Tnfsf11 (TNF superfamily member 11) - Rat Genome Database

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Gene: Tnfsf11 (TNF superfamily member 11) Rattus norvegicus
Analyze
Symbol: Tnfsf11
Name: TNF superfamily member 11
RGD ID: 620784
Description: Predicted to have cytokine activity; identical protein binding activity; and tumor necrosis factor receptor superfamily binding activity. Involved in several processes, including positive regulation of bone resorption; positive regulation of osteoclast differentiation; and response to immobilization stress. Predicted to localize to extracellular space; integral component of membrane; and plasma membrane. Biomarker of mucopolysaccharidosis IV and myocarditis. Human ortholog(s) of this gene implicated in autosomal recessive osteopetrosis 2 and osteoporosis. Orthologous to human TNFSF11 (TNF superfamily member 11); PARTICIPATES IN interleukin-6 signaling pathway; cytokine mediated signaling pathway; rheumatoid arthritis pathway; INTERACTS WITH (20S)-ginsenoside Rg3; (S)-nicotine; 1-naphthyl isothiocyanate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC103689974; ODF; OPGL; osteoclast differentiation factor; osteoprotegerin ligand; RANKL; receptor activator of nuclear factor kappa B ligand; receptor activator of nuclear factor kappa-B ligand; TNF-related activation-induced cytokine; TRANCE; tumor necrosis factor (ligand) superfamily, member 11; tumor necrosis factor ligand superfamily member 11; tumor necrosis factor superfamily member 11
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
mRatBN7.21553,674,990 - 53,705,171 (-)NCBI
Rnor_6.0 Ensembl1560,482,527 - 60,512,704 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01560,482,527 - 60,512,704 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01565,726,538 - 65,757,935 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01564,155,680 - 64,186,116 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41559,397,837 - 59,428,014 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11559,413,616 - 59,443,794 (-)NCBI
Celera1553,271,197 - 53,300,935 (-)NCBICelera
Cytogenetic Map15q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-anisomycin  (ISO)
(20S)-ginsenoside Rg3  (EXP)
(S)-nicotine  (EXP)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2-amino-2-deoxy-D-glucopyranose  (ISO)
2-aminopurine  (ISO)
2-tert-butylhydroquinone  (ISO)
23-epi-26-deoxyactein  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (ISO)
4',5,7-trihydroxy-3'-methoxyflavone  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-amino-5-chloro-N-[1-[3-(4-fluorophenoxy)propyl]-3-methoxy-4-piperidinyl]-2-methoxybenzamide  (ISO)
4-nitroquinoline N-oxide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (ISO)
alendronic acid  (EXP,ISO)
all-trans-retinoic acid  (ISO)
alpha-naphthoflavone  (ISO)
ammonium chloride  (EXP)
amsacrine  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antimycin A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
ATP  (ISO)
belinostat  (ISO)
benzamide  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
Bergenin  (ISO)
beta-D-glucosamine  (ISO)
betulinic acid  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
calciol  (ISO)
calcitriol  (EXP,ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
cannabidiol  (ISO)
carbocyclic thromboxane A2  (ISO)
carbon nanotube  (ISO)
chlormequat chloride  (EXP)
chlorpromazine  (ISO)
chondroitin sulfate  (ISO)
chromium(3+) trichloride  (ISO)
cisapride  (ISO)
cobalt dichloride  (ISO)
corticosterone  (EXP)
crocin-1  (ISO)
curcumin  (ISO)
cycloheximide  (ISO)
cyclosporin A  (ISO)
decabromodiphenyl ether  (EXP)
dehydrocostus lactone  (ISO)
desferrioxamine B  (ISO)
dexamethasone  (EXP,ISO)
diarsenic trioxide  (ISO)
dihydro-beta-erythroidine  (EXP)
dimethyl fumarate  (ISO)
dimethylarsinic acid  (ISO)
dioscin  (ISO)
diosgenin  (ISO)
dorsomorphin  (ISO)
ellagic acid  (ISO)
entinostat  (ISO)
ethanol  (EXP,ISO)
etoposide  (ISO)
fluoxetine  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
furosemide  (EXP)
gadolinium trichloride  (ISO)
genistein  (ISO)
gentamycin  (EXP)
ginsenoside Rb1  (ISO)
glycerol 2-phosphate  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
icariin  (ISO)
icariside II  (EXP)
indometacin  (EXP)
iron dextran  (EXP)
kaempferol  (ISO)
KN-93  (ISO)
KT 5720  (EXP)
L-ascorbic acid  (ISO)
lead diacetate  (EXP)
levonorgestrel  (ISO)
lipopolysaccharide  (EXP,ISO)
lithocholic acid  (ISO)
lovastatin  (ISO)
LY294002  (ISO)
mangiferin  (ISO)
menadione  (ISO)
menaquinone  (ISO)
menatetrenone  (ISO)
methapyrilene  (ISO)
methimazole  (EXP)
methotrexate  (EXP,ISO)
methylglyoxal  (ISO)
methylmercury chloride  (ISO)
mifepristone  (EXP)
miquelianin  (ISO)
modafinil  (EXP)
morin  (EXP)
myricitrin  (ISO)
N-acetyl-L-cysteine  (ISO)
N-ethyl-5'-carboxamidoadenosine  (EXP)
N-nitrosodiethylamine  (EXP)
naringin  (ISO)
nickel atom  (ISO)
niclosamide  (ISO)
nicotinamide  (ISO)
nicotine  (EXP)
nimesulide  (ISO)
o-anisidine  (ISO)
ozagrel  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paricalcitol  (EXP)
pentobarbital  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
phenethyl caffeate  (EXP)
phenobarbital  (EXP,ISO)
phenylephrine  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
platycodin D  (EXP,ISO)
poly(ethylene)  (ISO)
prazosin  (ISO)
progesterone  (EXP,ISO)
promethazine  (ISO)
quercetin  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
riboflavin  (ISO)
Ro 41-5253  (ISO)
rotenone  (ISO)
rubiadin  (EXP)
SB 203580  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sirolimus  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (EXP,ISO)
sulfasalazine  (ISO)
tacrolimus hydrate  (ISO)
testosterone  (EXP)
thalidomide  (ISO)
thymol  (ISO)
thymol sulfate(1-)  (ISO)
titanium atom  (EXP)
titanium dioxide  (ISO)
tofacitinib  (EXP,ISO)
tributylstannane  (ISO)
Tributyltin oxide  (ISO)
trichostatin A  (ISO)
trifluoperazine  (ISO)
triphenylstannane  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
uranium atom  (EXP,ISO)
valproic acid  (EXP,ISO)
vitamin D  (ISO)
vorinostat  (ISO)
xanthohumol  (ISO)
zinc dichloride  (EXP)
zinc sulfate  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of JUN kinase activity  (ISO)
animal organ morphogenesis  (ISO)
bone development  (ISO)
bone resorption  (ISO)
calcium ion homeostasis  (ISO)
calcium-mediated signaling  (ISO,ISS)
cellular response to leukemia inhibitory factor  (ISO)
cytokine-mediated signaling pathway  (ISO)
ERK1 and ERK2 cascade  (ISO)
immune response  (IEA)
mammary gland alveolus development  (ISO)
mammary gland epithelial cell proliferation  (ISO)
monocyte chemotaxis  (ISO)
ossification  (ISO)
osteoclast development  (ISO)
osteoclast differentiation  (ISO)
osteoclast proliferation  (ISO)
paracrine signaling  (ISO)
positive regulation of bone resorption  (IMP,ISO)
positive regulation of corticotropin-releasing hormone secretion  (ISO)
positive regulation of DNA-binding transcription factor activity  (ISO)
positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling  (ISO)
positive regulation of fever generation by positive regulation of prostaglandin secretion  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of homotypic cell-cell adhesion  (ISO)
positive regulation of I-kappaB kinase/NF-kappaB signaling  (ISO)
positive regulation of intracellular signal transduction  (ISO)
positive regulation of JNK cascade  (ISO)
positive regulation of MAP kinase activity  (ISO)
positive regulation of NF-kappaB transcription factor activity  (ISO)
positive regulation of osteoclast development  (ISO)
positive regulation of osteoclast differentiation  (IMP,ISO)
positive regulation of phosphorylation  (ISO)
positive regulation of protein kinase B signaling  (ISO)
positive regulation of T cell activation  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
regulation of actin binding  (ISO)
regulation of osteoclast differentiation  (ISO)
response to immobilization stress  (IEP)
response to radiation  (IEP)
signal transduction  (IEA)
TNFSF11-mediated signaling pathway  (ISO)
tooth eruption  (ISO)
tumor necrosis factor-mediated signaling pathway  (ISO)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9367155   PMID:9950424   PMID:11051546   PMID:11859102   PMID:12490655   PMID:14662855   PMID:14672351   PMID:14734743   PMID:15248232   PMID:15304486   PMID:15485831   PMID:15657444  
PMID:15704000   PMID:15724149   PMID:15750601   PMID:15844004   PMID:16874862   PMID:17053831   PMID:17241109   PMID:17442941   PMID:17476578   PMID:17608585   PMID:18166509   PMID:18269914  
PMID:18432284   PMID:18476557   PMID:18597628   PMID:18606301   PMID:19008464   PMID:19040304   PMID:19105036   PMID:19252502   PMID:19298785   PMID:19325147   PMID:19501680   PMID:19537860  
PMID:19539794   PMID:19560569   PMID:19714640   PMID:19715671   PMID:19940926   PMID:20439489   PMID:20444587   PMID:20480144   PMID:20595654   PMID:21048959   PMID:21078845   PMID:21176538  
PMID:21602131   PMID:21771583   PMID:21841309   PMID:21982707   PMID:22027774   PMID:22073305   PMID:22194983   PMID:22298642   PMID:22353912   PMID:22428075   PMID:22437732   PMID:22451653  
PMID:22848465   PMID:22878484   PMID:22948539   PMID:23271279   PMID:23334376   PMID:23395171   PMID:23404413   PMID:23500899   PMID:23553492   PMID:23636419   PMID:23769040   PMID:23954550  
PMID:23980096   PMID:24039232   PMID:24190884   PMID:24321069   PMID:25200151   PMID:25257532   PMID:25406873   PMID:26234751   PMID:26270535   PMID:26489619   PMID:26677102   PMID:26722385  
PMID:26962001   PMID:27122093   PMID:27154288   PMID:28092862   PMID:28473060   PMID:28774557   PMID:28898718   PMID:29211121   PMID:29240821   PMID:29297549   PMID:30199848   PMID:31773672  
PMID:31828174   PMID:32307402   PMID:32372426   PMID:32722636  


Genomics

Comparative Map Data
Tnfsf11
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21553,674,990 - 53,705,171 (-)NCBI
Rnor_6.0 Ensembl1560,482,527 - 60,512,704 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01560,482,527 - 60,512,704 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01565,726,538 - 65,757,935 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01564,155,680 - 64,186,116 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41559,397,837 - 59,428,014 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11559,413,616 - 59,443,794 (-)NCBI
Celera1553,271,197 - 53,300,935 (-)NCBICelera
Cytogenetic Map15q11NCBI
TNFSF11
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1342,562,736 - 42,608,013 (+)EnsemblGRCh38hg38GRCh38
GRCh381342,562,736 - 42,608,013 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371343,136,872 - 43,182,149 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361342,043,795 - 42,080,148 (+)NCBINCBI36hg18NCBI36
Build 341342,043,794 - 42,080,148NCBI
Celera1324,194,611 - 24,239,896 (+)NCBI
Cytogenetic Map13q14.11NCBI
HuRef1323,940,423 - 23,985,716 (+)NCBIHuRef
CHM1_11343,104,338 - 43,149,624 (+)NCBICHM1_1
Tnfsf11
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391478,514,886 - 78,545,483 (-)NCBIGRCm39mm39
GRCm39 Ensembl1478,514,885 - 78,545,483 (-)Ensembl
GRCm381478,277,446 - 78,308,043 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1478,277,445 - 78,308,043 (-)EnsemblGRCm38mm10GRCm38
MGSCv371478,677,253 - 78,707,850 (-)NCBIGRCm37mm9NCBIm37
MGSCv361477,009,005 - 77,042,170 (-)NCBImm8
Celera1475,790,488 - 75,821,164 (-)NCBICelera
Cytogenetic Map14D3NCBI
cM Map1441.26NCBI
Tnfsf11
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955518430,642 - 462,705 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955518431,401 - 462,063 (+)NCBIChiLan1.0ChiLan1.0
TNFSF11
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Mhudiblu_PPA_v01323,750,835 - 23,784,740 (+)NCBIMhudiblu_PPA_v0panPan3
TNFSF11
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1228,226,931 - 8,257,926 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl228,227,555 - 8,258,645 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha228,218,782 - 8,249,783 (-)NCBI
ROS_Cfam_1.0228,445,691 - 8,476,717 (-)NCBI
UMICH_Zoey_3.1228,136,967 - 8,174,247 (-)NCBI
UNSW_CanFamBas_1.0228,193,944 - 8,224,951 (-)NCBI
UU_Cfam_GSD_1.0228,205,225 - 8,236,245 (-)NCBI
Tnfsf11
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945152,785,812 - 152,819,281 (+)NCBI
SpeTri2.0NW_0049367471,255,803 - 1,288,252 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TNFSF11
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1124,466,586 - 24,505,422 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11124,468,011 - 24,505,421 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21125,117,332 - 25,154,855 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TNFSF11
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1320,717,884 - 20,761,520 (+)NCBI
ChlSab1.1 Ensembl320,727,592 - 20,760,408 (+)Ensembl
Vero_WHO_p1.0NW_02366605723,446,636 - 23,492,542 (-)NCBI
Tnfsf11
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474812,527,221 - 12,555,551 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15162301382Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151549236072568189Rat
9590272Scort14Serum corticosterone level QTL 142.780.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)151698090761980907Rat
8694427Bw163Body weight QTL 1634.820.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)151698090761980907Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151724964162249641Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151809320881255430Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151851391388036354Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1526381041106550657Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1526381041106550657Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1526381041106550657Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152870974173709741Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)153321910189640841Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)153321910189640841Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)153321910189640841Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)153948079762596410Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153974955779033707Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153974955779033707Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)154106809486068094Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1543097470106550657Rat
724545Niddm54Non-insulin dependent diabetes mellitus QTL 540.02blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)155752897081263988Rat
2317050Aia24Adjuvant induced arthritis QTL 242.06joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)155965115181255430Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:28
Count of miRNA genes:25
Interacting mature miRNAs:26
Transcripts:ENSRNOT00000013210
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


Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000013210   ⟹   ENSRNOP00000013210
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1562,067,565 - 62,097,749 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000049056   ⟹   ENSRNOP00000044212
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1560,482,527 - 60,512,704 (-)Ensembl
RefSeq Acc Id: NM_057149   ⟹   NP_476490
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21553,674,990 - 53,705,171 (-)NCBI
Rnor_6.01560,482,527 - 60,512,704 (-)NCBI
Rnor_5.01564,155,680 - 64,186,116 (-)NCBI
RGSC_v3.41559,397,837 - 59,428,014 (-)RGD
Celera1553,271,197 - 53,300,935 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_476490 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAG17031 (Get FASTA)   NCBI Sequence Viewer  
  AAL23963 (Get FASTA)   NCBI Sequence Viewer  
  EDM02337 (Get FASTA)   NCBI Sequence Viewer  
  Q9ESE2 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_476490   ⟸   NM_057149
- UniProtKB: Q9ESE2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000044212   ⟸   ENSRNOT00000049056
RefSeq Acc Id: ENSRNOP00000013210   ⟸   ENSRNOT00000013210
Protein Domains
TNF_2

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620784 AgrOrtholog
  RGD:9144322 AgrOrtholog
Ensembl Genes ENSRNOG00000009559 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000049547 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000013210 UniProtKB/TrEMBL
  ENSRNOP00000044212 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013210 UniProtKB/TrEMBL
  ENSRNOT00000049056 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro TNF_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNF_ligand_10/11 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tumour_necrosis_fac-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:103689974 UniProtKB/TrEMBL
  rno:117516 UniProtKB/Swiss-Prot
NCBI Gene 117516 ENTREZGENE
Pfam TNF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tnfsf11 PhenoGen
PIRSF TNF10_TNF11 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE TNF_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART TNF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49842 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V794_RAT UniProtKB/TrEMBL
  Q9ESE2 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary D3ZXV1 UniProtKB/TrEMBL
  Q91ZI9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Tnfsf11  TNF superfamily member 11  LOC103689974  tumor necrosis factor ligand superfamily member 11  Data Merged 737654 PROVISIONAL
2017-03-21 Tnfsf11  TNF superfamily member 11  Tnfsf11  tumor necrosis factor superfamily member 11  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-25 Tnfsf11  tumor necrosis factor superfamily member 11  Tnfsf11  tumor necrosis factor (ligand) superfamily, member 11  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-08-25 LOC103689974  tumor necrosis factor ligand superfamily member 11      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-09-10 Tnfsf11  tumor necrosis factor (ligand) superfamily, member 11      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Tnfsf11  tumor necrosis factor (ligand) superfamily, member 11      Symbol and Name status set to provisional 70820 PROVISIONAL