Cacna1g (calcium voltage-gated channel subunit alpha1 G) - Rat Genome Database

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Gene: Cacna1g (calcium voltage-gated channel subunit alpha1 G) Rattus norvegicus
Analyze
Symbol: Cacna1g
Name: calcium voltage-gated channel subunit alpha1 G
RGD ID: 68942
Description: Exhibits low voltage-gated calcium channel activity. Involved in several processes, including artery smooth muscle contraction; calcium ion transport; and cellular response to dexamethasone stimulus. Localizes to several cellular components, including dendrite; neuronal cell body; and perinuclear region of cytoplasm. Human ortholog(s) of this gene implicated in cerebellar ataxia type 42. Orthologous to human CACNA1G (calcium voltage-gated channel subunit alpha1 G); PARTICIPATES IN acebutolol pharmacodynamics pathway; adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway; amiodarone pharmacodynamics pathway; INTERACTS WITH (S)-amphetamine; 17beta-estradiol; 3-isobutyl-1-methyl-7H-xanthine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: calcium channel, voltage-dependent, T type, alpha 1G subunit; voltage-dependent T-type calcium channel subunit alpha-1G; voltage-gated calcium channel subunit alpha Cav3.1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Cacna1gm1Mcwi  
Genetic Models: SS-Cacna1gm1Mcwi
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
Rnor_6.0 Ensembl1082,129,506 - 82,197,848 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01082,129,071 - 82,197,828 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01081,950,594 - 82,017,885 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41083,043,636 - 83,112,886 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11083,058,005 - 83,127,256 (-)NCBI
Celera1078,143,865 - 78,211,268 (-)NCBICelera
RH 3.4 Map10617.6RGD
Cytogenetic Map10q26NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-amphetamine  (EXP)
1,2-dichloroethane  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (EXP)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
acrylamide  (EXP)
actinomycin D  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
allethrin  (EXP)
ammonium chloride  (EXP)
androgen antagonist  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
barium(0)  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Butylparaben  (EXP)
C60 fullerene  (EXP)
cadmium dichloride  (ISO)
calcium atom  (EXP,ISO)
calcium(0)  (EXP,ISO)
cannabidiol  (EXP)
cerium  (ISO)
choline  (ISO)
cisplatin  (ISO)
colforsin daropate hydrochloride  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
daunorubicin  (ISO)
DDE  (EXP)
diazinon  (ISO)
dibutyl phthalate  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
enzacamene  (EXP)
epoxiconazole  (EXP)
erbium  (ISO)
ethanol  (ISO)
fluoxetine  (EXP)
folic acid  (ISO)
gadolinium atom  (ISO)
genistein  (ISO)
holmium atom  (ISO)
indole-3-methanol  (EXP)
L-methionine  (ISO)
lanthanum atom  (ISO)
linuron  (EXP)
menadione  (ISO)
methapyrilene  (ISO)
methylmercury chloride  (ISO)
Mibefradil  (EXP,ISO)
mitoxantrone  (ISO)
N-acetyl-L-cysteine  (EXP)
N-nitrosodiethylamine  (EXP)
neodymium atom  (ISO)
nickel atom  (EXP)
p-menthan-3-ol  (ISO)
paracetamol  (EXP)
pentanal  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
potassium dichromate  (ISO)
prochloraz  (EXP)
procymidone  (EXP)
progesterone  (EXP,ISO)
propanal  (ISO)
SB 203580  (EXP)
SB 431542  (ISO)
scandium atom  (ISO)
silicon dioxide  (ISO)
tamoxifen  (ISO)
telmisartan  (EXP)
titanium dioxide  (ISO)
toluene  (EXP)
trichostatin A  (ISO)
triphenyl phosphate  (ISO)
triptonide  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
ytterbium  (ISO)
yttrium atom  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
acebutolol pharmacodynamics pathway  (ISO)
adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway  (ISO)
amiodarone pharmacodynamics pathway  (ISO)
amlodipine pharmacodynamics pathway  (ISO)
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)
carvedilol pharmacodynamics pathway  (ISO)
diltiazem pharmacodynamics pathway  (ISO)
disopyramide pharmacodynamics pathway  (ISO)
dobutamine pharmacodynamics pathway  (ISO)
esmolol pharmacodynamics pathway  (ISO)
flecainde pharmacodynamics pathway  (ISO)
fosphenytoin pharmacodynamics pathway  (ISO)
ibutilide pharmacodynamics pathway  (ISO)
isoprenaline pharmacodynamics pathway  (ISO)
isradipine pharmacodynamics pathway  (ISO)
levobunolol pharmacodynamics pathway  (ISO)
lidocaine pharmacodynamics pathway  (ISO)
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)

References

References - curated
1. BenMohamed F, etal., Mol Cell Biochem. 2009 Jan;320(1-2):173-83. Epub 2008 Sep 27.
2. Catterall WA Cold Spring Harb Perspect Biol. 2011 Aug 1;3(8):a003947. doi: 10.1101/cshperspect.a003947.
3. Dogrul A, etal., Pain 2003 Sep;105(1-2):159-68.
4. Ferron L, etal., Circ Res. 2003 Dec 12;93(12):1241-8. Epub 2003 Nov 13.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. GOA data from the GO Consortium
7. Hansen PB, etal., Circ Res. 2001 Sep 28;89(7):630-8.
8. Iftinca M, etal., Neuroscience. 2006 Nov 3;142(4):1031-42. Epub 2006 Aug 28.
9. Kang HW, etal., Biochim Biophys Acta. 2008 Dec;1778(12):2740-8. Epub 2008 Aug 9.
10. Kase M, etal., Neurosci Lett. 1999 Jun 18;268(2):77-80.
11. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
12. Latour I, etal., Glia 2003 Mar;41(4):347-53.
13. McKay BE, etal., Eur J Neurosci. 2006 Nov;24(9):2581-94.
14. McRory JE, etal., J Biol Chem 2001 Feb 9;276(6):3999-4011.
15. MGD data from the GO Consortium
16. Navarro-Gonzalez MF, etal., Clin Exp Pharmacol Physiol. 2009 Jan;36(1):55-66. Epub 2008 Aug 26.
17. NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. Perez-Reyes E, etal., Nature 1998 Feb 26;391(6670):896-900.
19. Pipeline to import KEGG annotations from KEGG into RGD
20. Pipeline to import SMPDB annotations from SMPDB into RGD
21. RGD automated data pipeline
22. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
23. RGD automated import pipeline for gene-chemical interactions
24. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
25. Zhou C, etal., Am J Physiol Lung Cell Mol Physiol. 2007 Apr;292(4):L833-44. Epub 2006 Dec 15.
26. Zhuang H, etal., Diabetes 2000 Jan;49(1):59-64.
Additional References at PubMed
PMID:11230107   PMID:16567615   PMID:16690884   PMID:17450521   PMID:17761775   PMID:18294617   PMID:18765948   PMID:18801335   PMID:18930057   PMID:19520861   PMID:19657020   PMID:19666840  
PMID:20505041   PMID:21084288   PMID:21123217   PMID:21148410   PMID:22972512   PMID:23103495   PMID:23250353   PMID:26456284   PMID:26656778   PMID:26715324   PMID:29578032   PMID:31871187  
PMID:32034930  


Genomics

Comparative Map Data
Cacna1g
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
Rnor_6.0 Ensembl1082,129,506 - 82,197,848 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01082,129,071 - 82,197,828 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01081,950,594 - 82,017,885 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41083,043,636 - 83,112,886 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11083,058,005 - 83,127,256 (-)NCBI
Celera1078,143,865 - 78,211,268 (-)NCBICelera
RH 3.4 Map10617.6RGD
Cytogenetic Map10q26NCBI
CACNA1G
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1750,560,715 - 50,627,474 (+)EnsemblGRCh38hg38GRCh38
GRCh381750,560,715 - 50,629,625 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371748,638,076 - 48,704,835 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361745,993,448 - 46,059,541 (+)NCBINCBI36hg18NCBI36
Build 341745,993,447 - 46,038,832NCBI
Celera1745,099,811 - 45,165,917 (+)NCBI
Cytogenetic Map17q21.33NCBI
HuRef1744,006,381 - 44,072,836 (+)NCBIHuRef
CHM1_11748,702,306 - 48,768,826 (+)NCBICHM1_1
Cacna1g
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391194,299,217 - 94,365,226 (-)NCBIGRCm39mm39
GRCm39 Ensembl1194,299,217 - 94,365,024 (-)Ensembl
GRCm381194,408,391 - 94,474,400 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1194,408,391 - 94,474,198 (-)EnsemblGRCm38mm10GRCm38
MGSCv371194,269,705 - 94,335,512 (-)NCBIGRCm37mm9NCBIm37
MGSCv361194,224,606 - 94,289,815 (-)NCBImm8
Celera11104,027,102 - 104,094,565 (-)NCBICelera
Cytogenetic Map11DNCBI
Cacna1g
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545111,137,214 - 11,194,036 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545111,136,885 - 11,194,321 (-)NCBIChiLan1.0ChiLan1.0
LOC100983419
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11749,528,819 - 49,595,487 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1749,529,402 - 49,595,166 (+)Ensemblpanpan1.1panPan2
PanPan1.1 Ensembl1749,603,268 - 49,659,318 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01744,654,558 - 44,786,037 (+)NCBIMhudiblu_PPA_v0panPan3
CACNA1G
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1926,481,148 - 26,544,511 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl926,481,652 - 26,544,845 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha925,874,088 - 25,937,055 (+)NCBI
ROS_Cfam_1.0927,275,576 - 27,338,562 (+)NCBI
UMICH_Zoey_3.1926,043,294 - 26,106,242 (+)NCBI
UNSW_CanFamBas_1.0926,301,905 - 26,364,906 (+)NCBI
UU_Cfam_GSD_1.0926,432,081 - 26,495,083 (+)NCBI
Cacna1g
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560225,917,385 - 25,981,187 (+)NCBI
SpeTri2.0NW_00493649011,093,600 - 11,157,756 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CACNA1G
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1226,844,079 - 26,912,054 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11226,838,633 - 26,912,344 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21226,991,543 - 27,052,231 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CACNA1G
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11642,710,640 - 42,776,736 (-)NCBI
ChlSab1.1 Ensembl1642,708,638 - 42,768,843 (-)Ensembl
Cacna1g
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247956,443,322 - 6,501,673 (+)NCBI

Position Markers
D10Wox53  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21079,361,543 - 79,361,708 (+)MAPPER
Rnor_6.01082,135,617 - 82,135,781NCBIRnor6.0
Rnor_5.01081,957,140 - 81,957,304UniSTSRnor5.0
RGSC_v3.41083,049,746 - 83,049,910UniSTSRGSC3.4
Celera1078,150,411 - 78,150,575UniSTS
Cytogenetic Map10q26-q31UniSTS
RH130173  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21079,355,437 - 79,355,617 (+)MAPPER
Rnor_6.01082,129,511 - 82,129,690NCBIRnor6.0
Rnor_5.01081,951,034 - 81,951,213UniSTSRnor5.0
RGSC_v3.41083,043,641 - 83,043,820UniSTSRGSC3.4
Celera1078,144,305 - 78,144,484UniSTS
RH 3.4 Map10631.2UniSTS
Cytogenetic Map10q26-q31UniSTS
RH142184  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21079,355,447 - 79,355,620 (+)MAPPER
Rnor_6.01082,129,521 - 82,129,693NCBIRnor6.0
Rnor_5.01081,951,044 - 81,951,216UniSTSRnor5.0
RGSC_v3.41083,043,651 - 83,043,823UniSTSRGSC3.4
Celera1078,144,315 - 78,144,487UniSTS
RH 3.4 Map10617.6UniSTS
Cytogenetic Map10q26-q31UniSTS
BE098192  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21079,357,051 - 79,357,225 (+)MAPPER
Rnor_6.01082,131,125 - 82,131,298NCBIRnor6.0
Rnor_5.01081,952,648 - 81,952,821UniSTSRnor5.0
RGSC_v3.41083,045,255 - 83,045,428UniSTSRGSC3.4
Celera1078,145,919 - 78,146,092UniSTS
RH 3.4 Map10719.39UniSTS
Cytogenetic Map10q26-q31UniSTS
RH137526  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21079,355,442 - 79,355,563 (+)MAPPER
Rnor_6.01082,129,516 - 82,129,636NCBIRnor6.0
Rnor_5.01081,951,039 - 81,951,159UniSTSRnor5.0
RGSC_v3.41083,043,646 - 83,043,766UniSTSRGSC3.4
Celera1078,144,310 - 78,144,430UniSTS
Cytogenetic Map10q26-q31UniSTS
CACNA1G-1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01081,959,678 - 81,960,532NCBIRnor5.0
RGSC_v3.41083,052,735 - 83,053,623UniSTSRGSC3.4
Celera1078,153,302 - 78,154,190UniSTS
Cytogenetic Map10q26-q31UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10642907599492409Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109841807108540162Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101482789492423564Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014827894107857673Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014827894110992275Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)1020170031102897474Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102152390683549467Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)12152390690312401Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102152390690312401Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102290149793886300Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1023861015112626471Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)1027237530101482600Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1027237530102427718Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)103618592982675365Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)103618592995845311Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)104051404485514044Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)104051404485514044Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1041260363106105607Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1043289657108540162Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104370495588704955Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104659302198939209Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104684834691848346Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104684834691848346Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104684834691848346Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)105063833795638337Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)105128920384596393Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)105128920384596393Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)105128920384596393Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)105128920384596393Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)105128920384596393Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105310471898104718Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1053621375112626471Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1053621375112626471Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105362581598939209Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105363748594807701Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)1055224855100224855Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1055678976112626471Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)1055679084102427604Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1056698730101698730Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1060450007105450007Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1060875260105875260Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1060875260105875260Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1060875260105875260Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1062096293107096293Rat
70363Bp71Blood pressure QTL 710.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)106464817584601269Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)1064648175101691360Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)1064648175102149713Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1064648175102149713Rat
61402Niddm3Non-insulin dependent diabetes mellitus QTL 34.58blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)106464831185513822Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1065590122110590122Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1065992275110992275Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1065992275110992275Rat
7387312Bw125Body weight QTL 12530.0047retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight (CMO:0000356)1067880046112626471Rat
1581559Eae18Experimental allergic encephalomyelitis QTL 180.00002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1067988218110992091Rat
2298481Eau9Experimental allergic uveoretinitis QTL 90.0169uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)106830503785514044Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1069123603101482600Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1069385595112626471Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1069385595112626471Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1070166960112626471Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1070800069112626471Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1071692298112626471Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1073008136112626471Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1073008136112626471Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1073008136112626471Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1073467158112626471Rat
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107504539197308358Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1075544754112626471Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1075544754112626471Rat
12880053Cm104Cardiac mass QTL 1040.009heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)107598366286419171Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107598380599492217Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107598380599492217Rat
12880050Am10Aortic mass QTL 100.016aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)107705574186962563Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107705574198282519Rat
631537Oia4Oil induced arthritis QTL 4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)107834302790042115Rat
2325836Bp346Blood pressure QTL 3460.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107897027986962563Rat
10450495Bp383Blood pressure QTL 3830.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107897027998282519Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1078970279112626471Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1079927661112626471Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1080239190112626471Rat
724516Uae17Urinary albumin excretion QTL 173.6urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)108094611088200662Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)1081515116101758478Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)108164977590297007Rat


Genetic Models
This gene Cacna1g is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:176
Count of miRNA genes:68
Interacting mature miRNAs:75
Transcripts:ENSRNOT00000055597, ENSRNOT00000067416
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 25 73 18 26
Low 3 18 29 22 10 22 6 9 1 17 8 11 6
Below cutoff 28 19 9 19 2 2 7 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001308302 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_031601 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767985 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767987 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767990 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767991 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767992 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767993 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767994 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767996 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767997 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767998 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767999 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768000 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597180 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597181 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597182 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597183 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597184 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597186 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597187 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597188 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597189 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597190 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597191 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597192 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597193 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085782 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085783 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085784 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085785 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085786 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085787 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085788 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085789 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085790 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF027984 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF125161 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF203698 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF290212 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF116282 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF116283 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF116284 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF116285 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF116286 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU293202 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU293203 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU293204 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU293205 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU293206 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU293207 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ227500 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000220 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000081307   ⟹   ENSRNOP00000071940
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1082,129,506 - 82,197,848 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092024   ⟹   ENSRNOP00000072061
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1082,129,541 - 82,197,520 (-)Ensembl
RefSeq Acc Id: NM_001308302   ⟹   NP_001295231
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,424 (-)NCBI
Rnor_6.01082,129,071 - 82,197,520 (-)NCBI
Celera1078,143,865 - 78,211,268 (-)NCBI
Sequence:
RefSeq Acc Id: NM_031601   ⟹   NP_113789
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,424 (-)NCBI
Rnor_6.01082,129,071 - 82,197,520 (-)NCBI
Rnor_5.01081,950,594 - 82,017,885 (-)NCBI
RGSC_v3.41083,043,636 - 83,112,886 (-)RGD
Celera1078,143,865 - 78,211,268 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767985   ⟹   XP_008766207
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
Rnor_6.01082,129,071 - 82,197,822 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767986   ⟹   XP_008766208
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
Rnor_6.01082,129,071 - 82,197,822 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767987   ⟹   XP_008766209
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
Rnor_6.01082,129,071 - 82,197,822 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767988   ⟹   XP_008766210
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
Rnor_6.01082,129,071 - 82,197,822 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767990   ⟹   XP_008766212
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
Rnor_6.01082,129,071 - 82,197,822 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767991   ⟹   XP_008766213
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
Rnor_6.01082,129,071 - 82,197,822 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767992   ⟹   XP_008766214
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
Rnor_6.01082,129,071 - 82,197,822 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767993   ⟹   XP_008766215
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
Rnor_6.01082,129,071 - 82,197,822 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767994   ⟹   XP_008766216
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
Rnor_6.01082,129,071 - 82,197,821 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767996   ⟹   XP_008766218
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
Rnor_6.01082,129,071 - 82,197,821 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767997   ⟹   XP_008766219
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
Rnor_6.01082,129,071 - 82,197,821 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767998   ⟹   XP_008766220
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
Rnor_6.01082,129,071 - 82,197,821 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767999   ⟹   XP_008766221
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
Rnor_6.01082,129,071 - 82,197,821 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008768000   ⟹   XP_008766222
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
Rnor_6.01082,129,071 - 82,197,821 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008768001   ⟹   XP_008766223
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
Rnor_6.01082,129,071 - 82,197,821 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597180   ⟹   XP_017452669
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01082,129,071 - 82,197,823 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597181   ⟹   XP_017452670
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01082,129,071 - 82,197,823 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597182   ⟹   XP_017452671
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01082,129,071 - 82,197,824 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597183   ⟹   XP_017452672
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01082,129,071 - 82,197,823 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597184   ⟹   XP_017452673
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01082,129,071 - 82,197,823 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597185   ⟹   XP_017452674
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01082,129,071 - 82,197,823 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597186   ⟹   XP_017452675
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01082,129,071 - 82,197,822 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597187   ⟹   XP_017452676
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01082,129,071 - 82,197,823 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597188   ⟹   XP_017452677
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
Rnor_6.01082,129,071 - 82,197,822 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597189   ⟹   XP_017452678
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
Rnor_6.01082,129,071 - 82,197,821 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597190   ⟹   XP_017452679
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01082,129,071 - 82,197,823 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597191   ⟹   XP_017452680
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01082,129,071 - 82,197,823 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597192   ⟹   XP_017452681
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,362,288 - 79,422,960 (-)NCBI
Rnor_6.01082,136,361 - 82,197,828 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597193   ⟹   XP_017452682
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,362,288 - 79,422,960 (-)NCBI
Rnor_6.01082,136,361 - 82,197,826 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039085782   ⟹   XP_038941710
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
RefSeq Acc Id: XM_039085783   ⟹   XP_038941711
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
RefSeq Acc Id: XM_039085784   ⟹   XP_038941712
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
RefSeq Acc Id: XM_039085785   ⟹   XP_038941713
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
RefSeq Acc Id: XM_039085786   ⟹   XP_038941714
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
RefSeq Acc Id: XM_039085787   ⟹   XP_038941715
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
RefSeq Acc Id: XM_039085788   ⟹   XP_038941716
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
RefSeq Acc Id: XM_039085789   ⟹   XP_038941717
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,354,998 - 79,422,960 (-)NCBI
RefSeq Acc Id: XM_039085790   ⟹   XP_038941718
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,362,288 - 79,422,960 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001295231 (Get FASTA)   NCBI Sequence Viewer  
  NP_113789 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766207 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766208 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766209 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766210 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766212 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766213 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766214 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766215 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766216 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766218 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766219 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766220 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766221 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766222 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766223 (Get FASTA)   NCBI Sequence Viewer  
  XP_017452677 (Get FASTA)   NCBI Sequence Viewer  
  XP_017452678 (Get FASTA)   NCBI Sequence Viewer  
  XP_017452681 (Get FASTA)   NCBI Sequence Viewer  
  XP_017452682 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941710 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941711 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941712 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941713 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941714 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941715 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941716 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941717 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941718 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAC67372 (Get FASTA)   NCBI Sequence Viewer  
  AAD26858 (Get FASTA)   NCBI Sequence Viewer  
  AAF26716 (Get FASTA)   NCBI Sequence Viewer  
  AAG35186 (Get FASTA)   NCBI Sequence Viewer  
  ABL63737 (Get FASTA)   NCBI Sequence Viewer  
  ABL63738 (Get FASTA)   NCBI Sequence Viewer  
  ABL63739 (Get FASTA)   NCBI Sequence Viewer  
  ABL63740 (Get FASTA)   NCBI Sequence Viewer  
  ABL63741 (Get FASTA)   NCBI Sequence Viewer  
  ABX89945 (Get FASTA)   NCBI Sequence Viewer  
  ABX89946 (Get FASTA)   NCBI Sequence Viewer  
  ABX89947 (Get FASTA)   NCBI Sequence Viewer  
  ABX89948 (Get FASTA)   NCBI Sequence Viewer  
  ABX89949 (Get FASTA)   NCBI Sequence Viewer  
  ABX89950 (Get FASTA)   NCBI Sequence Viewer  
  ACJ71730 (Get FASTA)   NCBI Sequence Viewer  
  O54898 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_113789   ⟸   NM_031601
- Peptide Label: isoform 2
- Sequence:
RefSeq Acc Id: XP_008766222   ⟸   XM_008768000
- Peptide Label: isoform X23
- Sequence:
RefSeq Acc Id: XP_008766223   ⟸   XM_008768001
- Peptide Label: isoform X24
- Sequence:
RefSeq Acc Id: XP_008766221   ⟸   XM_008767999
- Peptide Label: isoform X21
- Sequence:
RefSeq Acc Id: XP_008766215   ⟸   XM_008767993
- Peptide Label: isoform X16
- Sequence:
RefSeq Acc Id: XP_008766210   ⟸   XM_008767988
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_008766219   ⟸   XM_008767997
- Peptide Label: isoform X19
- Sequence:
RefSeq Acc Id: XP_008766220   ⟸   XM_008767998
- Peptide Label: isoform X20
- Sequence:
RefSeq Acc Id: XP_008766214   ⟸   XM_008767992
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_008766212   ⟸   XM_008767990
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_008766208   ⟸   XM_008767986
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008766218   ⟸   XM_008767996
- Peptide Label: isoform X18
- Sequence:
RefSeq Acc Id: XP_008766213   ⟸   XM_008767991
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: XP_008766209   ⟸   XM_008767987
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008766216   ⟸   XM_008767994
- Peptide Label: isoform X17
- Sequence:
RefSeq Acc Id: XP_008766207   ⟸   XM_008767985
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: NP_001295231   ⟸   NM_001308302
- Peptide Label: isoform 1
- Sequence:
RefSeq Acc Id: XP_017452671   ⟸   XM_017597182
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017452680   ⟸   XM_017597191
- Peptide Label: isoform X21
- Sequence:
RefSeq Acc Id: XP_017452679   ⟸   XM_017597190
- Peptide Label: isoform X19
- Sequence:
RefSeq Acc Id: XP_017452673   ⟸   XM_017597184
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017452674   ⟸   XM_017597185
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017452670   ⟸   XM_017597181
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017452672   ⟸   XM_017597183
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017452676   ⟸   XM_017597187
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_017452669   ⟸   XM_017597180
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017452675   ⟸   XM_017597186
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017452677   ⟸   XM_017597188
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_017452678   ⟸   XM_017597189
- Peptide Label: isoform X15
- Sequence:
RefSeq Acc Id: XP_017452681   ⟸   XM_017597192
- Peptide Label: isoform X26
- Sequence:
RefSeq Acc Id: XP_017452682   ⟸   XM_017597193
- Peptide Label: isoform X27
- Sequence:
RefSeq Acc Id: ENSRNOP00000072061   ⟸   ENSRNOT00000092024
RefSeq Acc Id: ENSRNOP00000071940   ⟸   ENSRNOT00000081307
RefSeq Acc Id: XP_038941717   ⟸   XM_039085789
- Peptide Label: isoform X25
RefSeq Acc Id: XP_038941710   ⟸   XM_039085782
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038941716   ⟸   XM_039085788
- Peptide Label: isoform X22
RefSeq Acc Id: XP_038941713   ⟸   XM_039085785
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038941711   ⟸   XM_039085783
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038941712   ⟸   XM_039085784
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038941714   ⟸   XM_039085786
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038941715   ⟸   XM_039085787
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038941718   ⟸   XM_039085790
- Peptide Label: isoform X28
Protein Domains
Ion_trans

Transcriptome

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

Promoters
RGD ID:13697605
Promoter ID:EPDNEW_R8127
Type:initiation region
Name:Cacna1g_1
Description:calcium voltage-gated channel subunit alpha1 G
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01082,197,810 - 82,197,870EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/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)
ACI/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
ACI/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
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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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
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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