Notch1 (notch receptor 1) - Rat Genome Database

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Gene: Notch1 (notch receptor 1) Rattus norvegicus
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Symbol: Notch1
Name: notch receptor 1
RGD ID: 3187
Description: Enables transmembrane signaling receptor activity. Involved in several processes, including nervous system development; positive regulation of cell differentiation; and positive regulation of macromolecule metabolic process. Located in several cellular components, including Golgi apparatus; acrosomal vesicle; and nucleus. Human ortholog(s) of this gene implicated in Adams-Oliver syndrome; adult T-cell leukemia; and aortic valve disease 1. Orthologous to human NOTCH1 (notch receptor 1); PARTICIPATES IN Notch signaling pathway; altered Notch signaling pathway; altered Notch signaling pathway involving the main players; INTERACTS WITH 1,2-dimethylhydrazine; 17alpha-ethynylestradiol; 2,2',4,4',5,5'-hexachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Drosophila Notch homolog 1; Drosophila Notch homolog 1 (controlling the the ectodermal and neural cell fate in Drosophila); neurogenic locus notch homolog protein 1; NOTCH; notch 1; Notch gene homolog 1; Notch gene homolog 1 (Drosophila); Notch homolog 1, translocation-associated; Notch homolog 1, translocation-associated (Drosophila); TAN1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.239,277,955 - 9,323,531 (-)NCBI
Rnor_6.0 Ensembl33,905,453 - 3,951,025 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.033,905,562 - 3,951,015 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.039,266,663 - 9,311,575 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.434,631,797 - 4,677,640 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.134,632,997 - 4,677,652 (-)NCBI
Celera34,097,915 - 4,143,369 (-)NCBICelera
Cytogenetic Map3p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Adams-Oliver syndrome  (ISO)
Adams-Oliver Syndrome 5  (ISO)
adenoid cystic carcinoma  (ISO)
adenoiditis  (ISO)
adult T-cell leukemia  (ISO)
amyotrophic lateral sclerosis  (ISO)
aortic valve disease  (ISO)
aortic valve disease 1  (ISO)
Aortic Valve, Calcification of  (ISO)
ARTERIAL DISSECTION  (ISO)
autosomal dominant non-syndromic intellectual disability 8  (ISO)
bicuspid aortic valve disease  (ISO)
Breast Neoplasms  (ISO)
calcinosis  (ISO)
Candidiasis, Familial, 2  (ISO)
Carotid Artery Injuries  (IEP)
Chemical and Drug Induced Liver Injury  (ISO)
cholangiocarcinoma  (ISO)
Colonic Neoplasms  (ISO)
Congenital Abnormalities  (ISO)
congenital heart disease  (ISO)
connective tissue disease  (ISO)
Craniofacial Abnormalities  (ISO)
developmental and epileptic encephalopathy 14  (ISO)
Ehlers-Danlos syndrome hypermobility type  (ISO)
endometrial cancer  (ISO)
epilepsy  (ISO)
esophageal atresia  (ISO)
esophagus squamous cell carcinoma  (ISO)
Experimental Liver Neoplasms  (IEP)
genetic disease  (ISO)
glioblastoma  (ISO)
heart valve disease  (ISO)
hemangioma  (ISO)
hypoplastic left heart syndrome  (ISO)
Joubert syndrome  (ISO)
Kleefstra syndrome 1  (ISO)
lung non-small cell carcinoma  (ISO)
lymphoma  (ISO)
malignant astrocytoma  (ISO)
Marfan syndrome  (ISO)
Marfanoid Hypermobility Syndrome  (ISO)
microphthalmia  (ISO)
Neoplastic Cell Transformation  (ISO)
nervous system disease  (ISO)
pancreatic cancer  (ISO)
pancreatic ductal carcinoma  (ISO)
Peritoneal Diseases  (IMP)
prion disease  (ISO)
scoliosis  (ISO)
SHONE COMPLEX  (ISO)
Skin Neoplasms  (ISO)
Splenomegaly  (ISO)
squamous cell carcinoma  (ISO)
syndromic microphthalmia 5  (ISO)
T-cell acute lymphoblastic leukemia  (ISO)
T-cell lymphoblastic leukemia/lymphoma  (ISO)
tetralogy of Fallot  (ISO)
thoracic aortic aneurysm  (ISO)
Uterine Cervical Neoplasms  (ISO)
visual epilepsy  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(+)-dexrazoxane  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2-acetamidofluorene  (ISO)
2-tert-butylhydroquinone  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',5,5'-tetrabromobisphenol A  (EXP)
3,4-methylenedioxymethamphetamine  (EXP)
4-hydroxynon-2-enal  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
aconitine  (EXP,ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
aspartame  (ISO)
baicalein  (ISO)
baicalin  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
beta-naphthoflavone  (ISO)
bis(2-chloroethyl) sulfide  (EXP)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
Botulinum toxin type A  (ISO)
cadmium dichloride  (EXP,ISO)
calciol  (ISO)
captan  (ISO)
carbon nanotube  (ISO)
chloroquine  (ISO)
chlorpyrifos  (EXP,ISO)
chromium(6+)  (ISO)
chrysene  (ISO)
cis-caffeic acid  (EXP)
cisplatin  (ISO)
clobetasol  (ISO)
cobalt dichloride  (EXP,ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
Cyclopamine  (ISO)
DAPT  (ISO)
DDT  (ISO)
dexamethasone  (EXP)
diallyl trisulfide  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
dieldrin  (EXP)
diethyl maleate  (ISO)
diethylstilbestrol  (ISO)
dimethylarsinic acid  (EXP)
dioxygen  (EXP,ISO)
doxorubicin  (EXP,ISO)
emodin  (EXP)
enzalutamide  (ISO)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
eugenol  (ISO)
fenamidone  (ISO)
fenofibrate  (ISO)
fluoxetine  (EXP)
folic acid  (EXP)
folpet  (ISO)
formaldehyde  (ISO)
furan  (EXP)
gemcitabine  (ISO)
gentamycin  (EXP)
glyphosate  (EXP,ISO)
hydrogen peroxide  (ISO)
isoflavones  (ISO)
Licochalcone B  (ISO)
lipopolysaccharide  (EXP,ISO)
lithium chloride  (ISO)
LY294002  (ISO)
mebendazole  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (EXP)
miconazole  (ISO)
Mitotane  (ISO)
monosodium L-glutamate  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (ISO)
nickel dichloride  (EXP,ISO)
niclosamide  (ISO)
nicotinic acid  (EXP)
ochratoxin A  (ISO)
oxaliplatin  (ISO)
oxidopamine  (EXP,ISO)
Paeonol  (EXP)
paracetamol  (ISO)
paraquat  (ISO)
pentachlorophenol  (ISO)
phenethyl isothiocyanate  (ISO)
picropodophyllotoxin  (ISO)
pirinixic acid  (ISO)
poly(ethylene)  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
propiconazole  (ISO)
propranolol  (ISO)
prostaglandin F2alpha  (EXP)
quercetin  (ISO)
resveratrol  (ISO)
retinyl acetate  (ISO)
Salidroside  (ISO)
SB 203580  (ISO)
simvastatin  (EXP)
sirolimus  (EXP)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
T-2 toxin  (EXP)
tamoxifen  (EXP)
temozolomide  (ISO)
testosterone  (ISO)
tetraphene  (ISO)
titanium dioxide  (ISO)
trans-caffeic acid  (EXP)
trichostatin A  (ISO)
triphenylstannane  (ISO)
Triptolide  (ISO)
triptonide  (ISO)
tungsten  (ISO)
tunicamycin  (ISO)
tyrphostin AG 1478  (ISO)
uranium atom  (EXP)
urethane  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
wortmannin  (ISO)
zalcitabine  (ISO)
zearalenone  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
animal organ regeneration  (IEP)
aortic valve morphogenesis  (ISO)
apoptotic process involved in embryonic digit morphogenesis  (ISO)
arterial endothelial cell differentiation  (ISO)
astrocyte differentiation  (IDA)
atrioventricular node development  (ISO)
atrioventricular valve morphogenesis  (ISO)
auditory receptor cell fate commitment  (ISO)
axonogenesis  (ISO)
brain development  (IEP)
branching morphogenesis of an epithelial tube  (ISO)
cardiac atrium morphogenesis  (ISO)
cardiac chamber formation  (ISO)
cardiac epithelial to mesenchymal transition  (ISO)
cardiac left ventricle morphogenesis  (ISO)
cardiac muscle cell proliferation  (ISO)
cardiac muscle tissue morphogenesis  (ISO)
cardiac right atrium morphogenesis  (ISO)
cardiac right ventricle formation  (ISO)
cardiac septum morphogenesis  (ISO)
cardiac vascular smooth muscle cell development  (ISO)
cardiac ventricle morphogenesis  (ISO)
cell differentiation  (ISO)
cell differentiation in spinal cord  (IEP)
cell fate commitment  (ISO)
cell fate specification  (ISO)
cell migration involved in endocardial cushion formation  (ISO)
cellular response to follicle-stimulating hormone stimulus  (ISO)
cellular response to vascular endothelial growth factor stimulus  (ISO,ISS)
central nervous system development  (IBA)
cilium assembly  (ISS)
collecting duct development  (ISO)
compartment pattern specification  (ISO)
coronary artery morphogenesis  (ISO)
coronary sinus valve morphogenesis  (ISO)
coronary vein morphogenesis  (ISO)
determination of left/right symmetry  (ISO)
distal tubule development  (ISO)
embryonic hindlimb morphogenesis  (ISO)
embryonic limb morphogenesis  (ISO)
endocardial cell differentiation  (ISO)
endocardial cushion development  (ISO)
endocardial cushion morphogenesis  (ISO)
endocardium development  (ISO)
endocardium morphogenesis  (ISO)
endoderm development  (ISO)
epidermis development  (ISO)
epithelial to mesenchymal transition  (ISO)
epithelial to mesenchymal transition involved in endocardial cushion formation  (ISO)
forebrain development  (ISO)
foregut morphogenesis  (ISO)
gene expression  (IEA,ISO)
glial cell differentiation  (ISO)
glomerular mesangial cell development  (ISO)
growth involved in heart morphogenesis  (ISO)
hair follicle morphogenesis  (ISO)
heart development  (ISO)
heart looping  (ISO)
heart trabecula morphogenesis  (ISO)
homeostasis of number of cells within a tissue  (ISO)
humoral immune response  (ISO)
in utero embryonic development  (ISO)
inflammatory response to antigenic stimulus  (ISO)
interleukin-17-mediated signaling pathway  (IEA,ISO)
keratinocyte differentiation  (ISO)
left/right axis specification  (ISO)
liver development  (ISO)
lung development  (ISO)
mesenchymal cell development  (ISO)
mitral valve formation  (ISO)
negative regulation of anoikis  (ISO)
negative regulation of biomineral tissue development  (ISO)
negative regulation of BMP signaling pathway  (ISO)
negative regulation of calcium ion-dependent exocytosis  (ISO)
negative regulation of canonical Wnt signaling pathway  (ISO)
negative regulation of cardiac muscle hypertrophy  (ISO)
negative regulation of catalytic activity  (ISO,ISS)
negative regulation of cell adhesion molecule production  (ISO)
negative regulation of cell death  (ISO)
negative regulation of cell differentiation  (ISO)
negative regulation of cell migration involved in sprouting angiogenesis  (ISO,ISS)
negative regulation of cell population proliferation  (ISO,ISS)
negative regulation of cell proliferation involved in heart valve morphogenesis  (ISO)
negative regulation of cell-cell adhesion mediated by cadherin  (ISO)
negative regulation of cell-substrate adhesion  (ISO)
negative regulation of cold-induced thermogenesis  (ISO,ISS)
negative regulation of endothelial cell chemotaxis  (ISO,ISS)
negative regulation of extracellular matrix constituent secretion  (ISO)
negative regulation of gene expression  (ISO)
negative regulation of glial cell proliferation  (ISO,ISS)
negative regulation of growth rate  (ISO)
negative regulation of inner ear auditory receptor cell differentiation  (ISO)
negative regulation of myoblast differentiation  (ISO)
negative regulation of myotube differentiation  (ISO,ISS)
negative regulation of neurogenesis  (ISO,ISS)
negative regulation of neuron differentiation  (IMP,ISO)
negative regulation of oligodendrocyte differentiation  (ISO,ISS)
negative regulation of ossification  (ISO)
negative regulation of osteoblast differentiation  (ISO)
negative regulation of photoreceptor cell differentiation  (ISO)
negative regulation of pro-B cell differentiation  (ISO,ISS)
negative regulation of stem cell differentiation  (ISO)
negative regulation of transcription by RNA polymerase II  (ISO,ISS)
negative regulation of transcription, DNA-templated  (ISO)
neural tube development  (ISO)
neuron differentiation  (ISO)
neuron fate commitment  (ISO)
neuronal stem cell population maintenance  (ISO)
Notch signaling involved in heart development  (ISO,ISS)
Notch signaling pathway  (IDA,IMP,ISO)
Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation  (ISO)
oligodendrocyte differentiation  (IEP)
outflow tract morphogenesis  (ISO)
pericardium morphogenesis  (ISO)
positive regulation of aorta morphogenesis  (ISO)
positive regulation of apoptotic process  (ISO)
positive regulation of apoptotic process involved in morphogenesis  (ISO)
positive regulation of astrocyte differentiation  (ISO,ISS)
positive regulation of BMP signaling pathway  (ISO,ISS)
positive regulation of cardiac epithelial to mesenchymal transition  (IGI)
positive regulation of cardiac muscle cell proliferation  (ISO)
positive regulation of cell migration  (ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of endothelial cell differentiation  (IMP)
positive regulation of epithelial cell proliferation  (ISO)
positive regulation of epithelial to mesenchymal transition  (ISO)
positive regulation of ERK1 and ERK2 cascade  (ISO)
positive regulation of gene expression  (IGI,IMP,ISO)
positive regulation of glial cell differentiation  (IMP)
positive regulation of keratinocyte differentiation  (ISO)
positive regulation of neuroblast proliferation  (IMP)
positive regulation of Notch signaling pathway  (ISO)
positive regulation of Ras protein signal transduction  (ISO)
positive regulation of receptor signaling pathway via JAK-STAT  (ISO,ISS)
positive regulation of transcription by RNA polymerase II  (IGI,IMP,ISO)
positive regulation of transcription from RNA polymerase II promoter in response to hypoxia  (ISO,ISS)
positive regulation of transcription of Notch receptor target  (IMP,ISO)
positive regulation of transcription, DNA-templated  (ISO,ISS)
positive regulation of viral genome replication  (ISO)
positive regulation of viral transcription  (ISO)
prostate gland epithelium morphogenesis  (ISO)
protein catabolic process  (IEA,ISO)
protein import into nucleus  (IEA,ISO)
pulmonary valve morphogenesis  (ISO)
regulation of cardioblast proliferation  (IMP)
regulation of cell cycle  (ISO)
regulation of cell migration  (ISO)
regulation of cell population proliferation  (IMP,ISO)
regulation of epithelial cell proliferation  (ISO)
regulation of epithelial cell proliferation involved in prostate gland development  (ISO)
regulation of extracellular matrix assembly  (ISO)
regulation of gene expression  (ISO)
regulation of inner ear auditory receptor cell differentiation  (ISO)
regulation of neurogenesis  (ISO)
regulation of Notch signaling pathway  (ISO)
regulation of somitogenesis  (ISO)
regulation of transcription by RNA polymerase II  (ISO)
regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation  (ISO)
response to corticosteroid  (IEP)
response to lipopolysaccharide  (IEP)
response to muramyl dipeptide  (ISO)
secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development  (ISO)
skeletal muscle cell differentiation  (ISO)
skeletal system development  (IBA)
somatic stem cell division  (ISO)
spermatogenesis  (IMP)
sprouting angiogenesis  (ISO)
T-helper 17 type immune response  (IEA,ISO)
tissue regeneration  (IEP)
tube formation  (ISO,ISS)
vasculogenesis involved in coronary vascular morphogenesis  (ISO)
venous blood vessel morphogenesis  (ISO)
venous endothelial cell differentiation  (ISO)
ventricular septum morphogenesis  (ISO)
ventricular trabecula myocardium morphogenesis  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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Additional References at PubMed
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PMID:21209419   PMID:21266778   PMID:21311046   PMID:21330605   PMID:21419176   PMID:21426641   PMID:21457232   PMID:21493891   PMID:21672385   PMID:21887253   PMID:22085497   PMID:22147266  
PMID:22302604   PMID:22334042   PMID:22474986   PMID:22525134   PMID:22713619   PMID:22833359   PMID:22833673   PMID:22964414   PMID:22989188   PMID:23056328   PMID:23132739   PMID:23160044  
PMID:23232913   PMID:23284756   PMID:23382219   PMID:23589286   PMID:23595520   PMID:23707238   PMID:23755752   PMID:23834718   PMID:23844238   PMID:23938602   PMID:23948289   PMID:24098462  
PMID:24098939   PMID:24217957   PMID:24223152   PMID:24397211   PMID:24406215   PMID:24563863   PMID:24667410   PMID:24677709   PMID:24715457   PMID:24751889   PMID:24866722   PMID:24974008  
PMID:25342127   PMID:25535395   PMID:25624721   PMID:25660475   PMID:25700513   PMID:26040933   PMID:26134952   PMID:26182882   PMID:26316699   PMID:26491108   PMID:26703474   PMID:26728369  
PMID:26817817   PMID:27011052   PMID:27057278   PMID:27107132   PMID:27259983   PMID:27655677   PMID:27804997   PMID:28025657   PMID:28129650   PMID:28210849   PMID:28273100   PMID:28677782  
PMID:28695984   PMID:28698260   PMID:28776666   PMID:29097792   PMID:29138545   PMID:29186476   PMID:29286063   PMID:29504377   PMID:29674611   PMID:29717517   PMID:30221657   PMID:30338818  
PMID:30515819   PMID:30653707   PMID:30714138   PMID:30768929   PMID:31002155   PMID:31035811   PMID:31209813   PMID:31210285   PMID:31433841   PMID:31476403   PMID:31585906   PMID:31640732  
PMID:31718671   PMID:31726181   PMID:31796120   PMID:31799679   PMID:31975567   PMID:32004541   PMID:32069075   PMID:32144600   PMID:32703409   PMID:32783102   PMID:32827575   PMID:33086033  
PMID:33236068   PMID:34018360  


Genomics

Comparative Map Data
Notch1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.239,277,955 - 9,323,531 (-)NCBI
Rnor_6.0 Ensembl33,905,453 - 3,951,025 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.033,905,562 - 3,951,015 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.039,266,663 - 9,311,575 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.434,631,797 - 4,677,640 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.134,632,997 - 4,677,652 (-)NCBI
Celera34,097,915 - 4,143,369 (-)NCBICelera
Cytogenetic Map3p13NCBI
NOTCH1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9136,494,433 - 136,546,048 (-)EnsemblGRCh38hg38GRCh38
GRCh389136,494,433 - 136,546,048 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh379139,388,885 - 139,440,500 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369138,508,717 - 138,560,059 (-)NCBINCBI36hg18NCBI36
Build 349136,664,733 - 136,716,075NCBI
Celera9109,903,340 - 109,955,631 (-)NCBI
Cytogenetic Map9q34.3NCBI
HuRef9108,848,155 - 108,928,442 (-)NCBIHuRef
CHM1_19139,537,630 - 139,588,846 (-)NCBICHM1_1
Notch1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39226,347,914 - 26,393,834 (-)NCBIGRCm39mm39
GRCm39 Ensembl226,347,915 - 26,406,675 (-)Ensembl
GRCm38226,457,902 - 26,503,822 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl226,457,903 - 26,516,663 (-)EnsemblGRCm38mm10GRCm38
MGSCv37226,313,422 - 26,359,342 (-)NCBIGRCm37mm9NCBIm37
MGSCv36226,280,033 - 26,325,646 (-)NCBImm8
Celera226,175,736 - 26,221,759 (-)NCBICelera
Cytogenetic Map2A3NCBI
cM Map218.91NCBI
Notch1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555134,225,956 - 4,263,259 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555134,225,939 - 4,264,875 (+)NCBIChiLan1.0ChiLan1.0
NOTCH1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19136,544,639 - 136,595,511 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9136,544,639 - 136,598,740 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v09107,568,670 - 107,621,032 (-)NCBIMhudiblu_PPA_v0panPan3
NOTCH1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1948,975,972 - 49,018,985 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl948,974,757 - 49,017,277 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha948,226,361 - 48,269,900 (+)NCBI
ROS_Cfam_1.0949,852,205 - 49,895,734 (+)NCBI
UMICH_Zoey_3.1948,633,237 - 48,676,758 (+)NCBI
UNSW_CanFamBas_1.0948,926,759 - 48,970,231 (+)NCBI
UU_Cfam_GSD_1.0948,974,423 - 49,017,941 (+)NCBI
Notch1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947202,040,997 - 202,083,042 (-)NCBI
SpeTri2.0NW_0049366691,292,016 - 1,334,061 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NOTCH1
(Sus scrofa - pig)
No map positions available.
NOTCH1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1121,656,815 - 1,707,566 (+)NCBI
ChlSab1.1 Ensembl121,656,918 - 1,709,585 (+)Ensembl
Vero_WHO_p1.0NW_0236660583,509,673 - 3,610,304 (-)NCBI
Notch1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247601,636,331 - 1,676,398 (-)NCBI

Position Markers
D3Rat195  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.239,286,002 - 9,286,237 (+)MAPPER
Rnor_6.033,913,490 - 3,913,724NCBIRnor6.0
Rnor_5.039,274,591 - 9,274,825UniSTSRnor5.0
RGSC_v3.434,639,724 - 4,639,959RGDRGSC3.4
RGSC_v3.434,639,725 - 4,639,959UniSTSRGSC3.4
RGSC_v3.134,639,724 - 4,639,959RGD
Celera34,105,843 - 4,106,077UniSTS
SHRSP x BN Map32.4699RGD
SHRSP x BN Map32.4699UniSTS
Cytogenetic Map3p13UniSTS
D3Rat281  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.239,325,263 - 9,325,417 (+)MAPPER
Rnor_6.033,952,748 - 3,952,901NCBIRnor6.0
Rnor_5.039,313,308 - 9,313,453UniSTSRnor5.0
Celera34,145,102 - 4,145,255UniSTS
SHRSP x BN Map32.4499RGD
SHRSP x BN Map32.4499UniSTS
Cytogenetic Map3p13UniSTS
PMC85812P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.239,285,189 - 9,285,550 (+)MAPPER
Rnor_6.033,912,677 - 3,913,037NCBIRnor6.0
Rnor_5.039,273,778 - 9,274,138UniSTSRnor5.0
RGSC_v3.434,638,912 - 4,639,272UniSTSRGSC3.4
Celera34,105,030 - 4,105,390UniSTS
Cytogenetic Map3p13UniSTS
RH133217  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.239,277,962 - 9,278,179 (+)MAPPER
Rnor_6.033,905,450 - 3,905,666NCBIRnor6.0
Rnor_5.039,266,551 - 9,266,767UniSTSRnor5.0
RGSC_v3.434,631,685 - 4,631,901UniSTSRGSC3.4
Celera34,097,803 - 4,098,019UniSTS
Cytogenetic Map3p13UniSTS
RH134624  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.239,279,595 - 9,279,775 (+)MAPPER
Rnor_6.033,907,083 - 3,907,262NCBIRnor6.0
Rnor_5.039,268,184 - 9,268,363UniSTSRnor5.0
RGSC_v3.434,633,318 - 4,633,497UniSTSRGSC3.4
Celera34,099,436 - 4,099,615UniSTS
Cytogenetic Map3p13UniSTS
UniSTS:265729  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.239,279,732 - 9,279,979 (+)MAPPER
Rnor_6.033,907,220 - 3,907,466NCBIRnor6.0
Rnor_5.039,268,321 - 9,268,567UniSTSRnor5.0
RGSC_v3.434,633,455 - 4,633,701UniSTSRGSC3.4
Celera34,099,573 - 4,099,819UniSTS
Cytogenetic Map3p13UniSTS
Notch1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.239,280,872 - 9,281,064 (+)MAPPER
Rnor_6.033,908,360 - 3,908,551NCBIRnor6.0
Rnor_5.039,269,461 - 9,269,652UniSTSRnor5.0
RGSC_v3.434,634,595 - 4,634,786UniSTSRGSC3.4
Celera34,100,713 - 4,100,904UniSTS
Cytogenetic Map3p13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3125786001Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3128136884Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3128500807Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3132972944Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3137891710Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3139773425Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3195176874Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35711366000866Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35711366000866Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3263142133477544Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3263142148562146Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3328592928136884Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3328592928136884Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:172
Count of miRNA genes:128
Interacting mature miRNAs:140
Transcripts:ENSRNOT00000026212
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

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 2 33 15 2 17 2 1 1 61 23 33 11 1
Low 1 10 42 39 2 39 7 10 13 12 8 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026212   ⟹   ENSRNOP00000026212
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl33,905,453 - 3,951,025 (-)Ensembl
RefSeq Acc Id: NM_001105721   ⟹   NP_001099191
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.239,278,075 - 9,323,531 (-)NCBI
Rnor_6.033,905,562 - 3,951,015 (-)NCBI
Rnor_5.039,266,663 - 9,311,575 (-)NCBI
RGSC_v3.434,631,797 - 4,677,640 (-)RGD
Celera34,097,915 - 4,143,369 (-)RGD
Sequence:
RefSeq Acc Id: XM_039104374   ⟹   XP_038960302
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.239,277,955 - 9,303,898 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001099191 (Get FASTA)   NCBI Sequence Viewer  
  XP_038960302 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL93491 (Get FASTA)   NCBI Sequence Viewer  
  Q07008 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001099191   ⟸   NM_001105721
- Peptide Label: precursor
- UniProtKB: Q07008 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000026212   ⟸   ENSRNOT00000026212
RefSeq Acc Id: XP_038960302   ⟸   XM_039104374
- Peptide Label: isoform X1
Protein Domains
EGF-like

Transcriptome

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

Promoters
RGD ID:13691908
Promoter ID:EPDNEW_R2433
Type:single initiation site
Name:Notch1_1
Description:notch 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_6.033,951,039 - 3,951,099EPDNEW

Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3187 AgrOrtholog
Ensembl Genes ENSRNOG00000019322 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000026212 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000026212 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.25.40.20 UniProtKB/Swiss-Prot
InterPro Ankyrin_rpt UniProtKB/Swiss-Prot
  Ankyrin_rpt-contain_dom UniProtKB/Swiss-Prot
  Ankyrin_rpt-contain_sf UniProtKB/Swiss-Prot
  DUF3454_notch UniProtKB/Swiss-Prot
  EGF-like_Ca-bd_dom UniProtKB/Swiss-Prot
  EGF-like_CS UniProtKB/Swiss-Prot
  EGF-like_dom UniProtKB/Swiss-Prot
  EGF-type_Asp/Asn_hydroxyl_site UniProtKB/Swiss-Prot
  EGF_Ca-bd_CS UniProtKB/Swiss-Prot
  Growth_fac_rcpt_cys_sf UniProtKB/Swiss-Prot
  Notch UniProtKB/Swiss-Prot
  Notch-like_dom_sf UniProtKB/Swiss-Prot
  Notch_1 UniProtKB/Swiss-Prot
  Notch_dom UniProtKB/Swiss-Prot
  Notch_NOD_dom UniProtKB/Swiss-Prot
  Notch_NODP_dom UniProtKB/Swiss-Prot
KEGG Report rno:25496 UniProtKB/Swiss-Prot
NCBI Gene 25496 ENTREZGENE
Pfam Ank_2 UniProtKB/Swiss-Prot
  DUF3454 UniProtKB/Swiss-Prot
  EGF UniProtKB/Swiss-Prot
  EGF_CA UniProtKB/Swiss-Prot
  hEGF UniProtKB/Swiss-Prot
  NOD UniProtKB/Swiss-Prot
  NODP UniProtKB/Swiss-Prot
  Notch UniProtKB/Swiss-Prot
PhenoGen Notch1 PhenoGen
PIRSF Notch UniProtKB/Swiss-Prot
PRINTS LNOTCHREPEAT UniProtKB/Swiss-Prot
  NOTCH1 UniProtKB/Swiss-Prot
PROSITE ANK_REP_REGION UniProtKB/Swiss-Prot
  ANK_REPEAT UniProtKB/Swiss-Prot
  ASX_HYDROXYL UniProtKB/Swiss-Prot
  EGF_1 UniProtKB/Swiss-Prot
  EGF_2 UniProtKB/Swiss-Prot
  EGF_3 UniProtKB/Swiss-Prot
  EGF_CA UniProtKB/Swiss-Prot
  LNR UniProtKB/Swiss-Prot
SMART ANK UniProtKB/Swiss-Prot
  DUF3454 UniProtKB/Swiss-Prot
  EGF UniProtKB/Swiss-Prot
  EGF_CA UniProtKB/Swiss-Prot
  NOD UniProtKB/Swiss-Prot
  NODP UniProtKB/Swiss-Prot
  SM00004 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48403 UniProtKB/Swiss-Prot
  SSF57184 UniProtKB/Swiss-Prot
  SSF90193 UniProtKB/Swiss-Prot
UniProt NOTC1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary F1M9E7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-04 Notch1  notch receptor 1  Notch1  notch 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-08-02 Notch1  notch 1  Notch1  Notch homolog 1, translocation-associated (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-26 Notch1  Notch homolog 1, translocation-associated (Drosophila)  Notch1  Notch gene homolog 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2001-10-23 Notch1  Notch gene homolog 1, (Drosophila)      Name updated to reflect Human and Mouse nomenclature 68913 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains 36 epidermal growth factor (EGF)-like repeats 728926
gene_expression expressed only in ventricular proliferative zones of embryonic neuroepithelia 728926