Cacna1a (calcium voltage-gated channel subunit alpha1 A) - Rat Genome Database

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Gene: Cacna1a (calcium voltage-gated channel subunit alpha1 A) Rattus norvegicus
Analyze
Symbol: Cacna1a
Name: calcium voltage-gated channel subunit alpha1 A
RGD ID: 2244
Description: Enables calmodulin binding activity and high voltage-gated calcium channel activity. Involved in several processes, including calcium ion import; regulation of voltage-gated calcium channel activity; and sensory perception of pain. Located in perikaryon and plasma membrane. Part of voltage-gated calcium channel complex. Is integral component of presynaptic active zone membrane. Used to study childhood absence epilepsy. Biomarker of temporal lobe epilepsy. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 42; hereditary ataxia (multiple); and migraine (multiple). Orthologous to human CACNA1A (calcium voltage-gated channel subunit alpha1 A); PARTICIPATES IN alfentanil pharmacodynamics pathway; bupivacaine pharmacodynamics pathway; buprenorphine pharmacodynamics pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: BccA1; BI; brain calcium channel 1; brain calcium channel I; brain class A; Calcium channel alpha 1A; calcium channel, L type, alpha-1 polypeptide; calcium channel, L type, alpha-1 polypeptide, isoform 4; calcium channel, voltage-dependent, alpha 1A subunit; calcium channel, voltage-dependent, P/Q type, alpha 1A subunit; Cav2.1; LOC688360; rbA-1; RBA-I; similar to Voltage-dependent P/Q-type calcium channel alpha-1A subunit (Voltage-gated calcium channel alpha subunit Cav2.1) (Calcium channel, L type, alpha-1 polypeptide isoform 4) (Brain calcium channel I) (BI); voltage-dependent P/Q-type calcium channel subunit alpha-1A; voltage-gated calcium channel subunit alpha Cav2.1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Cacna1agry  
Genetic Models: GRY/Idr
Is Marker For: Strains:   WTC.GRY-Cacna1agry/Kyo   F344-Cacna1agryScn1am1Kyo/Okym  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21923,520,741 - 23,819,971 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1923,520,741 - 23,823,225 (-)Ensembl
Rnor_6.01925,453,236 - 25,749,550 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1925,526,751 - 25,749,550 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01936,502,533 - 36,727,039 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41925,188,170 - 25,424,495 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11925,194,294 - 25,429,321 (-)NCBI
Celera1923,074,249 - 23,295,970 (-)NCBICelera
Cytogenetic Map19q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (ISO)
1,2-dimethylhydrazine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
4-hydroxynon-2-enal  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
allethrin  (EXP)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsenous acid  (ISO)
aspartame  (ISO)
barium(0)  (EXP)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
Butylparaben  (EXP)
calcium atom  (EXP)
calcium(0)  (EXP)
cannabidiol  (EXP)
carbamazepine  (ISO)
choline  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
clozapine  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
DDE  (EXP)
DDT  (EXP)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP,ISO)
dichlorine  (EXP)
dorsomorphin  (ISO)
entinostat  (ISO)
enzacamene  (EXP)
epoxiconazole  (EXP)
ethanol  (ISO)
fenvalerate  (EXP)
folic acid  (ISO)
gabapentin  (EXP,ISO)
gamma-aminobutyric acid  (EXP)
haloperidol  (EXP,ISO)
L-methionine  (ISO)
linuron  (EXP)
methotrexate  (ISO)
methoxychlor  (EXP)
monosodium L-glutamate  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-ethyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (EXP)
nitric oxide  (EXP)
Nor-9-carboxy-delta9-THC  (ISO)
ozone  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
permethrin  (EXP)
phenethyl caffeate  (EXP)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium chloride  (EXP,ISO)
prochloraz  (EXP)
procymidone  (EXP)
rotenone  (ISO)
SB 431542  (ISO)
silver atom  (EXP)
silver(0)  (EXP)
sodium arsenite  (EXP)
succimer  (ISO)
temozolomide  (ISO)
testosterone  (ISO)
Testosterone propionate  (ISO)
tetrachloromethane  (EXP)
thapsigargin  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
triptonide  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adult walking behavior  (ISO)
behavioral response to pain  (ISO)
calcium ion import  (IBA,IDA,IMP)
calcium ion transmembrane transport  (IEA,ISO)
calcium ion transport  (IBA,IDA,IMP,ISO)
calcium ion-regulated exocytosis of neurotransmitter  (ISO)
calcium-ion regulated exocytosis  (ISO)
cell death  (ISO)
cellular chloride ion homeostasis  (ISO)
cellular response to amyloid-beta  (ISO)
central nervous system neuron differentiation  (ISO)
cerebellar molecular layer development  (ISO)
cerebellar Purkinje cell differentiation  (ISO)
cerebellar Purkinje cell layer development  (ISO)
cerebellum maturation  (ISO)
chemical synaptic transmission  (IBA,IMP,ISO)
dendrite morphogenesis  (ISO)
gamma-aminobutyric acid secretion  (ISO)
gamma-aminobutyric acid signaling pathway  (ISO)
glucose homeostasis  (ISO)
membrane depolarization  (ISO)
modulation of chemical synaptic transmission  (ISO)
musculoskeletal movement, spinal reflex action  (ISO)
negative regulation of hormone biosynthetic process  (ISO)
negative regulation of neuron apoptotic process  (ISO)
nervous system process  (ISO)
neuromuscular process  (ISO)
neuromuscular process controlling balance  (ISO)
neuromuscular synaptic transmission  (ISO)
neuron-neuron synaptic transmission  (ISO)
positive regulation of cytosolic calcium ion concentration  (ISO,ISS)
receptor clustering  (ISO)
regulation of acetylcholine secretion, neurotransmission  (ISO)
regulation of axonogenesis  (ISO)
regulation of calcium ion-dependent exocytosis  (ISO)
regulation of hormone levels  (ISO)
regulation of ion transmembrane transport  (IEA)
regulation of membrane potential  (ISO)
regulation of neurotransmitter levels  (ISO)
regulation of presynaptic cytosolic calcium ion concentration  (IEA)
regulation of sulfur amino acid metabolic process  (ISO)
regulation of voltage-gated calcium channel activity  (IMP)
response to amyloid-beta  (ISO)
response to pain  (ISO)
rhythmic synaptic transmission  (ISO)
sensory perception of pain  (IMP)
spinal cord motor neuron differentiation  (ISO)
synapse assembly  (ISO)
synaptic transmission, GABAergic  (ISO)
synaptic transmission, glutamatergic  (ISO)
transmission of nerve impulse  (ISO)
vestibular nucleus development  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
alfentanil pharmacodynamics pathway  (ISO)
bupivacaine pharmacodynamics pathway  (ISO)
buprenorphine pharmacodynamics pathway  (ISO)
calcium transport pathway  (ISO)
calcium/calcium-mediated signaling pathway  (IEA,ISO)
chloroprocaine pharmacodynamics pathway  (ISO)
citalopram pharmacodynamics pathway  (ISO)
cocaine pharmacodynamics pathway  (ISO)
codeine and morphine pharmacodynamics pathway  (ISO)
desipramine pharmacodynamics pathway  (ISO)
diphenoxylate pharmacodynamics pathway  (ISO)
escitalopram pharmacodynamics pathway  (ISO)
ethylmorphine pharmacodynamics pathway  (ISO)
fentanyl pharmacodynamics pathway  (ISO)
fluoxetine pharmacodynamics pathway  (ISO)
gliclazide pharmacodynamics pathway  (ISO)
glutamate signaling pathway  (IEA)
glyburide pharmacodynamics pathway  (ISO)
heroin pharmacodynamics pathway  (ISO)
hydrocodone pharmacodynamics pathway  (ISO)
hydromorphone pharmacodynamics pathway  (ISO)
imipramine pharmacodynamics pathway  (ISO)
insulin secretion pathway  (TAS)
levacetylmethadol pharmacodynamics pathway  (ISO)
levobupivacaine phgarmacodynamics pathway  (ISO)
levorphanol pharmacodynamics pathway  (ISO)
lidocaine pharmacodynamics pathway  (ISO)
long term depression  (IEA)
mepivacaine pharmacodynamics pathway  (ISO)
methadone pharmacodynamics pathway  (ISO)
mitogen activated protein kinase signaling pathway  (IEA)
nalbuphine pharmacodynamics pathway  (ISO)
naloxone pharmacodynamics pathway  (ISO)
naltrexone pharmacodynamics pathway  (ISO)
nicotine pharmacodynamics pathway  (ISO)
oxybuprocaine pharmacodynamics pathway  (ISO)
oxycodone pharmacodynamics pathway  (ISO)
oxymorphone pharmacodynamics pathway  (ISO)
pentazocine pharmacodynamics pathway  (ISO)
potassium channel inhibitors pharmacodynamics pathway  (ISO)
prilocaine pharmacodynamics pathway  (ISO)
procaine pharmacodynamics pathway  (ISO)
remifentanil pharmacodynamics pathway  (ISO)
ropivacaine pharmacodynamics pathway  (ISO)
tramadol pharmacodynamics pathway  (ISO)
type 2 diabetes mellitus pathway  (IEA)

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. Berkefeld H, etal., Science. 2006 Oct 27;314(5799):615-20.
2. Carrera P, etal., Neurology. 1999 Jul 13;53(1):26-33.
3. Catterall WA Cold Spring Harb Perspect Biol. 2011 Aug 1;3(8):a003947. doi: 10.1101/cshperspect.a003947.
4. Cens T, etal., Pflugers Arch. 2011 Aug;462(2):303-14. doi: 10.1007/s00424-011-0974-x. Epub 2011 May 25.
5. Charvin N, etal., EMBO J. 1997 Aug 1;16(15):4591-6.
6. Chioza B, etal., Neurology 2001 May 8;56(9):1245-6.
7. Condliffe SB, etal., J Biol Chem. 2013 Nov 22;288(47):33873-83. doi: 10.1074/jbc.M113.497701. Epub 2013 Oct 9.
8. Doyle J, etal., Mamm Genome. 1997 Feb;8(2):113-20.
9. Ferron L, etal., Nat Commun. 2014 Apr 7;5:3628. doi: 10.1038/ncomms4628.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. Holderith N, etal., Nat Neurosci. 2012 Jun 10;15(7):988-97. doi: 10.1038/nn.3137.
12. Ishikawa K, etal., Hum Mol Genet. 1999 Jul;8(7):1185-93.
13. Jiang X, etal., Proc Natl Acad Sci U S A. 2008 Jan 8;105(1):341-6. Epub 2007 Dec 27.
14. Kaeser PS, etal., Cell. 2011 Jan 21;144(2):282-95. doi: 10.1016/j.cell.2010.12.029.
15. Kato T, etal., Clin Genet 2000 Jul;58(1):69-73.
16. Kaunisto MA, etal., Neurogenetics 2004 Feb;5(1):69-73. Epub 2003 Oct 7.
17. Lautermilch NJ, etal., J Neurosci. 2005 Jul 27;25(30):7062-70.
18. Lee A, etal., Nat Neurosci 2002 Mar;5(3):210-7.
19. Lee A, etal., Proc Natl Acad Sci U S A 2003 Dec 23;100(26):16059-64. Epub 2003 Dec 12.
20. Ligon B, etal., J Biol Chem 1998 May 29;273(22):13905-11.
21. MGD data from the GO Consortium
22. N'Gouemo P and Morad M, Neuroscience 2003;120(3):815-26.
23. NCBI rat LocusLink and RefSeq merged data July 26, 2002
24. OMIM Disease Annotation Pipeline
25. Pipeline to import KEGG annotations from KEGG into RGD
26. Pipeline to import SMPDB annotations from SMPDB into RGD
27. Restituito S, etal., J Neurosci. 2000 Sep 1;20(17):6394-403.
28. RGD automated data pipeline
29. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
30. RGD automated import pipeline for gene-chemical interactions
31. Scheuber A, etal., J Neurosci. 2004 Nov 17;24(46):10402-9.
32. Starr TV, etal., Proc Natl Acad Sci U S A 1991 Jul 1;88(13):5621-5.
33. Su X, etal., J Urol. 2008 Jun;179(6):2464-9. doi: 10.1016/j.juro.2008.01.088. Epub 2008 Apr 23.
34. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
35. Tokuda S, etal., Brain Res. 2006 Dec 28;.
36. Vigues S, etal., Neurobiol Dis. 1999 Aug;6(4):288-301.
37. Witkovsky P, etal., J Comp Neurol. 2006 Jul 20;497(3):384-96.
38. Yang SN and Berggren PO, Endocr Rev. 2006 Oct;27(6):621-76. Epub 2006 Jul 25.
39. Yu AS, etal., Proc Natl Acad Sci U S A 1992 Nov 1;89(21):10494-8.
40. Zhou H, etal., J Biol Chem. 2005 Aug 19;280(33):29612-9. Epub 2005 Jun 26.
41. Zhuchenko O, etal., Nat Genet. 1997 Jan;15(1):62-9.
Additional References at PubMed
PMID:572084   PMID:1306163   PMID:1355109   PMID:1469420   PMID:1485534   PMID:1486501   PMID:1572065   PMID:1686215   PMID:1692134   PMID:4799944   PMID:4941467   PMID:6167317  
PMID:6462226   PMID:6945603   PMID:7697385   PMID:7834360   PMID:8100981   PMID:8158221   PMID:8229069   PMID:8565963   PMID:8632762   PMID:8692999   PMID:8719615   PMID:8719807  
PMID:8929530   PMID:8957685   PMID:9614225   PMID:9742139   PMID:9857013   PMID:9882694   PMID:10322048   PMID:10328888   PMID:10336181   PMID:10611370   PMID:10630211   PMID:10670432  
PMID:10686170   PMID:10753886   PMID:10899223   PMID:10908603   PMID:11160387   PMID:11182254   PMID:11344116   PMID:11718712   PMID:11756409   PMID:12040045   PMID:12065603   PMID:12151514  
PMID:12401561   PMID:12451115   PMID:12624181   PMID:12827191   PMID:13950100   PMID:14973254   PMID:15090043   PMID:15451373   PMID:15548652   PMID:15577901   PMID:15728831   PMID:15750602  
PMID:15768038   PMID:15953418   PMID:16049184   PMID:16278278   PMID:16373336   PMID:16474392   PMID:16540584   PMID:16595610   PMID:16820014   PMID:16890369   PMID:17156092   PMID:17893194  
PMID:18216187   PMID:18390553   PMID:18536931   PMID:19883739   PMID:20511524   PMID:21389298   PMID:21883149   PMID:22504905   PMID:22589533   PMID:22869375   PMID:23376566   PMID:24205277  
PMID:24344901   PMID:24453334   PMID:24836863   PMID:25483588   PMID:25741235   PMID:26283199   PMID:26507659   PMID:26716990   PMID:27260834   PMID:28167673   PMID:29277284   PMID:30756238  
PMID:30922876   PMID:31104951   PMID:32318899   PMID:32630015   PMID:32803504   PMID:33045260  


Genomics

Comparative Map Data
Cacna1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21923,520,741 - 23,819,971 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1923,520,741 - 23,823,225 (-)Ensembl
Rnor_6.01925,453,236 - 25,749,550 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1925,526,751 - 25,749,550 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01936,502,533 - 36,727,039 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41925,188,170 - 25,424,495 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11925,194,294 - 25,429,321 (-)NCBI
Celera1923,074,249 - 23,295,970 (-)NCBICelera
Cytogenetic Map19q11NCBI
CACNA1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1913,206,442 - 13,633,025 (-)EnsemblGRCh38hg38GRCh38
GRCh381913,206,442 - 13,506,479 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371913,317,256 - 13,617,293 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361913,178,256 - 13,478,274 (-)NCBINCBI36hg18NCBI36
Build 341913,179,114 - 13,478,317NCBI
Celera1913,207,639 - 13,507,772 (-)NCBI
Cytogenetic Map19p13.13NCBI
HuRef1912,889,634 - 13,189,171 (-)NCBIHuRef
CHM1_11913,318,256 - 13,618,198 (-)NCBICHM1_1
Cacna1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39885,065,257 - 85,366,880 (+)NCBIGRCm39mm39
GRCm39 Ensembl885,065,268 - 85,366,875 (+)Ensembl
GRCm38884,338,631 - 84,640,251 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl884,338,639 - 84,640,246 (+)EnsemblGRCm38mm10GRCm38
MGSCv37886,939,263 - 87,164,148 (+)NCBIGRCm37mm9NCBIm37
MGSCv36887,305,469 - 87,530,351 (+)NCBImm8
Celera888,715,985 - 88,942,662 (+)NCBICelera
Cytogenetic Map8C2- C3NCBI
cM Map840.95NCBI
Cacna1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541532,183,442 - 32,400,595 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541532,182,536 - 32,457,511 (-)NCBIChiLan1.0ChiLan1.0
CACNA1A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11913,506,232 - 13,804,815 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1913,507,102 - 13,804,729 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01912,769,586 - 13,189,022 (-)NCBIMhudiblu_PPA_v0panPan3
CACNA1A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12048,747,087 - 49,036,627 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2048,821,025 - 49,036,032 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2048,694,916 - 48,910,172 (+)NCBI
ROS_Cfam_1.02049,339,396 - 49,554,755 (+)NCBI
ROS_Cfam_1.0 Ensembl2049,280,733 - 49,553,801 (+)Ensembl
UMICH_Zoey_3.12048,549,923 - 48,765,101 (+)NCBI
UNSW_CanFamBas_1.02048,976,279 - 49,191,383 (+)NCBI
UU_Cfam_GSD_1.02049,219,720 - 49,435,029 (+)NCBI
LOC101960999
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118208,078,478 - 208,143,320 (+)NCBI
SpeTri2.0NW_0049366592,201,606 - 2,269,625 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CACNA1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1265,491,784 - 65,871,068 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2265,921,411 - 66,176,189 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CACNA1A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1611,883,353 - 12,307,023 (-)NCBIChlSab1.1chlSab2
ChlSab1.1611,883,353 - 12,307,023 (-)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660747,403,914 - 7,900,327 (+)NCBIVero_WHO_p1.0
Cacna1a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624901707,322 - 932,658 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
Cacna1a  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21923,528,755 - 23,529,138 (-)MAPPERmRatBN7.2
Rnor_6.01925,741,154 - 25,741,536NCBIRnor6.0
Rnor_5.01936,718,569 - 36,718,951UniSTSRnor5.0
RGSC_v3.41925,194,835 - 25,195,218UniSTSRGSC3.4
Celera1923,082,377 - 23,082,759UniSTS
Cytogenetic Map19q11UniSTS
RH143033  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21923,746,224 - 23,746,369 (-)MAPPERmRatBN7.2
mRatBN7.21923,745,974 - 23,746,369 (-)MAPPERmRatBN7.2
Rnor_6.01925,525,749 - 25,525,893NCBIRnor6.0
Rnor_6.01925,525,749 - 25,526,172NCBIRnor6.0
Rnor_5.01936,501,531 - 36,501,954UniSTSRnor5.0
Rnor_5.01936,501,531 - 36,501,675UniSTSRnor5.0
RGSC_v3.41925,425,115 - 25,425,259UniSTSRGSC3.4
Celera1923,296,539 - 23,296,683UniSTS
Cytogenetic Map19q11UniSTS
RH137733  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21923,642,907 - 23,643,067 (-)MAPPERmRatBN7.2
Rnor_6.01925,629,237 - 25,629,396NCBIRnor6.0
Rnor_5.01936,604,642 - 36,604,801UniSTSRnor5.0
RGSC_v3.41925,318,888 - 25,319,047UniSTSRGSC3.4
Celera1923,193,847 - 23,194,006UniSTS
Cytogenetic Map19q11UniSTS
RH140588  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21923,557,895 - 23,558,114 (-)MAPPERmRatBN7.2
Rnor_6.01925,712,179 - 25,712,397NCBIRnor6.0
Rnor_5.01936,689,645 - 36,689,863UniSTSRnor5.0
RGSC_v3.41925,225,045 - 25,225,263UniSTSRGSC3.4
Celera1923,112,051 - 23,112,269UniSTS
Cytogenetic Map19q11UniSTS


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


Related Rat Strains
The following Strains have been annotated to Cacna1a


Genetic Models
This gene Cacna1a is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:109
Count of miRNA genes:93
Interacting mature miRNAs:100
Transcripts:ENSRNOT00000067921, ENSRNOT00000068563
Prediction methods: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 58
Low 3 43 19 4 18 4 8 11 16 35 40 11 8
Below cutoff 34 33 1 33 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_012918 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772347 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772348 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772349 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772351 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772352 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772354 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772356 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772358 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772359 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772360 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601177 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601178 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601179 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601180 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601182 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097478 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097479 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097480 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097481 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097482 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097483 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097484 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097485 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097486 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097487 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097488 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097489 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097490 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097491 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097492 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097493 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005496615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005496616 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005496617 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC120246 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF051526 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF051527 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AM040228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AM040229 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AM040230 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AM040231 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AM040232 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AM040233 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AM040234 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB582288 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473972 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000313 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M64373 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M99222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000083448   ⟹   ENSRNOP00000070304
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1923,520,741 - 23,745,646 (-)Ensembl
Rnor_6.0 Ensembl1925,526,751 - 25,749,550 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000102295   ⟹   ENSRNOP00000080121
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1923,520,741 - 23,823,225 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106526   ⟹   ENSRNOP00000096924
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1923,520,741 - 23,823,225 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000114797   ⟹   ENSRNOP00000078109
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1923,520,741 - 23,565,281 (-)Ensembl
RefSeq Acc Id: NM_012918   ⟹   NP_037050
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,520,741 - 23,745,646 (-)NCBI
Rnor_6.01925,526,751 - 25,749,550 (+)NCBI
Rnor_5.01936,502,533 - 36,727,039 (+)NCBI
RGSC_v3.41925,188,170 - 25,424,495 (-)RGD
Celera1923,074,249 - 23,295,970 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039097478   ⟹   XP_038953406
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,521,989 - 23,819,964 (-)NCBI
RefSeq Acc Id: XM_039097479   ⟹   XP_038953407
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,521,989 - 23,819,964 (-)NCBI
RefSeq Acc Id: XM_039097480   ⟹   XP_038953408
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,521,989 - 23,819,964 (-)NCBI
RefSeq Acc Id: XM_039097481   ⟹   XP_038953409
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,521,989 - 23,819,964 (-)NCBI
RefSeq Acc Id: XM_039097482   ⟹   XP_038953410
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,521,989 - 23,819,963 (-)NCBI
RefSeq Acc Id: XM_039097483   ⟹   XP_038953411
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,521,989 - 23,819,964 (-)NCBI
RefSeq Acc Id: XM_039097484   ⟹   XP_038953412
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,521,989 - 23,819,963 (-)NCBI
RefSeq Acc Id: XM_039097485   ⟹   XP_038953413
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,521,989 - 23,819,962 (-)NCBI
RefSeq Acc Id: XM_039097486   ⟹   XP_038953414
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,521,989 - 23,819,962 (-)NCBI
RefSeq Acc Id: XM_039097487   ⟹   XP_038953415
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,521,989 - 23,819,963 (-)NCBI
RefSeq Acc Id: XM_039097488   ⟹   XP_038953416
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,522,511 - 23,819,964 (-)NCBI
RefSeq Acc Id: XM_039097489   ⟹   XP_038953417
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,521,989 - 23,819,963 (-)NCBI
RefSeq Acc Id: XM_039097490   ⟹   XP_038953418
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,521,989 - 23,819,965 (-)NCBI
RefSeq Acc Id: XM_039097491   ⟹   XP_038953419
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,522,875 - 23,819,961 (-)NCBI
RefSeq Acc Id: XM_039097492   ⟹   XP_038953420
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,542,811 - 23,819,966 (-)NCBI
RefSeq Acc Id: XM_039097493   ⟹   XP_038953421
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,562,656 - 23,819,971 (-)NCBI
RefSeq Acc Id: XR_005496615
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,548,823 - 23,819,970 (-)NCBI
RefSeq Acc Id: XR_005496616
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,558,714 - 23,819,970 (-)NCBI
RefSeq Acc Id: XR_005496617
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,548,823 - 23,819,970 (-)NCBI
Protein Sequences
Protein RefSeqs NP_037050 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953406 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953407 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953408 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953409 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953410 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953411 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953412 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953413 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953414 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953415 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953416 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953417 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953418 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953419 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953420 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953421 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA40806 (Get FASTA)   NCBI Sequence Viewer  
  AAA40896 (Get FASTA)   NCBI Sequence Viewer  
  AAC24516 (Get FASTA)   NCBI Sequence Viewer  
  AAC24517 (Get FASTA)   NCBI Sequence Viewer  
  CAJ09863 (Get FASTA)   NCBI Sequence Viewer  
  CAJ09864 (Get FASTA)   NCBI Sequence Viewer  
  CAJ09865 (Get FASTA)   NCBI Sequence Viewer  
  CAJ09866 (Get FASTA)   NCBI Sequence Viewer  
  CAJ09867 (Get FASTA)   NCBI Sequence Viewer  
  CAJ09868 (Get FASTA)   NCBI Sequence Viewer  
  CAJ09869 (Get FASTA)   NCBI Sequence Viewer  
  EDL92217 (Get FASTA)   NCBI Sequence Viewer  
  EDL92218 (Get FASTA)   NCBI Sequence Viewer  
  EDL92219 (Get FASTA)   NCBI Sequence Viewer  
  EDL92220 (Get FASTA)   NCBI Sequence Viewer  
  EDL92221 (Get FASTA)   NCBI Sequence Viewer  
  EDL92222 (Get FASTA)   NCBI Sequence Viewer  
  EDL92223 (Get FASTA)   NCBI Sequence Viewer  
  P54282 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_037050   ⟸   NM_012918
- Sequence:
RefSeq Acc Id: ENSRNOP00000070304   ⟸   ENSRNOT00000083448
RefSeq Acc Id: XP_038953418   ⟸   XM_039097490
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038953411   ⟸   XM_039097483
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038953409   ⟸   XM_039097481
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038953408   ⟸   XM_039097480
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038953406   ⟸   XM_039097478
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038953407   ⟸   XM_039097479
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038953415   ⟸   XM_039097487
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038953412   ⟸   XM_039097484
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038953410   ⟸   XM_039097482
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038953417   ⟸   XM_039097489
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038953414   ⟸   XM_039097486
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038953413   ⟸   XM_039097485
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038953416   ⟸   XM_039097488
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038953419   ⟸   XM_039097491
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038953420   ⟸   XM_039097492
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038953421   ⟸   XM_039097493
- Peptide Label: isoform X16
RefSeq Acc Id: ENSRNOP00000096924   ⟸   ENSRNOT00000106526
RefSeq Acc Id: ENSRNOP00000080121   ⟸   ENSRNOT00000102295
RefSeq Acc Id: ENSRNOP00000078109   ⟸   ENSRNOT00000114797
Protein Domains
Ca_chan_IQ   Ion_trans

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 (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)
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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
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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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
F344/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
F344/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
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
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)
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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
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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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
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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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
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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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
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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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)
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
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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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)
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
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (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
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (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
Damaging Variants


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
19 25469933 25469934 G T snv FHL/EurMcwi (RGD), FHH/EurMcwi (2019), FHH/EurMcwi (RGD), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW)
19 25470111 25470112 G A snv WKY/N (MCW), F344/NRrrc (MCW)
19 25470150 25470151 C T snv Buf/N (MCW)
19 25632386 25632387 G T snv F344/NRrrc (MCW), WKY/N (MCW), M520/N (MCW)
19 25676963 25676964 G T snv BN/SsN (MCW)
19 25698634 25698635 G T snv BN/SsN (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2244 AgrOrtholog
Ensembl Genes ENSRNOG00000052707 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000070304 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000080121 ENTREZGENE
Ensembl Transcript ENSRNOT00000083448 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000102295 ENTREZGENE
Gene3D-CATH 1.20.120.350 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CACNA1A 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
  VDCCAlpha1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Volt_channel_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25398 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 25398 ENTREZGENE
Pfam Ca_chan_IQ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPHH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ion_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cacna1a PhenoGen
PRINTS CACHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PQVDCCALPHA1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Ca_chan_IQ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC228655
UniProt A0A0G2JXK1_RAT UniProtKB/TrEMBL
  CAC1A_RAT UniProtKB/Swiss-Prot
  O70368_RAT UniProtKB/TrEMBL
  P54282 ENTREZGENE
  Q2YS33_RAT UniProtKB/TrEMBL
  Q2YS34_RAT UniProtKB/TrEMBL
  Q2YS35_RAT UniProtKB/TrEMBL
  Q2YS36_RAT UniProtKB/TrEMBL
  Q2YS37_RAT UniProtKB/TrEMBL
  Q2YS38_RAT UniProtKB/TrEMBL
  Q2YS39_RAT UniProtKB/TrEMBL
UniProt Secondary Q01541 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Cacna1a  calcium voltage-gated channel subunit alpha1 A  Cacna1a  calcium channel, voltage-dependent, P/Q type, alpha 1A subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-03-29 Cacna1a  calcium channel, voltage-dependent, P/Q type, alpha 1A subunit  LOC688360  similar to Voltage-dependent P/Q-type calcium channel alpha-1A subunit (Voltage-gated calcium channel alpha subunit Cav2.1) (Calcium channel, L type, alpha-1 polypeptide isoform 4) (Brain calcium channel I) (BI)  Data Merged 737654 PROVISIONAL
2006-11-20 LOC688360  similar to Voltage-dependent P/Q-type calcium channel alpha-1A subunit (Voltage-gated calcium channel alpha subunit Cav2.1) (Calcium channel, L type, alpha-1 polypeptide isoform 4) (Brain calcium channel I) (BI)      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-09-10 Cacna1a  calcium channel, voltage-dependent, P/Q type, alpha 1A subunit    calcium channel, voltage-dependent, alpha 1A subunit  Name updated 1299863 APPROVED
2002-11-06 Cacna1a  calcium channel, voltage-dependent, alpha 1A subunit    Calcium channel alpha 1A  Name updated 625702 APPROVED
2002-06-10 Cacna1a  Calcium channel alpha 1A      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in central nervous system, heart and pituitary and not expressed in spleen, kidney or liver 1299846
gene_function a voltage-gated calcium channel 634678
gene_process involved in secretion coupling in beta cells 634678