Cacna1c (calcium voltage-gated channel subunit alpha1 C) - Rat Genome Database

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Gene: Cacna1c (calcium voltage-gated channel subunit alpha1 C) Rattus norvegicus
Analyze
Symbol: Cacna1c
Name: calcium voltage-gated channel subunit alpha1 C
RGD ID: 2245
Description: Exhibits several functions, including high voltage-gated calcium channel activity; ion channel binding activity; and protein phosphatase 2A binding activity. Involved in calcium ion transport; cellular response to amyloid-beta; and positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel. Localizes to several cellular components, including L-type voltage-gated calcium channel complex; Z disc; and integral component of synaptic membrane. Human ortholog(s) of this gene implicated in Brugada syndrome 3 and Timothy syndrome. Orthologous to human CACNA1C (calcium voltage-gated channel subunit alpha1 C); PARTICIPATES IN acebutolol pharmacodynamics pathway; adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway; amiodarone pharmacodynamics pathway; INTERACTS WITH (R)-mevalonic acid; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: brain class C; Ca channel voltage-dependent L type alpha 1c subunit; Ca channel, voltage-dependent, L type, alpha 1c subunit; calcium channel, L type, alpha-1 polypeptide, isoform 1, cardiac muscle; calcium channel, voltage-dependent, alpha 1C subunit; calcium channel, voltage-dependent, L type, alpha 1C subunit; L-type calcium channel alpha-1 subunit; RATIVS302; RBC; voltage-dependent L-type calcium channel subunit alpha-1C; voltage-gated calcium channel subunit alpha Cav1.2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Cacna1cem1Sage  
Genetic Models: SD-Cacna1cem1Sage
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24151,764,138 - 152,379,454 (-)NCBI
Rnor_6.0 Ensembl4150,641,066 - 150,829,913 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04150,635,808 - 151,270,790 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04216,562,477 - 217,184,927 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44154,895,691 - 155,517,389 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14155,140,531 - 155,762,230 (-)NCBI
Celera4140,633,057 - 141,244,304 (-)NCBICelera
Cytogenetic Map4q42NCBI
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
(+)-pilocarpine  (ISO)
(R)-mevalonic acid  (EXP)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
acetamide  (EXP)
aconitine  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (EXP)
allethrin  (EXP)
amiodarone  (ISO)
amphetamine  (EXP)
androgen antagonist  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atenolol  (ISO)
barium(0)  (EXP)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butanal  (ISO)
Butylparaben  (EXP)
calcium atom  (EXP,ISO)
calcium(0)  (EXP,ISO)
chloroprene  (ISO)
chlorpyrifos  (EXP)
cisplatin  (ISO)
crizotinib  (ISO)
DDE  (EXP)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
diltiazem  (ISO)
disodium selenite  (ISO)
doxorubicin  (EXP,ISO)
endosulfan  (EXP)
enzacamene  (EXP)
epoxiconazole  (EXP)
ethanol  (ISO)
ezogabine  (ISO)
fenvalerate  (EXP)
formaldehyde  (EXP)
furan  (EXP)
iron dextran  (ISO)
isoprenaline  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
linsidomine  (ISO)
linuron  (EXP)
methamphetamine  (ISO)
methapyrilene  (ISO)
methotrexate  (ISO)
methylene blue  (ISO)
N-nitrosodiethylamine  (ISO)
nefazodone  (ISO)
nicotine  (ISO)
nifedipine  (ISO)
nimodipine  (ISO)
Nor-9-carboxy-delta9-THC  (ISO)
paracetamol  (EXP)
paraquat  (EXP)
peroxynitrous acid  (ISO)
pioglitazone  (ISO)
potassium chloride  (ISO)
pregabalin  (EXP)
prochloraz  (EXP)
procymidone  (EXP)
progesterone  (EXP)
Ptaquiloside  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium cyanide  (ISO)
streptozocin  (ISO)
sunitinib  (ISO)
tetrachloromethane  (EXP)
thalidomide  (ISO)
torcetrapib  (ISO)
trichloroethene  (ISO)
triptonide  (ISO)
tunicamycin  (ISO)
valproic acid  (EXP,ISO)
verapamil  (EXP,ISO)
vinclozolin  (EXP)
zinc atom  (EXP)
zinc sulfate  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adult walking behavior  (ISO)
calcium ion import  (IBA,IMP)
calcium ion import across plasma membrane  (ISO)
calcium ion transmembrane transport  (IEA,ISO)
calcium ion transmembrane transport via high voltage-gated calcium channel  (IDA,IEA,ISO,ISS)
calcium ion transport  (IBA,IMP,ISO)
calcium ion transport into cytosol  (ISS)
calcium-ion regulated exocytosis  (ISO)
camera-type eye development  (IEA,ISO)
cardiac conduction  (ISO,ISS)
cardiac muscle cell action potential involved in contraction  (ISO,ISS)
cell communication involved in cardiac conduction  (ISO)
cellular calcium ion homeostasis  (ISO)
cellular response to amyloid-beta  (IEP)
chemical synaptic transmission  (ISO)
embryonic forelimb morphogenesis  (IEA,ISO)
glucose homeostasis  (ISO)
growth hormone secretion  (ISO)
heart development  (IEA,ISO)
immune system development  (IEA,ISO)
insulin secretion  (ISO)
membrane depolarization during atrial cardiac muscle cell action potential  (IEA,ISO,ISS)
membrane depolarization during AV node cell action potential  (IEA,ISO,ISS)
membrane depolarization during cardiac muscle cell action potential  (ISO,ISS)
positive regulation of adenylate cyclase activity  (ISO,ISS)
positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel  (IMP)
positive regulation of cytosolic calcium ion concentration  (IEA,ISO)
regulation of blood pressure  (ISO)
regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion  (ISS)
regulation of heart rate by cardiac conduction  (IEA,ISO,ISS)
regulation of ion transmembrane transport  (IEA)
regulation of organ growth  (ISO)
regulation of postsynaptic membrane potential  (IEA)
regulation of vasoconstriction  (ISO)
regulation of ventricular cardiac muscle cell action potential  (IEA,ISO,ISS)
smooth muscle contraction  (ISO)
smooth muscle contraction involved in micturition  (ISO)
visual learning  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
acebutolol pharmacodynamics pathway  (ISO)
adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway  (ISO)
Alzheimer's disease pathway  (IEA)
amiodarone pharmacodynamics pathway  (ISO)
amlodipine pharmacodynamics pathway  (ISO)
arrhythmogenic right ventricular cardiomyopathy pathway  (IEA)
atenolol pharmacodynamics pathway  (ISO)
betaxolol pharmacodynamics pathway  (ISO)
bisoprolol pharmacodynamics pathway  (ISO)
bupranolol drug pathway  (ISO)
bupranolol pharmacodynamics pathway  (ISO)
calcium transport pathway  (ISO)
calcium/calcium-mediated signaling pathway  (IEA,ISO)
calcium/calmodulin dependent kinase 2 signaling pathway  (ISO)
carvedilol pharmacodynamics pathway  (ISO)
dilated cardiomyopathy pathway  (IEA)
diltiazem pharmacodynamics pathway  (ISO)
disopyramide pharmacodynamics pathway  (ISO)
dobutamine pharmacodynamics pathway  (ISO)
esmolol pharmacodynamics pathway  (ISO)
felodipine pharmacokinetics pathway  (ISO)
flecainde pharmacodynamics pathway  (ISO)
fosphenytoin pharmacodynamics pathway  (ISO)
glutamate signaling pathway  (IEA)
gonadotropin-releasing hormone signaling pathway  (IEA)
hypertrophic cardiomyopathy pathway  (IEA)
ibutilide pharmacodynamics pathway  (ISO)
insulin secretion pathway  (TAS)
isoprenaline pharmacodynamics pathway  (ISO)
isradipine pharmacodynamics pathway  (ISO)
levobunolol pharmacodynamics pathway  (ISO)
lidocaine pharmacodynamics pathway  (ISO)
long term potentiation  (IEA)
metoprolol pharmacodynamics pathway  (ISO)
mexiletine pharmacodynamics pathway  (ISO)
mitogen activated protein kinase signaling pathway  (IEA)
nadolol pharmacodynamics pathway  (ISO)
nebivolol pharmacodynamics pathway  (ISO)
nifedipine pharmacodynamics pathway  (ISO)
nimodipine pharmacodynamics pathway  (ISO)
nisoldipine pharmacodynamics pathway  (ISO)
nitrendipine pharmacodynamics pathway  (ISO)
penbutolol pharmacodynamics pathway  (ISO)
phenytoin pharmacodynamics pathway  (ISO)
pindolol pharmacodynamics pathway  (ISO)
procainamide pharmacodynamics pathway  (ISO)
propranolol pharmacodynamics pathway  (ISO)
quinidine pharmacodynamics pathway  (ISO)
sotalol pharmacodynamics pathway  (ISO)
timolol pharmacodynamics pathway  (ISO)
type 2 diabetes mellitus pathway  (IEA)
verapamil pharmacodynamics pathway  (ISO)

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
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5. Catterall WA Cold Spring Harb Perspect Biol. 2011 Aug 1;3(8):a003947. doi: 10.1101/cshperspect.a003947.
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12. GOA data from the GO Consortium
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23. Lichvárová L and Lacinová L, Gen Physiol Biophys. 2015 Apr;34(2):157-65. doi: 10.4149/gpb_2014045. Epub 2015 Feb 12.
24. Ma YP and Pan ZH, Vis Neurosci 2003 Mar-Apr;20(2):131-9.
25. MGD data from the GO Consortium
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28. N'Gouemo P and Morad M, Neuroscience 2003;120(3):815-26.
29. NCBI rat LocusLink and RefSeq merged data July 26, 2002
30. OMIM Disease Annotation Pipeline
31. Pipeline to import KEGG annotations from KEGG into RGD
32. Pipeline to import SMPDB annotations from SMPDB into RGD
33. Pravenec M, etal., J Am Soc Nephrol 2000 Jul;11(7):1261-5
34. Redecker TM, etal., Behav Brain Res. 2019 Jul 23;367:35-52. doi: 10.1016/j.bbr.2019.03.032. Epub 2019 Mar 19.
35. RGD automated data pipeline
36. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
37. RGD automated import pipeline for gene-chemical interactions
38. Rokita AG and Anderson ME, Circulation. 2012 Oct 23;126(17):2125-39. doi: 10.1161/CIRCULATIONAHA.112.124990.
39. Scriven DR, etal., Biophys J. 2000 Nov;79(5):2682-91.
40. Scriven DR, etal., Biophys J. 2005 Sep;89(3):1893-901. Epub 2005 Jun 24.
41. Snutch TP, etal., Neuron 1991 Jul;7(1):45-57.
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45. Tippens AL, etal., J Comp Neurol. 2008 Feb 1;506(4):569-83.
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Additional References at PubMed
PMID:1311102   PMID:1385406   PMID:1692134   PMID:7485440   PMID:7598723   PMID:7635187   PMID:7814415   PMID:8392192   PMID:8396138   PMID:9882694   PMID:11206130   PMID:12130699  
PMID:12190108   PMID:12359330   PMID:12711087   PMID:12881419   PMID:14140941   PMID:14561827   PMID:14609949   PMID:14665691   PMID:15044319   PMID:15087548   PMID:15090038   PMID:15132976  
PMID:15454078   PMID:15504730   PMID:15728831   PMID:15750602   PMID:15755491   PMID:15786728   PMID:16251435   PMID:16267232   PMID:16319140   PMID:16530828   PMID:16636102   PMID:16636499  
PMID:16648270   PMID:16809371   PMID:16906520   PMID:16979758   PMID:16980347   PMID:17110593   PMID:17224476   PMID:17626895   PMID:17636479   PMID:17640527   PMID:17699517   PMID:17893194  
PMID:17916557   PMID:18045623   PMID:18070605   PMID:18296710   PMID:18369156   PMID:18499609   PMID:18562674   PMID:18566917   PMID:18596041   PMID:18718913   PMID:18765948   PMID:18848828  
PMID:19383796   PMID:19502562   PMID:19506339   PMID:19520861   PMID:19665524   PMID:20110531   PMID:20137275   PMID:20226536   PMID:20616314   PMID:20639649   PMID:20929812   PMID:20929813  
PMID:21156134   PMID:21178109   PMID:21186355   PMID:21408608   PMID:21486818   PMID:21619826   PMID:21670503   PMID:21674494   PMID:21745450   PMID:21804529   PMID:21998324   PMID:22329900  
PMID:22355118   PMID:22385640   PMID:22473424   PMID:22871113   PMID:23103495   PMID:23337371   PMID:23537331   PMID:23576750   PMID:23807706   PMID:23926129   PMID:23943510   PMID:24033980  
PMID:24086669   PMID:24278424   PMID:24352630   PMID:24506535   PMID:24535566   PMID:24728418   PMID:24775099   PMID:25209265   PMID:25556199   PMID:25614710   PMID:25648081   PMID:25841350  
PMID:25888683   PMID:26253506   PMID:26471941   PMID:26507659   PMID:27076616   PMID:27140189   PMID:27368804   PMID:27905406   PMID:28514967   PMID:28566490   PMID:29330129   PMID:29436604  
PMID:30304534   PMID:31628460   PMID:31717392   PMID:31770099   PMID:31862418   PMID:32047116  


Genomics

Candidate Gene Status
Cacna1c is a candidate Gene for QTL Coreg2
Comparative Map Data
Cacna1c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24151,764,138 - 152,379,454 (-)NCBI
Rnor_6.0 Ensembl4150,641,066 - 150,829,913 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04150,635,808 - 151,270,790 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04216,562,477 - 217,184,927 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44154,895,691 - 155,517,389 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14155,140,531 - 155,762,230 (-)NCBI
Celera4140,633,057 - 141,244,304 (-)NCBICelera
Cytogenetic Map4q42NCBI
CACNA1C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl121,970,786 - 2,697,950 (+)EnsemblGRCh38hg38GRCh38
GRCh38121,969,552 - 2,697,950 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37122,162,153 - 2,807,116 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36122,032,725 - 2,677,376 (+)NCBINCBI36hg18NCBI36
Build 34122,032,724 - 2,672,368NCBI
Celera123,770,102 - 4,421,688 (+)NCBI
Cytogenetic Map12p13.33NCBI
HuRef122,016,425 - 2,664,566 (+)NCBIHuRef
CHM1_1122,161,408 - 2,806,152 (+)NCBICHM1_1
Cacna1c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396118,564,201 - 119,174,345 (-)NCBIGRCm39mm39
GRCm39 Ensembl6118,564,201 - 119,173,851 (-)Ensembl
GRCm386118,587,240 - 119,197,384 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6118,587,240 - 119,196,890 (-)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl6118,587,240 - 119,196,418 (-)EnsemblGRCm38mm10GRCm38
MGSCv376118,542,314 - 119,146,427 (-)NCBIGRCm37mm9NCBIm37
MGSCv366118,558,083 - 119,074,173 (-)NCBImm8
MGSCv366119,385,868 - 119,901,054 (-)NCBImm8
Celera6120,420,625 - 121,028,854 (-)NCBICelera
Cytogenetic Map6F1NCBI
cM Map655.86NCBI
Cacna1c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554544,490,923 - 5,198,506 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554544,573,647 - 5,199,046 (+)NCBIChiLan1.0ChiLan1.0
CACNA1C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1122,031,317 - 2,745,113 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl122,114,140 - 2,744,826 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0122,166,672 - 2,817,827 (+)NCBIMhudiblu_PPA_v0panPan3
CACNA1C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12744,007,363 - 44,748,251 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2744,008,020 - 44,746,429 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha271,930,129 - 2,677,673 (-)NCBI
ROS_Cfam_1.02744,377,759 - 45,118,301 (+)NCBI
UMICH_Zoey_3.12744,305,678 - 45,048,124 (+)NCBI
UNSW_CanFamBas_1.02744,278,568 - 45,019,930 (+)NCBI
UU_Cfam_GSD_1.0271,287,600 - 2,035,369 (-)NCBI
Cacna1c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945106,316,518 - 106,936,642 (-)NCBI
SpeTri2.0NW_0049366062,168,104 - 2,867,560 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CACNA1C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1569,016,954 - 69,448,428 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2571,339,366 - 71,731,255 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CACNA1C
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1112,107,722 - 2,753,970 (+)NCBI
ChlSab1.1 Ensembl112,508,705 - 2,752,991 (+)Ensembl
Cacna1c
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473510,201,030 - 10,927,349 (-)NCBI

Position Markers
D4Arb4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24151,805,502 - 151,805,662 (+)MAPPER
Rnor_6.04150,682,435 - 150,682,594NCBIRnor6.0
Rnor_5.04216,606,296 - 216,606,455UniSTSRnor5.0
RGSC_v3.44154,937,067 - 154,937,227RGDRGSC3.4
RGSC_v3.44154,937,068 - 154,937,227UniSTSRGSC3.4
RGSC_v3.14155,181,908 - 155,182,068RGD
Celera4140,674,416 - 140,674,575UniSTS
Cytogenetic Map4q42UniSTS
D4Mgh30  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24151,805,495 - 151,805,620 (+)MAPPER
Rnor_6.04150,682,428 - 150,682,552NCBIRnor6.0
Rnor_5.04216,606,289 - 216,606,413UniSTSRnor5.0
RGSC_v3.44154,937,060 - 154,937,185RGDRGSC3.4
RGSC_v3.44154,937,061 - 154,937,185UniSTSRGSC3.4
RGSC_v3.14155,181,901 - 155,182,026RGD
Celera4140,674,409 - 140,674,533UniSTS
RH 3.4 Map4971.0UniSTS
RH 3.4 Map4971.0RGD
RH 2.0 Map4962.7RGD
Cytogenetic Map4q42UniSTS
D4Rat137  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.04151,102,607 - 151,102,848NCBIRnor6.0
Rnor_5.04217,018,694 - 217,018,935UniSTSRnor5.0
RGSC_v3.44155,346,854 - 155,347,095UniSTSRGSC3.4
RGSC_v3.44155,346,853 - 155,347,095RGDRGSC3.4
RGSC_v3.14155,591,694 - 155,591,936RGD
Celera4141,077,421 - 141,077,662UniSTS
RH 3.4 Map4982.1RGD
RH 3.4 Map4982.1UniSTS
RH 2.0 Map4975.2RGD
SHRSP x BN Map475.9099RGD
Cytogenetic Map4q42UniSTS
D4Got269  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24152,006,437 - 152,006,685 (+)MAPPER
Rnor_6.04150,885,590 - 150,885,837NCBIRnor6.0
Rnor_5.04216,806,463 - 216,806,710UniSTSRnor5.0
RGSC_v3.44155,138,808 - 155,139,055UniSTSRGSC3.4
Celera4140,874,330 - 140,874,573UniSTS
Cytogenetic Map4q42UniSTS
BF387868  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24151,917,968 - 151,918,181 (+)MAPPER
Rnor_6.04150,796,460 - 150,796,672NCBIRnor6.0
Rnor_5.04216,717,763 - 216,717,975UniSTSRnor5.0
RGSC_v3.44155,050,033 - 155,050,245UniSTSRGSC3.4
Celera4140,786,880 - 140,787,092UniSTS
RH 3.4 Map4972.3UniSTS
Cytogenetic Map4q42UniSTS
RH144194  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24152,136,086 - 152,136,242 (+)MAPPER
Rnor_6.04151,017,204 - 151,017,359NCBIRnor6.0
Rnor_5.04216,935,551 - 216,935,706UniSTSRnor5.0
RGSC_v3.44155,269,083 - 155,269,238UniSTSRGSC3.4
Celera4141,003,665 - 141,003,820UniSTS
RH 3.4 Map4975.1UniSTS
Cytogenetic Map4q42UniSTS
RH144587  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24152,380,229 - 152,380,383 (+)MAPPER
Rnor_6.04151,269,935 - 151,270,088NCBIRnor6.0
Rnor_5.04217,185,703 - 217,185,856UniSTSRnor5.0
RGSC_v3.44155,518,165 - 155,518,318UniSTSRGSC3.4
Celera4141,245,080 - 141,245,233UniSTS
RH 3.4 Map4973.9UniSTS
Cytogenetic Map4q42UniSTS
RH138902  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24152,174,992 - 152,175,163 (+)MAPPER
Rnor_6.04151,056,101 - 151,056,271NCBIRnor6.0
Rnor_5.04216,974,448 - 216,974,618UniSTSRnor5.0
RGSC_v3.44155,308,706 - 155,308,876UniSTSRGSC3.4
Celera4141,042,560 - 141,042,730UniSTS
RH 3.4 Map4984.5UniSTS
Cytogenetic Map4q42UniSTS
BE119369  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24152,046,482 - 152,046,687 (+)MAPPER
Rnor_6.04150,925,629 - 150,925,833NCBIRnor6.0
Rnor_5.04216,846,502 - 216,846,706UniSTSRnor5.0
RGSC_v3.44155,178,850 - 155,179,054UniSTSRGSC3.4
Celera4140,914,365 - 140,914,569UniSTS
RH 3.4 Map4986.5UniSTS
Cytogenetic Map4q42UniSTS
UniSTS:259196  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24151,842,824 - 151,843,363 (+)MAPPER
Rnor_6.04150,719,769 - 150,720,307NCBIRnor6.0
Rnor_5.04216,643,630 - 216,644,168UniSTSRnor5.0
RGSC_v3.44154,974,388 - 154,974,926UniSTSRGSC3.4
Celera4140,711,716 - 140,712,254UniSTS
Cytogenetic Map4q42UniSTS
UniSTS:495979  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24151,918,691 - 151,918,782 (+)MAPPER
Rnor_6.04150,797,183 - 150,797,273NCBIRnor6.0
Rnor_5.04216,718,486 - 216,718,576UniSTSRnor5.0
RGSC_v3.44155,050,756 - 155,050,846UniSTSRGSC3.4
Celera4140,787,603 - 140,787,693UniSTS
Cytogenetic Map4q42UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)47850904182171018Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)423850384169318094Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)443414605155469929Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)458640017154427984Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)458640017154427984Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)458640017154427984Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)463537179157286626Rat
70177Xhs1X-ray hypersensitivity QTL 125.1intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)481959983152055009Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)484475257178931073Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)486438317168047091Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)494893247168046938Rat
61406Scwia1Streptococcal cell wall induced arthritis QTL 12.3joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)4105682594150682594Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4105971071168047091Rat
731165Uae21Urinary albumin excretion QTL 212.40.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)4106347236151347236Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4108876717169215811Rat
1549832Bss3Bone structure and strength QTL 311femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)4109636356154636356Rat
7207480Bss105Bone structure and strength QTL 1058.1femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)4109636356154636356Rat
6478760Anxrr45Anxiety related response QTL 450.06717locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110702761155702761Rat
6478763Anxrr46Anxiety related response QTL 460.07428locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110702761155702761Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4112807675157807675Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4116726724157291438Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4117926139162926139Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4123111827168111827Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123478354168478354Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4123587009168587009Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4124442168169442168Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4125884464168047091Rat
1358364Sradr4Stress Responsive Adrenal Weight QTL 44.92adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)4128602727173602727Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131532269168047091Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131532269168047091Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4131834282176834282Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4131864442176864442Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132455408168047091Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (VE) (CMO:0000132)4134917642179917642Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4136351734174694858Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4136351734174694858Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4136351734180689124Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4136908430182878540Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4137171018182171018Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4145373934176509907Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4145547014184226339Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4145547014184226339Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4145547014184226339Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4145547014184226339Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4145547014184226339Rat
12798525Anxrr57Anxiety related response QTL 573.210.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4146086918168047091Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4146497452184226339Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4146942075168998263Rat
61446Coreg2Compensatory renal growth QTL 23.5kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)4147274055157294090Rat


Genetic Models
This gene Cacna1c is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:306
Count of miRNA genes:90
Interacting mature miRNAs:95
Transcripts:ENSRNOT00000009268, ENSRNOT00000041571, ENSRNOT00000051846, ENSRNOT00000052017
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 43 8 58 6 10
Low 3 16 8 18 8 8 9 16 34 35 1 8
Below cutoff 31 31 1 31 2 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_012517 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237159 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237175 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763216 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592434 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF394938 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF394939 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF394940 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH002191 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY323810 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY594691 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY974797 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ538522 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000149 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M59786 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M67515 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M67516 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  S80558 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U31815 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000041571   ⟹   ENSRNOP00000051397
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4150,642,427 - 150,829,913 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000051846   ⟹   ENSRNOP00000048580
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4150,641,066 - 150,829,741 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000052017   ⟹   ENSRNOP00000048790
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4150,642,534 - 150,829,741 (-)Ensembl
RefSeq Acc Id: NM_012517   ⟹   NP_036649
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24151,764,138 - 152,379,454 (-)NCBI
Rnor_6.04150,641,066 - 151,269,159 (-)NCBI
Rnor_5.04216,562,477 - 217,184,927 (-)NCBI
RGSC_v3.44154,895,691 - 155,517,389 (-)RGD
Celera4140,633,057 - 141,244,304 (-)RGD
Sequence:
RefSeq Acc Id: XM_006237159   ⟹   XP_006237221
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04150,635,808 - 151,270,790 (-)NCBI
Rnor_5.04216,562,477 - 217,184,927 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237175   ⟹   XP_006237237
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04150,635,808 - 151,176,709 (-)NCBI
Rnor_5.04216,562,477 - 217,184,927 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763216   ⟹   XP_008761438
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04150,635,808 - 151,148,698 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592434   ⟹   XP_017447923
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04150,635,808 - 151,176,709 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036649   ⟸   NM_012517
- UniProtKB: P22002 (UniProtKB/Swiss-Prot),   A0SLC4 (UniProtKB/TrEMBL),   Q71QJ6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237221   ⟸   XM_006237159
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006237237   ⟸   XM_006237175
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008761438   ⟸   XM_008763216
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017447923   ⟸   XM_017592434
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000048580   ⟸   ENSRNOT00000051846
RefSeq Acc Id: ENSRNOP00000051397   ⟸   ENSRNOT00000041571
RefSeq Acc Id: ENSRNOP00000048790   ⟸   ENSRNOT00000052017
Protein Domains
Ca_chan_IQ

Transcriptome

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


Strain Variation

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


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 150757945 150757946 G A snv M520/N (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 154901875 154901876 C T snv LE/Stm (KNAW), LE/Stm (ICL)
4 155012561 155012562 G T snv LE/Stm (KNAW)
4 155012564 155012565 G A snv M520/N (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2245 AgrOrtholog
BIND 128229
  130593
Ensembl Genes ENSRNOG00000007090 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000048580 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000048790 UniProtKB/TrEMBL
  ENSRNOP00000051397 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041571 UniProtKB/TrEMBL
  ENSRNOT00000051846 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000052017 UniProtKB/TrEMBL
Gene3D-CATH 1.20.120.350 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CAC1F_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPHH_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ion_trans_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VDCC_a1su_IQ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VDCC_L_a1csu UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VDCC_L_a1su UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VDCCAlpha1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Volt_channel_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24239 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 24239 ENTREZGENE
Pfam Ca_chan_IQ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CAC1F_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPHH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ion_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB CACNA1C RGD
PhenoGen Cacna1c PhenoGen
PRINTS CACHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LVDCCALPHA1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LVDCCALPHA1C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Ca_chan_IQ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2QC25_RAT UniProtKB/TrEMBL
  A0PJ39_RAT UniProtKB/TrEMBL
  A0SLC4 ENTREZGENE, UniProtKB/TrEMBL
  CAC1C_RAT UniProtKB/Swiss-Prot
  E9PT56_RAT UniProtKB/TrEMBL
  F1MA84_RAT UniProtKB/TrEMBL
  P22002 ENTREZGENE
  Q71QJ6 ENTREZGENE, UniProtKB/TrEMBL
  Q8VHT2_RAT UniProtKB/TrEMBL
  Q8VHT3_RAT UniProtKB/TrEMBL
UniProt Secondary F1LMN0 UniProtKB/TrEMBL
  F1M5G9 UniProtKB/TrEMBL
  P27733 UniProtKB/Swiss-Prot
  P27734 UniProtKB/Swiss-Prot
  Q62816 UniProtKB/Swiss-Prot
  Q63271 UniProtKB/Swiss-Prot
  Q64178 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Cacna1c  calcium voltage-gated channel subunit alpha1 C  Cacna1c  calcium channel, voltage-dependent, L type, alpha 1C subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Cacna1c  calcium channel, voltage-dependent, L type, alpha 1C subunit    calcium channel, voltage-dependent, alpha 1C subunit  Name updated 1299863 APPROVED
2002-11-06 Cacna1c  calcium channel, voltage-dependent, alpha 1C subunit    Ca channel, voltage-dependent, L type, alpha 1c subunit  Name updated 625702 APPROVED
2002-06-10 Cacna1c  Ca channel, voltage-dependent, L type, alpha 1c subunit      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in kidney proximal tubule epithelial cells 61074
gene_expression expressed in osteoblasts 634679
gene_function subunit of an L-type Ca2+ channel 625474
gene_process may mediate compensatory renal growth 61074
gene_process may be involved in the transduction of extracellular signals regulating bone metabolism 634679
gene_transcript promoter region contains putative response elements for MEF-2, Nkx2.5, NFAT and CRE binding protein 1 625537
gene_transcript 8.6 kb mRNA 634679