Cacna1d (calcium voltage-gated channel subunit alpha1 D) - Rat Genome Database

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Gene: Cacna1d (calcium voltage-gated channel subunit alpha1 D) Rattus norvegicus
Analyze
Symbol: Cacna1d
Name: calcium voltage-gated channel subunit alpha1 D
RGD ID: 70973
Description: Enables PDZ domain binding activity; ankyrin binding activity; and high voltage-gated calcium channel activity. Involved in several processes, including cellular response to amyloid-beta; positive regulation of CREB transcription factor activity; and positive regulation of transport. Located in several cellular components, including apical plasma membrane; dendrite membrane; and sarcolemma. Biomarker of sciatic neuropathy. Human ortholog(s) of this gene implicated in type 2 diabetes mellitus. Orthologous to human CACNA1D (calcium voltage-gated channel subunit alpha1 D); PARTICIPATES IN calcium transport pathway; calcium/calcium-mediated signaling pathway; Alzheimer's disease pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: brain class D; calcium channel alpha-1 subunit; calcium channel, L type, alpha-1 polypeptide; calcium channel, L type, alpha-1 polypeptide, isoform 2; calcium channel, voltage-dependent, L type, alpha 1D subunit; CaV1.3alpha1; RBD; voltage-dependent calcium channel subunit alpha1D; voltage-dependent L-type calcium channel subunit alpha-1D; voltage-gated calcium channel pore forming subunit CaV1.3alpha1 IVS3-IVS4 extracellular linker; voltage-gated calcium channel subunit alpha Cav1.3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2165,227,157 - 5,521,163 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl165,228,306 - 5,668,215 (-)Ensembl
Rnor_6.0166,110,294 - 6,405,022 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl166,112,150 - 6,405,117 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0166,044,524 - 6,339,170 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4165,383,259 - 5,703,361 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1165,383,256 - 5,703,359NCBI
Celera169,667,490 - 9,955,564 (+)NCBICelera
RH 3.4 Map161.3RGD
Cytogenetic Map16p16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (ISO)
(S)-nicotine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
acetamide  (EXP)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amphetamine  (ISO)
androgen antagonist  (EXP)
Aroclor 1254  (EXP)
arsenite(3-)  (ISO)
barium(0)  (EXP,ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
buta-1,3-diene  (ISO)
butanal  (ISO)
Butylparaben  (EXP)
C60 fullerene  (EXP)
cadmium dichloride  (EXP)
calcium atom  (EXP,ISO)
calcium(0)  (EXP,ISO)
chloroprene  (ISO)
chlorpyrifos  (ISO)
cisplatin  (ISO)
cobalt dichloride  (EXP)
cocaine  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
DDE  (EXP)
deoxynivalenol  (ISO)
dibutyl phthalate  (EXP)
enzacamene  (EXP)
epoxiconazole  (EXP)
folic acid  (ISO)
formaldehyde  (EXP)
gabapentin  (EXP)
glyphosate  (ISO)
linuron  (EXP)
MeIQx  (ISO)
metformin  (EXP)
methapyrilene  (ISO)
N-Nitrosopyrrolidine  (ISO)
nickel atom  (ISO)
nicotine  (ISO)
nitrofen  (EXP)
O-methyleugenol  (ISO)
p-menthan-3-ol  (ISO)
paracetamol  (EXP)
perfluorooctanoic acid  (EXP)
phenobarbital  (EXP)
pirinixic acid  (EXP)
pregnenolone 16alpha-carbonitrile  (ISO)
prochloraz  (EXP)
procymidone  (EXP)
progesterone  (ISO)
quercetin  (EXP)
scopolamine  (EXP)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
tebuconazole  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP)
trichloroethene  (EXP)
triclosan  (ISO)
trimellitic anhydride  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adenylate cyclase-modulating G protein-coupled receptor signaling pathway  (ISO)
aging  (IEP)
calcium ion import  (IBA,IEA,IMP,ISO)
calcium ion transmembrane transport  (IEA,ISO)
calcium ion transport  (IBA,IDA,ISO)
calcium-mediated signaling  (IDA)
cardiac muscle cell action potential involved in contraction  (IEA,ISO)
cellular response to amyloid-beta  (IEP)
heart development  (IEP)
induction of synaptic vesicle exocytosis by positive regulation of presynaptic cytosolic calcium ion concentration  (IEA)
membrane depolarization during cardiac muscle cell action potential  (IC)
membrane depolarization during SA node cell action potential  (IEA,ISO)
memory  (IEP)
metal ion transport  (IMP)
positive regulation of adenylate cyclase activity  (ISO,ISS)
positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel  (IMP)
positive regulation of calcium ion transport  (IEA,ISO)
positive regulation of CREB transcription factor activity  (IMP)
positive regulation of insulin secretion involved in cellular response to glucose stimulus  (IMP)
regulation of atrial cardiac muscle cell membrane repolarization  (ISO)
regulation of calcium ion transport  (IDA)
regulation of heart rate by cardiac conduction  (IEA,ISO)
regulation of ion transmembrane transport  (IEA)
regulation of potassium ion transmembrane transport  (ISO)
regulation of potassium ion transmembrane transporter activity  (ISO)
response to estradiol  (IEP)
sensory perception of sound  (IEA,ISO)

References

References - curated
1. Barry EL, etal., Proc Natl Acad Sci U S A 1995 Nov 21;92(24):10914-8.
2. Calin-Jageman I, etal., J Neurosci. 2007 Feb 7;27(6):1374-85.
3. Catterall WA Cold Spring Harb Perspect Biol. 2011 Aug 1;3(8):a003947. doi: 10.1101/cshperspect.a003947.
4. Chen J, etal., Neuroreport. 2013 Apr 17;24(6):313-7. doi: 10.1097/WNR.0b013e32835fa79c.
5. Cunha SR, etal., Circulation. 2011 Sep 13;124(11):1212-22. Epub 2011 Aug 22.
6. Dobremez E, etal., Eur J Neurosci. 2005 Jun;21(12):3321-33.
7. Dubel SJ, etal., Proc Natl Acad Sci U S A 1992 Jun 1;89(11):5058-62.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. GOA data from the GO Consortium
10. Grant L and Fuchs P, J Neurophysiol. 2008 May;99(5):2183-93. doi: 10.1152/jn.01174.2007. Epub 2008 Mar 5.
11. Huang L, etal., Am J Physiol Cell Physiol. 2004 Feb;286(2):C213-21. doi: 10.1152/ajpcell.00346.2003. Epub 2003 Oct 8.
12. Hui A, etal., Neuron 1991 Jul;7(1):35-44.
13. Ihara Y, etal., Mol Endocrinol 1995 Jan;9(1):121-30.
14. Ishida H, etal., FEBS Lett. 2018 Aug;592(16):2786-2797. doi: 10.1002/1873-3468.13209. Epub 2018 Aug 12.
15. Karnabi E, etal., Biochem Biophys Res Commun. 2009 Jul 10;384(4):409-14. doi: 10.1016/j.bbrc.2009.04.150. Epub 2009 May 5.
16. Kim S and Rhim H, Mol Cells. 2011 Sep;32(3):289-94. doi: 10.1007/s10059-011-0075-x. Epub 2011 Aug 4.
17. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
18. Latour I, etal., Glia 2003 Mar;41(4):347-53.
19. Lichvárová L and Lacinová L, Gen Physiol Biophys. 2015 Apr;34(2):157-65. doi: 10.4149/gpb_2014045. Epub 2015 Feb 12.
20. MGD Curation, June 12, 2002
21. MGD data from the GO Consortium
22. Morgan EL, etal., Biochem Biophys Res Commun. 2003 Dec 12;312(2):487-93.
23. Morgan EL, etal., J Physiol. 2007 Apr 15;580(Pt. 2):593-604. Epub 2007 Feb 1.
24. N'Gouemo P and Morad M, Neuroscience 2003;120(3):815-26.
25. NCBI rat LocusLink and RefSeq merged data July 26, 2002
26. OMIM Disease Annotation Pipeline
27. Park HW, etal., FEBS Lett. 2010 Aug 4;584(15):3317-22. doi: 10.1016/j.febslet.2010.07.014. Epub 2010 Jul 11.
28. Pipeline to import KEGG annotations from KEGG into RGD
29. Platzer J, etal., Cell 2000 Jul 7;102(1):89-97.
30. Qu Y, etal., Pediatr Res. 2011 Jun;69(6):479-84.
31. Reinbothe TM, etal., Diabetologia. 2013 Feb;56(2):340-9. doi: 10.1007/s00125-012-2758-z. Epub 2012 Nov 15.
32. RGD automated data pipeline
33. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
34. RGD automated import pipeline for gene-chemical interactions
35. Safa P, etal., J Biol Chem 2001 Oct 19;276(42):38727-37.
36. Schuster S, etal., Biol Psychiatry. 2009 Mar 15;65(6):518-26. Epub 2008 Oct 23.
37. Sukiasyan N, etal., Neuroscience. 2009 Mar 3;159(1):217-35. doi: 10.1016/j.neuroscience.2008.12.011. Epub 2008 Dec 14.
38. Veng LM and Browning MD, Brain Res Mol Brain Res. 2002 Nov 15;107(2):120-7.
39. Veng LM, etal., Brain Res Mol Brain Res 2003 Feb 20;110(2):193-202.
40. Xu W and Lipscombe D, J Neurosci 2001 Aug 15;21(16):5944-51.
41. Yang SN and Berggren PO, Endocr Rev. 2006 Oct;27(6):621-76. Epub 2006 Jul 25.
42. Yu AS, etal., Proc Natl Acad Sci U S A 1992 Nov 1;89(21):10494-8.
43. Zhang H, etal., Eur J Neurosci. 2006 May;23(9):2297-310.
44. Zhou QG, etal., Zhonghua Nan Ke Xue. 2009 Jun;15(6):511-6.
Additional References at PubMed
PMID:1309651   PMID:1692134   PMID:7553731   PMID:9232351   PMID:10468580   PMID:11160515   PMID:12531517   PMID:12700358   PMID:12900400   PMID:15689539   PMID:15932895   PMID:16354915  
PMID:16973824   PMID:17074442   PMID:17110593   PMID:17272349   PMID:17823125   PMID:17909852   PMID:18562674   PMID:18832177   PMID:19074150   PMID:19665524   PMID:20007466   PMID:20112737  
PMID:20137275   PMID:20142517   PMID:20218309   PMID:20392935   PMID:21131953   PMID:21408608   PMID:21998309   PMID:22760075   PMID:23807706   PMID:24033980   PMID:24086669   PMID:25620733  
PMID:25648081   PMID:27231046   PMID:27255217   PMID:27905406   PMID:28402855   PMID:28472301   PMID:28665272   PMID:28807144   PMID:28916724   PMID:31770099   PMID:31983427   PMID:33124763  
PMID:34681928  


Genomics

Comparative Map Data
Cacna1d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2165,227,157 - 5,521,163 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl165,228,306 - 5,668,215 (-)Ensembl
Rnor_6.0166,110,294 - 6,405,022 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl166,112,150 - 6,405,117 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0166,044,524 - 6,339,170 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4165,383,259 - 5,703,361 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1165,383,256 - 5,703,359NCBI
Celera169,667,490 - 9,955,564 (+)NCBICelera
RH 3.4 Map161.3RGD
Cytogenetic Map16p16NCBI
CACNA1D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl353,328,963 - 53,813,733 (+)EnsemblGRCh38hg38GRCh38
GRCh38353,494,611 - 53,813,733 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37353,528,638 - 53,847,760 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36353,504,116 - 53,821,001 (+)NCBINCBI36hg18NCBI36
Build 34353,504,115 - 53,821,001NCBI
Celera353,496,179 - 53,813,773 (+)NCBI
Cytogenetic Map3p21.1NCBI
HuRef353,577,566 - 53,895,012 (+)NCBIHuRef
CHM1_1353,480,800 - 53,798,135 (+)NCBICHM1_1
Cacna1d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391429,761,898 - 30,213,113 (-)NCBIGRCm39mm39
GRCm39 Ensembl1429,761,896 - 30,213,412 (-)Ensembl
GRCm381430,039,941 - 30,491,156 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1430,039,939 - 30,491,455 (-)EnsemblGRCm38mm10GRCm38
MGSCv371430,853,125 - 31,304,342 (-)NCBIGRCm37mm9NCBIm37
MGSCv361428,871,082 - 29,320,165 (-)NCBImm8
Celera1426,295,784 - 26,747,696 (-)NCBICelera
Cytogenetic Map14A3- BNCBI
cM Map1418.43NCBI
Cacna1d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554303,268,953 - 3,794,592 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554303,450,151 - 3,796,983 (+)NCBIChiLan1.0ChiLan1.0
CACNA1D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1354,654,121 - 54,972,755 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl354,495,952 - 54,970,444 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0353,432,189 - 53,751,347 (+)NCBIMhudiblu_PPA_v0panPan3
CACNA1D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12036,189,986 - 36,488,460 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2036,191,810 - 36,613,686 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2036,127,167 - 36,425,020 (-)NCBI
ROS_Cfam_1.02036,464,261 - 36,765,714 (-)NCBI
ROS_Cfam_1.0 Ensembl2036,464,264 - 36,891,695 (-)Ensembl
UMICH_Zoey_3.12035,905,766 - 36,203,511 (-)NCBI
UNSW_CanFamBas_1.02036,264,311 - 36,565,496 (-)NCBI
UU_Cfam_GSD_1.02036,481,867 - 36,779,827 (-)NCBI
Cacna1d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118171,026,002 - 171,341,293 (+)NCBI
SpeTri2.0NW_0049364734,164,633 - 4,479,866 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CACNA1D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1335,436,519 - 35,909,662 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11335,568,534 - 35,911,483 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21338,638,092 - 38,980,243 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CACNA1D
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12214,868,459 - 15,195,002 (+)NCBIChlSab1.1chlSab2
ChlSab1.12214,868,459 - 15,195,002 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2215,027,565 - 15,197,101 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041151,696,363 - 152,023,286 (-)NCBIVero_WHO_p1.0
Cacna1d
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248223,391,045 - 3,734,258 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D16Got114  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2165,372,764 - 5,372,903 (+)MAPPERmRatBN7.2
Rnor_6.0166,257,045 - 6,257,183NCBIRnor6.0
Rnor_5.0166,189,933 - 6,190,071UniSTSRnor5.0
RGSC_v3.4165,527,912 - 5,528,050UniSTSRGSC3.4
Cytogenetic Map16p16UniSTS
RH143397  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2165,411,525 - 5,411,767 (+)MAPPERmRatBN7.2
Rnor_6.0166,295,088 - 6,295,329NCBIRnor6.0
Rnor_5.0166,227,976 - 6,228,217UniSTSRnor5.0
RGSC_v3.4165,565,955 - 5,566,196UniSTSRGSC3.4
Celera169,773,472 - 9,773,713UniSTS
RH 3.4 Map1622.3UniSTS
Cytogenetic Map16p16UniSTS
AI555146  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2165,242,726 - 5,242,946 (+)MAPPERmRatBN7.2
Rnor_6.0166,126,571 - 6,126,790NCBIRnor6.0
Rnor_5.0166,060,094 - 6,060,313UniSTSRnor5.0
RGSC_v3.4165,397,680 - 5,397,899UniSTSRGSC3.4
Celera169,940,922 - 9,941,141UniSTS
RH 3.4 Map163.5UniSTS
Cytogenetic Map16p16UniSTS
BE113526  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2165,264,430 - 5,264,598 (+)MAPPERmRatBN7.2
Rnor_6.0166,148,271 - 6,148,438NCBIRnor6.0
Rnor_5.0166,081,794 - 6,081,961UniSTSRnor5.0
RGSC_v3.4165,419,380 - 5,419,547UniSTSRGSC3.4
Celera169,919,305 - 9,919,472UniSTS
RH 3.4 Map1611.6UniSTS
Cytogenetic Map16p16UniSTS
BE113723  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0166,182,626 - 6,182,793NCBIRnor5.0
Rnor_5.0166,182,029 - 6,182,196NCBIRnor5.0
RGSC_v3.4165,520,606 - 5,520,772UniSTSRGSC3.4
RGSC_v3.4165,519,959 - 5,520,125UniSTSRGSC3.4
Celera169,819,468 - 9,819,634UniSTS
RH 3.4 Map1622.3UniSTS
Cytogenetic Map16p16UniSTS
RH94500  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2165,245,312 - 5,245,497 (+)MAPPERmRatBN7.2
Rnor_6.0166,129,155 - 6,129,339NCBIRnor6.0
Rnor_5.0166,062,678 - 6,062,862UniSTSRnor5.0
RGSC_v3.4165,400,264 - 5,400,448UniSTSRGSC3.4
Celera169,938,403 - 9,938,587UniSTS
RH 3.4 Map161.3UniSTS
Cytogenetic Map16p16UniSTS
PMC18246P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2165,295,194 - 5,295,984 (+)MAPPERmRatBN7.2
Rnor_6.0166,179,034 - 6,179,823NCBIRnor6.0
Rnor_5.0166,112,557 - 6,113,346UniSTSRnor5.0
RGSC_v3.4165,450,144 - 5,450,933UniSTSRGSC3.4
Celera169,887,920 - 9,888,709UniSTS
Cytogenetic Map16p16UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1619639137Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8hepatic copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
2301406Kidm39Kidney mass QTL 390.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)16285170915884239Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338015021361552Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat
737825Alc13Alcohol consumption QTL 134.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760916039848Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16422760943025077Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
61372Bp40Blood pressure QTL 402.2blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)16422773017696785Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1701
Count of miRNA genes:298
Interacting mature miRNAs:375
Transcripts:ENSRNOT00000017975, ENSRNOT00000040759, ENSRNOT00000043180, ENSRNOT00000045459, ENSRNOT00000047737, ENSRNOT00000048459, ENSRNOT00000049531, ENSRNOT00000051371
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 4 6 58 21 8
Low 3 35 51 41 19 41 2 2 16 35 20 3 2
Below cutoff 4 6 9 6

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001389225 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_017298 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252590 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252594 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252595 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252597 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770991 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770992 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600055 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600056 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600057 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600058 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600059 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600060 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600061 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600062 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600063 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600064 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600065 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600066 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600067 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600068 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600069 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600070 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094434 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094435 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005494597 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005494598 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005494599 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC142010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF370009 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF370010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF370011 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF370012 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF439401 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH011547 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D38101 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D38102 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232509 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M57682 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M99221 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U14005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U31772 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U49126 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U49127 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U49128 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000040759   ⟹   ENSRNOP00000041766
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl165,228,306 - 5,519,336 (-)Ensembl
Rnor_6.0 Ensembl166,113,168 - 6,245,644 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000047737   ⟹   ENSRNOP00000042492
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl165,228,306 - 5,520,993 (-)Ensembl
Rnor_6.0 Ensembl166,129,089 - 6,405,117 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000048459   ⟹   ENSRNOP00000043046
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl165,228,306 - 5,520,993 (-)Ensembl
Rnor_6.0 Ensembl166,112,150 - 6,404,957 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000051371   ⟹   ENSRNOP00000051407
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl165,228,306 - 5,668,215 (-)Ensembl
Rnor_6.0 Ensembl166,129,800 - 6,404,578 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095730   ⟹   ENSRNOP00000084179
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl165,228,306 - 5,520,993 (-)Ensembl
RefSeq Acc Id: NM_001389225   ⟹   NP_001376154
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,227,165 - 5,521,059 (-)NCBI
RefSeq Acc Id: XM_006252590   ⟹   XP_006252652
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,229,324 - 5,521,075 (-)NCBI
Rnor_6.0166,113,168 - 6,404,605 (-)NCBI
Rnor_5.0166,044,524 - 6,339,170 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252594   ⟹   XP_006252656
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,229,324 - 5,521,075 (-)NCBI
Rnor_6.0166,113,168 - 6,404,605 (-)NCBI
Rnor_5.0166,044,524 - 6,339,170 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252595   ⟹   XP_006252657
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,229,324 - 5,521,075 (-)NCBI
Rnor_6.0166,113,168 - 6,404,605 (-)NCBI
Rnor_5.0166,044,524 - 6,339,170 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252597   ⟹   XP_006252659
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,229,324 - 5,521,075 (-)NCBI
Rnor_6.0166,113,168 - 6,404,605 (-)NCBI
Rnor_5.0166,044,524 - 6,339,170 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600055   ⟹   XP_017455544
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,227,157 - 5,521,075 (-)NCBI
Rnor_6.0166,110,294 - 6,405,022 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600056   ⟹   XP_017455545
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,227,157 - 5,521,075 (-)NCBI
Rnor_6.0166,110,294 - 6,405,022 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600057   ⟹   XP_017455546
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,227,157 - 5,521,075 (-)NCBI
Rnor_6.0166,110,294 - 6,405,022 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600058   ⟹   XP_017455547
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,227,157 - 5,521,075 (-)NCBI
Rnor_6.0166,110,294 - 6,405,021 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600059   ⟹   XP_017455548
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,227,157 - 5,521,075 (-)NCBI
Rnor_6.0166,110,294 - 6,405,021 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600060   ⟹   XP_017455549
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,227,157 - 5,521,075 (-)NCBI
Rnor_6.0166,110,294 - 6,405,021 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600061   ⟹   XP_017455550
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,227,157 - 5,521,075 (-)NCBI
Rnor_6.0166,110,294 - 6,405,021 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600062   ⟹   XP_017455551
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,227,157 - 5,521,075 (-)NCBI
Rnor_6.0166,113,168 - 6,405,022 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600064   ⟹   XP_017455553
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,227,157 - 5,521,075 (-)NCBI
Rnor_6.0166,110,294 - 6,405,021 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600065   ⟹   XP_017455554
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,227,157 - 5,521,075 (-)NCBI
Rnor_6.0166,110,294 - 6,405,021 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600066   ⟹   XP_017455555
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,237,021 - 5,521,078 (-)NCBI
Rnor_6.0166,120,920 - 6,405,022 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039094434   ⟹   XP_038950362
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,227,157 - 5,521,075 (-)NCBI
RefSeq Acc Id: XM_039094435   ⟹   XP_038950363
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,265,799 - 5,521,079 (-)NCBI
RefSeq Acc Id: XR_005494597
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,238,073 - 5,521,078 (-)NCBI
RefSeq Acc Id: XR_005494598
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,238,073 - 5,521,078 (-)NCBI
RefSeq Acc Id: XR_005494599
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2165,238,073 - 5,521,163 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001376154 (Get FASTA)   NCBI Sequence Viewer  
  XP_006252652 (Get FASTA)   NCBI Sequence Viewer  
  XP_006252656 (Get FASTA)   NCBI Sequence Viewer  
  XP_006252657 (Get FASTA)   NCBI Sequence Viewer  
  XP_006252659 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455544 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455545 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455546 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455547 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455548 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455549 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455550 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455551 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455553 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455554 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455555 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950362 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950363 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA40895 (Get FASTA)   NCBI Sequence Viewer  
  AAA42015 (Get FASTA)   NCBI Sequence Viewer  
  AAA89156 (Get FASTA)   NCBI Sequence Viewer  
  AAB60515 (Get FASTA)   NCBI Sequence Viewer  
  AAB61634 (Get FASTA)   NCBI Sequence Viewer  
  AAB61635 (Get FASTA)   NCBI Sequence Viewer  
  AAB61636 (Get FASTA)   NCBI Sequence Viewer  
  AAK72959 (Get FASTA)   NCBI Sequence Viewer  
  AAK72960 (Get FASTA)   NCBI Sequence Viewer  
  AAK72961 (Get FASTA)   NCBI Sequence Viewer  
  AAK72962 (Get FASTA)   NCBI Sequence Viewer  
  AAL58322 (Get FASTA)   NCBI Sequence Viewer  
  AAL89640 (Get FASTA)   NCBI Sequence Viewer  
  AAL89641 (Get FASTA)   NCBI Sequence Viewer  
  AAL89642 (Get FASTA)   NCBI Sequence Viewer  
  BAA07282 (Get FASTA)   NCBI Sequence Viewer  
  BAA07283 (Get FASTA)   NCBI Sequence Viewer  
  EDL89001 (Get FASTA)   NCBI Sequence Viewer  
  EDL89002 (Get FASTA)   NCBI Sequence Viewer  
  EDL89003 (Get FASTA)   NCBI Sequence Viewer  
  EDL89004 (Get FASTA)   NCBI Sequence Viewer  
  EDL89005 (Get FASTA)   NCBI Sequence Viewer  
  P27732 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_006252657   ⟸   XM_006252595
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: XP_006252652   ⟸   XM_006252590
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_006252659   ⟸   XM_006252597
- Peptide Label: isoform X15
- Sequence:
RefSeq Acc Id: XP_006252656   ⟸   XM_006252594
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_017455546   ⟸   XM_017600057
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017455544   ⟸   XM_017600055
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017455545   ⟸   XM_017600056
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017455548   ⟸   XM_017600059
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017455554   ⟸   XM_017600065
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_017455553   ⟸   XM_017600064
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_017455550   ⟸   XM_017600061
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_017455547   ⟸   XM_017600058
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017455549   ⟸   XM_017600060
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017455551   ⟸   XM_017600062
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_017455555   ⟸   XM_017600066
- Peptide Label: isoform X16
- Sequence:
RefSeq Acc Id: ENSRNOP00000042492   ⟸   ENSRNOT00000047737
RefSeq Acc Id: ENSRNOP00000043046   ⟸   ENSRNOT00000048459
RefSeq Acc Id: ENSRNOP00000051407   ⟸   ENSRNOT00000051371
RefSeq Acc Id: ENSRNOP00000041766   ⟸   ENSRNOT00000040759
RefSeq Acc Id: XP_038950362   ⟸   XM_039094434
- Peptide Label: isoform X3
RefSeq Acc Id: NP_001376154   ⟸   NM_001389225
RefSeq Acc Id: XP_038950363   ⟸   XM_039094435
- Peptide Label: isoform X17
RefSeq Acc Id: ENSRNOP00000084179   ⟸   ENSRNOT00000095730
Protein Domains
Ca_chan_IQ

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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)
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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 (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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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
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)
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
LL/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (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
LN/MavRrrcAek (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: 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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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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)
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: 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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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_5.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 6122533 6122534 T A snv ZF (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:70973 AgrOrtholog
Ensembl Genes ENSRNOG00000013147 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000041766 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000042492 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000043046 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000051407 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000084179 ENTREZGENE
Ensembl Transcript ENSRNOT00000040759 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000047737 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000048459 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000051371 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000095730 ENTREZGENE
Gene3D-CATH 1.20.120.350 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CAC1F_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPHH_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ion_trans_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LVDCC_a1dsu UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VDCC_a1su_IQ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VDCC_L_a1su UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VDCCAlpha1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Volt_channel_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 29716 ENTREZGENE
Pfam Ca_chan_IQ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CAC1F_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPHH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ion_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cacna1d PhenoGen
PRINTS CACHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LVDCCALPHA1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LVDCCALPHA1D UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Ca_chan_IQ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt CAC1D_RAT UniProtKB/Swiss-Prot
  E9PSN0_RAT UniProtKB/TrEMBL
  E9PT50_RAT UniProtKB/TrEMBL
  E9PTK1_RAT UniProtKB/TrEMBL
  F1LNB7_RAT UniProtKB/TrEMBL
  P27732 ENTREZGENE
UniProt Secondary O09022 UniProtKB/Swiss-Prot
  O09023 UniProtKB/Swiss-Prot
  O09024 UniProtKB/Swiss-Prot
  Q01542 UniProtKB/Swiss-Prot
  Q62691 UniProtKB/Swiss-Prot
  Q62815 UniProtKB/Swiss-Prot
  Q63491 UniProtKB/Swiss-Prot
  Q63492 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Cacna1d  calcium voltage-gated channel subunit alpha1 D  Cacna1d  calcium channel, voltage-dependent, L type, alpha 1D subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-07-09 Cacna1d  calcium channel, voltage-dependent, L type, alpha 1D subunit      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains QXXER motif of the C terminus is not sufficient to confer sensitivity to inhibitory G proteins 628461
gene_expression expressed in brain and neuroendocrine GH3 cells 628461
gene_function voltage-activated Ca2+ channel 628461
gene_function alpha 1 subunit is the main component of the Ca2+ channel 628461
gene_process mediates parathyroid hormone induction of increase in intracellular calcium 634679
gene_process may mediate hormone release in pituitary and pancreatic neuroendocrine cells 628461
gene_protein neuroendocrine isoform of pore forming subunit of L-type calcium channel 634679
gene_protein alpha 1 subunit is the main component of the Ca2+ channel  
gene_regulation channel activity is inhibited by activation of somatostatin and muscarinic receptors in the growth hormone- and prolactin-secreting anterior pituitary GH3 cell line 628461