Tnfrsf1a (TNF receptor superfamily member 1A) - Rat Genome Database
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Gene: Tnfrsf1a (TNF receptor superfamily member 1A) Rattus norvegicus
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Symbol: Tnfrsf1a
Name: TNF receptor superfamily member 1A
RGD ID: 621237
Description: Exhibits protease binding activity; tumor necrosis factor binding activity; and tumor necrosis factor-activated receptor activity. Involved in several processes, including cellular response to estradiol stimulus; regulation of apoptotic process; and regulation of cytokine production. Localizes to several cellular components, including cell surface; membrane raft; and mitochondrion. Used to study ischemia (multiple); middle cerebral artery infarction; myocardial infarction; uveitis; and visual epilepsy. Biomarker of several diseases, including colon carcinoma; root resorption; sciatic neuropathy; transient cerebral ischemia; and ureteral obstruction. Human ortholog(s) of this gene implicated in several diseases, including IgA glomerulonephritis; acne; allergic bronchopulmonary aspergillosis; autoimmune disease (multiple); and autosomal dominant familial periodic fever. Orthologous to human TNFRSF1A (TNF receptor superfamily member 1A); PARTICIPATES IN tumor necrosis factor mediated signaling pathway; ceramide signaling pathway; nuclear factor kappa B signaling pathway; INTERACTS WITH (+)-pilocarpine; (S)-nicotine; 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: MGC105478; p55; p60; TNF-R1; TNF-RI; TNFR-1; TNFR-I; Tnfr1; Tumor necrosis factor receptor; tumor necrosis factor receptor 1; tumor necrosis factor receptor superfamily member 1A; tumor necrosis factor receptor superfamily, member 1a; tumor necrosis factor receptor type I
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: Strains:   BN   LEW   DA   ACI/N   F344/NRrrc  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.04157,864,905 - 157,877,634 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4157,864,969 - 157,877,633 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04224,881,368 - 224,894,089 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44162,172,563 - 162,185,252 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14162,417,498 - 162,430,188 (+)NCBI
Celera4146,886,949 - 146,899,646 (+)NCBICelera
Cytogenetic Map4q42NCBI
RH 3.4 Map41000.9RGD
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acne  (ISO)
acquired immunodeficiency syndrome  (ISO)
acute kidney failure  (ISO)
adult respiratory distress syndrome  (ISO)
allergic bronchopulmonary aspergillosis  (ISO)
allergic disease  (ISO)
Alzheimer's disease  (ISO)
amyloidosis  (ISO)
anemia  (ISO)
Anorexia  (ISO)
Anti-Neutrophil Cytoplasmic Antibody-Associated Vasculitis  (ISO)
arteriosclerosis  (ISO)
asthma  (ISO)
autoimmune disease  (ISO)
autosomal dominant familial periodic fever  (ISO)
autosomal recessive pseudohypoaldosteronism type 1  (ISO)
bacterial pneumonia  (ISO)
Behcet's disease  (ISO)
Brain Injuries  (IEP,ISO)
brain ischemia  (IDA,ISO)
bronchiectasis  (ISO)
Cachexia  (IEP,ISO)
CHARGE syndrome  (ISO)
Chronic Hepatitis C  (ISO)
chronic obstructive pulmonary disease  (ISO)
colon carcinoma  (IEP)
colorectal adenoma  (ISO)
congestive heart failure  (ISO)
coronary artery disease  (ISO)
Crohn's disease  (IEP)
cryptogenic organizing pneumonia  (ISO)
cystic fibrosis  (ISO)
cytomegalovirus retinitis  (ISO)
Diabetic Nephropathies  (ISO)
End Stage Liver Disease  (IMP)
end stage renal disease  (ISO)
endometrial cancer  (ISO)
Enterovirus Infections  (ISO)
Experimental Arthritis  (IDA,IEP,ISO)
Experimental Autoimmune Uveoretinitis  (ISO)
Experimental Colitis  (IMP)
Experimental Diabetes Mellitus  (IEP,ISO)
Experimental Pancreatitis, Acute  (IEP)
extrinsic allergic alveolitis  (ISO)
familial Mediterranean fever  (ISO)
Febrile Seizures  (ISO)
Fever  (ISO)
fibrosarcoma  (ISO)
focal segmental glomerulosclerosis  (ISO)
genetic disease  (ISO)
glomerulonephritis  (ISO)
Human Influenza  (ISO)
Hyperalgesia  (IEP,IMP,ISO)
Hyperoxia  (ISO)
Hyperphosphatemic Familial Tumoral Calcinosis 1  (ISO)
IgA glomerulonephritis  (ISO)
infantile Refsum disease  (ISO)
Insulin Resistance  (ISO)
ischemia  (IDA)
kidney disease  (ISO)
Kidney Reperfusion Injury  (ISO)
Legionnaires' disease  (ISO)
Liver Reperfusion Injury  (IEP)
Lung Injury  (ISO)
lung non-small cell carcinoma  (ISO)
lupus nephritis  (ISO)
Metabolic Syndrome  (ISO)
middle cerebral artery infarction  (IMP)
multiple sclerosis  (ISO)
Muscle Weakness  (ISO)
myocardial infarction  (IDA,IEP,IMP)
Nasal Polyps  (ISO)
Nematode Infections  (IEP)
Neurogenic Inflammation  (IDA)
obesity  (ISO)
obstructive sleep apnea  (ISO)
Optic Nerve Injuries  (IEP,ISO)
ovarian cancer  (ISO)
Pain  (IEP)
pneumonia  (ISO)
polymyositis  (ISO)
primary biliary cholangitis  (ISO)
Pseudomonas Infections  (ISO)
psoriasis  (ISO)
Radiation Pneumonitis  (ISO)
renal cell carcinoma  (ISO)
renal fibrosis  (ISO)
Reperfusion Injury  (IEP)
retinal detachment  (ISO)
rheumatoid arthritis  (ISO)
root resorption  (IEP)
sciatic neuropathy  (IEP,ISO)
silicosis  (ISO)
Spinal Cord Compression  (IEP)
Spinal Cord Injuries  (IEP)
squamous cell carcinoma  (ISO)
systemic lupus erythematosus  (ISO)
transient cerebral ischemia  (IEP)
type 2 diabetes mellitus  (IEP,ISO)
ureteral obstruction  (IEP)
uveitis  (IMP,ISO)
visual epilepsy  (IDA)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(-)-citrinin  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(S)-colchicine  (ISO)
(S)-nicotine  (EXP,ISO)
1'-acetoxychavicol acetate  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
1-naphthyl isothiocyanate  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-amino-2-deoxy-D-glucopyranose  (ISO)
2-methylcholine  (ISO)
2-naphthylamine  (ISO)
3,3'-diindolylmethane  (ISO)
3-chloropropane-1,2-diol  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
4-tert-butylphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
[des-Arg(9)]-bradykinin  (ISO)
acetamide  (EXP)
acetylsalicylic acid  (ISO)
acrolein  (ISO)
AH23848  (ISO)
AICA ribonucleotide  (ISO)
aldehydo-D-glucosamine  (ISO)
all-trans-retinoic acid  (ISO)
Aloe emodin  (ISO)
alpha-pinene  (ISO)
aminoguanidine  (ISO)
amphetamine  (EXP)
amphibole asbestos  (ISO)
antirheumatic drug  (ISO)
arachidonic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
asbestos  (ISO)
asperentin  (ISO)
atorvastatin calcium  (ISO)
azathioprine  (ISO)
Bandrowski's base  (ISO)
benzene  (EXP)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-D-glucosamine  (ISO)
beta-naphthoflavone  (EXP)
bexarotene  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (ISO)
boric acid  (ISO)
butylated hydroxyanisole  (ISO)
Butylparaben  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
capsaicin  (ISO)
capsazepine  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carbonyl sulfide  (EXP)
cefaloridine  (EXP)
chloroform  (EXP)
chloroquine  (ISO)
cholesterol  (EXP)
cisplatin  (ISO)
clobetasol  (ISO)
clofibrate  (EXP)
cobalt dichloride  (ISO)
cocaine  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
DDT  (EXP)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dibutyl phthalate  (EXP)
diclofenac  (ISO)
dieldrin  (EXP)
dimethyl sulfoxide  (ISO)
dimethylarsinic acid  (EXP)
dioscin  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
elemental selenium  (ISO)
erythromycin estolate  (EXP)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
fenamidone  (ISO)
flutamide  (EXP)
folic acid  (ISO)
fumonisin B1  (ISO)
furosemide  (EXP)
gadolinium trichloride  (ISO)
genistein  (ISO)
gentamycin  (EXP)
glafenine  (EXP)
glutathione  (ISO)
glyphosate  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
hexachlorobenzene  (EXP)
hydrogen peroxide  (ISO)
indometacin  (ISO)
irinotecan  (EXP)
isoflurane  (EXP)
isoprenaline  (EXP,ISO)
ketoconazole  (ISO)
L-mimosine  (ISO)
lead nitrate  (ISO)
leflunomide  (ISO)
lenalidomide  (ISO)
lignan  (ISO)
lipopolysaccharide  (EXP,ISO)
magnesium atom  (EXP)
magnesium oxide  (ISO)
mercury atom  (EXP)
mercury(0)  (EXP)
metformin  (ISO)
methacholine chloride  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylarsonic acid  (EXP)
methylmercury chloride  (ISO)
methylmercury(1+)  (EXP)
mifepristone  (ISO)
Mitotane  (EXP)
monodansylcadaverine  (ISO)
motexafin gadolinium  (ISO)
mycophenolic acid  (ISO)
mycotoxin  (ISO)
N-acetyl-L-cysteine  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
naloxone  (EXP)
nefazodone  (EXP)
neoechinulin A  (ISO)
nickel atom  (ISO)
nickel dichloride  (EXP)
nickel sulfate  (ISO)
nicotine  (EXP,ISO)
nimesulide  (EXP)
nitrates  (EXP)
Nonidet P-40  (ISO)
notoginsenoside R1  (ISO)
o-anisidine  (ISO)
ochratoxin A  (EXP,ISO)
octreotide  (EXP)
osthole  (ISO)
ozone  (ISO)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
pentobarbital  (EXP)
perfluorononanoic acid  (EXP)
perfluorooctanoic acid  (EXP)
phenobarbital  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
phosphoramide mustard  (EXP)
prochloraz  (EXP)
progesterone  (EXP,ISO)
propylparaben  (ISO)
prostaglandin E2  (ISO)
quercetin  (ISO)
quercetin 3-O-beta-D-galactopyranoside  (ISO)
quercetin 3-O-beta-D-glucofuranoside  (EXP)
quercetin 3-O-beta-D-glucopyranoside  (EXP)
quercitrin  (ISO)
quinidine  (EXP)
resiniferatoxin  (ISO)
resveratrol  (ISO)
rotenone  (EXP,ISO)
SB 203580  (ISO)
selenium atom  (ISO)
serpentine asbestos  (ISO)
sesquiterpene  (ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
sodium stibogluconate  (ISO)
Soman  (EXP)
sterigmatocystin  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
tetracycline  (EXP)
thalidomide  (ISO)
titanium dioxide  (ISO)
tolcapone  (EXP)
Tributyltin oxide  (ISO)
trichloroethene  (EXP)
trichostatin A  (EXP,ISO)
trimethyltin  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
WR-1065  (ISO)
zerumbone  (ISO)
zinc acetate  (ISO)
zinc atom  (ISO)
zinc molecular entity  (ISO)
zinc protoporphyrin  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
aortic valve development  (IEA,ISO)
cell surface receptor signaling pathway  (ISO,ISS)
cellular response to estradiol stimulus  (IEP)
cellular response to mechanical stimulus  (IEA,ISO)
cytokine-mediated signaling pathway  (ISO,ISS)
defense response  (ISO,ISS)
defense response to bacterium  (IEA,ISO)
inflammatory response  (IBA,IEA,IEP,ISO,ISS)
intrinsic apoptotic signaling pathway in response to DNA damage  (IEA,ISO)
negative regulation of apoptotic process  (IMP)
negative regulation of cardiac muscle hypertrophy  (IEA,ISO)
negative regulation of extracellular matrix constituent secretion  (IEA,ISO)
negative regulation of gene expression  (IDA)
negative regulation of inflammatory response  (IEA,ISO)
negative regulation of interleukin-6 production  (IDA)
positive regulation of angiogenesis  (IMP)
positive regulation of apoptotic process involved in morphogenesis  (IEA,ISO)
positive regulation of gene expression  (IMP)
positive regulation of I-kappaB kinase/NF-kappaB signaling  (IEA,ISO)
positive regulation of inflammatory response  (IEA,ISO,ISS)
positive regulation of neuron apoptotic process  (IMP)
positive regulation of protein import into nucleus  (IMP)
positive regulation of transcription by RNA polymerase II  (IEA,ISO,ISS)
positive regulation of tumor necrosis factor production  (IMP)
positive regulation of tyrosine phosphorylation of STAT protein  (IEA,ISO)
prostaglandin metabolic process  (IEA)
protein localization to plasma membrane  (IEA,ISO)
pulmonary valve development  (IEA,ISO)
regulation of apoptotic process  (IMP)
regulation of establishment of endothelial barrier  (IEA,ISO)
response to alkaloid  (IEP)
response to amino acid  (IEP)
response to ethanol  (IEP)
response to hypoxia  (IEP)
response to lipopolysaccharide  (IEP)
response to wounding  (IEP)
tumor necrosis factor-mediated signaling pathway  (IEA,IMP,ISO)

Cellular Component
axon  (IDA)
cell surface  (IDA,IEA,ISO)
cytosol  (IDA)
extracellular space  (IDA,IEA,ISO)
Golgi membrane  (IEA,ISO,ISS)
integral component of membrane  (IEA)
membrane raft  (IBA,IDA,IEA,ISO)
mitochondrion  (IBA,IDA)
nucleus  (IDA)
plasma membrane  (IEA)
protein-containing complex  (IDA)
receptor complex  (IBA,IEA,ISO)
synapse  (IDA)

Molecular Function

References

References - curated
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Additional References at PubMed
PMID:1645445   PMID:7758105   PMID:8387893   PMID:9324362   PMID:9435233   PMID:9551933   PMID:9843922   PMID:11588035   PMID:12477932   PMID:12761501   PMID:12849708   PMID:12851692  
PMID:13130484   PMID:14625205   PMID:14743216   PMID:15033431   PMID:15464762   PMID:16675114   PMID:16705482   PMID:16804967   PMID:17010968   PMID:17049356   PMID:17242187   PMID:17468886  
PMID:17873366   PMID:17917074   PMID:18205044   PMID:18938092   PMID:18990246   PMID:19180511   PMID:19593445   PMID:20092780   PMID:20619468   PMID:21410936   PMID:21692635   PMID:21871121  
PMID:21930713   PMID:21988832   PMID:23134577   PMID:23382219   PMID:23706525   PMID:23756688   PMID:24211183   PMID:24599692   PMID:25738414   PMID:25816133   PMID:26078221   PMID:26491108  
PMID:26504355   PMID:27239114   PMID:27979472   PMID:28710070   PMID:30358805   PMID:33066952  


Genomics

Candidate Gene Status
Tnfrsf1a is a candidate Gene for QTL Ciaa4
Tnfrsf1a is a candidate Gene for QTL Cia24
Comparative Map Data
Tnfrsf1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.04157,864,905 - 157,877,634 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4157,864,969 - 157,877,633 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04224,881,368 - 224,894,089 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44162,172,563 - 162,185,252 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14162,417,498 - 162,430,188 (+)NCBI
Celera4146,886,949 - 146,899,646 (+)NCBICelera
Cytogenetic Map4q42NCBI
RH 3.4 Map41000.9RGD
TNFRSF1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl126,328,757 - 6,342,114 (-)EnsemblGRCh38hg38GRCh38
GRCh38126,328,771 - 6,342,076 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37126,437,923 - 6,451,283 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36126,308,184 - 6,321,522 (-)NCBINCBI36hg18NCBI36
Build 34126,308,184 - 6,321,522NCBI
Celera128,054,567 - 8,067,927 (-)NCBI
Cytogenetic Map12p13.31NCBI
HuRef126,291,179 - 6,304,533 (-)NCBIHuRef
CHM1_1126,437,153 - 6,450,509 (-)NCBICHM1_1
Tnfrsf1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396125,326,686 - 125,339,446 (+)NCBIGRCm39mm39
GRCm386125,349,723 - 125,362,483 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6125,349,362 - 125,362,484 (+)EnsemblGRCm38mm10GRCm38
MGSCv376125,299,741 - 125,312,501 (+)NCBIGRCm37mm9NCBIm37
MGSCv366125,315,374 - 125,328,104 (+)NCBImm8
Celera6127,020,792 - 127,033,747 (+)NCBICelera
Cytogenetic Map6F3NCBI
cM Map659.32NCBI
Tnfrsf1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554133,981,400 - 3,996,021 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554133,982,670 - 3,996,320 (-)NCBIChiLan1.0ChiLan1.0
TNFRSF1A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1126,374,256 - 6,387,613 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl126,374,257 - 6,387,613 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0126,457,617 - 6,470,969 (-)NCBIMhudiblu_PPA_v0panPan3
TNFRSF1A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2738,638,753 - 38,700,282 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12738,641,837 - 38,654,693 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Tnfrsf1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049367091,407,327 - 1,421,448 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TNFRSF1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl564,319,073 - 64,331,909 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1564,319,349 - 64,331,876 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2566,780,726 - 66,793,255 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TNFRSF1A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1116,364,544 - 6,378,880 (-)NCBI
ChlSab1.1 Ensembl116,364,330 - 6,378,902 (-)Ensembl
Tnfrsf1a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248603,111,244 - 3,123,041 (-)NCBI

Position Markers
RH94826  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.04157,877,279 - 157,877,391NCBIRnor6.0
Rnor_5.04224,893,734 - 224,893,846UniSTSRnor5.0
RGSC_v3.44162,184,898 - 162,185,010UniSTSRGSC3.4
Celera4146,899,292 - 146,899,404UniSTS
Cytogenetic Map4q42UniSTS
RH 3.4 Map41000.9UniSTS
RH142087  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.04157,877,258 - 157,877,455NCBIRnor6.0
Rnor_5.04224,893,713 - 224,893,910UniSTSRnor5.0
RGSC_v3.44162,184,877 - 162,185,074UniSTSRGSC3.4
Celera4146,899,271 - 146,899,468UniSTS
Cytogenetic Map4q42UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4125884464168047091Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4117926139162926139Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4131834282176834282Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4136351734180689124Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4108876717169215811Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4105971071168047091Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4123111827168111827Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131532269168047091Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4146942075168998263Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4136351734174694858Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131532269168047091Rat
1581566Eae21Experimental allergic encephalomyelitis QTL 216.2body mass (VT:0001259)maximum body weight loss to initial body weight ratio (CMO:0001400)4157399119158564471Rat
1581574Eae20Experimental allergic encephalomyelitis QTL 207.8nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)4152482121158564471Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4136908430182878540Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)494893247168046938Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4145373934176509907Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123478354168478354Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)484475257178931073Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4137171018182171018Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157423126184226339Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)47850904182171018Rat
1358364Sradr4Stress Responsive Adrenal Weight QTL 44.92adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)4128602727173602727Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)486438317168047091Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (VE) (CMO:0000132)4134917642179917642Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4131864442176864442Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4136351734174694858Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132455408168047091Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4145547014184226339Rat
6478720Alc23Alcohol consumption QTL 230.00509drinking behavior trait (VT:0001422)ethanol drink intake rate to body weight ratio (CMO:0001616)4155386197184226339Rat
6478728Anxrr36Anxiety related response QTL 360.01061locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478733Anxrr37Anxiety related response QTL 370.00095locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478737Anxrr38Anxiety related response QTL 380.00159locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4145547014184226339Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4145547014184226339Rat
6478757Anxrr44Anxiety related response QTL 440.01087locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4123587009168587009Rat
6478782Anxrr52Anxiety related response QTL 520.02091locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478785Anxrr53Anxiety related response QTL 530.01397locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4145547014184226339Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4145547014184226339Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4124442168169442168Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4156855449184226339Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4146497452184226339Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)423850384169318094Rat
12798525Anxrr57Anxiety related response QTL 573.210.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4146086918168047091Rat


Related Rat Strains
The following Strains have been annotated to Tnfrsf1a

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:202
Count of miRNA genes:142
Interacting mature miRNAs:152
Transcripts:ENSRNOT00000048529
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 37 57 41 19 41 2 5 57 35 34 11 2
Low 6 6 6 17 7 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000048529   ⟹   ENSRNOP00000042371
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4157,864,969 - 157,877,633 (+)Ensembl
RefSeq Acc Id: NM_013091   ⟹   NP_037223
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04157,864,990 - 157,877,633 (+)NCBI
Rnor_5.04224,881,368 - 224,894,089 (+)NCBI
RGSC_v3.44162,172,563 - 162,185,252 (+)RGD
Celera4146,886,949 - 146,899,646 (+)RGD
Sequence:
RefSeq Acc Id: XM_006237334   ⟹   XP_006237396
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04157,864,905 - 157,877,634 (+)NCBI
Rnor_5.04224,881,368 - 224,894,089 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_037223   ⟸   NM_013091
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_006237396   ⟸   XM_006237334
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000042371   ⟸   ENSRNOT00000048529
Protein Domains
Death   TNFR-Cys

Transcriptome

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

Promoters
RGD ID:13693412
Promoter ID:EPDNEW_R3937
Type:initiation region
Name:Tnfrsf1a_1
Description:TNF receptor superfamily member 1A
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_6.04157,864,947 - 157,865,007EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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)
ACI/EurMcwi (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
ACI/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
BBDP/Wor (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
BN/SsN (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
Buf/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
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/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
F344/NRrrc (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
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 224892989 224892990 C A snv MHS/Gib (KNAW), WAG/Rij (KNAW), GK/Ox (KNAW), BUF/N (KNAW), BBDP/WorN (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 157876534 157876535 C A snv CDS, Buf/N (MCW), WAG/Rij (RGD), MHS/Gib (RGD), GK/Ox (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 162184153 162184154 C A snv BUF/N (KNAW), BBDP/WorN (ICL), GK/Ox (ICL), HCR/2Mco (UMich), WAG/Rij (ICL), HCR/1Mco (UMich), MHS/Gib (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621237 AgrOrtholog
Ensembl Genes ENSRNOG00000031312 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000042371 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000048529 ENTREZGENE, UniProtKB/TrEMBL
InterPro DEATH-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Death_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR/NGFR_Cys_rich_reg UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR_1A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFRSF1A_death UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFRSF1A_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25625 UniProtKB/Swiss-Prot
NCBI Gene 25625 ENTREZGENE
Pfam Death UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR_c6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB TNFRSF1A RGD
PhenoGen Tnfrsf1a PhenoGen
PRINTS TNFACTORR1A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE DEATH_DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR_NGFR_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR_NGFR_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART DEATH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47986 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.11119 ENTREZGENE
UniProt A0A0G2JSU9_RAT UniProtKB/TrEMBL
  P22934 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q5U1X6 UniProtKB/Swiss-Prot
  Q91V30 UniProtKB/Swiss-Prot
  Q91Y93 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-05 Tnfrsf1a  TNF receptor superfamily member 1A  Tnfrsf1a  tumor necrosis factor receptor superfamily, member 1a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Tnfrsf1a  tumor necrosis factor receptor superfamily, member 1a      Symbol and Name updated 629477 APPROVED
2003-03-12 Tnfrsf1a  tumor necrosis factor receptor superfamily, member 1a  Tnfr1  Tumor necrosis factor receptor  Data Merged 628472 PROVISIONAL
2002-08-07 Tnfrsf1a        Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Tnfr1  Tumor necrosis factor receptor      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease nucleotide sequence variants between rat strains may be associated with collagen induced arthritis QTL Cia13 619594
gene_process may contribute to collagen induced arthritis severity QTL Cia13 619594
gene_process human homolog induces MAP kinase activation and may mediate inflammatory response in airway muscle cells 730191