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 transmembrane transport via high voltage-gated calcium channel; calcium ion transport into cytosol; and regulation of membrane repolarization during action potential. Part of L-type voltage-gated calcium channel complex. Is active in glutamatergic synapse; postsynaptic membrane; and presynaptic active zone membrane. Biomarker of brain infarction. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 110. 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 2,3,7,8-tetrachlorodibenzodioxine; 2-acetamidofluorene; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously 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 Orthologs
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
GRCr8419,902,324 - 20,330,287 (-)NCBIGRCr8
mRatBN7.2418,950,611 - 19,374,969 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl418,951,002 - 19,374,969 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx424,107,697 - 24,535,090 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0419,924,586 - 20,351,968 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0418,305,637 - 18,733,033 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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  (EXP,ISO)
2-acetamidofluorene  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
acetamide  (EXP)
aflatoxin B1  (ISO)
allethrin  (EXP)
alpha-Zearalanol  (EXP)
amitriptyline  (EXP)
ammonium chloride  (EXP)
androgen antagonist  (EXP)
aristolochic acid A  (ISO)
arsenous acid  (ISO)
asbestos  (ISO)
barium(0)  (EXP,ISO)
benzene  (EXP)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
Brodifacoum  (EXP)
butanal  (ISO)
Butylparaben  (EXP)
cadmium dichloride  (EXP)
calcium atom  (EXP,ISO)
calcium(0)  (EXP,ISO)
cannabidiol  (EXP)
cantharidin  (ISO)
carbon nanotube  (ISO)
chenodeoxycholic acid  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
cisplatin  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
cyhalothrin  (EXP)
cypermethrin  (EXP)
deoxycholic acid  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dorsomorphin  (ISO)
entinostat  (ISO)
enzacamene  (EXP)
ethanol  (EXP,ISO)
fenvalerate  (EXP)
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 diacetate  (ISO)
lead(0)  (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)
oxybenzone  (ISO)
paclitaxel  (ISO)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorooctanoic acid  (EXP)
phenylmercury acetate  (ISO)
PhIP  (EXP)
potassium chloride  (ISO)
potassium chromate  (ISO)
pregabalin  (EXP,ISO)
progesterone  (ISO)
pyrethrins  (EXP)
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  (EXP,ISO)
trichloroethene  (EXP)
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

References - curated
# Reference Title Reference Citation
1. The increased trafficking of the calcium channel subunit alpha2delta-1 to presynaptic terminals in neuropathic pain is inhibited by the alpha2delta ligand pregabalin. Bauer CS, etal., J Neurosci. 2009 Apr 1;29(13):4076-88. doi: 10.1523/JNEUROSCI.0356-09.2009.
2. Molecular determinants of the CaVbeta-induced plasma membrane targeting of the CaV1.2 channel. Bourdin B, etal., J Biol Chem. 2010 Jul 23;285(30):22853-63. doi: 10.1074/jbc.M110.111062. Epub 2010 May 17.
3. Functional characterization of CaValpha2delta mutations associated with sudden cardiac death. Bourdin B, etal., J Biol Chem. 2015 Jan 30;290(5):2854-69. doi: 10.1074/jbc.M114.597930. Epub 2014 Dec 19.
4. Identification of new therapeutic targets by genome-wide analysis of gene expression in the ipsilateral cortex of aged rats after stroke. Buga AM, etal., PLoS One. 2012;7(12):e50985. doi: 10.1371/journal.pone.0050985. Epub 2012 Dec 12.
5. Two sets of amino acids of the domain I of Cav2.3 Ca(2+) channels contribute to their high sensitivity to extracellular protons. Cens T, etal., Pflugers Arch. 2011 Aug;462(2):303-14. doi: 10.1007/s00424-011-0974-x. Epub 2011 May 25.
6. Molecular cloning of calcium channel alpha(2)delta-subunits from rat atria and the differential regulation of their expression by IGF-1. Chu PJ and Best PM, J Mol Cell Cardiol 2003 Feb;35(2):207-15.
7. Gabapentin receptor alpha2delta-1 is a neuronal thrombospondin receptor responsible for excitatory CNS synaptogenesis. Eroglu C, etal., Cell. 2009 Oct 16;139(2):380-92. doi: 10.1016/j.cell.2009.09.025. Epub 2009 Oct 8.
8. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
10. Rat brain expresses an alternatively spliced form of the dihydropyridine-sensitive L-type calcium channel alpha 2 subunit. Kim HL, etal., Proc Natl Acad Sci U S A 1992 Apr 15;89(8):3251-5.
11. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
12. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
13. GOA pipeline RGD automated data pipeline
14. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
15. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
16. Transcriptome analysis of frontal cortex in alcohol-preferring and nonpreferring rats. Worst TJ, etal., J Neurosci Res 2005 May 15;80(4):529-38.
17. Cloning of a functional splice variant of L-type calcium channel beta 2 subunit from rat heart. Yamada Y, etal., J Biol Chem 2001 Dec 14;276(50):47163-70.
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:33811955   PMID:33986433   PMID:35053304  
PMID:35352799  


Genomics

Comparative Map Data
Cacna2d1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8419,902,324 - 20,330,287 (-)NCBIGRCr8
mRatBN7.2418,950,611 - 19,374,969 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl418,951,002 - 19,374,969 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx424,107,697 - 24,535,090 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0419,924,586 - 20,351,968 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0418,305,637 - 18,733,033 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh38781,946,444 - 82,443,956 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl781,946,444 - 82,443,956 (-)EnsemblGRCh38hg38GRCh38
GRCh37781,575,760 - 82,073,272 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36781,417,354 - 81,910,967 (-)NCBINCBI36Build 36hg18NCBI36
Build 34781,224,068 - 81,717,682NCBI
Celera776,279,569 - 76,773,517 (-)NCBICelera
Cytogenetic Map7q21.11NCBI
HuRef776,182,274 - 76,676,613 (-)NCBIHuRef
CHM1_1781,509,503 - 82,003,079 (-)NCBICHM1_1
T2T-CHM13v2.0783,197,632 - 83,695,210 (-)NCBIT2T-CHM13v2.0
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 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl516,139,786 - 16,579,502 (+)EnsemblGRCm39 Ensembl
GRCm38515,934,264 - 16,374,511 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl515,934,691 - 16,374,511 (+)EnsemblGRCm38mm10GRCm38
MGSCv37515,440,509 - 15,880,329 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36515,446,612 - 15,882,875 (+)NCBIMGSCv36mm8
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
NHGRI_mPanPan1-v2699,798,532 - 100,295,629 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan17148,063,168 - 148,557,074 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0773,917,439 - 74,410,627 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1787,575,054 - 88,068,480 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl787,579,004 - 88,068,482 (-)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01822,009,947 - 22,485,359 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1822,009,954 - 22,485,691 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11821,646,522 - 22,121,006 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01821,182,147 - 21,656,514 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01821,836,185 - 22,311,929 (-)NCBIUU_Cfam_GSD_1.0
Cacna2d1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511863,375,924 - 63,825,676 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936734581,538 - 1,027,018 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936734577,656 - 1,027,412 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CACNA2D1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl997,781,090 - 98,266,969 (+)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 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2166,770,578 - 66,934,898 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604237,008,715 - 37,508,631 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cacna2d1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473930,436,568 - 30,864,468 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473930,436,662 - 30,864,482 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cacna2d1
3323 total Variants
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.


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

Markers in Region
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


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

Nucleotide Sequences
RefSeq Transcripts NM_001110847 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001110848 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_012919 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006235981 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006235982 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006235983 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592485 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063285604 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063285605 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063285606 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063285607 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063285608 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063285609 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063285610 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063285611 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC123251 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF286488 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF400662 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF486276 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220567 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000004 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M86621 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000034969   ⟹   ENSRNOP00000034572
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl415,710,805 - 16,130,563 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000042914   ⟹   ENSRNOP00000044940
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
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl415,710,793 - 16,130,563 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000110623   ⟹   ENSRNOP00000079383
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl419,239,836 - 19,374,969 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115152   ⟹   ENSRNOP00000079129
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
GRCr8419,906,137 - 20,329,874 (-)NCBI
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
GRCr8419,906,140 - 20,329,862 (-)NCBI
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
GRCr8419,905,751 - 20,330,147 (-)NCBI
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:
RefSeq Acc Id: XM_063285604   ⟹   XP_063141674
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8419,902,324 - 20,330,138 (-)NCBI
RefSeq Acc Id: XM_063285605   ⟹   XP_063141675
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8419,902,324 - 20,330,138 (-)NCBI
RefSeq Acc Id: XM_063285606   ⟹   XP_063141676
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8419,902,324 - 20,330,287 (-)NCBI
RefSeq Acc Id: XM_063285607   ⟹   XP_063141677
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8419,902,324 - 20,330,138 (-)NCBI
RefSeq Acc Id: XM_063285608   ⟹   XP_063141678
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8419,902,324 - 20,330,152 (-)NCBI
RefSeq Acc Id: XM_063285609   ⟹   XP_063141679
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8419,937,303 - 20,330,145 (-)NCBI
RefSeq Acc Id: XM_063285610   ⟹   XP_063141680
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8419,937,303 - 20,330,138 (-)NCBI
RefSeq Acc Id: XM_063285611   ⟹   XP_063141681
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8419,902,324 - 19,953,088 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_037051   ⟸   NM_012919
- Peptide Label: isoform 1 precursor
- UniProtKB: P54290 (UniProtKB/Swiss-Prot),   Q9ERS3 (UniProtKB/TrEMBL),   F7F134 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001104317   ⟸   NM_001110847
- Peptide Label: isoform 3 precursor
- UniProtKB: P54290 (UniProtKB/Swiss-Prot),   Q8VHS9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001104318   ⟸   NM_001110848
- Peptide Label: isoform 2 precursor
- UniProtKB: P54290 (UniProtKB/Swiss-Prot),   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
RefSeq Acc Id: XP_063141676   ⟸   XM_063285606
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063141678   ⟸   XM_063285608
- Peptide Label: isoform X5
RefSeq Acc Id: XP_063141677   ⟸   XM_063285607
- Peptide Label: isoform X4
RefSeq Acc Id: XP_063141675   ⟸   XM_063285605
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063141674   ⟸   XM_063285604
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063141681   ⟸   XM_063285611
- Peptide Label: isoform X8
RefSeq Acc Id: XP_063141679   ⟸   XM_063285609
- Peptide Label: isoform X6
RefSeq Acc Id: XP_063141680   ⟸   XM_063285610
- Peptide Label: isoform X7
Protein Domains
Cache   Voltage-dependent calcium channel alpha-2/delta   VWFA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P54290-F1-model_v2 AlphaFold P54290 1-1091 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2247 AgrOrtholog
BioCyc Gene G2FUF-45894 BioCyc
Ensembl Genes ENSRNOG00000033531 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000042914 ENTREZGENE
  ENSRNOT00000042914.5 UniProtKB/TrEMBL
  ENSRNOT00000082161.2 UniProtKB/TrEMBL
  ENSRNOT00000110623.1 UniProtKB/TrEMBL
  ENSRNOT00000115152.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.410 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PAS domain 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
PANTHER VOLTAGE-DEPENDENT CALCIUM CHANNEL SUBUNIT ALPHA-2/DELTA-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VOLTAGE-DEPENDENT CALCIUM CHANNEL SUBUNIT ALPHA-2/DELTA-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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
RatGTEx ENSRNOG00000033531 RatGTEx
SMART VWA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K8L7_RAT UniProtKB/TrEMBL
  A0A8I5ZMB5_RAT UniProtKB/TrEMBL
  A0A8I5ZNC6_RAT UniProtKB/TrEMBL
  A0A8J8XTR6_RAT UniProtKB/TrEMBL
  A6K5F0_RAT UniProtKB/TrEMBL
  A6K5F1_RAT UniProtKB/TrEMBL
  A6K5F2_RAT UniProtKB/TrEMBL
  A6K5F3_RAT UniProtKB/TrEMBL
  CA2D1_RAT UniProtKB/Swiss-Prot
  F7F134 ENTREZGENE
  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