Cacna1b (calcium voltage-gated channel subunit alpha1 B) - Rat Genome Database

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Gene: Cacna1b (calcium voltage-gated channel subunit alpha1 B) Rattus norvegicus
Analyze
Symbol: Cacna1b
Name: calcium voltage-gated channel subunit alpha1 B
RGD ID: 628852
Description: Exhibits high voltage-gated calcium channel activity; protein phosphatase 2A binding activity; and voltage-gated calcium channel activity involved in positive regulation of presynaptic cytosolic calcium levels. Involved in several processes, including positive regulation of neurotransmitter secretion; response to ethanol; and response to testosterone. Localizes to several cellular components, including Schaffer collateral - CA1 synapse; dendritic shaft; and glutamatergic synapse. Human ortholog(s) of this gene implicated in Lambert-Eaton myasthenic syndrome and dystonia 23. Orthologous to human CACNA1B (calcium voltage-gated channel subunit alpha1 B); PARTICIPATES IN calcium transport pathway; calcium/calcium-mediated signaling pathway; mitogen activated protein kinase signaling pathway; INTERACTS WITH 1,2-dimethylhydrazine; 6-propyl-2-thiouracil; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: BIII; brain calcium channel III; calcium channel, L type, alpha-1 polypeptide; calcium channel, voltage-dependent, N type, alpha 1B subunit; LOC102553311; voltage gated N-type calcium channel Ca(v)2.2; voltage-dependent N-type calcium channel subunit alpha-1B; voltage-dependent N-type calcium channel subunit alpha-1B-like; voltage-gated calcium channel subunit alpha Cav2.2
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
mRatBN7.237,380,892 - 7,546,104 (-)NCBI
Rnor_6.0 Ensembl31,740,024 - 1,924,827 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.031,740,026 - 1,924,959 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.031,727,915 - 1,910,475 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.432,842,948 - 3,039,747 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.132,873,390 - 3,039,747 (-)NCBI
Celera32,215,805 - 2,379,072 (-)NCBICelera
Cytogenetic Map3p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

References

References - curated
1. Altier C, etal., J Neurosci. 2007 Jun 13;27(24):6363-73.
2. Berkefeld H, etal., Science. 2006 Oct 27;314(5799):615-20.
3. Brittain JM, etal., J Biol Chem. 2009 Nov 6;284(45):31375-90. Epub 2009 Sep 15.
4. Catterall WA Cold Spring Harb Perspect Biol. 2011 Aug 1;3(8):a003947. doi: 10.1101/cshperspect.a003947.
5. Chapman ER, etal., J Biol Chem. 1998 Dec 4;273(49):32966-72.
6. Fang H, etal., J Biol Chem. 2006 Jul 21;281(29):20011-7. Epub 2006 May 16.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Khanna R, etal., J Biochem Mol Biol. 2007 May 31;40(3):302-14.
9. Kornek B, etal., Brain. 2001 Jun;124(Pt 6):1114-24.
10. Latour I, etal., Glia 2003 Mar;41(4):347-53.
11. Lewis RJ, etal., J Biol Chem. 2000 Nov 10;275(45):35335-44.
12. Li D, etal., J Neurosci. 2005 Feb 23;25(8):1914-23.
13. Lin Z, etal., Neuron 1997 Jan;18(1):153-66.
14. Maingret F, etal., Neuron. 2008 Aug 14;59(3):439-49. doi: 10.1016/j.neuron.2008.05.026.
15. Martin-Moutot N, etal., Neurobiol Dis. 2006 Apr;22(1):57-63. Epub 2005 Nov 11.
16. Maximov A and Bezprozvanny I, J Neurosci 2002 Aug 15;22(16):6939-52.
17. MGD data from the GO Consortium
18. N'Gouemo P and Morad M, Neuroscience 2003;120(3):815-26.
19. N'Gouemo P, etal., Brain Res. 2006 Sep 7;1108(1):216-20. Epub 2006 Jul 24.
20. Nudler SI, etal., Neuroscience. 2005;134(3):817-26.
21. Ohno S, etal., Sci Rep. 2016 Jun 7;6:27192. doi: 10.1038/srep27192.
22. OMIM Disease Annotation Pipeline
23. Pan JQ and Lipscombe D, J Neurosci 2000 Jul 1;20(13):4769-75.
24. Pipeline to import KEGG annotations from KEGG into RGD
25. RGD automated data pipeline
26. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
27. RGD automated import pipeline for gene-chemical interactions
28. Scheuber A, etal., J Neurosci. 2004 Nov 17;24(46):10402-9.
29. Su X, etal., J Urol. 2008 Jun;179(6):2464-9. doi: 10.1016/j.juro.2008.01.088. Epub 2008 Apr 23.
30. Wheeler DB, etal., Science. 1994 Apr 1;264(5155):107-11.
31. Witkovsky P, etal., J Comp Neurol. 2006 Jul 20;497(3):384-96.
Additional References at PubMed
PMID:1317580   PMID:1692134   PMID:7509046   PMID:8125957   PMID:10328888   PMID:10377343   PMID:11036064   PMID:11160515   PMID:11296258   PMID:11438518   PMID:11567049   PMID:12074836  
PMID:12827191   PMID:12890773   PMID:14715140   PMID:15451373   PMID:15768038   PMID:16049174   PMID:16760341   PMID:17293861   PMID:17686036   PMID:17686037   PMID:18054859   PMID:18971475  
PMID:19125229   PMID:19364492   PMID:20181083   PMID:20511524   PMID:21233207   PMID:21521766   PMID:21763275   PMID:22871113   PMID:23022559   PMID:23376566   PMID:23396054   PMID:23648579  
PMID:23807706   PMID:24513289   PMID:24566975   PMID:24646700   PMID:24889613   PMID:25878262   PMID:25966687   PMID:26283199   PMID:26507659   PMID:27489103   PMID:28837380   PMID:28957379  
PMID:29198756   PMID:29208674   PMID:29335317   PMID:29341826   PMID:29436604   PMID:31359322   PMID:31775826   PMID:31923392  


Genomics

Comparative Map Data
Cacna1b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.237,380,892 - 7,546,104 (-)NCBI
Rnor_6.0 Ensembl31,740,024 - 1,924,827 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.031,740,026 - 1,924,959 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.031,727,915 - 1,910,475 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.432,842,948 - 3,039,747 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.132,873,390 - 3,039,747 (-)NCBI
Celera32,215,805 - 2,379,072 (-)NCBICelera
Cytogenetic Map3p13NCBI
CACNA1B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9137,877,782 - 138,124,624 (+)EnsemblGRCh38hg38GRCh38
GRCh389137,877,782 - 138,124,619 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh379140,772,234 - 141,019,071 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369139,892,062 - 140,136,449 (+)NCBINCBI36hg18NCBI36
Build 349138,048,077 - 138,292,468NCBI
Cytogenetic Map9q34.3NCBI
HuRef9110,240,583 - 110,486,666 (+)NCBIHuRef
CHM1_19140,920,972 - 141,166,813 (+)NCBICHM1_1
Cacna1b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39224,493,872 - 24,653,210 (-)NCBIGRCm39mm39
GRCm39 Ensembl224,493,899 - 24,653,164 (-)Ensembl
GRCm38224,603,860 - 24,763,200 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl224,603,887 - 24,763,152 (-)EnsemblGRCm38mm10GRCm38
MGSCv37224,461,895 - 24,618,672 (-)NCBIGRCm37mm9NCBIm37
MGSCv36224,428,384 - 24,585,161 (-)NCBImm8
Celera224,325,634 - 24,485,472 (-)NCBICelera
Cytogenetic Map2A3NCBI
cM Map216.58NCBI
Cacna1b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555135,654,238 - 5,824,386 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555135,654,915 - 5,823,094 (+)NCBIChiLan1.0ChiLan1.0
CACNA1B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19137,935,165 - 138,147,969 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v09108,989,621 - 109,256,841 (+)NCBIMhudiblu_PPA_v0panPan3
CACNA1B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1947,813,625 - 48,009,532 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl947,816,393 - 48,009,406 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha947,000,692 - 47,196,388 (-)NCBI
ROS_Cfam_1.0948,674,418 - 48,870,501 (-)NCBI
UMICH_Zoey_3.1947,454,379 - 47,647,489 (-)NCBI
UNSW_CanFamBas_1.0947,750,936 - 47,946,938 (-)NCBI
UU_Cfam_GSD_1.0947,799,821 - 47,993,105 (-)NCBI
Cacna1b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947203,066,422 - 203,243,631 (+)NCBI
SpeTri2.0NW_004936669133,488 - 308,623 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CACNA1B
(Sus scrofa - pig)
No map positions available.
CACNA1B
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11275,441 - 335,980 (-)NCBI
ChlSab1.1 Ensembl1278,011 - 335,820 (-)Ensembl
Cacna1b
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476078,754 - 257,901 (-)NCBI

Position Markers
D10Wox55  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.237,381,856 - 7,381,967 (+)MAPPER
Rnor_6.031,740,963 - 1,741,075NCBIRnor6.0
Rnor_5.031,728,880 - 1,728,992UniSTSRnor5.0
Celera32,216,742 - 2,216,854UniSTS
Cytogenetic Map3p13UniSTS
AW060892  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.237,382,448 - 7,382,531 (+)MAPPER
Rnor_6.031,741,554 - 1,741,636NCBIRnor6.0
Rnor_5.031,729,471 - 1,729,553UniSTSRnor5.0
RGSC_v3.432,874,894 - 2,874,976UniSTSRGSC3.4
Celera32,217,334 - 2,217,416UniSTS
Cytogenetic Map3p13UniSTS
AW050276  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.237,468,801 - 7,468,887 (+)MAPPER
Rnor_6.031,847,736 - 1,847,821NCBIRnor6.0
Rnor_5.031,832,858 - 1,832,943UniSTSRnor5.0
RGSC_v3.432,962,190 - 2,962,275UniSTSRGSC3.4
Celera32,302,025 - 2,302,110UniSTS
Cytogenetic Map3p13UniSTS
RH138323  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.237,425,353 - 7,425,485 (+)MAPPER
Rnor_6.031,799,514 - 1,799,645NCBIRnor6.0
Rnor_5.031,784,657 - 1,784,788UniSTSRnor5.0
RGSC_v3.432,918,897 - 2,919,028UniSTSRGSC3.4
Celera32,259,411 - 2,259,542UniSTS
Cytogenetic Map3p13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3125786001Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3128136884Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3128500807Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3132972944Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3137891710Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3139773425Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3195176874Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35711366000866Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35711366000866Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1201
Count of miRNA genes:308
Interacting mature miRNAs:415
Transcripts:ENSRNOT00000006162, ENSRNOT00000048945
Prediction methods:Microtar, Miranda, 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 60
Low 2 8 14 8 25
Below cutoff 1 25 24 16 17 16 7 7 14 16 11 7

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001195199 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_147141 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233569 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233570 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233572 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233573 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233574 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233575 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233576 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233577 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233578 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761578 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591500 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591501 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591502 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591503 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591504 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591505 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104389 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104390 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104391 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001837030 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005501788 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF055477 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF222337 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF222338 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF389419 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH007822 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY211499 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY211500 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CS184990 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ431206 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HQ008360 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000115 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M92905 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000006162   ⟹   ENSRNOP00000006162
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl31,742,627 - 1,924,827 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000048945   ⟹   ENSRNOP00000044223
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl31,740,024 - 1,868,015 (-)Ensembl
RefSeq Acc Id: NM_001195199   ⟹   NP_001182128
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.237,383,519 - 7,545,957 (-)NCBI
Rnor_6.031,742,624 - 1,924,827 (-)NCBI
Rnor_5.031,727,915 - 1,910,475 (-)NCBI
Celera32,218,404 - 2,378,990 (-)NCBI
Sequence:
RefSeq Acc Id: NM_147141   ⟹   NP_671482
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.237,380,920 - 7,546,039 (-)NCBI
Rnor_6.031,740,026 - 1,924,909 (-)NCBI
Rnor_5.031,727,915 - 1,910,475 (-)NCBI
RGSC_v3.432,842,948 - 3,039,747 (-)RGD
Celera32,215,805 - 2,379,072 (-)RGD
Sequence:
RefSeq Acc Id: XM_006233569   ⟹   XP_006233631
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.237,380,892 - 7,546,103 (-)NCBI
Rnor_6.031,740,031 - 1,924,959 (-)NCBI
Rnor_5.031,727,915 - 1,910,475 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233570   ⟹   XP_006233632
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.237,380,892 - 7,546,103 (-)NCBI
Rnor_6.031,740,031 - 1,924,959 (-)NCBI
Rnor_5.031,727,915 - 1,910,475 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233572   ⟹   XP_006233634
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.237,383,519 - 7,546,103 (-)NCBI
Rnor_6.031,740,031 - 1,924,959 (-)NCBI
Rnor_5.031,727,915 - 1,910,475 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233573   ⟹   XP_006233635
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.237,380,892 - 7,546,103 (-)NCBI
Rnor_6.031,740,031 - 1,924,959 (-)NCBI
Rnor_5.031,727,915 - 1,910,475 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233574   ⟹   XP_006233636
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.237,380,892 - 7,546,103 (-)NCBI
Rnor_6.031,740,031 - 1,924,959 (-)NCBI
Rnor_5.031,727,915 - 1,910,475 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233575   ⟹   XP_006233637
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.237,380,892 - 7,546,103 (-)NCBI
Rnor_6.031,740,031 - 1,924,959 (-)NCBI
Rnor_5.031,727,915 - 1,910,475 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233576   ⟹   XP_006233638
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.237,380,892 - 7,546,103 (-)NCBI
Rnor_6.031,740,031 - 1,924,959 (-)NCBI
Rnor_5.031,727,915 - 1,910,475 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233577   ⟹   XP_006233639
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.237,383,519 - 7,545,957 (-)NCBI
Rnor_6.031,740,031 - 1,924,959 (-)NCBI
Rnor_5.031,727,915 - 1,910,475 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233578   ⟹   XP_006233640
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.237,383,519 - 7,545,957 (-)NCBI
Rnor_6.031,740,031 - 1,924,959 (-)NCBI
Rnor_5.031,727,915 - 1,910,475 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008761578   ⟹   XP_008759800
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.031,740,031 - 1,924,959 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591500   ⟹   XP_017446989
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.237,380,892 - 7,546,103 (-)NCBI
Rnor_6.031,740,031 - 1,924,959 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591501   ⟹   XP_017446990
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.031,740,031 - 1,924,959 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591502   ⟹   XP_017446991
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.237,380,892 - 7,545,957 (-)NCBI
Rnor_6.031,740,031 - 1,924,959 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591503   ⟹   XP_017446992
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.031,740,031 - 1,924,324 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591504   ⟹   XP_017446993
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.031,774,435 - 1,924,959 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591505   ⟹   XP_017446994
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.237,380,892 - 7,546,103 (-)NCBI
Rnor_6.031,740,031 - 1,924,959 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039104389   ⟹   XP_038960317
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.237,383,519 - 7,546,103 (-)NCBI
RefSeq Acc Id: XM_039104390   ⟹   XP_038960318
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.237,428,221 - 7,546,104 (-)NCBI
RefSeq Acc Id: XM_039104391   ⟹   XP_038960319
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.237,380,892 - 7,461,046 (-)NCBI
RefSeq Acc Id: XR_001837030
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.031,774,450 - 1,924,959 (-)NCBI
Sequence:
RefSeq Acc Id: XR_005501788
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.237,396,107 - 7,546,104 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001182128 (Get FASTA)   NCBI Sequence Viewer  
  NP_671482 (Get FASTA)   NCBI Sequence Viewer  
  XP_006233631 (Get FASTA)   NCBI Sequence Viewer  
  XP_006233632 (Get FASTA)   NCBI Sequence Viewer  
  XP_006233634 (Get FASTA)   NCBI Sequence Viewer  
  XP_006233635 (Get FASTA)   NCBI Sequence Viewer  
  XP_006233636 (Get FASTA)   NCBI Sequence Viewer  
  XP_006233637 (Get FASTA)   NCBI Sequence Viewer  
  XP_006233638 (Get FASTA)   NCBI Sequence Viewer  
  XP_006233639 (Get FASTA)   NCBI Sequence Viewer  
  XP_006233640 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446989 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446991 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446994 (Get FASTA)   NCBI Sequence Viewer  
  XP_038960317 (Get FASTA)   NCBI Sequence Viewer  
  XP_038960318 (Get FASTA)   NCBI Sequence Viewer  
  XP_038960319 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA42014 (Get FASTA)   NCBI Sequence Viewer  
  AAC29043 (Get FASTA)   NCBI Sequence Viewer  
  AAD31922 (Get FASTA)   NCBI Sequence Viewer  
  AAF70136 (Get FASTA)   NCBI Sequence Viewer  
  AAF70137 (Get FASTA)   NCBI Sequence Viewer  
  AAK71643 (Get FASTA)   NCBI Sequence Viewer  
  AAO53228 (Get FASTA)   NCBI Sequence Viewer  
  AAO53229 (Get FASTA)   NCBI Sequence Viewer  
  AAO53230 (Get FASTA)   NCBI Sequence Viewer  
  ACJ61258 (Get FASTA)   NCBI Sequence Viewer  
  ADM13675 (Get FASTA)   NCBI Sequence Viewer  
  CAJ41867 (Get FASTA)   NCBI Sequence Viewer  
  Q02294 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_671482   ⟸   NM_147141
- Peptide Label: isoform 2
- UniProtKB: O89089 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001182128   ⟸   NM_001195199
- Peptide Label: isoform 1
- UniProtKB: E1AW38 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233640   ⟸   XM_006233578
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_006233638   ⟸   XM_006233576
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_006233639   ⟸   XM_006233577
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_006233637   ⟸   XM_006233575
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_006233632   ⟸   XM_006233570
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006233636   ⟸   XM_006233574
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_006233635   ⟸   XM_006233573
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006233634   ⟸   XM_006233572
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006233631   ⟸   XM_006233569
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008759800   ⟸   XM_008761578
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017446991   ⟸   XM_017591502
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_017446994   ⟸   XM_017591505
- Peptide Label: isoform X15
- Sequence:
RefSeq Acc Id: XP_017446989   ⟸   XM_017591500
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017446990   ⟸   XM_017591501
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017446992   ⟸   XM_017591503
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_017446993   ⟸   XM_017591504
- Peptide Label: isoform X15
- Sequence:
RefSeq Acc Id: ENSRNOP00000006162   ⟸   ENSRNOT00000006162
RefSeq Acc Id: ENSRNOP00000044223   ⟸   ENSRNOT00000048945
RefSeq Acc Id: XP_038960319   ⟸   XM_039104391
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038960317   ⟸   XM_039104389
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038960318   ⟸   XM_039104390
- Peptide Label: isoform X13
Protein Domains
EF-hand   GPHH

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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 1775907 1775908 T G snv SR/JrHsd (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 2910147 2910148 T G snv SR/JrHsd (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:628852 AgrOrtholog
BIND 128230
  130592
Ensembl Genes ENSRNOG00000004560 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000006162 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000044223 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006162 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000048945 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.20.120.350 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro EF_hand_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPHH_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ion_trans_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VDCC_a1su_IQ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VDCC_N_a1su UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VDCCAlpha1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VGCC_Ca_Na UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Volt_channel_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:257648 UniProtKB/TrEMBL
NCBI Gene 257648 ENTREZGENE
PANTHER PTHR10037 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10037:SF289 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR45628:SF6 UniProtKB/TrEMBL
Pfam Ca_chan_IQ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPHH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ion_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cacna1b PhenoGen
PRINTS CACHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NVDCCALPHA1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE EF_HAND_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Ca_chan_IQ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B7U4V7_RAT UniProtKB/TrEMBL
  CAC1B_RAT UniProtKB/Swiss-Prot
  E1AW38 ENTREZGENE, UniProtKB/TrEMBL
  F1LQ87_RAT UniProtKB/TrEMBL
  F1LRE0_RAT UniProtKB/TrEMBL
  O89089 ENTREZGENE, UniProtKB/TrEMBL
  Q02294 ENTREZGENE
  Q6XS92_RAT UniProtKB/TrEMBL
  Q6XS93_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Cacna1b  calcium voltage-gated channel subunit alpha1 B  LOC102553311  voltage-dependent N-type calcium channel subunit alpha-1B-like  Data Merged 737654 PROVISIONAL
2016-02-11 Cacna1b  calcium voltage-gated channel subunit alpha1 B  Cacna1b  calcium channel, voltage-dependent, N type, alpha 1B subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-12-18 LOC102553311  voltage-dependent N-type calcium channel subunit alpha-1B-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-12-14 Cacna1b  calcium channel, voltage-dependent, N type, alpha 1B subunit      Symbol and Name status set to approved 1299863 APPROVED
2003-02-27 Cacna1b  calcium channel, voltage-dependent, N type, alpha 1B subunit      Symbol and Name status set to provisional 70820 PROVISIONAL