Calm3 (calmodulin 3) - Rat Genome Database

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Gene: Calm3 (calmodulin 3) Rattus norvegicus
Analyze
Symbol: Calm3
Name: calmodulin 3
RGD ID: 2259
Description: Enables several functions, including enzyme binding activity; nitric-oxide synthase regulator activity; and transmembrane transporter binding activity. Involved in several processes, including activation of adenylate cyclase activity; regulation of calcium ion transmembrane transporter activity; and regulation of vesicle-mediated transport. Located in 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 familial hypertrophic cardiomyopathy. Orthologous to human CALM3 (calmodulin 3); PARTICIPATES IN adenosine monophosphate-activated protein kinase (AMPK) signaling pathway; calcium/calcium-mediated signaling pathway; calcium/calmodulin dependent kinase 2 signaling pathway; INTERACTS WITH 2,2,2-tetramine; 2,3,7,8-Tetrachlorodibenzofuran; amphetamine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: calmodulin; calmodulin III; calmodulin-3; caM; Cam3; Camc; CaMIII; RNCAMIII
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
mRatBN7.2177,590,668 - 77,597,776 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl178,843,080 - 78,851,719 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0178,844,520 - 78,851,628 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0180,092,078 - 80,099,186 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4177,245,609 - 77,252,717 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1177,322,279 - 77,330,919 (-)NCBI
Celera172,075,982 - 72,079,075 (-)NCBICelera
RH 3.4 Map1793.6RGD
Cytogenetic Map1q21NCBI
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)
17alpha-ethynylestradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,2,2-tetramine  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
acetylsalicylic acid  (ISO)
afimoxifene  (ISO)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
C60 fullerene  (EXP)
calcium dichloride  (ISO)
carbon nanotube  (ISO)
chloropicrin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
dibutyl phthalate  (EXP,ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
Enterolactone  (ISO)
ethanol  (EXP,ISO)
finasteride  (EXP)
fluoranthene  (ISO)
flutamide  (EXP)
folic acid  (ISO)
glyphosate  (ISO)
isoprenaline  (ISO)
leflunomide  (ISO)
mechlorethamine  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
methotrexate  (ISO)
microcystin-LR  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodimethylamine  (EXP)
nickel atom  (ISO)
ozone  (EXP)
PCB138  (ISO)
pirinixic acid  (ISO)
sarin  (ISO)
selenium atom  (ISO)
serpentine asbestos  (ISO)
sodium arsenite  (EXP)
streptozocin  (EXP)
sulindac  (EXP,ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP,ISO)
thimerosal  (ISO)
titanium dioxide  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
venlafaxine hydrochloride  (EXP)
vinclozolin  (EXP)
vitamin E  (ISO)
zinc atom  (EXP)
zinc sulfate  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of adenylate cyclase activity  (IDA)
autophagosome membrane docking  (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  (ISO,ISS)
negative regulation of calcium ion export across plasma membrane  (IEA)
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 calcium-mediated signaling  (IEA)
regulation of cardiac muscle cell action potential  (ISO,ISS)
regulation of cardiac muscle contraction  (ISO)
regulation of cyclase 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)
substantia nigra development  (ISO)

Cellular Component

References

References - curated
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18. Grant L and Fuchs P, J Neurophysiol. 2008 May;99(5):2183-93. doi: 10.1152/jn.01174.2007. Epub 2008 Mar 5.
19. Hawley SA, etal., Cell Metab. 2005 Jul;2(1):9-19.
20. Hou W, etal., PLoS Biol. 2015 Sep 3;13(9):e1002233. doi: 10.1371/journal.pbio.1002233. eCollection 2015.
21. KEGG
22. Kosenko A, etal., EMBO J. 2012 May 29;31(14):3147-56. doi: 10.1038/emboj.2012.156.
23. Kubota Y, etal., J Neurophysiol. 2008 Jan;99(1):264-76. Epub 2007 Oct 24.
24. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
25. Li H and Villalobo A, Biochem J. 2002 Mar 1;362(Pt 2):499-505.
26. Li H, etal., Nat Cell Biol. 2013 Jul;15(7):773-85. doi: 10.1038/ncb2791. Epub 2013 Jun 23.
27. Li H, etal., Oncogene. 2005 Jun 16;24(26):4206-19.
28. Liu Y, etal., J Biol Chem. 2012 Dec 14;287(51):43030-41. doi: 10.1074/jbc.M112.380964. Epub 2012 Oct 29.
29. Macdougall DA, etal., J Biol Chem. 2009 Jun 5;284(23):15573-88. doi: 10.1074/jbc.M809585200. Epub 2009 Mar 21.
30. Majava V, etal., Amino Acids. 2010 Jun;39(1):59-71. doi: 10.1007/s00726-009-0364-2. Epub 2009 Oct 24.
31. MGD data from the GO Consortium
32. Michelhaugh SK and Gnegy ME, Neuroscience. 2000;98(2):275-85.
33. Morsink MC, etal., J Neuroendocrinol. 2006 Apr;18(4):239-52.
34. 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.
35. Natsukari N, etal., Neurochem Int. 1995 May;26(5):465-76.
36. NCBI rat LocusLink and RefSeq merged data July 26, 2002
37. Nojima H J Mol Biol 1989 Jul 20;208(2):269-82.
38. Oda T, etal., Circ Res. 2013 Feb 1;112(3):487-97. doi: 10.1161/CIRCRESAHA.111.300290. Epub 2012 Dec 11.
39. Pipeline to import KEGG annotations from KEGG into RGD
40. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
41. 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.
42. RGD automated data pipeline
43. RGD automated import pipeline for gene-chemical interactions
44. RGD comprehensive gene curation
45. Rokita AG and Anderson ME, Circulation. 2012 Oct 23;126(17):2125-39. doi: 10.1161/CIRCULATIONAHA.112.124990.
46. Russo LC, etal., FEBS J. 2009 Aug;276(16):4358-71. doi: 10.1111/j.1742-4658.2009.07144.x. Epub 2009 Jul 15.
47. Russo LC, etal., Proteomics. 2012 Aug;12(17):2641-55. doi: 10.1002/pmic.201200032. Epub 2012 Jul 26.
48. Schumacher MA, etal., Nature. 2001 Apr 26;410(6832):1120-4.
49. Schumacher MA, etal., Structure. 2004 May;12(5):849-60.
50. Sherbany AA, etal., DNA. 1987 Jun;6(3):267-72.
51. Sorensen SD, etal., Mol Pharmacol. 2002 Jun;61(6):1303-12.
52. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
53. Tejero J, etal., J Biol Chem. 2010 Aug 20;285(34):25941-9. doi: 10.1074/jbc.M110.126797. Epub 2010 Jun 7.
54. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
55. Yurimoto S, etal., Biochemistry. 2009 May 12;48(18):3946-55. doi: 10.1021/bi900260y.
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Additional References at PubMed
PMID:2469574   PMID:7607248   PMID:8631777   PMID:11694536   PMID:11807546   PMID:11984006   PMID:12223552   PMID:15294163   PMID:15632291   PMID:16760425   PMID:20226167   PMID:20668654  
PMID:21167176   PMID:22067155   PMID:22926577   PMID:23040497   PMID:25089838   PMID:26164367   PMID:26969752   PMID:27165696   PMID:27516456   PMID:27564677   PMID:28153703   PMID:28765142  


Genomics

Comparative Map Data
Calm3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2177,590,668 - 77,597,776 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl178,843,080 - 78,851,719 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0178,844,520 - 78,851,628 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0180,092,078 - 80,099,186 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4177,245,609 - 77,252,717 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1177,322,279 - 77,330,919 (-)NCBI
Celera172,075,982 - 72,079,075 (-)NCBICelera
RH 3.4 Map1793.6RGD
Cytogenetic Map1q21NCBI
CALM3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1946,601,074 - 46,610,782 (+)EnsemblGRCh38hg38GRCh38
GRCh381946,601,074 - 46,610,782 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371947,104,331 - 47,114,039 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361951,796,352 - 51,805,879 (+)NCBINCBI36hg18NCBI36
Build 341951,796,351 - 51,805,878NCBI
Celera1943,908,038 - 43,917,566 (+)NCBI
Cytogenetic Map19q13.32NCBI
HuRef1943,529,569 - 43,539,096 (+)NCBIHuRef
CHM1_11947,106,370 - 47,115,897 (+)NCBICHM1_1
Calm3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39716,649,304 - 16,657,957 (-)NCBIGRCm39mm39
GRCm39 Ensembl716,649,304 - 16,658,039 (-)Ensembl
GRCm38716,915,379 - 16,924,032 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl716,915,379 - 16,924,114 (-)EnsemblGRCm38mm10GRCm38
MGSCv37717,500,728 - 17,509,381 (-)NCBIGRCm37mm9NCBIm37
MGSCv36716,073,901 - 16,082,476 (-)NCBImm8
Celera714,121,809 - 14,130,463 (-)NCBICelera
Cytogenetic Map7A2NCBI
cM Map79.15NCBI
Calm3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955574672,300 - 680,924 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955574672,441 - 680,924 (+)NCBIChiLan1.0ChiLan1.0
CALM3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11952,121,687 - 52,131,135 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1952,121,687 - 52,131,135 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01943,593,069 - 43,602,550 (+)NCBIMhudiblu_PPA_v0panPan3
CALM3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11109,284,729 - 109,294,491 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1109,286,155 - 109,294,391 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1108,764,035 - 108,773,479 (-)NCBI
ROS_Cfam_1.01109,810,758 - 109,820,206 (-)NCBI
UMICH_Zoey_3.11109,487,893 - 109,497,333 (-)NCBI
UNSW_CanFamBas_1.01109,121,990 - 109,131,419 (-)NCBI
UU_Cfam_GSD_1.01109,990,749 - 110,000,195 (-)NCBI
Calm3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934918,853,317 - 18,861,294 (+)NCBI
SpeTri2.0NW_004936664471,446 - 480,858 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CALM3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl652,506,674 - 52,516,703 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1652,506,979 - 52,516,704 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2647,824,454 - 47,834,181 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CALM3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1639,957,012 - 39,966,562 (+)NCBI
ChlSab1.1 Ensembl639,957,320 - 39,966,581 (+)Ensembl
ChlSab1.1 Ensembl2468,133,428 - 68,145,180 (+)Ensembl
ChlSab1.1 Ensembl1460,027,801 - 60,044,951 (+)Ensembl
Vero_WHO_p1.0NW_02366607319,668,290 - 19,677,858 (+)NCBI
Calm3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248326,957,775 - 6,966,505 (-)NCBI

Position Markers
D1Wox12  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2177,593,079 - 77,593,226 (+)MAPPERmRatBN7.2
Rnor_6.0178,846,932 - 78,847,078NCBIRnor6.0
Rnor_5.0180,094,490 - 80,094,636UniSTSRnor5.0
RGSC_v3.4177,248,020 - 77,248,167RGDRGSC3.4
RGSC_v3.4177,248,021 - 77,248,167UniSTSRGSC3.4
RGSC_v3.1177,326,131 - 77,326,278RGD
Celera172,078,394 - 72,078,540UniSTS
RH 3.4 Map1791.5RGD
RH 3.4 Map1791.5UniSTS
RH 2.0 Map1511.8RGD
Cytogenetic Map1q22UniSTS
D1Arb35  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2177,592,984 - 77,593,234 (+)MAPPERmRatBN7.2
Rnor_6.0178,846,837 - 78,847,086NCBIRnor6.0
Rnor_5.0180,094,395 - 80,094,644UniSTSRnor5.0
RGSC_v3.4177,247,926 - 77,248,175UniSTSRGSC3.4
RGSC_v3.4177,247,925 - 77,248,175RGDRGSC3.4
RGSC_v3.1177,326,036 - 77,326,286RGD
Celera172,078,299 - 72,078,548UniSTS
FHH x ACI Map139.05RGD
FHH x ACI Map139.05UniSTS
Cytogenetic Map1q22UniSTS
D1Mgh27  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2177,598,766 - 77,598,961 (+)MAPPERmRatBN7.2
Rnor_6.0178,852,619 - 78,852,813NCBIRnor6.0
Rnor_5.0180,100,177 - 80,100,371UniSTSRnor5.0
RGSC_v3.4177,253,707 - 77,253,902RGDRGSC3.4
RGSC_v3.4177,253,708 - 77,253,902UniSTSRGSC3.4
RGSC_v3.1177,331,818 - 77,332,013RGD
Celera172,083,915 - 72,084,109UniSTS
RH 3.4 Map1790.5RGD
RH 3.4 Map1790.5UniSTS
Cytogenetic Map1q22UniSTS
D1Mco19  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2177,592,972 - 77,593,244 (+)MAPPERmRatBN7.2
Rnor_6.0178,846,825 - 78,847,096NCBIRnor6.0
Rnor_5.0180,094,383 - 80,094,654UniSTSRnor5.0
RGSC_v3.4177,247,913 - 77,248,185RGDRGSC3.4
RGSC_v3.4177,247,914 - 77,248,185UniSTSRGSC3.4
RGSC_v3.1177,326,024 - 77,326,296RGD
Celera172,078,287 - 72,078,558UniSTS
Cytogenetic Map1q22UniSTS
RH128262  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25102,623,675 - 102,623,875 (+)MAPPERmRatBN7.2
mRatBN7.2177,589,281 - 77,589,472 (+)MAPPERmRatBN7.2
Rnor_6.0178,843,134 - 78,843,324NCBIRnor6.0
Rnor_6.05106,467,083 - 106,467,282NCBIRnor6.0
Rnor_5.0180,090,692 - 80,090,882UniSTSRnor5.0
Rnor_5.05110,448,523 - 110,448,722UniSTSRnor5.0
RGSC_v3.4177,244,223 - 77,244,413UniSTSRGSC3.4
Celera5100,486,767 - 100,486,966UniSTS
Celera172,074,596 - 72,074,786UniSTS
Cytogenetic Map5q32UniSTS
Cytogenetic Map1q22UniSTS
UniSTS:141218  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25102,623,667 - 102,623,851 (+)MAPPERmRatBN7.2
mRatBN7.2177,589,273 - 77,589,448 (+)MAPPERmRatBN7.2
Rnor_6.0178,843,126 - 78,843,300NCBIRnor6.0
Rnor_6.05106,467,075 - 106,467,258NCBIRnor6.0
Rnor_5.0180,090,684 - 80,090,858UniSTSRnor5.0
Rnor_5.05110,448,515 - 110,448,698UniSTSRnor5.0
RGSC_v3.4177,244,215 - 77,244,389UniSTSRGSC3.4
Celera5100,486,791 - 100,486,974UniSTS
Celera172,074,588 - 72,074,762UniSTS
Cytogenetic Map5q32UniSTS
Cytogenetic Map1q22UniSTS
RH137447  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2177,590,696 - 77,590,999 (+)MAPPERmRatBN7.2
Rnor_6.0178,844,549 - 78,844,851NCBIRnor6.0
Rnor_5.0180,092,107 - 80,092,409UniSTSRnor5.0
RGSC_v3.4177,245,638 - 77,245,940UniSTSRGSC3.4
Celera172,076,011 - 72,076,313UniSTS
Cytogenetic Map1q22UniSTS
Calm3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2177,594,298 - 77,594,557 (+)MAPPERmRatBN7.2
Rnor_6.0178,848,151 - 78,848,409NCBIRnor6.0
Rnor_5.0180,095,709 - 80,095,967UniSTSRnor5.0
RGSC_v3.4177,249,240 - 77,249,498UniSTSRGSC3.4
Celera172,079,613 - 72,079,871UniSTS
RH 3.4 Map1793.6UniSTS
Cytogenetic Map1q22UniSTS
MARC_7076-7077:992008234:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2177,590,677 - 77,591,018 (+)MAPPERmRatBN7.2
Rnor_6.0178,844,530 - 78,844,870NCBIRnor6.0
Rnor_5.0180,092,088 - 80,092,428UniSTSRnor5.0
RGSC_v3.4177,245,619 - 77,245,959UniSTSRGSC3.4
Celera172,075,992 - 72,076,332UniSTS
Cytogenetic Map1q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)125439386904217Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15655769122614963Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1565577285706974Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11131448983657083Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11131448983657083Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11131448983657083Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11131448983657083Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123406428108057505Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)125951907130917265Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)13148945479689689Rat
1354643Foco2Food consumption QTL 27.170.0001eating behavior trait (VT:0001431)food intake rate (CMO:0000427)13444911279449112Rat
1354599Bw29Body weight QTL 293.460.001body mass (VT:0001259)body weight (CMO:0000012)13444911279449112Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13537750894364229Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
9589820Insglur3Insulin/glucose ratio QTL 310.750.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)13585416780854167Rat
8552900Pigfal1Plasma insulin-like growth factor 1 level QTL 17.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13585416780854167Rat
8552948Pigfal11Plasma insulin-like growth factor 1 level QTL 114.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13585416780854167Rat
1331732Srn4Serum renin concentration QTL 44.467renin activity (VT:0005581)plasma renin activity level (CMO:0000116)13603316579689689Rat
1331792Rf29Renal function QTL 294.589urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)13603316579689689Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14190724986907249Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143579208126240667Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143579208126240667Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143579208126240667Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143579208126240667Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143579208126240667Rat
1331778Rf28Renal function QTL 284.66urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)14611346179689689Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)149147799156446783Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14954732883657083Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14957857794578577Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149578577169852184Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15052271494225616Rat
4889919Bss86Bone structure and strength QTL 864.1tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)15385134883657083Rat
4889929Bss87Bone structure and strength QTL 876.7tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)15385134883657083Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)157761301104391981Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)158209327103209327Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)158354072161711996Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)164588516125875986Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)166113339122614963Rat
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)16722768394201552Rat

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mir1rno-miR-1-3pMirtarbaseexternal_infoqRT-PCRFunctional MTI (Weak)19188439

Predicted Target Of
Summary Value
Count of predictions:340
Count of miRNA genes:186
Interacting mature miRNAs:212
Transcripts:ENSRNOT00000022603
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


Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022603   ⟹   ENSRNOP00000022603
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl178,843,080 - 78,851,719 (-)Ensembl
RefSeq Acc Id: NM_012518   ⟹   NP_036650
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2177,590,668 - 77,597,776 (-)NCBI
Rnor_6.0178,844,520 - 78,851,628 (-)NCBI
Rnor_5.0180,092,078 - 80,099,186 (-)NCBI
RGSC_v3.4177,245,609 - 77,252,717 (-)RGD
Celera172,075,982 - 72,079,075 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036650   ⟸   NM_012518
- UniProtKB: P0DP31 (UniProtKB/Swiss-Prot),   P0DP30 (UniProtKB/Swiss-Prot),   P0DP29 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022603   ⟸   ENSRNOT00000022603
Protein Domains
EF-hand

Transcriptome

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

Promoters
RGD ID:13689745
Promoter ID:EPDNEW_R269
Type:initiation region
Name:Calm2_1
Description:calmodulin 2
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_6.0178,851,694 - 78,851,754EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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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
LEXF1C/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
LEXF2B/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
LEXF3/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
LEXF4/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
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
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)
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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/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
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)
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)
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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)
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
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:2259 AgrOrtholog
Ensembl Genes ENSRNOG00000004060 UniProtKB/Swiss-Prot
  ENSRNOG00000016770 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000022603 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000063822 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000022603 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000064679 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:6890866 IMAGE-MGC_LOAD
InterPro EF-hand-dom_pair UniProtKB/Swiss-Prot
  EF_Hand_1_Ca_BS UniProtKB/Swiss-Prot
  EF_hand_dom UniProtKB/Swiss-Prot
KEGG Report rno:24242 UniProtKB/Swiss-Prot
  rno:24244 UniProtKB/Swiss-Prot
  rno:50663 UniProtKB/Swiss-Prot
MGC_CLONE MGC:73021 IMAGE-MGC_LOAD
NCBI Gene 24244 ENTREZGENE
Pfam EF-hand_7 UniProtKB/Swiss-Prot
PhenoGen Calm3 PhenoGen
PROSITE EF_HAND_1 UniProtKB/Swiss-Prot
  EF_HAND_2 UniProtKB/Swiss-Prot
SMART EFh UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot
TIGR TC204370
UniProt CALM1_RAT UniProtKB/Swiss-Prot
  CALM2_RAT UniProtKB/Swiss-Prot
  CALM3_RAT UniProtKB/Swiss-Prot
  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
2002-11-06 Calm3  calmodulin 3    Calmodulin III  Name updated 625702 APPROVED
2002-06-10 Calm3  Calmodulin III      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed mainly in skeletal muscle and brain 634687
gene_protein 2.2 and 0.75 kb mRNA 634686