64,162,751 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11564,177,420 - 64,178,531 (-)NCBI
Celera66,842,934 - 6,855,590 (+)NCBICelera
Cytogenetic Map6q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,6-dinitrotoluene  (EXP)
3,3'-diindolylmethane  (ISO)
acrolein  (ISO)
aflatoxin B1  (ISO)
aflatoxin M1  (ISO)
aldehydo-D-glucose  (EXP)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
Aroclor 1254  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
buspirone  (EXP)
butan-1-ol  (ISO)
cerium trichloride  (ISO)
chlordecone  (ISO)
chloropicrin  (ISO)
cisplatin  (ISO)
clofibric acid  (EXP)
clozapine  (EXP)
cocaine  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
D-glucose  (EXP)
dicrotophos  (ISO)
dieldrin  (EXP)
dimethylarsinic acid  (EXP)
dioxygen  (EXP)
diuron  (EXP)
ethanol  (EXP,ISO)
folic acid  (ISO)
fumonisin B1  (ISO)
gentamycin  (EXP)
glucose  (EXP)
glyphosate  (ISO)
haloperidol  (EXP)
hydrogen peroxide  (ISO)
maneb  (ISO)
methotrexate  (ISO)
methylparaben  (ISO)
microcystin-LR  (ISO)
mifepristone  (ISO)
N-nitrosodiethylamine  (EXP)
nefazodone  (EXP)
nickel dichloride  (EXP)
nimesulide  (EXP)
nitroglycerin  (EXP)
okadaic acid  (ISO)
ozone  (ISO)
paraquat  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
phencyclidine  (ISO)
phenobarbital  (ISO)
phenytoin  (ISO)
progesterone  (ISO)
risperidone  (EXP)
rotenone  (EXP)
sodium fluoride  (ISO)
Tributyltin oxide  (ISO)
trichloroethene  (EXP)
tunicamycin  (ISO)
uranium atom  (ISO)
valproic acid  (ISO)
vincristine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of adenylate cyclase activity  (IDA)
autophagosome membrane docking  (IEA,ISO,ISS)
calcium-mediated signaling  (IMP)
detection of calcium ion  (ISO)
establishment of protein localization to membrane  (IMP)
establishment of protein localization to mitochondrial membrane  (IMP)
G2/M transition of mitotic cell cycle  (ISO)
mitochondrion-endoplasmic reticulum membrane tethering  (IEA,ISO,ISS)
negative regulation of high voltage-gated calcium channel activity  (ISO,ISS)
negative regulation of ryanodine-sensitive calcium-release channel activity  (ISO,ISS)
organelle localization by membrane tethering  (ISO,ISS)
positive regulation of cyclic-nucleotide phosphodiesterase activity  (ISO)
positive regulation of DNA binding  (IEA)
positive regulation of nitric-oxide synthase activity  (IDA)
positive regulation of phosphoprotein phosphatase activity  (ISO)
positive regulation of protein dephosphorylation  (ISO)
positive regulation of ryanodine-sensitive calcium-release channel activity  (IBA,ISO)
regulation of cardiac muscle cell action potential  (ISO,ISS)
regulation of cardiac muscle contraction  (ISO)
regulation of catalytic activity  (IEA)
regulation of cytokinesis  (ISO)
regulation of heart rate  (ISO)
regulation of high voltage-gated calcium channel activity  (IMP)
regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum  (ISO)
regulation of ryanodine-sensitive calcium-release channel activity  (IBA,IDA,ISO,ISS)
regulation of store-operated calcium channel activity  (IC)
regulation of synaptic vesicle endocytosis  (IMP)
regulation of synaptic vesicle exocytosis  (IMP)
response to amphetamine  (IEP)
response to calcium ion  (ISO)
response to corticosterone  (IEP)
substantia nigra development  (ISO)

Cellular Component

References

References - curated
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18. Hawley SA, etal., Cell Metab. 2005 Jul;2(1):9-19.
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20. Kang HJ, etal., Nat Med. 2012 Aug 12. doi: 10.1038/nm.2886.
21. KEGG
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23. Kubota Y, etal., J Neurophysiol. 2008 Jan;99(1):264-76. Epub 2007 Oct 24.
24. Li H and Villalobo A, Biochem J. 2002 Mar 1;362(Pt 2):499-505.
25. Li H, etal., Nat Cell Biol. 2013 Jul;15(7):773-85. doi: 10.1038/ncb2791. Epub 2013 Jun 23.
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27. Liu Y, etal., J Biol Chem. 2012 Dec 14;287(51):43030-41. doi: 10.1074/jbc.M112.380964. Epub 2012 Oct 29.
28. Macdougall DA, etal., J Biol Chem. 2009 Jun 5;284(23):15573-88. doi: 10.1074/jbc.M809585200. Epub 2009 Mar 21.
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30. MGD data from the GO Consortium
31. Michelhaugh SK and Gnegy ME, Neuroscience. 2000;98(2):275-85.
32. Morsink MC, etal., J Neuroendocrinol. 2006 Apr;18(4):239-52.
33. Mullins FM, etal., Proc Natl Acad Sci U S A. 2009 Sep 8;106(36):15495-500. doi: 10.1073/pnas.0906781106. Epub 2009 Aug 21.
34. Natsukari N, etal., Neurochem Int. 1995 May;26(5):465-76.
35. NCBI rat LocusLink and RefSeq merged data July 26, 2002
36. Nojima H, etal., Mol Cell Biol 1987 May;7(5):1873-80.
37. Oda T, etal., Circ Res. 2013 Feb 1;112(3):487-97. doi: 10.1161/CIRCRESAHA.111.300290. Epub 2012 Dec 11.
38. Pipeline to import KEGG annotations from KEGG into RGD
39. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
40. Ravindran A, etal., Proc Natl Acad Sci U S A. 2008 Jun 10;105(23):8154-9. doi: 10.1073/pnas.0711624105. Epub 2008 Jun 5.
41. RGD automated data pipeline
42. RGD automated import pipeline for gene-chemical interactions
43. RGD comprehensive gene curation
44. Rokita AG and Anderson ME, Circulation. 2012 Oct 23;126(17):2125-39. doi: 10.1161/CIRCULATIONAHA.112.124990.
45. Russo LC, etal., FEBS J. 2009 Aug;276(16):4358-71. doi: 10.1111/j.1742-4658.2009.07144.x. Epub 2009 Jul 15.
46. Russo LC, etal., Proteomics. 2012 Aug;12(17):2641-55. doi: 10.1002/pmic.201200032. Epub 2012 Jul 26.
47. Schumacher MA, etal., Nature. 2001 Apr 26;410(6832):1120-4.
48. Schumacher MA, etal., Structure. 2004 May;12(5):849-60.
49. SenGupta B, etal., J Biol Chem 1987 Dec 5;262(34):16663-70.
50. Sorensen SD, etal., Mol Pharmacol. 2002 Jun;61(6):1303-12.
51. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
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53. Yurimoto S, etal., Biochemistry. 2009 May 12;48(18):3946-55. doi: 10.1021/bi900260y.
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Additional References at PubMed
PMID:201628   PMID:1315919   PMID:2469574   PMID:2527998   PMID:2885164   PMID:3035194   PMID:3145979   PMID:3990807   PMID:7607248   PMID:8631777   PMID:11807546   PMID:11984006  
PMID:12223552   PMID:12392717   PMID:15294163   PMID:15489334   PMID:15632291   PMID:16760425   PMID:20226167   PMID:20668654   PMID:21091651   PMID:21167176   PMID:22067155   PMID:22926577  
PMID:23040497   PMID:26084473   PMID:26164367   PMID:26399481   PMID:26969752   PMID:27165696   PMID:27516456   PMID:27564677   PMID:28153703   PMID:30225708   PMID:30361391   PMID:31429119  


Genomics

Comparative Map Data
Calm2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.267,091,624 - 7,104,284 (+)NCBI
Rnor_6.0 Ensembl1565,506,874 - 65,507,968 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0611,067,675 - 11,080,078 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0621,052,945 - 21,068,133 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4664,161,641 - 64,162,751 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11564,177,420 - 64,178,531 (-)NCBI
Celera66,842,934 - 6,855,590 (+)NCBICelera
Cytogenetic Map6q12NCBI
CALM2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl247,160,083 - 47,176,921 (-)EnsemblGRCh38hg38GRCh38
GRCh38247,160,082 - 47,176,936 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37247,387,221 - 47,404,075 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36247,240,809 - 47,257,154 (-)NCBINCBI36hg18NCBI36
Build 34247,298,955 - 47,315,301NCBI
Celera247,226,054 - 47,242,551 (-)NCBI
Cytogenetic Map2p21NCBI
HuRef247,124,359 - 47,140,853 (-)NCBIHuRef
CHM1_1247,317,465 - 47,334,257 (-)NCBICHM1_1
Calm2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391787,740,829 - 87,754,363 (-)NCBIGRCm39mm39
GRCm39 Ensembl1787,740,840 - 87,754,363 (-)Ensembl
GRCm381787,433,401 - 87,446,935 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12100,199,435 - 100,209,814 (+)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl1787,433,412 - 87,446,935 (-)EnsemblGRCm38mm10GRCm38
MGSCv371787,832,741 - 87,846,275 (-)NCBIGRCm37mm9NCBIm37
MGSCv361787,341,743 - 87,355,168 (-)NCBImm8
Celera1791,831,455 - 91,844,939 (-)NCBICelera
Cytogenetic Map17E4NCBI
Calm2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495544113,973,147 - 13,988,665 (-)NCBIChiLan1.0ChiLan1.0
CALM2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A48,204,518 - 48,220,697 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A48,204,518 - 48,220,697 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A47,274,722 - 47,290,861 (-)NCBIMhudiblu_PPA_v0panPan3
CALM2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11049,299,698 - 49,314,533 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1049,299,897 - 49,314,457 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1049,152,937 - 49,167,816 (-)NCBI
ROS_Cfam_1.01050,169,941 - 50,184,842 (-)NCBI
UMICH_Zoey_3.11049,877,637 - 49,892,535 (-)NCBI
UNSW_CanFamBas_1.01050,167,136 - 50,182,012 (-)NCBI
UU_Cfam_GSD_1.01050,351,274 - 50,366,152 (-)NCBI
Calm2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629233,779,344 - 33,795,171 (+)NCBI
SpeTri2.0NW_0049365085,207,909 - 5,223,780 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CALM2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl393,372,045 - 93,438,068 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1393,371,765 - 93,386,378 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2399,567,552 - 99,582,160 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CALM2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11460,027,884 - 60,042,041 (+)NCBI
ChlSab1.1 Ensembl1460,027,801 - 60,044,951 (+)Ensembl
ChlSab1.1 Ensembl2468,133,428 - 68,145,180 (+)Ensembl
ChlSab1.1 Ensembl639,957,320 - 39,966,581 (+)Ensembl
Calm2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473828,525,290 - 28,541,562 (-)NCBI

Position Markers
RH137765  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0611,064,877 - 11,065,026NCBIRnor6.0
Rnor_5.0621,053,072 - 21,053,221UniSTSRnor5.0
RGSC_v3.4610,949,517 - 10,949,666UniSTSRGSC3.4
Celera66,858,239 - 6,858,388UniSTS
Cytogenetic Map6q11-q12UniSTS
PMC18246P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01565,507,716 - 65,507,957NCBIRnor6.0
Rnor_5.01569,147,488 - 69,147,729UniSTSRnor5.0
RGSC_v3.41564,162,483 - 64,162,724UniSTSRGSC3.4
Celera1557,664,694 - 57,664,935UniSTS
Cytogenetic Map6q11-q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6143665660Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6141917988Rat
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6135623029Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6144570292Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6123620518Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6135623029Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6135623029Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6143665660Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6143665660Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)71017386255173862Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6125048718Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)6616172276002731Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6616172276002731Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6135623029Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6175623393Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)6112039375023446Rat
1359023Bp272Blood pressure QTL 2722.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6112039328706721Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6135623029Rat
1358190Ept1Estrogen-induced pituitary tumorigenesis QTL 14.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6808322221515439Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6112039346120393Rat
2292616Ept15Estrogen-induced pituitary tumorigenesis QTL 154.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6808322221515439Rat
8693645Alc31Alcohol consumption QTL 313.70.038drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)613505323600274Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142388212Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6144015370Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6142388212Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6142388212Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6142388212Rat
8693699Alc37Alcohol consumption QTL 372.60.224drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)6997427722477622Rat
8693690Alc35Alcohol consumption QTL 352.20.606drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)6997427722477622Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6142388212Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mir1rno-miR-1-3pMirtarbaseexternal_infoReporter assay;Western blot;qRT-PCRFunctional MTI19188439

Predicted Target Of
Summary Value
Count of predictions:645
Count of miRNA genes:283
Interacting mature miRNAs:344
Transcripts:ENSRNOT00000046240
Prediction methods:Microtar, Miranda
Result types:miRGate_prediction

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

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


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 3 170 7 2
Medium 6 129 171 123 57 123 24 33 52 103 116 31 24
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_017326 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC058485 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211494 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211970 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212357 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212579 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212640 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212685 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212691 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212774 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212789 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212869 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212884 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213028 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213029 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213062 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213091 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213115 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213200 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213216 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213236 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213310 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213314 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213358 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213366 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213496 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213520 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213526 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213581 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213598 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213637 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213695 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213703 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213760 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213762 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213913 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213941 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213967 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213969 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213981 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213985 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213999 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214059 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214092 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214181 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214262 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214271 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214338 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214370 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214461 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214491 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214500 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214519 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214525 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214540 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215159 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215317 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215600 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216397 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216471 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218091 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219917 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220040 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220250 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220325 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220377 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220540 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220698 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220774 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220779 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222184 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223357 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224257 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225272 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226994 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227274 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229478 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229580 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229619 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229790 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229905 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231022 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231702 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233337 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233496 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234377 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235266 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000163 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M17069 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M19312 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X13834 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X13835 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000046240   ⟹   ENSRNOP00000040477
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1565,506,874 - 65,507,968 (-)Ensembl
RefSeq Acc Id: NM_017326   ⟹   NP_059022
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.267,091,624 - 7,104,284 (+)NCBI
Rnor_6.0611,067,675 - 11,080,078 (-)NCBI
Rnor_5.0621,052,945 - 21,068,133 (-)NCBI
RGSC_v3.4664,161,641 - 64,162,751 (-)RGD
Celera66,842,934 - 6,855,590 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_059022   ⟸   NM_017326
- UniProtKB: P0DP31 (UniProtKB/Swiss-Prot),   P0DP30 (UniProtKB/Swiss-Prot),   P0DP29 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000040477   ⟸   ENSRNOT00000046240
Protein Domains
EF-hand

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)
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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/SsN (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
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)
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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
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
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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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)
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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
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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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)
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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)
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)
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
SS/Jr (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
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)
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
WKY/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
WKY/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
WKY/NHsd (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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2258 AgrOrtholog
Ensembl Genes ENSRNOG00000004060 UniProtKB/Swiss-Prot
  ENSRNOG00000016770 UniProtKB/Swiss-Prot
  ENSRNOG00000030871 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000022603 UniProtKB/Swiss-Prot
  ENSRNOP00000040477 UniProtKB/TrEMBL
  ENSRNOP00000063822 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000022603 UniProtKB/Swiss-Prot
  ENSRNOT00000046240 UniProtKB/TrEMBL
  ENSRNOT00000064679 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:6921326 IMAGE-MGC_LOAD
InterPro EF-hand-dom_pair UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_Hand_1_Ca_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_hand_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24242 UniProtKB/Swiss-Prot
  rno:24244 UniProtKB/Swiss-Prot
  rno:50663 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72870 IMAGE-MGC_LOAD
NCBI Gene 50663 ENTREZGENE
Pfam EF-hand_7 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Calm2 PhenoGen
PROSITE EF_HAND_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_HAND_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART EFh UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt CALM1_RAT UniProtKB/Swiss-Prot
  CALM2_RAT UniProtKB/Swiss-Prot
  CALM3_RAT UniProtKB/Swiss-Prot
  D4ABV5_RAT UniProtKB/TrEMBL
  P0DP29 ENTREZGENE
  P0DP30 ENTREZGENE
  P0DP31 ENTREZGENE
UniProt Secondary P02593 UniProtKB/Swiss-Prot
  P62161 UniProtKB/Swiss-Prot
  P70667 UniProtKB/Swiss-Prot
  P99014 UniProtKB/Swiss-Prot
  Q61379 UniProtKB/Swiss-Prot
  Q61380 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Calm2  Calmodulin 2 (phosphorylase kinase, delta)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed mainly in brain 634684
gene_function bovine homolog binds and activates the reductase domain of Nos 634685
gene_transcript 1.4 kb 634684