Trpc6 (transient receptor potential cation channel, subfamily C, member 6) - Rat Genome Database

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Gene: Trpc6 (transient receptor potential cation channel, subfamily C, member 6) Rattus norvegicus
Analyze
Symbol: Trpc6
Name: transient receptor potential cation channel, subfamily C, member 6
RGD ID: 619788
Description: Enables several functions, including ATPase binding activity; clathrin binding activity; and cytoskeletal protein binding activity. Involved in several processes, including cellular response to hydrogen peroxide; generation of neurons; and positive regulation of peptidyl-threonine phosphorylation. Located in plasma membrane. Used to study focal segmental glomerulosclerosis; kidney disease; and transient cerebral ischemia. Biomarker of type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in chronic fatigue syndrome; focal segmental glomerulosclerosis; focal segmental glomerulosclerosis 2; and nephrotic syndrome type 2. Orthologous to human TRPC6 (transient receptor potential cation channel subfamily C member 6); PARTICIPATES IN endothelin signaling pathway; erythropoietin signaling pathway; INTERACTS WITH 1-Oleoyl-2-acetyl-sn-glycerol; 17alpha-ethynylestradiol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: short transient receptor potential channel 6; transient receptor protein 6; Trrp6
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Trpc6em3Mcwi   Trpc6em4Mcwi   Trpc6em1Mcwi  
Genetic Models: SS-Trpc6em1Mcwi SS-Trpc6em4Mcwi SS-Trpc6em3Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
NCBI Annotation Information: Annotation category: suggests misassembly; Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.285,759,387 - 5,864,000 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl85,758,935 - 5,828,092 (+)Ensembl
Rnor_6.086,811,543 - 6,917,534 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl86,811,543 - 6,917,535 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.086,799,564 - 6,904,623 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.485,472,515 - 5,577,537 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.185,472,514 - 5,577,536 (+)NCBI
Celera87,300,179 - 7,404,007 (+)NCBICelera
Cytogenetic Map8q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(+)-conocarpan  (ISO)
1-Oleoyl-2-acetyl-sn-glycerol  (EXP,ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (EXP)
8-bromo-3',5'-cyclic GMP  (EXP,ISO)
acetylcholine  (EXP)
aflatoxin B1  (ISO)
alpha-Zearalanol  (ISO)
amiloride  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
barium(0)  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Butylbenzyl phthalate  (EXP)
cadmium atom  (ISO)
caesium atom  (ISO)
calcium atom  (EXP,ISO)
calcium(0)  (EXP,ISO)
carbachol  (ISO)
cefaloridine  (EXP)
chlordecone  (ISO)
chloroprene  (ISO)
Cuprizon  (EXP)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dibenziodolium  (ISO)
dibutyl phthalate  (EXP)
diethyl phthalate  (EXP)
diisobutyl phthalate  (EXP)
diisononyl phthalate  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP)
endosulfan  (EXP)
entinostat  (ISO)
fasudil  (ISO)
flavonoids  (EXP)
flufenamic acid  (EXP,ISO)
furan  (EXP)
gadolinium atom  (ISO)
GDP-beta-S  (ISO)
geldanamycin  (ISO)
guanosine 5'-[gamma-thio]triphosphate  (ISO)
hydrogen peroxide  (ISO)
iron atom  (ISO)
iron(0)  (ISO)
KT 5823  (EXP,ISO)
lanthanum atom  (ISO)
lead diacetate  (ISO)
lithium atom  (ISO)
lithium hydride  (ISO)
manganese atom  (EXP,ISO)
manganese(0)  (EXP,ISO)
ML-7  (ISO)
nickel atom  (ISO)
nitrofen  (EXP)
ouabain  (EXP)
oxaliplatin  (EXP)
panobinostat  (ISO)
phenylephrine  (EXP)
pirinixic acid  (ISO)
potassium atom  (ISO)
progesterone  (EXP,ISO)
reactive oxygen species  (EXP)
resveratrol  (EXP)
rubidium atom  (ISO)
S-nitroso-N-acetyl-D-penicillamine  (EXP)
salvianolic acid B  (EXP)
SB 431542  (ISO)
sildenafil citrate  (ISO)
SKF-96365 hydrochloride  (EXP,ISO)
sodium arsenite  (ISO)
sodium atom  (ISO)
strontium atom  (ISO)
sulforaphane  (ISO)
tetrachloromethane  (EXP)
tetraphene  (ISO)
thapsigargin  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
U-73122  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
Y-27632  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. Alessandri-Haber N, etal., J Neurosci. 2009 May 13;29(19):6217-28. doi: 10.1523/JNEUROSCI.0893-09.2009.
2. Du W, etal., J Clin Invest. 2010 Oct;120(10):3480-92. doi: 10.1172/JCI43165. Epub 2010 Sep 1.
3. Erac Y, etal., Age (Dordr). 2010 Jun;32(2):223-30. doi: 10.1007/s11357-009-9126-z. Epub 2010 Jan 13.
4. Fortin DA, etal., J Neurosci. 2012 Jun 13;32(24):8127-37. doi: 10.1523/JNEUROSCI.6034-11.2012.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. Goel M, etal., Pflugers Arch. 2005 Oct;451(1):87-98. Epub 2005 Jul 16.
7. Graham S, etal., J Biol Chem. 2010 Jul 23;285(30):23466-76. doi: 10.1074/jbc.M109.093500. Epub 2010 May 25.
8. He Z, etal., J Neurosci. 2012 Jul 4;32(27):9383-95. doi: 10.1523/JNEUROSCI.6363-11.2012.
9. Jung S, etal., Am J Physiol Cell Physiol 2002 Feb;282(2):C347-59.
10. Li H, etal., J Neurochem. 2012 Dec;123(6):1010-8. doi: 10.1111/jnc.12045. Epub 2012 Nov 1.
11. Lin Y, etal., J Mol Neurosci. 2013 Jul;50(3):504-13. doi: 10.1007/s12031-013-9977-8. Epub 2013 Feb 23.
12. Liu X, etal., J Thorac Cardiovasc Surg. 2013 Mar 24. pii: S0022-5223(13)00274-2. doi: 10.1016/j.jtcvs.2013.02.076.
13. Liu Y, etal., Am J Nephrol. 2010;31(1):36-44. doi: 10.1159/000254060. Epub 2009 Oct 30.
14. Lu W, etal., Am J Physiol Cell Physiol. 2010 Jan;298(1):C114-23. doi: 10.1152/ajpcell.00629.2008. Epub 2009 Nov 4.
15. Luan J, etal., J Pharmacol Sci. 2012;119(2):167-76. Epub 2012 May 22.
16. Marshall-Gradisnik S, etal., J Int Med Res. 2016 Dec;44(6):1381-1394. doi: 10.1177/0300060516671622. Epub 2016 Nov 11.
17. MGD data from the GO Consortium
18. Mir S, etal., Nephrol Dial Transplant. 2012 Jan;27(1):205-9. doi: 10.1093/ndt/gfr202. Epub 2011 Apr 21.
19. Mita M, etal., Clin Exp Pharmacol Physiol. 2010 Jul;37(7):670-8. doi: 10.1111/j.1440-1681.2010.05373.x. Epub 2010 Mar 12.
20. NCBI rat LocusLink and RefSeq merged data July 26, 2002
21. Nijenhuis T, etal., Am J Pathol. 2011 Oct;179(4):1719-32. doi: 10.1016/j.ajpath.2011.06.033. Epub 2011 Aug 11.
22. Obeidova L, etal., Folia Biol (Praha). 2012;58(4):173-6.
23. OMIM Disease Annotation Pipeline
24. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
25. Reiser J, etal., Nat Genet. 2005 Jul;37(7):739-44. Epub 2005 May 27.
26. RGD automated data pipeline
27. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
28. RGD automated import pipeline for gene-chemical interactions
29. Shin HY, etal., PLoS One. 2010 May 7;5(5):e10359. doi: 10.1371/journal.pone.0010359.
30. Sonneveld R, etal., Am J Pathol. 2013 Apr;182(4):1196-204. doi: 10.1016/j.ajpath.2012.12.011. Epub 2013 Feb 4.
31. Spires D, etal., Am J Physiol Renal Physiol. 2018 Oct 1;315(4):F1091-F1097. doi: 10.1152/ajprenal.00155.2018. Epub 2018 Jun 20.
32. Wang X, etal., Invest Ophthalmol Vis Sci. 2010 Nov;51(11):5751-8. Epub 2010 Jun 16.
33. Welsh DG, etal., Circ Res 2002 Feb 22;90(3):248-50.
34. Winn MP, etal., Science. 2005 Jun 17;308(5729):1801-4. Epub 2005 May 5.
35. Xie J, etal., Nat Commun. 2012;3:1238. doi: 10.1038/ncomms2240.
36. Yu Y, etal., Proc Natl Acad Sci U S A. 2004 Sep 21;101(38):13861-6. Epub 2004 Sep 9.
37. Zhang L and Saffen D, J Biol Chem 2001 Apr 20;276(16):13331-9.
Additional References at PubMed
PMID:8646775   PMID:9368034   PMID:10998353   PMID:14505576   PMID:15194687   PMID:15199065   PMID:15623527   PMID:15672411   PMID:16204251   PMID:17082763   PMID:17112478   PMID:17141310  
PMID:17533154   PMID:17684020   PMID:17699554   PMID:17699555   PMID:17723267   PMID:17977908   PMID:18559891   PMID:18835357   PMID:19246091   PMID:19386284   PMID:19443836   PMID:19936226  
PMID:19961855   PMID:20177073   PMID:20179889   PMID:20307499   PMID:20426773   PMID:20622104   PMID:21487005   PMID:21525431   PMID:21799177   PMID:22129453   PMID:22865594   PMID:22926417  
PMID:23149561   PMID:23171048   PMID:23193081   PMID:23224895   PMID:23291369   PMID:23494294   PMID:23526217   PMID:23526219   PMID:23764398   PMID:24037962   PMID:24336649   PMID:24553432  
PMID:24731445   PMID:25041367   PMID:25203114   PMID:25292315   PMID:25365342   PMID:25467798   PMID:25649357   PMID:25740156   PMID:25939574   PMID:26155749   PMID:26193076   PMID:26248296  
PMID:26327362   PMID:26718737   PMID:26823720   PMID:27147559   PMID:28039055   PMID:28263796   PMID:28300348   PMID:28331185   PMID:28495616   PMID:28596571   PMID:28627661   PMID:28646178  
PMID:28902407   PMID:28983729   PMID:29785489   PMID:30476735   PMID:30664212   PMID:31236585   PMID:31310676   PMID:31683954   PMID:31778750   PMID:32844288   PMID:33667520   PMID:33918778  
PMID:33924991  


Genomics

Comparative Map Data
Trpc6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.285,759,387 - 5,864,000 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl85,758,935 - 5,828,092 (+)Ensembl
Rnor_6.086,811,543 - 6,917,534 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl86,811,543 - 6,917,535 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.086,799,564 - 6,904,623 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.485,472,515 - 5,577,537 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.185,472,514 - 5,577,536 (+)NCBI
Celera87,300,179 - 7,404,007 (+)NCBICelera
Cytogenetic Map8q11NCBI
TRPC6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl11101,451,564 - 101,872,562 (-)EnsemblGRCh38hg38GRCh38
GRCh3811101,451,470 - 101,584,007 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3711101,322,295 - 101,454,738 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3611100,827,584 - 100,959,869 (-)NCBINCBI36hg18NCBI36
Build 3411100,827,582 - 100,959,869NCBI
Celera1198,491,501 - 98,623,915 (-)NCBI
Cytogenetic Map11q22.1NCBI
HuRef1197,256,362 - 97,388,472 (-)NCBIHuRef
CHM1_111101,205,451 - 101,337,498 (-)NCBICHM1_1
Trpc6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3998,543,868 - 8,680,753 (+)NCBIGRCm39mm39
GRCm39 Ensembl98,544,143 - 8,680,742 (+)Ensembl
GRCm3898,543,867 - 8,680,752 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl98,544,142 - 8,680,741 (+)EnsemblGRCm38mm10GRCm38
MGSCv3798,544,142 - 8,680,741 (+)NCBIGRCm37mm9NCBIm37
MGSCv3698,544,711 - 8,642,583 (+)NCBImm8
Celera95,924,518 - 6,060,945 (+)NCBICelera
Cytogenetic Map9A1NCBI
cM Map92.46NCBI
Trpc6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554124,906,650 - 4,950,525 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554124,905,039 - 5,019,678 (-)NCBIChiLan1.0ChiLan1.0
TRPC6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11199,918,382 - 100,051,110 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1199,919,410 - 100,050,685 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01196,414,498 - 96,551,670 (-)NCBIMhudiblu_PPA_v0panPan3
TRPC6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1529,897,378 - 30,007,885 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl529,897,210 - 30,007,723 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha529,849,049 - 29,959,895 (+)NCBI
ROS_Cfam_1.0529,962,647 - 30,073,659 (+)NCBI
UMICH_Zoey_3.1530,016,217 - 30,126,413 (+)NCBI
UNSW_CanFamBas_1.0529,864,510 - 29,975,743 (+)NCBI
UU_Cfam_GSD_1.0530,042,168 - 30,153,079 (+)NCBI
Trpc6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494785,253,510 - 85,362,868 (-)NCBI
SpeTri2.0NW_0049365516,173,588 - 6,282,971 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TRPC6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl932,332,769 - 32,439,184 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1932,332,768 - 32,439,184 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2936,257,623 - 36,364,097 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TRPC6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1192,828,546 - 92,970,224 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl192,829,253 - 92,885,086 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604332,920,602 - 33,049,610 (+)NCBIVero_WHO_p1.0
Trpc6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248781,321,022 - 1,469,964 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
Trpc6  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.086,904,442 - 6,905,652NCBIRnor6.0
Rnor_5.086,891,531 - 6,892,741UniSTSRnor5.0
RGSC_v3.485,564,444 - 5,565,654UniSTSRGSC3.4
Celera87,390,915 - 7,392,125UniSTS
Cytogenetic Map8q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat


Genetic Models
This gene Trpc6 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:156
Count of miRNA genes:95
Interacting mature miRNAs:100
Transcripts:ENSRNOT00000008905, ENSRNOT00000042553
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 6 6 6
Low 3 39 36 22 17 22 7 7 68 35 30 5 7
Below cutoff 4 16 14 2 14 1 4 3 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008905   ⟹   ENSRNOP00000008905
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl85,758,935 - 5,828,092 (+)Ensembl
Rnor_6.0 Ensembl86,811,543 - 6,917,535 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000042553   ⟹   ENSRNOP00000043514
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl86,811,617 - 6,907,623 (+)Ensembl
RefSeq Acc Id: NM_053559   ⟹   NP_446011
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.285,759,387 - 5,864,000 (+)NCBI
Rnor_6.086,811,543 - 6,917,534 (+)NCBI
Rnor_5.086,799,564 - 6,904,623 (+)NCBI
RGSC_v3.485,472,515 - 5,577,537 (+)RGD
Celera87,300,179 - 7,404,007 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_446011   ⟸   NM_053559
- UniProtKB: Q99N78 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008905   ⟸   ENSRNOT00000008905
RefSeq Acc Id: ENSRNOP00000043514   ⟸   ENSRNOT00000042553
Protein Domains
Ankyrin_rpt-contain_dom   Ion_trans   TRP_2

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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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)
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/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (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
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (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)
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)
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/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (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
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 6904590 6904591 C T snv WN/N (KNAW), LE/OrlBarth (UDEL), ZFDM (KyushuU), ZF (KyushuU), Crl:SD (UDEL)


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 6917501 6917502 C T snv WN/N (2020), WN/N (MCW)


Assembly: RGSC_v3.4
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 5577503 5577504 C T snv WN/N (KNAW), HCR/1Mco (UMich), LCR/2Mco (UMich), HCR/2Mco (UMich), LCR/1Mco (UMich)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619788 AgrOrtholog
Ensembl Genes ENSRNOG00000006324 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008905 UniProtKB/TrEMBL
  ENSRNOP00000043514 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008905 UniProtKB/TrEMBL
  ENSRNOT00000042553 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.20 UniProtKB/TrEMBL
InterPro Ankyrin_rpt UniProtKB/TrEMBL
  Ankyrin_rpt-contain_dom UniProtKB/TrEMBL
  Ankyrin_rpt-contain_sf UniProtKB/TrEMBL
  Ion_trans UniProtKB/TrEMBL
  TRP_dom UniProtKB/TrEMBL
  TRPC6_channel UniProtKB/TrEMBL
  TRPC_channel UniProtKB/TrEMBL
KEGG Report rno:89823 UniProtKB/TrEMBL
NCBI Gene 89823 ENTREZGENE
PANTHER PTHR10117 UniProtKB/TrEMBL
  PTHR10117:SF7 UniProtKB/TrEMBL
Pfam Ank_2 UniProtKB/TrEMBL
  Ion_trans UniProtKB/TrEMBL
  TRP_2 UniProtKB/TrEMBL
PhenoGen Trpc6 PhenoGen
PRINTS TRNSRECEPTRP UniProtKB/TrEMBL
  TRPCHANNEL6 UniProtKB/TrEMBL
PROSITE ANK_REPEAT UniProtKB/TrEMBL
SMART ANK UniProtKB/TrEMBL
Superfamily-SCOP ANK UniProtKB/TrEMBL
UniProt F1MAN2_RAT UniProtKB/TrEMBL
  Q99N78 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Trpc6  transient receptor potential cation channel, subfamily C, member 6    transient receptor protein 6  Name updated 1299863 APPROVED
2004-09-10 Trpc6  transient receptor protein 6  Trrp6    Symbol and Name updated 1299863 APPROVED
2002-08-07 Trrp6  transient receptor protein 6      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_regulation activated by diacylglycerol 634440