Cacna1i (calcium voltage-gated channel subunit alpha1 I) - Rat Genome Database

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Gene: Cacna1i (calcium voltage-gated channel subunit alpha1 I) Rattus norvegicus
Analyze
Symbol: Cacna1i
Name: calcium voltage-gated channel subunit alpha1 I
RGD ID: 68944
Description: Exhibits low voltage-gated calcium channel activity. Involved in calcium ion import; calcium ion transport into cytosol; and regulation of membrane potential. Predicted to localize to neuron projection and voltage-gated sodium channel complex. Biomarker of sciatic neuropathy. Human ortholog(s) of this gene implicated in schizophrenia. Orthologous to human CACNA1I (calcium voltage-gated channel subunit alpha1 I); PARTICIPATES IN calcium transport pathway; calcium/calcium-mediated signaling pathway; mitogen activated protein kinase signaling pathway; INTERACTS WITH 3-isobutyl-1-methyl-7H-xanthine; ammonium chloride; androgen antagonist.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: calcium channel, voltage-dependent, alpha 1I subunit; calcium channel, voltage-dependent, T type, alpha 1I subunit; caVT.3; hypothetical gene supported by NM_020084; LOC497824; low voltage-activated T-type calcium channel alpha-1 subunit (CACNA1I); voltage-dependent calcium channel; voltage-dependent T-type calcium channel subunit alpha-1I; voltage-gated calcium channel subunit alpha Cav3.3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27111,835,996 - 111,947,418 (+)NCBI
Rnor_6.0 Ensembl7121,511,097 - 121,619,283 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07121,521,787 - 121,619,300 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07121,509,362 - 121,609,542 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47118,582,279 - 118,681,537 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17118,604,777 - 118,715,750 (+)NCBI
Celera7108,173,442 - 108,270,677 (+)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Catterall WA Cold Spring Harb Perspect Biol. 2011 Aug 1;3(8):a003947. doi: 10.1101/cshperspect.a003947.
2. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. GOA data from the GO Consortium
4. González B, etal., Addict Biol. 2016 May;21(3):589-602. doi: 10.1111/adb.12249. Epub 2015 Apr 14.
5. Iftinca M, etal., Neuroscience. 2006 Nov 3;142(4):1031-42. Epub 2006 Aug 28.
6. Kang HW, etal., Biochim Biophys Acta. 2008 Dec;1778(12):2740-8. Epub 2008 Aug 9.
7. Lee JH, etal., J Neurophysiol 2002 Jun;87(6):2844-50.
8. Lee JH, etal., J Neurosci 1999 Mar 15;19(6):1912-21.
9. Ma YP and Pan ZH, Vis Neurosci 2003 Mar-Apr;20(2):131-9.
10. McRory JE, etal., J Biol Chem 2001 Feb 9;276(6):3999-4011.
11. Murbartian J, etal., FEBS Lett 2002 Sep 25;528(1-3):272-8.
12. NCBI rat LocusLink and RefSeq merged data July 26, 2002
13. Pipeline to import KEGG annotations from KEGG into RGD
14. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
15. RGD automated import pipeline for gene-chemical interactions
16. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
17. Wen XJ, etal., Acta Pharmacol Sin. 2006 Dec;27(12):1547-52. doi: 10.1111/j.1745-7254.2006.00461.x.
18. Xie Y, etal., Hereditas. 2018 Jan 2;155:16. doi: 10.1186/s41065-017-0054-0. eCollection 2018.
19. Xu W, etal., Hereditas. 2017 Jul 17;155:5. doi: 10.1186/s41065-017-0037-1. eCollection 2018.
20. Yue J, etal., Spine (Phila Pa 1976). 2013 Mar 15;38(6):463-70. doi: 10.1097/BRS.0b013e318272fbf8.
Additional References at PubMed
PMID:16505194   PMID:16567615   PMID:21808016   PMID:25454347   PMID:28974111   PMID:31666636  


Genomics

Comparative Map Data
Cacna1i
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27111,835,996 - 111,947,418 (+)NCBI
Rnor_6.0 Ensembl7121,511,097 - 121,619,283 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07121,521,787 - 121,619,300 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07121,509,362 - 121,609,542 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47118,582,279 - 118,681,537 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17118,604,777 - 118,715,750 (+)NCBI
Celera7108,173,442 - 108,270,677 (+)NCBICelera
Cytogenetic Map7q34NCBI
CACNA1I
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2239,570,753 - 39,689,735 (+)EnsemblGRCh38hg38GRCh38
GRCh382239,570,753 - 39,689,737 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372239,966,758 - 40,085,740 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362238,296,704 - 38,415,686 (+)NCBINCBI36hg18NCBI36
Build 342238,291,257 - 38,410,238NCBI
Celera2223,768,830 - 23,887,794 (+)NCBI
Cytogenetic Map22q13.1NCBI
HuRef2222,931,166 - 23,048,848 (+)NCBIHuRef
CHM1_12239,925,499 - 40,044,841 (+)NCBICHM1_1
Cacna1i
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391580,171,439 - 80,282,493 (+)NCBIGRCm39mm39
GRCm39 Ensembl1580,171,439 - 80,282,480 (+)Ensembl
GRCm381580,287,238 - 80,398,292 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1580,287,238 - 80,398,279 (+)EnsemblGRCm38mm10GRCm38
MGSCv371580,117,668 - 80,228,722 (+)NCBIGRCm37mm9NCBIm37
MGSCv361580,114,300 - 80,225,547 (+)NCBImm8
Celera1582,404,367 - 82,516,148 (+)NCBICelera
Cytogenetic Map15E1NCBI
Cacna1i
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541325,453,703 - 25,535,530 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541325,440,533 - 25,538,367 (+)NCBIChiLan1.0ChiLan1.0
CACNA1I
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12238,325,411 - 38,412,923 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2238,296,436 - 38,414,963 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02220,463,511 - 20,595,253 (+)NCBIMhudiblu_PPA_v0panPan3
CACNA1I
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11025,381,446 - 25,493,680 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1025,380,943 - 25,482,852 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1025,317,909 - 25,429,936 (-)NCBI
ROS_Cfam_1.01026,133,456 - 26,245,748 (-)NCBI
UMICH_Zoey_3.11025,845,366 - 25,946,629 (-)NCBI
UNSW_CanFamBas_1.01026,167,842 - 26,279,957 (-)NCBI
UU_Cfam_GSD_1.01026,337,549 - 26,455,352 (-)NCBI
Cacna1i
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049458,980,016 - 9,035,382 (-)NCBI
SpeTri2.0NW_0049364921,990,430 - 2,030,744 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CACNA1I
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl58,595,142 - 8,712,393 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.158,593,014 - 8,702,734 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.255,894,595 - 6,011,363 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CACNA1I
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11922,129,795 - 22,264,485 (+)NCBI
ChlSab1.1 Ensembl1922,143,980 - 22,261,098 (+)Ensembl
Cacna1i
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247528,702,320 - 8,795,192 (-)NCBI

Position Markers
D7Hmgc1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.07121,536,547 - 121,536,752NCBIRnor6.0
Rnor_5.07121,524,620 - 121,524,825UniSTSRnor5.0
RGSC_v3.47118,596,768 - 118,596,974RGDRGSC3.4
RGSC_v3.47118,596,769 - 118,596,974UniSTSRGSC3.4
Celera7108,189,147 - 108,189,352UniSTS
RH 3.4 Map7860.8RGD
RH 3.4 Map7860.8UniSTS
Cytogenetic Map7q34UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)748118835128611831Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)750704769128085642Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)755072862123602998Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)755072862123602998Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)755072862123602998Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)771448715145729302Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)777428105127748511Rat
1357338Stl17Serum triglyceride level QTL 173.23blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)777428234122421148Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)781645773140745067Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)788365265121986709Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)788365265133365265Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)788365265134673427Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)791018361136018361Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)793726906138726906Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)793726906138726906Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)796630946141630946Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7100028953145729302Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)7100160423140335001Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)7100192194145192194Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)7103815550126525386Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)7103867802126080176Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)7106564316145729302Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7111519266143965591Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7112429186126525386Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7114825174145729302Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7115922628145729302Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7120746024145692398Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:93
Count of miRNA genes:75
Interacting mature miRNAs:80
Transcripts:ENSRNOT00000048790
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

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 42
Low 26 8 23
Below cutoff 12 19 8 17 8 6 7 6 14 18 7 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000084352
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7121,521,787 - 121,619,194 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000086192
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7121,511,097 - 121,614,469 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092608
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7121,511,097 - 121,619,283 (+)Ensembl
RefSeq Acc Id: NM_020084   ⟹   NP_064469
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27111,846,738 - 111,944,705 (+)NCBI
Rnor_6.07121,521,787 - 121,619,300 (+)NCBI
Rnor_5.07121,509,362 - 121,609,542 (+)NCBI
RGSC_v3.47118,582,279 - 118,681,537 (+)RGD
Celera7108,173,442 - 108,270,677 (+)RGD
Sequence:
RefSeq Acc Id: XM_039079795   ⟹   XP_038935723
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27111,835,997 - 111,947,418 (+)NCBI
RefSeq Acc Id: XM_039079796   ⟹   XP_038935724
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27111,835,996 - 111,947,418 (+)NCBI
RefSeq Acc Id: XM_039079797   ⟹   XP_038935725
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27111,835,997 - 111,947,418 (+)NCBI
RefSeq Acc Id: XM_039079798   ⟹   XP_038935726
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27111,835,997 - 111,947,418 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_064469   ⟸   NM_020084
- Sequence:
RefSeq Acc Id: XP_038935724   ⟸   XM_039079796
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038935723   ⟸   XM_039079795
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038935725   ⟸   XM_039079797
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038935726   ⟸   XM_039079798
- Peptide Label: isoform X4

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 (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 (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/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (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
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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)
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
FHH/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)
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)
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)
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
GH/OmrMcwi (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)
GK/Ox (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
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 (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary 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/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 (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 (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 (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:68944 AgrOrtholog
Ensembl Genes ENSRNOG00000060407 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000092608 ENTREZGENE
Gene3D-CATH 1.20.120.350 UniProtKB/Swiss-Prot
InterPro CACNA1I UniProtKB/Swiss-Prot
  Ion_trans_dom UniProtKB/Swiss-Prot
  VDCC_T_a1 UniProtKB/Swiss-Prot
  VDCCAlpha1 UniProtKB/Swiss-Prot
  VGCC_Ca_Na UniProtKB/Swiss-Prot
  Volt_channel_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:56827 UniProtKB/Swiss-Prot
NCBI Gene 56827 ENTREZGENE
PANTHER PTHR10037 UniProtKB/Swiss-Prot
  PTHR10037:SF209 UniProtKB/Swiss-Prot
Pfam Ion_trans UniProtKB/Swiss-Prot
PhenoGen Cacna1i PhenoGen
PRINTS CACHANNEL UniProtKB/Swiss-Prot
  TVDCCALPHA1 UniProtKB/Swiss-Prot
TIGR TC209367
UniProt CAC1I_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q9EQ59 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Cacna1i  calcium voltage-gated channel subunit alpha1 I  Cacna1i  calcium voltage-gated channel subunit alpha1 I  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-11 Cacna1i  calcium voltage-gated channel subunit alpha1 I  Cacna1i  calcium channel, voltage-dependent, T type, alpha 1I subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-04-17 Cacna1i  calcium channel, voltage-dependent, T type, alpha 1I subunit  LOC497824  hypothetical gene supported by NM_020084  Data Merged 737654 PROVISIONAL
2008-09-29 Cacna1i  calcium channel, voltage-dependent, T type, alpha 1I subunit  Cacna1i  calcium channel, voltage-dependent, alpha 1I subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC497824  hypothetical gene supported by NM_020084      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-09-10 Cacna1i  calcium channel, voltage-dependent, alpha 1I subunit    calcium channel, voltage-dependent, T type, alpha 1I subunit  Name updated 1299863 APPROVED
2002-06-10 Cacna1i  calcium channel, voltage-dependent, T type, alpha 1I subunit      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed throughout the newborn and juvenile brain 62421
gene_expression mRNA expression is restricted to the striatum 68748
gene_process mediates voltage-dependent entry of calcium into nerve, muscle, and endocrine cells 68748
gene_process responsible for central neuron rebound burst firing and implicated in slow wave sleep and epilepsy 68748
gene_process may play a role in hormone secretion and smooth muscle excitability 68748