Tlr4 (toll-like receptor 4) - Rat Genome Database

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Gene: Tlr4 (toll-like receptor 4) Rattus norvegicus
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Symbol: Tlr4
Name: toll-like receptor 4
RGD ID: 3870
Description: Exhibits lipopolysaccharide binding activity and phosphatidylinositol 3-kinase binding activity. Involved in several processes, including cellular response to lipid; detection of stimulus involved in sensory perception of pain; and response to steroid hormone. Localizes to cell surface and cytoplasm. Colocalizes with membrane raft. Used to study several diseases, including carotid stenosis; ileitis; neuropathy (multiple); obesity; and renal fibrosis. Biomarker of several diseases, including kidney failure (multiple); mastitis; perinatal necrotizing enterocolitis; pulpitis; and sciatic neuropathy. Human ortholog(s) of this gene implicated in several diseases, including allergic contact dermatitis (multiple); artery disease (multiple); autoimmune disease (multiple); eye disease (multiple); and lung disease (multiple). Orthologous to human TLR4 (toll like receptor 4); PARTICIPATES IN Toll-like receptor signaling pathway; titanium dioxide nanoparticle response pathway; Chagas disease pathway; INTERACTS WITH (+)-pilocarpine; (S)-nicotine; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: toll4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Tlr4m1Mcwi   Tlr4em1Geh   Tlr4em5Mcwi  
Genetic Models: WI-Tlr4em1Geh BBDR.BBDP-(D4Mit6-D4Mit7)-Tlr4em5Mcwi FHH-Tlr4m1Mcwi
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2580,145,867 - 80,159,501 (+)NCBI
Rnor_6.0 Ensembl582,587,420 - 82,601,052 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0582,587,424 - 82,601,056 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0586,690,670 - 86,704,302 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4583,564,100 - 83,577,735 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1583,569,212 - 83,582,848 (+)NCBI
Celera579,045,293 - 79,058,928 (+)NCBICelera
RH 3.4 Map5643.7RGD
Cytogenetic Map5q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Acanthamoeba Keratitis  (IEP)
acne  (ISO)
Acne Conglobata  (ISO)
Acute Coronary Syndrome  (ISO)
acute kidney failure  (IDA,ISO)
Acute Liver Failure  (IEP,IMP)
Acute Lung Injury  (IEP)
Acute Necrotizing Pancreatitis  (IEP)
acute pancreatitis  (ISO)
Acute Tubulointerstitial Nephritis  (ISO)
Acute-On-Chronic Liver Failure  (IEP)
age related macular degeneration 10  (ISO)
Alcoholic Fatty Liver  (ISO)
allergic conjunctivitis  (ISO)
allergic contact dermatitis  (ISO)
allergic rhinitis  (ISO)
Alzheimer's disease  (ISO)
Angina, Stable  (ISO)
ankylosing spondylitis  (ISO)
anogenital venereal wart  (ISO)
anterior uveitis  (ISO)
arteriosclerosis  (ISO)
arthritis  (ISO)
asthma  (ISO)
atherosclerosis  (ISO)
atopic dermatitis  (ISO)
Bacteremia  (ISO)
Bacterial Keratitis  (ISO)
bacterial pneumonia  (ISO)
Behcet's disease  (ISO)
Brain Injuries  (IEP,ISO)
brain ischemia  (ISO)
breast cancer  (ISO)
Bronchial Hyperreactivity  (ISO)
carcinoma  (ISO)
carotid artery disease  (ISO)
carotid stenosis  (IDA)
Chemical and Drug Induced Liver Injury  (IEP)
cholesteatoma  (ISO)
cholesteatoma of middle ear  (ISO)
Chronic Hepatitis B  (ISO)
Chronic Hepatitis C  (ISO)
chronic obstructive pulmonary disease  (ISO)
Chronic Pain  (ISO)
Chronic Periodontitis  (ISO)
colitis  (IEP,ISO)
Colorectal Neoplasms  (ISO)
contact dermatitis  (ISO)
coronary artery disease  (ISO)
Crohn's disease  (ISO)
cutaneous leishmaniasis  (ISO)
cystic echinococcosis  (ISO)
cystic fibrosis  (ISO)
dermatomyositis  (ISO)
diabetes mellitus  (ISO)
Diabetic Foot  (ISO)
Diabetic Nephropathies  (ISO)
diabetic neuropathy  (IDA,ISO)
diabetic retinopathy  (ISO)
dry eye syndrome  (ISO)
end stage renal disease  (ISO)
Endotoxemia  (IDA,ISO)
Entamoebiasis  (ISO)
Eosinophilia  (ISO)
esophagus adenocarcinoma  (ISO)
eumycotic mycetoma  (ISO)
exfoliation syndrome  (ISO)
Experimental Autoimmune Encephalomyelitis  (IEP)
Experimental Autoimmune Neuritis  (IEP)
Experimental Autoimmune Uveitis  (ISO)
Experimental Diabetes Mellitus  (IEP)
Experimental Liver Cirrhosis  (IDA,ISO)
extrahepatic cholestasis  (ISO)
eye disease  (ISO)
familial Mediterranean fever  (ISO)
fatty liver disease  (ISO)
Fibrosis  (ISO)
Fungal Eye Infections  (IEP)
Fungal Keratitis  (ISO)
glomerulonephritis  (ISO)
Hearing Loss  (ISO)
Hemorrhagic Shock  (ISO)
hepatocellular carcinoma  (ISO)
hepatorenal syndrome  (IEP)
Herpes Simplex Encephalitis  (IEP)
herpes simplex virus keratitis  (ISO)
Hyperalgesia  (IMP,ISO)
hypertension  (ISO)
ileitis  (IMP,ISO)
Inflammation  (ISO)
Insulin Resistance  (ISO)
invasive aspergillosis  (ISO)
Kawasaki disease  (ISO)
keratitis  (ISO)
kidney failure  (IEP,ISO)
Kidney Reperfusion Injury  (IDA,ISO)
learning disability  (ISO)
leptospirosis  (ISO)
liver cirrhosis  (IEP,ISO)
Liver Injury  (ISO)
Liver Reperfusion Injury  (IEP,ISO)
low tension glaucoma  (ISO)
lung disease  (IDA,IEP,ISO)
Lung Injury  (ISO)
Lung Neoplasms  (ISO)
Lung Reperfusion Injury  (IEP)
Lymphatic Metastasis  (ISO)
macular degeneration  (ISO)
mastitis  (IEP)
mastoiditis  (ISO)
melanoma  (ISO)
membranoproliferative glomerulonephritis  (ISO)
Meningitis, Escherichia Coli  (ISO)
meningococcal meningitis  (ISO)
multiple sclerosis  (ISO)
myocardial infarction  (ISO)
Myocardial Reperfusion Injury  (IDA)
Nasal Polyps  (ISO)
Neoplasm Invasiveness  (ISO)
Neoplasm Metastasis  (ISO)
Neuralgia  (IEP)
non-alcoholic fatty liver disease  (IEP,ISO)
obesity  (IMP,ISO)
Onchocerciasis, Ocular  (ISO)
Optic Nerve Injuries  (ISO)
Oral Lichen Planus  (ISO)
otitis media  (ISO)
Otitis Media with Effusion  (ISO)
Ovarian Neoplasms  (ISO)
Pain  (IMP)
Painful Neuropathy  (ISO)
pancreatitis  (IEP,ISO)
perinatal necrotizing enterocolitis  (IEP,ISO)
Plaque, Atherosclerotic  (ISO)
pleural tuberculosis  (ISO)
Pneumococcal Meningitis  (ISO)
pneumonia  (ISO)
pre-eclampsia  (ISO)
primary open angle glaucoma  (ISO)
Prostatic Neoplasms  (ISO)
Pseudomonas Aeruginosa Keratitis  (ISO)
psoriasis  (ISO)
pulmonary edema  (ISO)
pulmonary emphysema  (ISO,ISS)
pulmonary fibrosis  (ISO)
pulmonary hypertension  (ISO)
pulmonary tuberculosis  (ISO)
pulpitis  (IEP)
renal fibrosis  (IMP)
Reperfusion Injury  (IEP,ISO)
respiratory allergy  (ISO)
Respiratory Sounds  (ISO)
respiratory syncytial virus infectious disease  (ISO)
Retina Reperfusion Injury  (ISO)
Rhinosinusitis  (ISO)
sciatic neuropathy  (IEP,IMP,ISO)
Seasonal Allergic Rhinitis  (ISO)
Sepsis  (IEP,ISO)
sinusitis  (ISO)
Spinal Cord Injuries  (ISO)
Spinal Cord Reperfusion Injury  (IMP)
sporotrichosis  (ISO)
Stroke  (ISO)
Subarachnoid Hemorrhage  (IEP)
suppurative otitis media  (ISO)
systemic lupus erythematosus  (ISO)
temporal arteritis  (ISO)
Transplant Rejection  (ISO)
tuberculosis  (ISO)
tympanosclerosis  (ISO)
type 1 diabetes mellitus  (ISO)
type 2 diabetes mellitus  (ISO)
urinary bladder cancer  (ISO)
urinary tract infection  (ISO)
uveitis  (IEP)
Ventricular Dysfunction, Left  (ISO)
Viral Bronchiolitis  (ISO)
viral meningitis  (ISO)
vitiligo  (ISO)
Wallerian Degeneration  (ISO)
Weight Loss  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(+)-epicatechin-3-O-gallate  (ISO)
(+)-pilocarpine  (EXP)
(-)-demecolcine  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(24S)-24-hydroxycholesterol  (ISO)
(25R)-cholest-5-ene-3beta,26-diol  (ISO)
(S)-nicotine  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (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)
17beta-estradiol  (EXP)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP,ISO)
2-(4-iodo-2,5-dimethoxyphenyl)-1-methylethylamine  (EXP)
2-amino-2-deoxy-D-galactopyranose  (ISO)
26-hydroxycholesterol  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',5,5'-tetrabromobisphenol A  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-phenylprop-2-enal  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxy-3-[4-(2-hydroxyphenyl)phenyl]-6-oxo-7H-thieno[2,3-b]pyridine-5-carbonitrile  (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)
5-aza-2'-deoxycytidine  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
7alpha-hydroxycholesterol  (ISO)
acetamide  (EXP)
acetate ester  (ISO)
acetic acid  (ISO)
acrolein  (ISO)
adenosine  (ISO)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (ISO)
all-trans-retinol  (ISO)
alpha-D-galactose  (ISO)
alpha-pinene  (ISO)
aluminium hydroxide  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arachidonic acid  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
artesunate  (EXP)
aspalathin  (ISO)
atorvastatin calcium  (EXP,ISO)
auranofin  (ISO)
azathioprine  (ISO)
baicalin  (EXP)
benazepril  (ISO)
benzalkonium chloride  (ISO)
benzo[a]pyrene  (ISO)
benzylpenicillin  (ISO)
berberine  (ISO)
Besigomsin  (ISO)
bicalutamide  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisdemethoxycurcumin  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol A diglycidyl ether  (EXP)
bisphenol F  (ISO)
bortezomib  (ISO)
butyric acid  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
calcitriol  (EXP)
capsaicin  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
casticin  (ISO)
catalpol  (ISO)
cerium trichloride  (ISO)
chaetoglobosin A  (ISO)
chitosan  (ISO)
chlorogenic acid  (EXP,ISO)
chloroquine  (ISO)
chlorpyrifos  (EXP)
cholesterol  (EXP)
choline  (ISO)
chromium atom  (ISO)
chrysin  (EXP,ISO)
cisplatin  (EXP,ISO)
cobalt dichloride  (EXP,ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
corticosterone  (ISO)
cortisol  (ISO)
crocin-1  (EXP)
curcumin  (EXP,ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
D-glucose  (EXP,ISO)
DAPT  (EXP)
daunorubicin  (ISO)
dehydroepiandrosterone  (EXP)
desferrioxamine B  (ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
diallyl trisulfide  (ISO)
diazinon  (ISO)
dienogest  (ISO)
dihydrogen  (EXP)
dimethylarsinous acid  (ISO)
dioxygen  (EXP,ISO)
diprotium  (EXP)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
enalapril  (ISO)
enalaprilat dihydrate  (EXP)
erythromycin A  (ISO)
esculetin  (ISO)
ethanol  (EXP,ISO)
ethion  (ISO)
ethyl methanesulfonate  (ISO)
eugenol  (ISO)
ferulic acid  (ISO)
fisetin  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
formaldehyde  (EXP)
fructose  (EXP,ISO)
furan  (EXP)
gadolinium trichloride  (EXP)
galactose  (ISO)
gallocatechin  (ISO)
ganglioside GM1  (EXP)
Gastrodin  (EXP)
geldanamycin  (ISO)
genistein  (ISO)
geraniol  (ISO)
Ginkgolide A  (ISO)
ginsenoside Re  (ISO)
glucose  (EXP,ISO)
glutathione  (ISO)
glycyrrhetinate  (ISO)
glycyrrhetinic acid  (ISO)
halothane  (ISO)
helenalin  (ISO)
hexadecanoic acid  (ISO)
hyaluronic acid  (ISO)
hydroquinone  (ISO)
ifosfamide  (ISO)
indometacin  (ISO)
irinotecan  (ISO)
iron(2+) sulfate (anhydrous)  (ISO)
isoamylol  (ISO)
isoprenaline  (EXP,ISO)
ivermectin  (ISO)
kaempferol 3-O-beta-D-glucosyl-(1->2)-beta-D-glucoside  (ISO)
ketamine  (ISO)
L-1,4-dithiothreitol  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lactulose  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
linsidomine  (ISO)
lipophosphoglycan  (ISO)
lipopolysaccharide  (EXP,ISO)
liquiritigenin  (EXP)
liquiritin  (EXP)
lithium chloride  (EXP)
LY294002  (ISO)
lycopene  (ISO)
magnesium dihydroxide  (ISO)
malathion  (ISO)
melatonin  (EXP)
melittin  (ISO)
melphalan  (ISO)
metformin  (EXP,ISO)
methadone  (EXP,ISO)
methamphetamine  (EXP,ISO)
methimazole  (EXP)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylisothiazolinone  (ISO)
Methylthiouracil  (ISO)
monocrotaline  (EXP,ISO)
monodansylcadaverine  (ISO)
morphine  (EXP,ISO)
Morphine-3-glucuronide  (EXP,ISO)
muramyl dipeptide  (ISO)
N-[2-(diethylamino)ethyl]-2-methoxy-5-methylsulfonylbenzamide  (EXP)
N-acetyl-L-cysteine  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (EXP)
N-nitrosodimethylamine  (EXP)
N-Nitrosopyrrolidine  (ISO)
naloxone  (ISO)
naproxen  (EXP)
nerolidol  (EXP)
nickel dichloride  (ISO)
nickel sulfate  (ISO)
nicorandil  (EXP)
nicotine  (EXP)
nitric oxide  (ISO)
Nonidet P-40  (ISO)
Nonylphenol  (EXP,ISO)
o-anisidine  (ISO)
omeprazole  (EXP)
oxaliplatin  (ISO)
ozone  (EXP,ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
PD 0325901  (ISO)
pelargonidin  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctanoic acid  (ISO)
permethrin  (ISO)
phenylmercury acetate  (ISO)
phenytoin  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
phosphatidylinositol dimannoside  (ISO)
phosphoramide mustard  (EXP)
picropodophyllotoxin  (ISO)
pipoxolan  (ISO)
pirinixic acid  (ISO)
platycodin D  (EXP)
polymyxin B2  (ISO)
potassium chromate  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
probenecid  (ISO)
progesterone  (ISO)
propofol  (ISO)
puerarin  (ISO)
Pyridostigmine bromide  (ISO)
quercetin  (EXP,ISO)
reactive oxygen species  (ISO)
resveratrol  (EXP,ISO)
rosmarinic acid  (EXP)
S-allylcysteine  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (EXP,ISO)
Salvianolic acid A  (ISO)
salvianolic acid B  (EXP)
SB 431542  (ISO)
Scoparone  (ISO)
scopoletin  (EXP)
silicon dioxide  (ISO)
simvastatin  (EXP,ISO)
sodium arsenite  (ISO)
sodium cholate  (EXP)
streptozocin  (EXP,ISO)
succimer  (ISO)
sulfasalazine  (ISO)
sulforaphane  (ISO)
sumatriptan  (EXP)
telmisartan  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP,ISO)
tetrachloropalladate(2-)  (ISO)
thioacetamide  (EXP)
thymoquinone  (ISO)
titanium atom  (EXP,ISO)
titanium dioxide  (ISO)
toluene  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vitamin D  (ISO)
zinc atom  (EXP)
zinc oxide  (ISO)
zinc protoporphyrin  (EXP)
zinc(0)  (EXP)
zingerone  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of innate immune response  (IEA,ISO)
activation of MAPK activity  (IEA,ISO)
astrocyte development  (IEA,ISO)
B cell proliferation involved in immune response  (IEA,ISO)
cellular response to amyloid-beta  (IEA,ISO)
cellular response to interferon-gamma  (IEA,ISO)
cellular response to lipopolysaccharide  (IEP,ISO)
cellular response to lipoteichoic acid  (IEA,ISO)
cellular response to mechanical stimulus  (IEA,IEP,ISO)
cellular response to oxidised low-density lipoprotein particle stimulus  (IEA,ISO)
cellular response to retinoic acid  (IEP)
defense response to bacterium  (ISO)
defense response to Gram-negative bacterium  (IBA,IEA,ISO)
detection of lipopolysaccharide  (IEA,ISO,ISS)
detection of mechanical stimulus involved in sensory perception of pain  (IMP)
detection of temperature stimulus involved in sensory perception of pain  (IMP)
I-kappaB phosphorylation  (IEA,ISO)
immunoglobulin mediated immune response  (IEP)
inflammatory response  (IBA,IEP)
innate immune response-activating signal transduction  (IMP)
intestinal epithelial structure maintenance  (IEA,ISO)
leukotriene metabolic process  (IDA)
lipopolysaccharide-mediated signaling pathway  (IEA,ISO)
macrophage activation  (IEA,ISO)
microglial cell activation  (IDA)
MyD88-dependent toll-like receptor signaling pathway  (IEA,ISO)
negative regulation of cold-induced thermogenesis  (ISO,ISS)
negative regulation of ERK1 and ERK2 cascade  (IEA,ISO)
negative regulation of interferon-gamma production  (IEA,ISO)
negative regulation of interleukin-17 production  (IEA,ISO)
negative regulation of interleukin-23 production  (IEA,ISO)
negative regulation of interleukin-6 production  (IEA,ISO)
negative regulation of tumor necrosis factor production  (IEA,ISO)
nitric oxide production involved in inflammatory response  (IEA,ISO)
phagocytosis  (IEA,ISO)
positive regulation of apoptotic process  (IMP)
positive regulation of B cell proliferation  (IEA,ISO)
positive regulation of cellular response to macrophage colony-stimulating factor stimulus  (IEA,ISO)
positive regulation of chemokine (C-X-C motif) ligand 2 production  (IEA,ISO)
positive regulation of chemokine production  (ISO)
positive regulation of cytokine production involved in inflammatory response  (IEA,ISO)
positive regulation of DNA binding  (IMP)
positive regulation of DNA-binding transcription factor activity  (IMP)
positive regulation of ERK1 and ERK2 cascade  (IEA,ISO)
positive regulation of gene expression  (ISO)
positive regulation of I-kappaB kinase/NF-kappaB signaling  (IEA,ISO)
positive regulation of inflammatory response  (IEA,IMP,ISO)
positive regulation of interferon-alpha production  (IEA,ISO)
positive regulation of interferon-beta production  (IEA,ISO)
positive regulation of interferon-gamma production  (IEA,ISO)
positive regulation of interleukin-1 beta production  (IEA,ISO,ISS)
positive regulation of interleukin-1 production  (ISO)
positive regulation of interleukin-10 production  (IEA,ISO)
positive regulation of interleukin-12 production  (IEA,ISO)
positive regulation of interleukin-6 production  (IEA,ISO)
positive regulation of interleukin-8 production  (IEA,ISO)
positive regulation of JNK cascade  (IEA,ISO)
positive regulation of keratinocyte proliferation  (IEA)
positive regulation of lymphocyte proliferation  (ISO)
positive regulation of macrophage activation  (IEA,ISO)
positive regulation of macrophage cytokine production  (IEA,ISO)
positive regulation of matrix metallopeptidase secretion  (IEA,ISO)
positive regulation of MHC class II biosynthetic process  (IEA,ISO)
positive regulation of NF-kappaB transcription factor activity  (IEA,IMP,ISO)
positive regulation of NIK/NF-kappaB signaling  (IEA,ISO)
positive regulation of nitric oxide biosynthetic process  (IEA,ISO)
positive regulation of nitric-oxide synthase biosynthetic process  (IEA,ISO)
positive regulation of NLRP3 inflammasome complex assembly  (IEA,ISO,ISS)
positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway  (IEA,ISO)
positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway  (IEA,ISO)
positive regulation of oxidative stress-induced neuron death  (IEA,ISO)
positive regulation of peptidyl-tyrosine phosphorylation  (IDA)
positive regulation of platelet activation  (IEA,ISO)
positive regulation of reactive oxygen species biosynthetic process  (IEA,ISO)
positive regulation of stress-activated MAPK cascade  (ISO)
positive regulation of transcription by RNA polymerase II  (IEA,ISO)
positive regulation of tumor necrosis factor production  (IEA,ISO)
regulation of dendritic cell cytokine production  (IEA,ISO)
regulation of inflammatory response  (ISO)
regulation of sensory perception of pain  (IMP)
regulation of tumor necrosis factor production  (IMP)
response to activity  (IEP)
response to bacterium  (ISO)
response to ethanol  (IMP)
response to fatty acid  (IDA)
response to glucocorticoid  (IEP)
response to gold nanoparticle  (IEP)
response to hypoxia  (IEP)
response to insulin  (IEP)
response to lipopolysaccharide  (IDA,IEP,ISO)
response to morphine  (IEP)
response to oxidative stress  (IMP)
response to progesterone  (IEP)
response to retinoic acid  (IEP)
response to toxic substance  (IEP)
skeletal muscle contraction  (IEP)
toll-like receptor 4 signaling pathway  (IEA,ISO)
toll-like receptor signaling pathway  (IBA,IDA)
TRIF-dependent toll-like receptor signaling pathway  (IEA,ISO)

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

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Additional References at PubMed
PMID:10229796   PMID:10430608   PMID:10549626   PMID:10607756   PMID:10623794   PMID:10835634   PMID:10880523   PMID:11274165   PMID:11294571   PMID:11432859   PMID:11489994   PMID:11672593  
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PMID:15841051   PMID:15935092   PMID:16260493   PMID:16338228   PMID:16386178   PMID:16489656   PMID:16514062   PMID:16522744   PMID:16543639   PMID:16870940   PMID:16879219   PMID:16954392  
PMID:17417665   PMID:17446308   PMID:17512285   PMID:17553348   PMID:17560208   PMID:17565820   PMID:17634395   PMID:17896797   PMID:17951129   PMID:17971865   PMID:17974996   PMID:18203139  
PMID:18204298   PMID:18261938   PMID:18343629   PMID:18397856   PMID:18476595   PMID:18592153   PMID:18677579   PMID:18756515   PMID:18787027   PMID:18820689   PMID:19034968   PMID:19047410  
PMID:19115402   PMID:19201895   PMID:19215923   PMID:19252480   PMID:19375882   PMID:19454685   PMID:19584052   PMID:19593445   PMID:19625374   PMID:19695174   PMID:19705455   PMID:19726014  
PMID:19734906   PMID:19740627   PMID:19824106   PMID:19852543   PMID:20016926   PMID:20021788   PMID:20037584   PMID:20043889   PMID:20051628   PMID:20107953   PMID:20113783   PMID:20127518  
PMID:20130368   PMID:20143470   PMID:20150961   PMID:20302880   PMID:20332628   PMID:20441697   PMID:20534845   PMID:20586888   PMID:20646617   PMID:20649597   PMID:20652722   PMID:20654065  
PMID:20665543   PMID:20670634   PMID:20717659   PMID:20945364   PMID:21109260   PMID:21151968   PMID:21186609   PMID:21227038   PMID:21248757   PMID:21329689   PMID:21343866   PMID:21368176  
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PMID:22422608   PMID:22496605   PMID:22523073   PMID:22564590   PMID:22577135   PMID:22590866   PMID:22735756   PMID:22737905   PMID:22837686   PMID:22850250   PMID:22870324   PMID:22927965  
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PMID:25853857   PMID:25880347   PMID:25895164   PMID:25931256   PMID:25978623   PMID:25979559   PMID:25986658   PMID:26033363   PMID:26056446   PMID:26065826   PMID:26085359   PMID:26116862  
PMID:26119193   PMID:26229403   PMID:26279421   PMID:26290459   PMID:26312770   PMID:26390417   PMID:26434622   PMID:26436391   PMID:26465095   PMID:26477505   PMID:26510582   PMID:26556957  
PMID:26585410   PMID:26617842   PMID:26637556   PMID:26657742   PMID:26699475   PMID:26707779   PMID:26744383   PMID:26770978   PMID:26802935   PMID:26806574   PMID:26859874   PMID:26895894  
PMID:26899371   PMID:26962463   PMID:26966782   PMID:27031871   PMID:27057550   PMID:27107073   PMID:27107801   PMID:27187237   PMID:27193049   PMID:27279424   PMID:27318790   PMID:27412936  
PMID:27413256   PMID:27431018   PMID:27494109   PMID:27506813   PMID:27519154   PMID:27538408   PMID:27539497   PMID:27590301   PMID:27665434   PMID:27681173   PMID:27714571   PMID:27756052  
PMID:27776340   PMID:27916733   PMID:27922677   PMID:27956802   PMID:27981756   PMID:27986929   PMID:28033732   PMID:28096568   PMID:28098138   PMID:28272417   PMID:28291959   PMID:28306133  
PMID:28359050   PMID:28410596   PMID:28412141   PMID:28432060   PMID:28525945   PMID:28542370   PMID:28547529   PMID:28623271   PMID:28690033   PMID:28692063   PMID:28692940   PMID:28714001  
PMID:28753906   PMID:28771774   PMID:28808786   PMID:28827130   PMID:28855278   PMID:28946139   PMID:28978536   PMID:29039447   PMID:29113143   PMID:29115455   PMID:29142263   PMID:29157986  
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PMID:32031699   PMID:32084554   PMID:32124969   PMID:32160960   PMID:32214070   PMID:32240615   PMID:32270948   PMID:32667865   PMID:33159115  


Genomics

Comparative Map Data
Tlr4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2580,145,867 - 80,159,501 (+)NCBI
Rnor_6.0 Ensembl582,587,420 - 82,601,052 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0582,587,424 - 82,601,056 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0586,690,670 - 86,704,302 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4583,564,100 - 83,577,735 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1583,569,212 - 83,582,848 (+)NCBI
Celera579,045,293 - 79,058,928 (+)NCBICelera
RH 3.4 Map5643.7RGD
Cytogenetic Map5q24NCBI
TLR4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9117,704,175 - 117,724,735 (+)EnsemblGRCh38hg38GRCh38
GRCh389117,704,403 - 117,724,735 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh379120,466,681 - 120,487,013 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369119,506,431 - 119,519,589 (+)NCBINCBI36hg18NCBI36
Build 349117,546,137 - 117,556,781NCBI
Celera991,114,228 - 91,127,535 (+)NCBI
Cytogenetic Map9q33.1NCBI
HuRef990,084,535 - 90,097,850 (+)NCBIHuRef
CHM1_19120,614,005 - 120,627,323 (+)NCBICHM1_1
Tlr4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39466,745,788 - 66,765,338 (+)NCBIGRCm39mm39
GRCm39 Ensembl466,745,821 - 66,848,521 (+)Ensembl
GRCm38466,827,551 - 66,846,581 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl466,827,584 - 66,930,284 (+)EnsemblGRCm38mm10GRCm38
MGSCv37466,488,845 - 66,503,831 (+)NCBIGRCm37mm9NCBIm37
MGSCv36466,314,172 - 66,329,158 (+)NCBImm8
Celera465,431,141 - 65,446,127 (+)NCBICelera
Cytogenetic Map4C1NCBI
cM Map434.66NCBI
Tlr4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541910,191,120 - 10,202,135 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541910,190,937 - 10,201,896 (-)NCBIChiLan1.0ChiLan1.0
TLR4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19117,180,250 - 117,193,510 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9117,180,550 - 117,190,711 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0988,827,495 - 88,840,458 (+)NCBIMhudiblu_PPA_v0panPan3
TLR4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11171,356,390 - 71,367,166 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1171,356,390 - 71,367,165 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1169,768,502 - 69,779,281 (+)NCBI
ROS_Cfam_1.01172,483,514 - 72,494,289 (+)NCBI
UMICH_Zoey_3.11171,012,889 - 71,023,665 (+)NCBI
UNSW_CanFamBas_1.01171,034,981 - 71,045,756 (+)NCBI
UU_Cfam_GSD_1.01171,767,611 - 71,778,394 (+)NCBI
Tlr4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947186,750,688 - 186,763,650 (+)NCBI
SpeTri2.0NW_0049364876,519,140 - 6,532,018 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TLR4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1258,044,610 - 258,059,004 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11258,044,610 - 258,054,641 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21289,775,816 - 289,785,847 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TLR4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11221,873,762 - 21,885,562 (-)NCBI
ChlSab1.1 Ensembl1221,871,773 - 21,885,515 (-)Ensembl
Tlr4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476017,596,516 - 17,608,955 (-)NCBI

Position Markers
PMC289161P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2580,158,544 - 80,158,848 (+)MAPPER
Rnor_6.0582,600,100 - 82,600,403NCBIRnor6.0
Rnor_5.0586,703,346 - 86,703,649UniSTSRnor5.0
RGSC_v3.4583,576,779 - 83,577,082UniSTSRGSC3.4
Celera579,057,972 - 79,058,275UniSTS
Cytogenetic Map5q24UniSTS
Tlr4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2580,158,060 - 80,158,238 (+)MAPPER
Rnor_6.0582,599,616 - 82,599,793NCBIRnor6.0
Rnor_5.0586,702,862 - 86,703,039UniSTSRnor5.0
RGSC_v3.4583,576,295 - 83,576,472UniSTSRGSC3.4
Celera579,057,488 - 79,057,665UniSTS
RH 3.4 Map5643.7UniSTS
Cytogenetic Map5q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5189432042Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5193273395Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51136640934Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)59514842103580403Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512651967117554267Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531926122136640934Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)535225432108092802Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)535661945117554267Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535788756147487820Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540777918154732375Rat
1331773Scl26Serum cholesterol level QTL 263.065blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)54440427689432042Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)544404276134502294Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)547745646167946134Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54872203893587756Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)551418671147487820Rat
9589025Epfw7Epididymal fat weight QTL 720.660.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)55180442696804426Rat
7411561Bw134Body weight QTL 134240.001body mass (VT:0001259)body weight gain (CMO:0000420)55180442696804426Rat
2303615Vencon7Ventilatory control QTL 70.001respiration trait (VT:0001943)respiration rate (CMO:0000289)55330956898309568Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)555903593100903593Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)556902367101902367Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)556991667137729065Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)560072951133313852Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)561086525149030144Rat
2316954Rf57Renal function QTL 570kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)56108665393273130Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)561086653117554114Rat
61386Bp49Blood pressure QTL 4916.6cerebrum integrity trait (VT:0010549)brain infarction volume (CMO:0001013)561612600102331727Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)561612600168109659Rat
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)565696672129038896Rat
2290005Mcs24Mammary carcinoma susceptibility QTL 24mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)568838385113838385Rat
1357396Bw44Body weight QTL 444.19body mass (VT:0001259)body weight (CMO:0000012)571154828108092802Rat
1357402Bw46Body weight QTL 464.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)571154828108092802Rat
2312671Scl64Serum cholesterol level QTL 640.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)571154828108092802Rat
2302381Bw84Body weight QTL 844.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)571154828108092802Rat
61380Edpm5Estrogen-dependent pituitary mass QTL 54.50.92pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)571154828108092802Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)571552569157225114Rat
1598845Mcs14Mammary carcinoma susceptibility QTL 140.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)57877754083269259Rat


Genetic Models
This gene Tlr4 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:75
Count of miRNA genes:65
Interacting mature miRNAs:73
Transcripts:ENSRNOT00000014020
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 9 4 11
Low 3 43 57 41 10 41 8 10 72 35 32 8
Below cutoff 1 2 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000014020   ⟹   ENSRNOP00000014020
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl582,587,420 - 82,601,052 (+)Ensembl
RefSeq Acc Id: NM_019178   ⟹   NP_062051
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2580,145,867 - 80,159,501 (+)NCBI
Rnor_6.0582,587,424 - 82,601,056 (+)NCBI
Rnor_5.0586,690,670 - 86,704,302 (+)NCBI
RGSC_v3.4583,564,100 - 83,577,735 (+)RGD
Celera579,045,293 - 79,058,928 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_062051 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAC13313 (Get FASTA)   NCBI Sequence Viewer  
  ACI15385 (Get FASTA)   NCBI Sequence Viewer  
  ACS45118 (Get FASTA)   NCBI Sequence Viewer  
  EDM10505 (Get FASTA)   NCBI Sequence Viewer  
  Q9QX05 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_062051   ⟸   NM_019178
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000014020   ⟸   ENSRNOT00000014020
Protein Domains
LRRCT   TIR

Transcriptome

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

Promoters
RGD ID:13693807
Promoter ID:EPDNEW_R4332
Type:initiation region
Name:Tlr4_1
Description:toll-like receptor 4
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_6.0582,587,365 - 82,587,425EPDNEW

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