Cacna1f (calcium voltage-gated channel subunit alpha1 F) - Rat Genome Database

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Gene: Cacna1f (calcium voltage-gated channel subunit alpha1 F) Rattus norvegicus
Analyze
Symbol: Cacna1f
Name: calcium voltage-gated channel subunit alpha1 F
RGD ID: 621535
Description: Predicted to have high voltage-gated calcium channel activity. Involved in visual perception. Localizes to perikaryon and photoreceptor outer segment. Used to study congenital stationary night blindness. Human ortholog(s) of this gene implicated in Aland Island eye disease; X-linked cone-rod dystrophy 3; congenital stationary night blindness; and congenital stationary night blindness 2A. Orthologous to human CACNA1F (calcium voltage-gated channel subunit alpha1 F); PARTICIPATES IN calcium transport pathway; calcium/calcium-mediated signaling pathway; Alzheimer's disease pathway; INTERACTS WITH atrazine; bisphenol A; Butylparaben.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: calcium channel, voltage-dependent, alpha 1F subunit; calcium channel, voltage-dependent, L type, alpha 1F subunit; voltage-dependent L-type calcium channel subunit alpha-1F
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Cacna1f csnb  
Genetic Models: SD-Cacna1f csnb
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X14,868,096 - 14,896,413 (-)NCBI
Rnor_6.0 EnsemblX15,712,713 - 15,741,103 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X15,712,709 - 15,741,135 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X16,504,174 - 16,532,670 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,908,850 - 26,937,165 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X26,962,318 - 26,990,634 (-)NCBI
CeleraX14,951,395 - 14,979,817 (-)NCBICelera
Cytogenetic MapXq12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
1. An J, etal., Gene. 2015 May 15;562(2):210-9. doi: 10.1016/j.gene.2015.02.073. Epub 2015 Mar 4.
2. An J, etal., J Neurogenet. 2012 Sep;26(3-4):363-73. doi: 10.3109/01677063.2012.684416. Epub 2012 Jul 16.
3. Catterall WA Cold Spring Harb Perspect Biol. 2011 Aug 1;3(8):a003947. doi: 10.1101/cshperspect.a003947.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. GOA data from the GO Consortium
6. Gu Y, etal., Mol Vis. 2008 Jan 9;14:20-8.
7. Jalkanen R, etal., Invest Ophthalmol Vis Sci. 2007 Jun;48(6):2498-502. doi: 10.1167/iovs.06-1103.
8. Jalkanen R, etal., J Med Genet. 2006 Aug;43(8):699-704. doi: 10.1136/jmg.2006.040741. Epub 2006 Feb 27.
9. MGD data from the GO Consortium
10. Morgans CW, etal., Mol Vis 2001 Aug 22;7:202-9.
11. NCBI rat LocusLink and RefSeq merged data July 26, 2002
12. OMIM Disease Annotation Pipeline
13. Pipeline to import KEGG annotations from KEGG into RGD
14. RGD automated data pipeline
15. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16. RGD automated import pipeline for gene-chemical interactions
17. Tao Y, etal., Invest Ophthalmol Vis Sci. 2013 Mar 19;54(3):1988-97. doi: 10.1167/iovs.12-10706.
18. Witkovsky P, etal., J Comp Neurol. 2006 Jul 20;497(3):384-96.
19. Wutz K, etal., Eur J Hum Genet 2002 Aug;10(8):449-56.
20. Zheng L, etal., Neurosci Lett. 2012 Jul 11;521(1):26-30. doi: 10.1016/j.neulet.2012.05.049. Epub 2012 May 24.
Additional References at PubMed
PMID:7571473   PMID:9662399   PMID:9662400   PMID:15897456   PMID:16155113   PMID:21052544   PMID:27226626  


Genomics

Comparative Map Data
Cacna1f
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X14,868,096 - 14,896,413 (-)NCBI
Rnor_6.0 EnsemblX15,712,713 - 15,741,103 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X15,712,709 - 15,741,135 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X16,504,174 - 16,532,670 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,908,850 - 26,937,165 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X26,962,318 - 26,990,634 (-)NCBI
CeleraX14,951,395 - 14,979,817 (-)NCBICelera
Cytogenetic MapXq12NCBI
CACNA1F
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX49,205,063 - 49,233,371 (-)EnsemblGRCh38hg38GRCh38
GRCh38X49,205,063 - 49,233,404 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X49,061,523 - 49,089,802 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X48,948,467 - 48,976,777 (-)NCBINCBI36hg18NCBI36
Build 34X48,817,894 - 48,846,204NCBI
CeleraX52,574,536 - 52,602,846 (+)NCBI
Cytogenetic MapXp11.23NCBI
HuRefX46,718,790 - 46,746,229 (-)NCBIHuRef
CHM1_1X49,093,823 - 49,122,134 (-)NCBICHM1_1
Cacna1f
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X7,473,342 - 7,501,435 (+)NCBIGRCm39mm39
GRCm39 EnsemblX7,473,322 - 7,501,435 (+)Ensembl
GRCm38X7,607,103 - 7,635,196 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX7,607,083 - 7,635,196 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X7,184,229 - 7,212,322 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X6,759,391 - 6,792,153 (+)NCBImm8
MGSCv36X3,776,675 - 3,808,487 (+)NCBImm8
CeleraX3,836,719 - 3,864,582 (-)NCBICelera
Cytogenetic MapXA1.1NCBI
cM MapX3.42NCBI
Cacna1f
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955543692,035 - 717,364 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955543692,035 - 717,364 (-)NCBIChiLan1.0ChiLan1.0
CACNA1F
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X49,356,994 - 49,385,678 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX49,356,994 - 49,385,678 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X41,504,804 - 41,533,501 (-)NCBIMhudiblu_PPA_v0panPan3
CACNA1F
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X42,302,971 - 42,327,787 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX42,303,158 - 42,326,774 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX16,681,688 - 16,706,446 (-)NCBI
ROS_Cfam_1.0X42,444,658 - 42,469,408 (-)NCBI
UMICH_Zoey_3.1X42,428,611 - 42,453,368 (-)NCBI
UNSW_CanFamBas_1.0X42,416,270 - 42,440,826 (-)NCBI
UU_Cfam_GSD_1.0X42,511,022 - 42,535,780 (-)NCBI
Cacna1f
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X34,838,179 - 34,865,828 (-)NCBI
SpeTri2.0NW_0049367211,078,570 - 1,106,153 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CACNA1F
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX43,246,786 - 43,283,990 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X43,250,449 - 43,284,458 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X48,098,467 - 48,132,377 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CACNA1F
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X46,304,831 - 46,330,562 (-)NCBI
Cacna1f
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624893945,378 - 968,041 (-)NCBI

Position Markers
RH139341  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X15,712,742 - 15,712,925NCBIRnor6.0
Rnor_5.0X16,504,207 - 16,504,390UniSTSRnor5.0
RGSC_v3.4X26,908,805 - 26,908,988UniSTSRGSC3.4
CeleraX14,951,350 - 14,951,533UniSTS
RH 3.4 Map5791.3UniSTS
Cytogenetic MapXq13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X144092703Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X166245321592783Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X166260933443848Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X183816624331837Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X428214049282140Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X595407850954078Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat


Genetic Models
This gene Cacna1f is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:41
Count of miRNA genes:39
Interacting mature miRNAs:41
Transcripts:ENSRNOT00000066489
Prediction methods:Miranda, Rnahybrid
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 hemolymphoid system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium
Low 1
Below cutoff 1 9 8 3 5 38 7 10 9 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000066489   ⟹   ENSRNOP00000061835
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX15,712,713 - 15,741,103 (-)Ensembl
RefSeq Acc Id: NM_053701   ⟹   NP_446153
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,868,096 - 14,896,413 (-)NCBI
Rnor_6.0X15,712,787 - 15,741,099 (-)NCBI
Rnor_5.0X16,504,174 - 16,532,670 (-)NCBI
RGSC_v3.4X26,908,850 - 26,937,165 (-)RGD
CeleraX14,951,395 - 14,979,817 (-)RGD
Sequence:
RefSeq Acc Id: XM_006256698   ⟹   XP_006256760
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X15,712,709 - 15,737,527 (-)NCBI
Rnor_5.0X16,504,174 - 16,532,670 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601894   ⟹   XP_017457383
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X15,712,709 - 15,741,135 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601895   ⟹   XP_017457384
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X15,712,709 - 15,736,489 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601896   ⟹   XP_017457385
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X15,717,430 - 15,741,135 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_446153 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAK71987 (Get FASTA)   NCBI Sequence Viewer  
  ABD52241 (Get FASTA)   NCBI Sequence Viewer  
  EDL83844 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_446153   ⟸   NM_053701
- Sequence:
RefSeq Acc Id: XP_006256760   ⟸   XM_006256698
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017457383   ⟸   XM_017601894
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457384   ⟸   XM_017601895
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017457385   ⟸   XM_017601896
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000061835   ⟸   ENSRNOT00000066489
Protein Domains
Ca_chan_IQ

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (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
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 16507949 16507950 C T snv SHRSP/Gcrc (KNAW), WKY/Gcrc (KNAW), GK/Ox (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), WKY/N (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 15716484 15716485 C T snv WKY/N (MCW), GK/Ox (RGD), WKY/Gcrc (RGD), WKY/NCrl (RGD), SHRSP/Gcrc (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621535 AgrOrtholog
Ensembl Genes ENSRNOG00000010348 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000061835 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066489 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.20.120.350 UniProtKB/TrEMBL
InterPro CAC1F_C UniProtKB/TrEMBL
  GPHH_dom UniProtKB/TrEMBL
  Ion_trans UniProtKB/TrEMBL
  VDCC_a1su_IQ UniProtKB/TrEMBL
  VDCC_L_a1su UniProtKB/TrEMBL
  VDCCAlpha1 UniProtKB/TrEMBL
  Volt_channel_dom_sf UniProtKB/TrEMBL
KEGG Report rno:114493 UniProtKB/TrEMBL
NCBI Gene 114493 ENTREZGENE
Pfam Ca_chan_IQ UniProtKB/TrEMBL
  CAC1F_C UniProtKB/TrEMBL
  GPHH UniProtKB/TrEMBL
  Ion_trans UniProtKB/TrEMBL
PhenoGen Cacna1f PhenoGen
PRINTS CACHANNEL UniProtKB/TrEMBL
  LVDCCALPHA1 UniProtKB/TrEMBL
SMART Ca_chan_IQ UniProtKB/TrEMBL
UniProt A1XIQ4_RAT UniProtKB/TrEMBL
  G3V9W8_RAT UniProtKB/TrEMBL
  Q923Z7_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Cacna1f  calcium voltage-gated channel subunit alpha1 F  Cacna1f  calcium channel, voltage-dependent, L type, alpha 1F subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-29 Cacna1f  calcium channel, voltage-dependent, L type, alpha 1F subunit  Cacna1f  calcium channel, voltage-dependent, alpha 1F subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Cacna1f  calcium channel, voltage-dependent, alpha 1F subunit      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Cacna1f  calcium channel, voltage-dependent, alpha 1F subunit      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference