Casp1 (caspase 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Casp1 (caspase 1) Rattus norvegicus
Analyze
Symbol: Casp1
Name: caspase 1
RGD ID: 2274
Description: Enables scaffold protein binding activity. Involved in several processes, including myoblast fusion; positive regulation of circadian sleep/wake cycle, non-REM sleep; and positive regulation of interleukin-1 beta production. Located in cytoplasm; neuron projection; and nucleus. Part of protein-containing complex. Used to study acute kidney failure and visual epilepsy. Orthologous to human CASP1 (caspase 1); PARTICIPATES IN interleukin-1 signaling pathway; type II interferon signaling pathway; amyotrophic lateral sclerosis pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: CASP-1; caspase 1 apoptosis-related cysteine protease (interleukin 1 beta convertase); caspase-1; Ice; IL-1 beta-converting enzyme; IL-1BC; Il1bc; interleukin 1 beta convertase; interleukin 1, beta, convertase; Interleukin 1beta converting enzyme; interleukin-1 beta convertase; interleukin-1 beta-converting enzyme; p45
RGD Orthologs
Human
Mouse
Bonobo
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.282,587,812 - 2,597,403 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl82,587,831 - 2,597,383 (+)Ensembl
Rnor_6.082,605,743 - 2,614,637 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl82,604,962 - 2,614,631 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.082,627,976 - 2,636,870 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.482,027,976 - 2,036,872 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.182,027,975 - 2,036,866 (+)NCBI
Celera82,455,483 - 2,464,376 (+)NCBICelera
Cytogenetic Map8q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-dexrazoxane  (ISO)
(-)-demecolcine  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(S)-nicotine  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1,4-benzoquinone  (ISO)
1,4-dithiothreitol  (ISO)
1,4-phenylenediamine  (ISO)
1-chloro-2,4,6-trinitrobenzene  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2,5-hexanedione  (EXP)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (ISO)
2-amino-2-deoxy-D-galactopyranose  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-mercaptopropanoic acid  (ISO)
3-methyladenine  (EXP,ISO)
3-phenylprop-2-enal  (ISO)
4'-epidoxorubicin  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4-Hydroxy-TEMPO  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-methyl-3-[[1-oxo-2-(propylamino)propyl]amino]-2-thiophenecarboxylic acid methyl ester  (ISO)
4-nonylphenol  (EXP)
4-phenylbutyric acid  (ISO)
5-fluorouracil  (ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (ISO)
7,9-dihydro-1H-purine-2,6,8(3H)-trione  (ISO)
7-ketocholesterol  (ISO)
acetamide  (EXP)
acetic acid  (EXP)
aclacinomycin A  (ISO)
aconitine  (EXP,ISO)
acrolein  (EXP,ISO)
acrylamide  (EXP,ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (ISO)
allicin  (ISO)
allopurinol  (EXP,ISO)
alpha-pinene  (ISO)
aluminium hydroxide  (ISO)
aluminium sulfate (anhydrous)  (ISO)
amitriptyline  (ISO)
ammonium chloride  (EXP)
amphibole asbestos  (ISO)
anthocyanin  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antimycin A  (ISO)
antirheumatic drug  (ISO)
apigenin  (ISO)
apocynin  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (EXP,ISO)
ATP  (EXP,ISO)
atrazine  (ISO)
benzene  (EXP)
benzo[a]pyrene  (ISO)
Bergenin  (EXP)
beta-eudesmol  (ISO)
beta-naphthoflavone  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A5  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
cadmium selenide  (ISO)
Calcimycin  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
CCCP  (ISO)
celastrol  (EXP)
chlorpyrifos  (ISO)
cholesterol  (EXP,ISO)
chrysin  (ISO)
cimetidine  (ISO)
cisplatin  (EXP,ISO)
cobalt atom  (EXP,ISO)
cobalt dichloride  (ISO)
colforsin daropate hydrochloride  (EXP)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cycloheximide  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
cypermethrin  (EXP)
D-glucose  (EXP,ISO)
dexamethasone  (ISO)
dexmedetomidine  (ISO)
dextran sulfate  (EXP,ISO)
diarsenic trioxide  (EXP,ISO)
diazinon  (EXP)
dibenziodolium  (ISO)
dibutyl phthalate  (ISO)
dibutylstannane  (ISO)
dichloromethane  (ISO)
dichlorvos  (EXP)
diclofenac  (EXP)
dicrotophos  (ISO)
diethyldithiocarbamic acid  (ISO)
diethylstilbestrol  (ISO)
dimethylarsinous acid  (ISO)
dimethyldithiocarbamate  (ISO)
dioxygen  (EXP,ISO)
diprotium oxide  (ISO)
dipyridamole  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
emodin  (ISO)
endosulfan  (ISO)
ergosterol  (EXP)
Erionite  (ISO)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
ethylenediaminetetraacetic acid  (ISO)
fluoxetine  (EXP)
fluvastatin  (ISO)
folic acid  (ISO)
formaldehyde  (EXP,ISO)
Fraxinellone  (ISO)
fructose  (EXP)
furan  (EXP)
furosemide  (EXP)
Fusaric acid  (ISO)
galangin  (ISO)
gefitinib  (ISO)
genistein  (ISO)
gentamycin  (EXP)
glucose  (EXP,ISO)
glyburide  (EXP,ISO)
glycidol  (EXP)
glycine betaine  (EXP)
glyphosate  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
hexachlorobenzene  (EXP)
hexadecanoic acid  (EXP,ISO)
homocysteine  (ISO)
HU-308  (ISO)
hyaluronic acid  (EXP)
hydrogen peroxide  (ISO)
hydrogen sulfide  (EXP)
ifosfamide  (ISO)
imiquimod  (ISO)
immunological adjuvant  (ISO)
indometacin  (EXP)
irinotecan  (EXP,ISO)
isoprenaline  (ISO)
kaempferol  (ISO)
L-1,4-dithiothreitol  (ISO)
lead diacetate  (ISO)
leflunomide  (ISO)
lenalidomide  (EXP)
leptomycin B  (ISO)
lipopolysaccharide  (EXP,ISO)
lithocholic acid  (ISO)
luteolin  (EXP,ISO)
LY294002  (ISO)
magnesium dihydroxide  (ISO)
maneb  (ISO)
melatonin  (ISO)
mercaptoethanol  (ISO)
mercury atom  (ISO)
mercury dichloride  (ISO)
mercury(0)  (ISO)
metformin  (ISO)
methamphetamine  (ISO)
methyl beta-cyclodextrin  (ISO)
methyl methanesulfonate  (ISO)
microcystin-LR  (ISO)
minocycline  (EXP,ISO)
Mitotane  (EXP)
morphine  (EXP)
mycophenolic acid  (ISO)
mycotoxin  (ISO)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-ethyl-5'-carboxamidoadenosine  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (ISO)
N-nitrosodimethylamine  (EXP)
nickel atom  (EXP,ISO)
nickel dichloride  (ISO)
niclosamide  (ISO)
nicotine  (ISO)
nigericin  (ISO)
nimustine  (ISO)
nitrates  (EXP)
nitric oxide  (ISO)
nitroflurbiprofen  (ISO)
nitroglycerin  (ISO)
NMN zwitterion  (EXP,ISO)
Nonidet P-40  (ISO)
ochratoxin A  (ISO)
octanoic acid  (ISO)
oxidopamine  (EXP)
oxybenzone  (EXP)
ozone  (EXP,ISO)
p-menthan-3-ol  (ISO)
paclitaxel  (ISO)
Palbinone  (EXP)
paracetamol  (ISO)
paraquat  (EXP,ISO)
patulin  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phencyclidine  (ISO)
phenethyl caffeate  (EXP)
phenobarbital  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
phosgene  (EXP)
phosphoramide mustard  (EXP)
pirinixic acid  (EXP)
Polpunonic acid  (ISO)
potassium atom  (ISO)
potassium chromate  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
probenecid  (ISO)
procyanidin B2  (EXP)
propylparaben  (ISO)
pyrrolidine dithiocarbamate  (EXP)
quercetin  (EXP,ISO)
quinolin-8-ol  (ISO)
resveratrol  (EXP,ISO)
rifampicin  (ISO)
ritonavir  (ISO)
rotenone  (EXP,ISO)
rutin  (EXP)
S-allylcysteine  (ISO)
S-nitroso-N-acetyl-D-penicillamine  (ISO)
salicylic acid  (ISO)
Salidroside  (EXP)
sanguinarine  (ISO)
SB 203580  (EXP,ISO)
serpentine asbestos  (ISO)
silicon dioxide  (EXP,ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (EXP)
sirolimus  (EXP,ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sodium fluoride  (ISO)
Sodium salicylate  (EXP)
sorafenib  (ISO)
staurosporine  (ISO)
sterigmatocystin  (ISO)
streptozocin  (EXP,ISO)
succimer  (ISO)
sulfasalazine  (EXP)
sulfur dioxide  (EXP)
suramin  (EXP)
taurine  (EXP,ISO)
tellurium atom  (EXP)
temozolomide  (ISO)
testosterone  (EXP,ISO)
tetrachloromethane  (ISO)
thapsigargin  (ISO)
thioacetamide  (ISO)
thiram  (ISO)
thymoquinone  (ISO)
titanium dioxide  (ISO)
toluene 2,4-diisocyanate  (ISO)
Tributyltin oxide  (ISO)
triclosan  (ISO)
tungsten  (EXP)
urethane  (ISO)
valproic acid  (ISO)
verapamil  (ISO)
vinclozolin  (EXP)
vincristine  (ISO)
water  (ISO)
wortmannin  (ISO)
Y-27632  (ISO)
zearalenone  (EXP,ISO)
zinc atom  (ISO)
zinc oxide  (ISO)
zinc pyrithione  (ISO)
zinc(0)  (ISO)
ziram  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of cysteine-type endopeptidase activity involved in apoptotic process  (IBA)
apoptotic process  (IEA,IEP)
apoptotic signaling pathway  (IEA)
cellular response to interferon-gamma  (IEA,ISO)
cellular response to lipopolysaccharide  (IEA,ISO)
cellular response to mechanical stimulus  (IEA,ISO)
cellular response to organic substance  (ISO)
cytokine precursor processing  (IEA,ISO)
defense response to Gram-negative bacterium  (IEA,ISO)
lung development  (IEP)
membrane hyperpolarization  (IEA,ISO)
memory  (IMP)
microglial cell activation  (IMP)
midgut development  (IEP)
mitochondrial depolarization  (IEA,ISO)
myoblast fusion  (IMP)
pattern recognition receptor signaling pathway  (ISO)
positive regulation of apoptotic process  (IMP)
positive regulation of circadian sleep/wake cycle, non-REM sleep  (IMP)
positive regulation of cysteine-type endopeptidase activity involved in apoptotic process  (IEA,ISO)
positive regulation of cytokine production  (IMP,ISO,ISS)
positive regulation of I-kappaB kinase/NF-kappaB signaling  (IEA,ISO)
positive regulation of inflammatory response  (ISO)
positive regulation of interleukin-1 alpha production  (IEA,ISO)
positive regulation of interleukin-1 beta production  (IEA,IMP,ISO,ISS)
positive regulation of neuron apoptotic process  (ISO)
positive regulation of release of cytochrome c from mitochondria  (ISO)
positive regulation of tumor necrosis factor-mediated signaling pathway  (IEA,ISO)
programmed necrotic cell death  (IEA,ISO)
protein autoprocessing  (IEA,ISO,ISS)
protein processing  (ISO)
proteolysis  (ISO)
pyroptosis  (IEA,ISO,ISS)
regulation of apoptotic process  (IEA)
regulation of autophagy  (IEA,ISO)
regulation of inflammatory response  (IBA,IEA,ISO,ISS)
response to ATP  (IEA,ISO)
response to bacterium  (ISO)
response to hypoxia  (IDA,IEA,ISO)
response to lipopolysaccharide  (IEA,IMP,ISO)
response to organic cyclic compound  (IDA)
response to toxic substance  (IEP)
response to xenobiotic stimulus  (IDA)
signaling receptor ligand precursor processing  (ISO)
toxin transport  (IEA,ISO)

Cellular Component

References

References - curated
1. Barnoy S and Kosower NS, FEBS Lett 2003 Jul 10;546(2-3):213-7.
2. Bhanoori M, etal., Oncogene 2003 Jan 9;22(1):117-30.
3. Boost KA, etal., Intensive Care Med. 2007 May;33(5):863-71. Epub 2007 Mar 24.
4. Cao Y, etal., Acta Pharmacol Sin. 2005 Feb;26(2):150-4.
5. Chong ZZ, etal., Exp Cell Res. 2004 Jun 10;296(2):196-207.
6. Clark AK, etal., J Neurochem. 2006 Nov;99(3):868-80. Epub 2006 Aug 29.
7. de Rivero Vaccari JP, etal., J Cereb Blood Flow Metab. 2009 Jul;29(7):1251-61. Epub 2009 Apr 29.
8. de Rivero Vaccari JP, etal., J Neurosci. 2008 Mar 26;28(13):3404-14.
9. Deng CH, etal., Zhonghua Nan Ke Xue. 2005 Nov;11(11):810-2.
10. Dinarello CA Annu Rev Immunol. 2009;27:519-50.
11. Dinis-Oliveira RJ, etal., Free Radic Biol Med. 2007 Jul 1;43(1):48-61. Epub 2007 Mar 24.
12. Flaws JA, etal., Endocrinology 1995 Nov;136(11):5042-53.
13. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
14. Gemma C, etal., Eur J Neurosci. 2005 Oct;22(7):1751-6.
15. GOA data from the GO Consortium
16. Grzegorczyk J, etal., Mediators Inflamm. 2002 Aug;11(4):225-33.
17. Gustavsson C, etal., Retina. 2008 Apr;28(4):645-52.
18. Homsi E, etal., Kidney Int. 2006 Apr;69(8):1385-92.
19. Hoshino T, etal., Am J Respir Cell Mol Biol. 2009 Dec;41(6):661-70. Epub 2009 Mar 5.
20. Imeri L, etal., Am J Physiol Regul Integr Comp Physiol. 2006 Jul;291(1):R197-204. Epub 2006 Feb 2.
21. Izawa M, etal., Asian J Androl 2001 Jun;3(2):105-8.
22. Keane KM, etal., Cytokine 1995 Feb;7(2):105-10.
23. KEGG
24. Kim NG, etal., Brain Res Mol Brain Res. 2003 Jun 10;114(2):107-14.
25. Kumral A, etal., Early Hum Dev. 2013 Mar;89(3):165-73. doi: 10.1016/j.earlhumdev.2012.09.016. Epub 2012 Oct 6.
26. Li WW, etal., Pain. 2009 Dec 15;147(1-3):277-86. Epub 2009 Oct 22.
27. Merkle S, etal., Circ Res. 2007 Mar 16;100(5):645-53. Epub 2007 Feb 15.
28. MGD data from the GO Consortium
29. NCBI rat LocusLink and RefSeq merged data July 26, 2002
30. Newman ZL, etal., Biochem Biophys Res Commun. 2010 Aug 6;398(4):785-9. Epub 2010 Jul 16.
31. O'Shea E, etal., Neuroscience. 2005;135(4):1095-105. Epub 2005 Sep 13.
32. Oh HA, etal., Int Immunopharmacol. 2011 Jan;11(1):39-45. Epub 2010 Oct 23.
33. Oshikawa K, etal., Proc Natl Acad Sci U S A. 1999 Nov 9;96(23):13351-6.
34. Pipeline to import KEGG annotations from KEGG into RGD
35. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
36. Pompl PN, etal., Arch Neurol. 2003 Mar;60(3):369-76.
37. Raju U, etal., Curr Genomics. 2006 Dec;7(8):523-532.
38. Ravizza T, etal., Epilepsia. 2006 Jul;47(7):1160-8.
39. RGD automated data pipeline
40. RGD automated import pipeline for gene-chemical interactions
41. Roe MF, etal., Clin Exp Immunol. 2004 Jul;137(1):139-45.
42. Ross J, etal., Neuropharmacology. 2007 Oct;53(5):638-42. Epub 2007 Aug 10.
43. Schroder K and Tschopp J, Cell. 2010 Mar 19;140(6):821-32. doi: 10.1016/j.cell.2010.01.040.
44. Sifringer M, etal., Neurobiol Dis. 2007 Mar;25(3):614-22. Epub 2006 Dec 22.
45. Silverman WR, etal., J Biol Chem. 2009 Jul 3;284(27):18143-51. Epub 2009 May 5.
46. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
47. Thomas PG, etal., Immunity. 2009 Apr 17;30(4):566-75. Epub 2009 Apr 9.
48. Wang B, etal., Biomed Pharmacother. 2019 Jun;114:108683. doi: 10.1016/j.biopha.2019.108683. Epub 2019 Apr 1.
49. Winter RN, etal., Cancer Res. 2001 Feb 1;61(3):1227-32.
50. Zhang XH, etal., World J Gastroenterol. 2007 Jan 28;13(4):623-7.
Additional References at PubMed
PMID:11016935   PMID:11432859   PMID:11536016   PMID:11684016   PMID:11821383   PMID:12191486   PMID:12477932   PMID:12761501   PMID:12888622   PMID:14663141   PMID:15030775   PMID:15190255  
PMID:15383541   PMID:15882992   PMID:16301672   PMID:16429160   PMID:16573645   PMID:16585594   PMID:16920334   PMID:17036048   PMID:17431085   PMID:18490713   PMID:18632279   PMID:18980715  
PMID:19158676   PMID:19158679   PMID:19317852   PMID:19593445   PMID:20025855   PMID:20595632   PMID:21832250   PMID:21874021   PMID:22002608   PMID:22267217   PMID:22297845   PMID:23028046  
PMID:23395675   PMID:23716698   PMID:24548080   PMID:24581500   PMID:24630722   PMID:24695748   PMID:24699513   PMID:25132762   PMID:25501827   PMID:26061900   PMID:26438340   PMID:27043298  
PMID:27289225   PMID:28823375   PMID:29101761   PMID:31195405   PMID:32186399   PMID:32461137  


Genomics

Comparative Map Data
Casp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.282,587,812 - 2,597,403 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl82,587,831 - 2,597,383 (+)Ensembl
Rnor_6.082,605,743 - 2,614,637 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl82,604,962 - 2,614,631 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.082,627,976 - 2,636,870 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.482,027,976 - 2,036,872 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.182,027,975 - 2,036,866 (+)NCBI
Celera82,455,483 - 2,464,376 (+)NCBICelera
Cytogenetic Map8q11NCBI
CASP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl11105,025,443 - 105,035,250 (-)EnsemblGRCh38hg38GRCh38
GRCh3811105,025,443 - 105,035,591 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3711104,896,170 - 104,905,871 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3611104,401,445 - 104,411,067 (-)NCBINCBI36hg18NCBI36
Build 3411104,401,448 - 104,411,067NCBI
Celera11102,060,400 - 102,070,022 (-)NCBI
Cytogenetic Map11q22.3NCBI
HuRef11100,827,223 - 100,836,872 (-)NCBIHuRef
CHM1_111104,779,164 - 104,788,813 (-)NCBICHM1_1
Casp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3995,298,517 - 5,307,281 (+)NCBIGRCm39mm39
GRCm39 Ensembl95,298,508 - 5,307,290 (+)Ensembl
GRCm3895,298,517 - 5,307,281 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl95,298,508 - 5,307,290 (+)EnsemblGRCm38mm10GRCm38
MGSCv3795,298,517 - 5,307,281 (+)NCBIGRCm37mm9NCBIm37
MGSCv3695,298,517 - 5,307,281 (+)NCBImm8
Celera3117,396,675 - 117,405,459 (-)NCBICelera
Cytogenetic Map9A1NCBI
cM Map92.46NCBI
CASP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.111103,448,497 - 103,468,367 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11103,448,497 - 103,458,149 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01199,965,964 - 99,975,640 (-)NCBIMhudiblu_PPA_v0panPan3
CASP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl935,186,420 - 35,200,328 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1935,188,066 - 35,199,364 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2939,210,251 - 39,221,559 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CASP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1196,389,697 - 96,400,610 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl196,389,657 - 96,400,849 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604329,497,194 - 29,506,147 (+)NCBIVero_WHO_p1.0

Position Markers
RH141870  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.282,596,234 - 2,597,352 (+)MAPPERmRatBN7.2
Rnor_6.082,613,473 - 2,614,590NCBIRnor6.0
Rnor_5.082,635,706 - 2,636,823UniSTSRnor5.0
RGSC_v3.482,035,705 - 2,036,825UniSTSRGSC3.4
Celera82,463,212 - 2,464,329UniSTS
Cytogenetic Map8q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
71120Niddm21Non-insulin dependent diabetes mellitus QTL 213.73blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)813402289Rat
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

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:60
Count of miRNA genes:54
Interacting mature miRNAs:57
Transcripts:ENSRNOT00000009993
Prediction methods:Microtar, 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

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 3 9 19 4 7 11
Low 33 48 41 41 8 11 66 31 32 8
Below cutoff 6 8 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009993   ⟹   ENSRNOP00000009993
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl82,587,938 - 2,597,383 (+)Ensembl
Rnor_6.0 Ensembl82,604,962 - 2,614,631 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000098719   ⟹   ENSRNOP00000086752
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl82,587,831 - 2,597,383 (+)Ensembl
RefSeq Acc Id: NM_012762   ⟹   NP_036894
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.282,587,938 - 2,597,403 (+)NCBI
Rnor_6.082,605,743 - 2,614,637 (+)NCBI
Rnor_5.082,627,976 - 2,636,870 (+)NCBI
RGSC_v3.482,027,976 - 2,036,872 (+)RGD
Celera82,455,483 - 2,464,376 (+)RGD
Sequence:
RefSeq Acc Id: XR_005487743
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.282,587,812 - 2,596,273 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_036894   ⟸   NM_012762
- Sequence:
RefSeq Acc Id: ENSRNOP00000009993   ⟸   ENSRNOT00000009993
RefSeq Acc Id: ENSRNOP00000086752   ⟸   ENSRNOT00000098719
Protein Domains
CARD   CASPASE_P10   CASPASE_P20

Transcriptome

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

Promoters
RGD ID:13695727
Promoter ID:EPDNEW_R6250
Type:multiple initiation site
Name:Casp1_1
Description:caspase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.082,605,157 - 2,605,217EPDNEW

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)
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/NHsdMcwi (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
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)
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
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)
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)
DA/OlaHsd (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: 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)
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
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)
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
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)
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/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
WKY/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
WN/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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2274 AgrOrtholog
Ensembl Genes ENSRNOG00000007372 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009993 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009993 UniProtKB/TrEMBL
Gene3D-CATH 1.10.533.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CARD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Caspase-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Caspase_cys_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Caspase_his_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DEATH-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pept_C14 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pept_C14_p10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pept_C14_p20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pept_C14A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25166 UniProtKB/TrEMBL
NCBI Gene 25166 ENTREZGENE
PANTHER PTHR10454 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CARD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Casp1 PhenoGen
PRINTS IL1BCENZYME UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CARD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CASPASE_CYS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CASPASE_HIS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CASPASE_P10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CASPASE_P20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CARD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CASc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47986 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52129 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC210778
UniProt CASP1_RAT UniProtKB/Swiss-Prot
  F1LQZ4_RAT UniProtKB/TrEMBL
  P43527 ENTREZGENE
  Q91W32_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Casp1  caspase 1      Symbol and Name status set to approved 70586 APPROVED
2001-07-23 Casp1  Interleukin 1beta converting enzyme      Name withdrawn 67952 WITHDRAWN
2001-07-23 Casp1  caspase 1      Name withdrawn 67952 WITHDRAWN

RGD Curation Notes
Note Type Note Reference
gene_expression expression upregulated in epithelial cells of ventral prostate and seminal vesicle in castrated rats 631309
gene_process may play a role in inflammation 634698
gene_process may play a role in apoptosis in male accessory sex organs 631309
gene_protein 402 amino acid protein 634698
gene_regulation expression upregulated by lipopolysaccharide 634698
gene_regulation active protein increased upon thiol alkylation in vascular smooth muscle cells 1299059