Cacna2d1 (calcium voltage-gated channel auxiliary subunit alpha2delta 1) - Rat Genome Database

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Gene: Cacna2d1 (calcium voltage-gated channel auxiliary subunit alpha2delta 1) Rattus norvegicus
Analyze
Symbol: Cacna2d1
Name: calcium voltage-gated channel auxiliary subunit alpha2delta 1
RGD ID: 2247
Description: Enables voltage-gated calcium channel activity. Involved in calcium ion transport and regulation of ion transmembrane transport. Part of L-type voltage-gated calcium channel complex. Is active in glutamatergic synapse. Is anchored component of postsynaptic membrane and anchored component of presynaptic active zone membrane. Orthologous to human CACNA2D1 (calcium voltage-gated channel auxiliary subunit alpha2delta 1); PARTICIPATES IN arrhythmogenic right ventricular cardiomyopathy pathway; dilated cardiomyopathy pathway; hypertrophic cardiomyopathy pathway; INTERACTS WITH 2-acetamidofluorene; acetamide; amitriptyline.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Cacna2; Calcium channel subunit alpha 2 delta (dihydropyridine - sensitive L-type); calcium channel, voltage-dependent, alpha2/delta subunit 1; CCHLA2; DHSCCA; voltage-dependent calcium channel subunit alpha-2/delta-1; voltage-gated calcium channel subunit alpha-2/delta-1
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
NCBI Annotation Information: Annotation category: suggests misassembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2418,950,611 - 19,374,969 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl418,951,002 - 19,374,969 (-)Ensembl
Rnor_6.0415,706,974 - 16,130,848 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl415,710,417 - 16,130,848 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0415,681,399 - 16,105,483 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4415,139,881 - 15,566,740 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1415,169,848 - 15,566,733 (-)NCBI
Celera414,480,196 - 14,898,934 (-)NCBICelera
Cytogenetic Map4q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-acetamidofluorene  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
acetamide  (EXP)
aflatoxin B1  (ISO)
amitriptyline  (EXP)
ammonium chloride  (EXP)
androgen antagonist  (EXP)
aristolochic acid  (ISO)
arsenous acid  (ISO)
asbestos  (ISO)
barium(0)  (EXP,ISO)
benzene  (EXP)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
butanal  (ISO)
Butylparaben  (EXP)
cadmium dichloride  (EXP)
calcium atom  (EXP,ISO)
calcium(0)  (EXP,ISO)
cannabidiol  (EXP)
carbon nanotube  (ISO)
chenodeoxycholic acid  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
cisplatin  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
deoxycholic acid  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dorsomorphin  (ISO)
entinostat  (ISO)
enzacamene  (EXP)
ethanol  (EXP,ISO)
flavonoids  (EXP)
folic acid  (ISO)
furan  (EXP)
gabapentin  (EXP,ISO)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
homocysteine  (EXP)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (ISO)
methamphetamine  (ISO)
N-nitrosodiethylamine  (EXP)
nefazodone  (ISO)
nicotine  (ISO)
nitrogen dioxide  (ISO)
Nor-9-carboxy-delta9-THC  (ISO)
O-methyleugenol  (ISO)
oxaliplatin  (ISO)
paclitaxel  (ISO)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
phenylmercury acetate  (ISO)
PhIP  (EXP)
potassium chloride  (ISO)
potassium chromate  (ISO)
pregabalin  (EXP,ISO)
progesterone  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
SCH 23390  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
sodium nitrate  (ISO)
sulpiride  (ISO)
sunitinib  (ISO)
Sunset Yellow FCF  (ISO)
tamoxifen  (ISO)
testosterone  (ISO)
tetracycline  (ISO)
thapsigargin  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
tungsten  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

References

Additional References at PubMed
PMID:1309651   PMID:11160515   PMID:14593108   PMID:15201306   PMID:15456823   PMID:15536090   PMID:16134135   PMID:17224476   PMID:17893194   PMID:18616987   PMID:19056867   PMID:19796812  
PMID:20080692   PMID:20888635   PMID:21239111   PMID:21383000   PMID:21464332   PMID:21695204   PMID:21700703   PMID:21804529   PMID:21883149   PMID:22054663   PMID:22949532   PMID:23376485  
PMID:23533145   PMID:23541831   PMID:24315988   PMID:24641886   PMID:24775099   PMID:24801623   PMID:24889613   PMID:24948814   PMID:25935199   PMID:25966687   PMID:26742847   PMID:27782881  
PMID:28957379   PMID:29355786   PMID:29476059   PMID:29490268   PMID:29580153   PMID:29921713   PMID:29971791   PMID:31805307   PMID:31914622   PMID:33986433  


Genomics

Comparative Map Data
Cacna2d1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2418,950,611 - 19,374,969 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl418,951,002 - 19,374,969 (-)Ensembl
Rnor_6.0415,706,974 - 16,130,848 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl415,710,417 - 16,130,848 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0415,681,399 - 16,105,483 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4415,139,881 - 15,566,740 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1415,169,848 - 15,566,733 (-)NCBI
Celera414,480,196 - 14,898,934 (-)NCBICelera
Cytogenetic Map4q12NCBI
CACNA2D1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl781,946,444 - 82,443,777 (-)EnsemblGRCh38hg38GRCh38
GRCh38781,946,444 - 82,443,956 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37781,575,760 - 82,073,272 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36781,417,354 - 81,910,967 (-)NCBINCBI36hg18NCBI36
Build 34781,224,068 - 81,717,682NCBI
Celera776,279,569 - 76,773,517 (-)NCBI
Cytogenetic Map7q21.11NCBI
HuRef776,182,274 - 76,676,613 (-)NCBIHuRef
CHM1_1781,509,503 - 82,003,079 (-)NCBICHM1_1
CRA_TCAGchr7v2780,910,288 - 81,405,123 (-)NCBI
Cacna2d1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39516,139,390 - 16,579,509 (+)NCBIGRCm39mm39
GRCm39 Ensembl516,139,689 - 16,579,509 (+)Ensembl
GRCm38515,934,264 - 16,374,511 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl515,934,691 - 16,374,511 (+)EnsemblGRCm38mm10GRCm38
MGSCv37515,440,509 - 15,880,329 (+)NCBIGRCm37mm9NCBIm37
MGSCv36515,446,612 - 15,882,875 (+)NCBImm8
Celera512,936,968 - 13,372,202 (+)NCBICelera
Cytogenetic Map5A2- A3NCBI
cM Map56.56NCBI
Cacna2d1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554103,619,740 - 3,964,239 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554103,544,398 - 3,963,582 (+)NCBIChiLan1.0ChiLan1.0
CACNA2D1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1787,575,054 - 88,068,480 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl787,579,004 - 88,068,482 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0773,917,439 - 74,410,627 (-)NCBIMhudiblu_PPA_v0panPan3
CACNA2D1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11821,561,091 - 21,949,970 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1821,564,676 - 21,949,544 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1821,233,630 - 21,714,674 (-)NCBI
ROS_Cfam_1.01822,009,947 - 22,485,359 (-)NCBI
UMICH_Zoey_3.11821,646,522 - 22,121,006 (-)NCBI
UNSW_CanFamBas_1.01821,182,147 - 21,656,514 (-)NCBI
UU_Cfam_GSD_1.01821,836,185 - 22,311,929 (-)NCBI
Cacna2d1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511863,375,924 - 63,825,676 (-)NCBI
SpeTri2.0NW_004936734577,656 - 1,027,412 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CACNA2D1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl997,780,742 - 98,266,573 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1997,781,057 - 98,265,925 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29108,068,038 - 108,554,997 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CACNA2D1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12166,449,154 - 66,937,643 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2166,770,578 - 66,934,898 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604237,008,715 - 37,508,631 (-)NCBIVero_WHO_p1.0
Cacna2d1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473930,436,662 - 30,864,482 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D4Rat149  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2419,303,240 - 19,303,440 (+)MAPPERmRatBN7.2
Rnor_6.0416,058,800 - 16,059,003NCBIRnor6.0
Rnor_5.0416,033,400 - 16,033,603UniSTSRnor5.0
RGSC_v3.4415,494,422 - 15,494,625UniSTSRGSC3.4
RGSC_v3.4415,493,809 - 15,494,008UniSTSRGSC3.4
Celera414,827,102 - 14,827,284UniSTS
SHRSP x BN Map46.7499UniSTS
SHRSP x BN Map46.7499RGD
Cytogenetic Map4q11UniSTS
RH131169  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2419,362,463 - 19,362,650 (+)MAPPERmRatBN7.2
Rnor_6.0416,118,349 - 16,118,535NCBIRnor6.0
Rnor_5.0416,092,949 - 16,093,135UniSTSRnor5.0
RGSC_v3.4415,554,241 - 15,554,427UniSTSRGSC3.4
Celera414,886,240 - 14,886,426UniSTS
Cytogenetic Map4q11UniSTS
RH142303  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2418,950,815 - 18,950,987 (+)MAPPERmRatBN7.2
Rnor_6.0415,710,616 - 15,710,787NCBIRnor6.0
Rnor_5.0415,685,039 - 15,685,210UniSTSRnor5.0
RGSC_v3.4415,140,093 - 15,140,264UniSTSRGSC3.4
Celera414,480,408 - 14,480,579UniSTS
Cytogenetic Map4q11UniSTS
RH144502  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2419,286,538 - 19,286,715 (+)MAPPERmRatBN7.2
Rnor_6.0416,042,100 - 16,042,276NCBIRnor6.0
Rnor_5.0416,016,700 - 16,016,876UniSTSRnor5.0
RGSC_v3.4415,477,109 - 15,477,285UniSTSRGSC3.4
Celera414,810,409 - 14,810,585UniSTS
Cytogenetic Map4q11UniSTS
AU048127  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2419,073,046 - 19,073,221 (+)MAPPERmRatBN7.2
Rnor_6.0415,830,027 - 15,830,201NCBIRnor6.0
Rnor_5.0415,804,495 - 15,804,669UniSTSRnor5.0
RGSC_v3.4415,263,055 - 15,263,229UniSTSRGSC3.4
Celera414,598,194 - 14,598,368UniSTS
Cytogenetic Map4q11UniSTS
Cacna2d1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2418,950,673 - 18,950,839 (+)MAPPERmRatBN7.2
Rnor_6.0415,710,476 - 15,710,639NCBIRnor6.0
Rnor_5.0415,684,899 - 15,685,062UniSTSRnor5.0
RGSC_v3.4415,139,953 - 15,140,116UniSTSRGSC3.4
Celera414,480,268 - 14,480,431UniSTS
Cytogenetic Map4q11UniSTS
RH139155  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2419,100,714 - 19,100,835 (+)MAPPERmRatBN7.2
Rnor_6.0416,917,585 - 16,917,705NCBIRnor6.0
Rnor_6.0415,856,501 - 15,856,621NCBIRnor6.0
Rnor_5.0415,830,969 - 15,831,089UniSTSRnor5.0
Rnor_5.0416,891,930 - 16,892,050UniSTSRnor5.0
RGSC_v3.4415,290,726 - 15,290,846UniSTSRGSC3.4
Celera414,625,857 - 14,625,977UniSTS
Cytogenetic Map4q11UniSTS
BE117531  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2419,358,892 - 19,359,042 (+)MAPPERmRatBN7.2
Rnor_6.0416,114,778 - 16,114,927NCBIRnor6.0
Rnor_5.0416,089,378 - 16,089,527UniSTSRnor5.0
RGSC_v3.4415,550,670 - 15,550,819UniSTSRGSC3.4
Celera414,882,655 - 14,882,804UniSTS
Cytogenetic Map4q11UniSTS
AU048896  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2418,961,088 - 18,961,308 (+)MAPPERmRatBN7.2
Rnor_6.0415,720,891 - 15,721,111NCBIRnor6.0
Rnor_5.0415,695,314 - 15,695,534UniSTSRnor5.0
RGSC_v3.4415,150,368 - 15,150,588UniSTSRGSC3.4
Celera414,490,674 - 14,490,894UniSTS
Cytogenetic Map4q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61351Bp33Blood pressure QTL 330.0018arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4127716890Rat
61408Scl23Serum cholesterol level QTL 230.0005blood HDL phospholipid amount (VT:0010504)serum high density lipoprotein phospholipid level (CMO:0001567)4127716890Rat
724557Plsm1Polydactyly-luxate syndrome (PLS) morphotypes QTL 10.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)4127716890Rat
1641905Colcr1Colorectal carcinoma resistance QTL 14.30.0003intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)4129494328Rat
61333Gluco16Glucose level QTL 164.30.00001adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)4130372989Rat
9589097Slep11Serum leptin concentration QTL 115.090.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)4131934116Rat
8552903Pigfal2Plasma insulin-like growth factor 1 level QTL 27.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)4131934116Rat
9589046Scfw2Subcutaneous fat weight QTL 25.540.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)4131934116Rat
9590100Sffal4Serum free fatty acids level QTL 47.360.05blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)4131934116Rat
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4132584199Rat
1357341Gluco5Glucose level QTL 56.4adipocyte free fatty acid secretion trait (VT:0010465)absolute change in adipocyte free fatty acid secretion per unit volume (CMO:0001446)4133250345Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4133250345Rat
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4139505420Rat
634323Hc2Hypercalciuria QTL 22.15urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)421079645210796Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
1358201Gluco12Glucose level QTL121.6adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake (CMO:0000870)4521839229593287Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat
631209Bw2Body weight QTL24.2retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)4994088544463908Rat
1300141Bp178Blood pressure QTL 178arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)41002490139524530Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41008408955084089Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41008408955084089Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41008408955084089Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41008408955084089Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41008408955084089Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41008408955084089Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41467806559678065Rat
2313401Anxrr27Anxiety related response QTL 27aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)41793350862933508Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:264
Count of miRNA genes:143
Interacting mature miRNAs:157
Transcripts:ENSRNOT00000034969, ENSRNOT00000042914
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 1 38 8 8 11 68 20 20 8 8
Low 2 5 38 30 19 30 6 15 21 3
Below cutoff 11 11 11

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000034969   ⟹   ENSRNOP00000034572
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl415,710,805 - 16,130,563 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000042914   ⟹   ENSRNOP00000044940
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl418,951,002 - 19,374,969 (-)Ensembl
Rnor_6.0 Ensembl415,710,417 - 16,130,848 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082161   ⟹   ENSRNOP00000074655
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl418,951,002 - 19,103,347 (-)Ensembl
Rnor_6.0 Ensembl415,710,802 - 15,859,132 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000090240   ⟹   ENSRNOP00000074171
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl415,710,793 - 16,130,563 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000110623   ⟹   ENSRNOP00000079383
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl419,239,836 - 19,374,969 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115152   ⟹   ENSRNOP00000079129
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl419,278,003 - 19,374,969 (-)Ensembl
RefSeq Acc Id: NM_001110847   ⟹   NP_001104317
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2418,950,990 - 19,374,696 (-)NCBI
Rnor_6.0415,710,790 - 16,130,575 (-)NCBI
Rnor_5.0415,681,399 - 16,105,483 (-)NCBI
RGSC_v3.4415,139,881 - 15,566,740 (-)RGD
Celera414,480,582 - 14,898,662 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001110848   ⟹   NP_001104318
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2418,950,993 - 19,374,684 (-)NCBI
Rnor_6.0415,710,793 - 16,130,563 (-)NCBI
Rnor_5.0415,681,399 - 16,105,483 (-)NCBI
RGSC_v3.4415,139,881 - 15,566,740 (-)RGD
Celera414,480,585 - 14,898,650 (-)NCBI
Sequence:
RefSeq Acc Id: NM_012919   ⟹   NP_037051
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2418,950,611 - 19,374,969 (-)NCBI
Rnor_6.0415,710,404 - 16,130,848 (-)NCBI
Rnor_5.0415,681,399 - 16,105,483 (-)NCBI
RGSC_v3.4415,139,881 - 15,566,740 (-)RGD
Celera414,480,196 - 14,898,934 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_037051   ⟸   NM_012919
- Peptide Label: isoform 1 precursor
- UniProtKB: Q9ERS3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001104317   ⟸   NM_001110847
- Peptide Label: isoform 3 precursor
- UniProtKB: Q8VHS9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001104318   ⟸   NM_001110848
- Peptide Label: isoform 2 precursor
- UniProtKB: Q8CFG7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074171   ⟸   ENSRNOT00000090240
RefSeq Acc Id: ENSRNOP00000074655   ⟸   ENSRNOT00000082161
RefSeq Acc Id: ENSRNOP00000034572   ⟸   ENSRNOT00000034969
RefSeq Acc Id: ENSRNOP00000044940   ⟸   ENSRNOT00000042914
RefSeq Acc Id: ENSRNOP00000079129   ⟸   ENSRNOT00000115152
RefSeq Acc Id: ENSRNOP00000079383   ⟸   ENSRNOT00000110623
Protein Domains
Cache   VWFA

Transcriptome

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

Promoters
RGD ID:13692829
Promoter ID:EPDNEW_R3346
Type:multiple initiation site
Name:Cacna2d1_1
Description:calcium voltage-gated channel auxiliary subunit alpha2delta 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R3347  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0416,130,632 - 16,130,692EPDNEW
RGD ID:13692822
Promoter ID:EPDNEW_R3347
Type:single initiation site
Name:Cacna2d1_2
Description:calcium voltage-gated channel auxiliary subunit alpha2delta 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R3346  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0416,130,831 - 16,130,891EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/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
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)
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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-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (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
BN/SsN (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
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)
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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
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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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
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)
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
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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
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)
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
M520/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
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)
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
MR/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
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (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
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2247 AgrOrtholog
Ensembl Genes ENSRNOG00000033531 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000034572 UniProtKB/TrEMBL
  ENSRNOP00000044940 UniProtKB/TrEMBL
  ENSRNOP00000074171 UniProtKB/TrEMBL
  ENSRNOP00000074655 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034969 UniProtKB/TrEMBL
  ENSRNOT00000042914 UniProtKB/TrEMBL
  ENSRNOT00000082161 UniProtKB/TrEMBL
  ENSRNOT00000090240 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.410 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro VDCC_a2/dsu UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VWA_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VWF_A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25399 UniProtKB/TrEMBL
NCBI Gene 25399 ENTREZGENE
Pfam VGCC_alpha2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VWA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VWA_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cacna2d1 PhenoGen
PROSITE VWFA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART VWA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K7E5_RAT UniProtKB/TrEMBL
  A0A0G2K8L7_RAT UniProtKB/TrEMBL
  CA2D1_RAT UniProtKB/Swiss-Prot
  D3ZKP9_RAT UniProtKB/TrEMBL
  P54290 ENTREZGENE
  Q8CFG7 ENTREZGENE, UniProtKB/TrEMBL
  Q8VHS9 ENTREZGENE, UniProtKB/TrEMBL
  Q9ERS3 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary F7F134 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Cacna2d1  calcium voltage-gated channel auxiliary subunit alpha2delta 1  Cacna2d1  calcium channel, voltage-dependent, alpha2/delta subunit 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-11-06 Cacna2d1  calcium channel, voltage-dependent, alpha2/delta subunit 1  Cacna2  Calcium channel subunit alpha 2 delta (dihydropyridine - sensitive L-type)  Name updated 625702 APPROVED
2002-06-10 Cacna2  Calcium channel subunit alpha 2 delta (dihydropyridine - sensitive L-type)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_drugs sensitive to dihydropyridine 625474
gene_transcript mRNA upregulated in frontal cortex of AA rat strain compared to ANA rat strain 1358772