Tnfrsf11b (TNF receptor superfamily member 11B) - Rat Genome Database

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Gene: Tnfrsf11b (TNF receptor superfamily member 11B) Rattus norvegicus
Analyze
Symbol: Tnfrsf11b
Name: TNF receptor superfamily member 11B
RGD ID: 619802
Description: Predicted to enable cytokine activity. Involved in several processes, including negative regulation of bone resorption; negative regulation of odontogenesis of dentin-containing tooth; and response to estrogen. Located in extracellular space. Biomarker of congestive heart failure; myocarditis; and periapical periodontitis. Human ortholog(s) of this gene implicated in Paget's disease of bone and osteoarthritis. Orthologous to human TNFRSF11B (TNF receptor superfamily member 11b); PARTICIPATES IN cytokine mediated signaling pathway; INTERACTS WITH (20S)-ginsenoside Rg3; (S)-nicotine; 1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: MGC93568; Opg; Osteoprotegerin; tumor necrosis factor receptor superfamily member 11B; tumor necrosis factor receptor superfamily, member 11b; tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2785,566,520 - 85,594,526 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl785,566,520 - 85,594,538 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx787,463,913 - 87,491,923 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0789,665,094 - 89,693,104 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0789,470,571 - 89,498,581 (-)NCBIRnor_WKY
Rnor_6.0793,798,580 - 93,826,586 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl793,798,545 - 93,826,665 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0794,436,612 - 94,464,618 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4790,606,424 - 90,634,431 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1790,640,654 - 90,668,661 (-)NCBI
Celera782,388,596 - 82,416,602 (-)NCBICelera
Cytogenetic Map7q32NCBI
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)
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (EXP)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-amino-2-deoxy-D-glucopyranose  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3-chloropropane-1,2-diol  (EXP,ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
aldehydo-D-glucosamine  (ISO)
aldehydo-D-glucose  (ISO)
alendronic acid  (EXP)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amsacrine  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antimycin A  (ISO)
aripiprazole  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (EXP,ISO)
avobenzone  (ISO)
benzo[a]pyrene  (ISO)
beta-D-glucosamine  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Butylbenzyl phthalate  (ISO)
Butylparaben  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
calciol  (ISO)
calcitriol  (EXP,ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
cannabidiol  (ISO)
carbamazepine  (ISO)
carbocyclic thromboxane A2  (ISO)
carbon nanotube  (ISO)
carbonyl sulfide  (EXP)
carmustine  (ISO)
celecoxib  (ISO)
CGP 52608  (ISO)
chloroprene  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
chondroitin sulfate  (ISO)
chromium(3+) trichloride  (ISO)
clothianidin  (ISO)
cobalt dichloride  (ISO)
cocaine  (ISO)
corticosterone  (EXP)
crocidolite asbestos  (ISO)
cycloheximide  (ISO)
cyclosporin A  (EXP,ISO)
D-glucose  (ISO)
DDE  (EXP)
DDT  (EXP)
decabromodiphenyl ether  (EXP)
dexamethasone  (EXP,ISO)
diarsenic trioxide  (EXP,ISO)
dibutyl phthalate  (EXP)
diethyl malate  (ISO)
dihydro-beta-erythroidine  (EXP)
dioscin  (ISO)
dioxygen  (ISO)
disodium selenite  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
ethanol  (EXP)
etoposide  (ISO)
fenofibrate  (ISO)
fenvalerate  (EXP)
flavonoids  (EXP)
flutamide  (ISO)
folic acid  (ISO)
fonofos  (ISO)
fulvestrant  (ISO)
furan  (EXP)
gadolinium trichloride  (ISO)
gemcitabine  (ISO)
genistein  (ISO)
glucose  (ISO)
glycerol 2-phosphate  (ISO)
glycidol  (EXP)
glyphosate  (ISO)
hydrogen peroxide  (ISO)
icariin  (ISO)
icariside II  (EXP)
indometacin  (ISO)
iron dextran  (EXP)
isoflurane  (EXP)
isonicotinamide  (ISO)
ketamine  (EXP)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lead diacetate  (EXP,ISO)
leflunomide  (ISO)
levonorgestrel  (ISO)
lipopolysaccharide  (EXP,ISO)
lovastatin  (ISO)
menadione  (ISO)
menaquinone-4  (ISO)
menaquinone-7  (ISO)
methotrexate  (EXP,ISO)
methylmercury chloride  (ISO)
mifepristone  (EXP)
Myrtucommulone A  (ISO)
N-methyl-N-nitrosourea  (EXP)
N-nitrosodiethylamine  (ISO)
naringin  (ISO)
nickel atom  (ISO)
nicotinamide  (ISO)
nicotine  (EXP)
O-methyleugenol  (ISO)
orphenadrine  (EXP)
ospemifene  (ISO)
ozagrel  (ISO)
ozone  (ISO)
p-menthan-3-ol  (ISO)
pamidronate  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
parathion  (ISO)
paricalcitol  (ISO)
pentobarbital  (EXP)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenethyl caffeate  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phosphorus atom  (ISO)
phosphorus(.)  (ISO)
pioglitazone  (ISO)
pirinixic acid  (EXP,ISO)
poly(ethylene)  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
prostaglandin D2  (ISO)
prostaglandin E1  (ISO)
prostaglandin E2  (ISO)
prostaglandin F2alpha  (ISO)
puerarin  (EXP)
quercetin  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
rotenone  (EXP,ISO)
rubiadin  (EXP)
SB 203580  (ISO)
SB 431542  (ISO)
silicon dioxide  (EXP,ISO)
simvastatin  (ISO)
sodium arsenate  (EXP,ISO)
sodium arsenite  (ISO)
sodium fluoride  (EXP,ISO)
streptozocin  (EXP)
sulfasalazine  (ISO)
sunitinib  (ISO)
tacrolimus hydrate  (EXP)
tamoxifen  (ISO)
terbufos  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
titanium atom  (EXP,ISO)
toluene  (EXP)
tributylstannane  (EXP,ISO)
trichloroethene  (EXP)
trichostatin A  (EXP,ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
uranium atom  (EXP,ISO)
valproic acid  (EXP,ISO)
vorinostat  (ISO)
zinc dichloride  (EXP)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Calcium metabolism in adults with severe aortic valve stenosis and preserved renal function. Akat K, etal., Am J Cardiol. 2010 Mar 15;105(6):862-4. doi: 10.1016/j.amjcard.2009.10.065.
2. Decreased serum osteoprotegerin levels in patients with cardiac syndrome X. Altun A, etal., J Endocrinol Invest. 2004 Oct;27(9):839-43.
3. Markers of bone metastases in breast and lung cancers. Bilgin E, etal., Asian Pac J Cancer Prev. 2012;13(9):4331-4.
4. Osteoprotegerin is associated with cardiovascular risk in hypertension and/or diabetes. Blazquez-Medela AM, etal., Eur J Clin Invest. 2012 May;42(5):548-56. doi: 10.1111/j.1365-2362.2011.02619.x. Epub 2011 Nov 4.
5. Long-term sequential receptor activator of NF-kappaB ligand (RANKL) and osteoprotegrin (OPG) expression in lipopolysaccharide-induced rat periapical lesions. Chuang FH, etal., J Oral Pathol Med. 2012 Feb;41(2):186-93. doi: 10.1111/j.1600-0714.2011.01065.x. Epub 2011 Jul 28.
6. Reduced bone resorption and inflammation in apical periodontitis evoked by dietary supplementation with probiotics in rats. Cosme-Silva L, etal., Int Endod J. 2020 Aug;53(8):1084-1092. doi: 10.1111/iej.13311. Epub 2020 May 21.
7. Serum levels of osteoprotegerin and RANKL in patients with ST elevation acute myocardial infarction. Crisafulli A, etal., Clin Sci (Lond). 2005 Oct;109(4):389-95.
8. A mutation in the gene TNFRSF11B encoding osteoprotegerin causes an idiopathic hyperphosphatasia phenotype. Cundy T, etal., Hum Mol Genet. 2002 Sep 1;11(18):2119-27.
9. Imbalance of RANK, RANKL and OPG expression during tibial fracture repair in diabetic rats. de Amorim FP, etal., J Mol Histol. 2008 Aug;39(4):401-8. Epub 2008 Jul 1.
10. Correlations of urinary biomarkers, TNF-like weak inducer of apoptosis (TWEAK), osteoprotegerin (OPG), monocyte chemoattractant protein-1 (MCP-1), and IL-8 with lupus nephritis. El-Shehaby A, etal., J Clin Immunol. 2011 Oct;31(5):848-56. doi: 10.1007/s10875-011-9555-1. Epub 2011 Jun 21.
11. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
12. Oral administration of a nonimmunosuppressant FKBP-12 ligand speeds nerve regeneration. Gold BG, etal., Neuroreport. 1998 Feb 16;9(3):553-8.
13. Early molecular responses of bone to obstructive nephropathy induced by unilateral ureteral obstruction in mice. Gu SS, etal., Nephrology (Carlton). 2012 Nov;17(8):767-73. doi: 10.1111/j.1440-1797.2012.01656.x.
14. Serum osteoprotegerin levels in patients with acute atherothrombotic stroke and lacunar infarct. Guldiken B, etal., Thromb Res. 2007 Jan 24;.
15. Osteoprotegerin concentrations and prognosis in acute ischaemic stroke. Jensen JK, etal., J Intern Med. 2010 Apr;267(4):410-7. doi: 10.1111/j.1365-2796.2009.02163.x. Epub 2009 Aug 26.
16. Combined effect of fluoride and arsenate on gene expression of osteoclast differentiation factor and osteoprotegerin. Jia L and Jin TY, Biomed Environ Sci. 2006 Oct;19(5):375-9.
17. Plasma osteoprotegerin levels predict cardiovascular and all-cause mortality and deterioration of kidney function in type 1 diabetic patients with nephropathy. Jorsal A, etal., Diabetologia. 2008 Nov;51(11):2100-7. doi: 10.1007/s00125-008-1123-8. Epub 2008 Aug 22.
18. Osteoprotegerin is a risk factor for progressive atherosclerosis and cardiovascular disease. Kiechl S, etal., Circulation. 2004 May 11;109(18):2175-80. Epub 2004 Apr 26.
19. Serum osteoprotegerin is a predictor of progression of atherosclerosis and coronary calcification in hemodialysis patients. Kurnatowska I, etal., Nephron Clin Pract. 2011;117(4):c297-304. doi: 10.1159/000321169. Epub 2010 Sep 22.
20. Sinomenine suppresses osteoclast formation and Mycobacterium tuberculosis H37Ra-induced bone loss by modulating RANKL signaling pathways. Li X, etal., PLoS One. 2013 Sep 16;8(9):e74274. doi: 10.1371/journal.pone.0074274. eCollection 2013.
21. [Serum osteoprotegerin level in children with nephrotic syndrome and the effect of glucocorticoid on it]. Li YL and Wang H, Zhongguo Dang Dai Er Ke Za Zhi. 2012 Sep;14(9):653-6.
22. Osteoprotegerin/RANK/RANKL axis in cardiac remodeling due to immuno-inflammatory myocardial disease. Liu W, etal., Exp Mol Pathol. 2008 Jun;84(3):213-7. Epub 2008 Mar 7.
23. [Effects of kangfengshi granules on expressions of osteoprotegerin, RANKL and M-CSF in bone tissues of rats with collagen-induced arthritis] Liu YH, etal., Zhong Xi Yi Jie He Xue Bao. 2006 May;4(3):307-10.
24. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
25. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
26. The RANKL/RANK/OPG signaling pathway mediates medial arterial calcification in diabetic Charcot neuroarthropathy. Ndip A, etal., Diabetes. 2011 Aug;60(8):2187-96. doi: 10.2337/db10-1220. Epub 2011 Jun 9.
27. Lovastatin raises serum osteoprotegerin level in people with type 2 diabetic nephropathy. Nezami N, etal., Clin Biochem. 2010 Nov;43(16-17):1294-9. doi: 10.1016/j.clinbiochem.2010.08.012. Epub 2010 Aug 19.
28. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
29. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
30. GOA pipeline RGD automated data pipeline
31. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
32. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
33. Comprehensive gene review and curation RGD comprehensive gene curation
34. Relationship of serum osteoprotegerin levels with coronary artery disease severity, left ventricular hypertrophy and C-reactive protein. Rhee EJ, etal., Clin Sci (Lond). 2005 Mar;108(3):237-43.
35. Osteoprotegerin reduces osteoclast numbers and prevents bone erosion in collagen-induced arthritis. Romas E, etal., Am J Pathol 2002 Oct;161(4):1419-27.
36. Effects of the RANKL inhibitor, osteoprotegerin, on the pain and histopathology of bone cancer in rats. Roudier MP, etal., Clin Exp Metastasis. 2006;23(3-4):167-75. Epub 2006 Aug 16.
37. Immunolocalization of RANKL is increased and OPG decreased during dietary magnesium deficiency in the rat. Rude RK, etal., Nutr Metab (Lond). 2005 Sep 14;2(1):24.
38. Osteoprotegerin: a novel secreted protein involved in the regulation of bone density. Simonet WS, etal., Cell 1997 Apr 18;89(2):309-19.
39. Prevalence and progression of peripheral vascular calcification in type 2 diabetes subjects with preserved kidney function. Singh DK, etal., Diabetes Res Clin Pract. 2012 Jul;97(1):158-65. doi: 10.1016/j.diabres.2012.01.038. Epub 2012 Mar 3.
40. Serum osteoprotegerin, RANKL and fibroblast growth factor-23 in children with chronic kidney disease. Siomou E, etal., Pediatr Nephrol. 2011 Jul;26(7):1105-14. doi: 10.1007/s00467-011-1870-5. Epub 2011 Apr 9.
41. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
42. Dysregulated osteoprotegerin/RANK ligand/RANK axis in clinical and experimental heart failure. Ueland T, etal., Circulation. 2005 May 17;111(19):2461-8. Epub 2005 May 9.
43. The relationship between insulin resistance assessed by HOMA-IR and serum osteoprotegerin levels in obesity. Ugur-Altun B, etal., Diabetes Res Clin Pract. 2005 Jun;68(3):217-22. Epub 2005 Jan 18.
44. Association study of candidate genes for the prevalence and progression of knee osteoarthritis. Valdes AM, etal., Arthritis Rheum. 2004 Aug;50(8):2497-507.
45. [Effect of estrogen on osteoprotegerin, osteoclast differentiation factor and macrophage colony stimulating factor mRNA expressions in ovariectomized rat bone tissue] Wang Q, etal., Nan Fang Yi Ke Da Xue Xue Bao. 2006 Apr;26(4):532-4.
46. Zhong xi yi jie he xue bao = Journal of Chinese integrative medicine Wang Q, etal., Zhong Xi Yi Jie He Xue Bao. 2006 May;4(3):303-6.
47. Inhibition of osteoclastogenesis by the secretion of osteoprotegerin in vitro by rat dental follicle cells and its implications for tooth eruption. Wise GE, etal., Arch Oral Biol 2002 Mar;47(3):247-54.
48. Injections of osteoprotegerin and PMA delay tooth eruption. Wise GE, etal., Clin Anat. 2006 Jan;19(1):19-24.
49. Protein Kinase C is a mediator of the synthesis and secretion of osteoprotegerin in osteoblast-like cells. Yang X, etal., Biochem Biophys Res Commun 2002 Jan 11;290(1):42-6.
50. [Indication of osteoprotegerin (OPG) and receptor activator of nuclear factor kappa B ligand (RANKL) in gingival crevicular fluid to remodeling of alveolar bone during retention]. Zhao NN, etal., Beijing Da Xue Xue Bao. 2012 Feb 18;44(1):108-12.
51. Association between increased serum osteoprotegerin levels and improvement in bone mineral density after parathyroidectomy in hemodialysis patients. Zheng CM, etal., Tohoku J Exp Med. 2012;226(1):19-27.
52. Osteoprotegerin plasma concentrations correlate with severity of peripheral artery disease. Ziegler S, etal., Atherosclerosis. 2005 Sep;182(1):175-80. Epub 2005 Apr 26.
Additional References at PubMed
PMID:14981127   PMID:15489334   PMID:15516325   PMID:15704000   PMID:16568210   PMID:17443309   PMID:17476578   PMID:17608585   PMID:17627577   PMID:18166509   PMID:18432284   PMID:18476557  
PMID:18757743   PMID:19040304   PMID:19105036   PMID:19257823   PMID:19537860   PMID:19539794   PMID:21519319   PMID:21602131   PMID:22027774   PMID:22878484   PMID:22948539   PMID:23404413  
PMID:23500899   PMID:23954550   PMID:24006456   PMID:24321069   PMID:25200151   PMID:25257532   PMID:26489619   PMID:26677102   PMID:27154288   PMID:28092862   PMID:28473060   PMID:28774557  
PMID:28931423   PMID:29529595   PMID:30077758   PMID:30951948   PMID:32000757   PMID:32307402   PMID:32722636   PMID:32856519   PMID:33834668   PMID:34610044   PMID:34948030   PMID:35842599  


Genomics

Comparative Map Data
Tnfrsf11b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2785,566,520 - 85,594,526 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl785,566,520 - 85,594,538 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx787,463,913 - 87,491,923 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0789,665,094 - 89,693,104 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0789,470,571 - 89,498,581 (-)NCBIRnor_WKY
Rnor_6.0793,798,580 - 93,826,586 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl793,798,545 - 93,826,665 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0794,436,612 - 94,464,618 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4790,606,424 - 90,634,431 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1790,640,654 - 90,668,661 (-)NCBI
Celera782,388,596 - 82,416,602 (-)NCBICelera
Cytogenetic Map7q32NCBI
TNFRSF11B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh388118,923,557 - 118,951,885 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl8118,923,557 - 118,951,885 (-)EnsemblGRCh38hg38GRCh38
GRCh378119,935,796 - 119,964,124 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 368120,004,977 - 120,033,564 (-)NCBINCBI36Build 36hg18NCBI36
Build 348120,004,977 - 120,033,492NCBI
Celera8116,124,073 - 116,152,621 (-)NCBICelera
Cytogenetic Map8q24.12NCBI
HuRef8115,263,331 - 115,291,874 (-)NCBIHuRef
CHM1_18119,976,820 - 120,005,398 (-)NCBICHM1_1
T2T-CHM13v2.08120,051,990 - 120,080,310 (-)NCBIT2T-CHM13v2.0
Tnfrsf11b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391554,114,014 - 54,141,880 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1554,114,015 - 54,141,880 (-)EnsemblGRCm39 Ensembl
GRCm381554,250,619 - 54,278,484 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1554,250,619 - 54,278,484 (-)EnsemblGRCm38mm10GRCm38
MGSCv371554,082,174 - 54,110,039 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361554,080,702 - 54,108,567 (-)NCBIMGSCv36mm8
Celera1555,801,719 - 55,829,545 (-)NCBICelera
Cytogenetic Map15D1NCBI
Tnfrsf11b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541724,804,664 - 24,831,894 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541724,804,708 - 24,831,338 (-)NCBIChiLan1.0ChiLan1.0
TNFRSF11B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.18118,134,305 - 118,162,422 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl8118,134,305 - 118,162,422 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v08115,614,778 - 115,643,387 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
TNFRSF11B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11318,155,765 - 18,183,263 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1318,156,367 - 18,183,444 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1318,157,696 - 18,185,164 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01318,475,888 - 18,503,357 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1318,475,887 - 18,503,320 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11318,206,469 - 18,233,953 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01318,302,728 - 18,330,220 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01318,533,442 - 18,560,917 (-)NCBIUU_Cfam_GSD_1.0
Tnfrsf11b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530320,145,169 - 20,172,626 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647027,571,270 - 27,599,089 (+)EnsemblSpeTri2.0
SpeTri2.0NW_00493647027,571,263 - 27,598,725 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TNFRSF11B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl419,850,350 - 19,879,125 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1419,850,212 - 19,879,132 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2421,129,878 - 21,158,557 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TNFRSF11B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.18113,520,711 - 113,549,370 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl8113,520,596 - 113,548,936 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603926,748,455 - 26,777,113 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tnfrsf11b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476317,138,847 - 17,166,453 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476317,139,109 - 17,166,398 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tnfrsf11b
114 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:184
Count of miRNA genes:127
Interacting mature miRNAs:156
Transcripts:ENSRNOT00000011344
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
634326Hc3Hypercalciuria QTL 32.1urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)74278731487787314Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)74322875088228750Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)743747012108555253Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)743747099102228765Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)74486753389867533Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)74659007091590070Rat
2293696Bmd32Bone mineral density QTL 325.10.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)74765143992651439Rat
2293707Bss32Bone structure and strength QTL 327.640.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)74765143992651439Rat
2300178Bmd54Bone mineral density QTL 545.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)74765143992651439Rat
2293644Bmd29Bone mineral density QTL 295.40.0001femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)74765143992651439Rat
2293667Bss42Bone structure and strength QTL 427.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)74765143992651439Rat
2293678Bss24Bone structure and strength QTL 246.710.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)74765143992651439Rat
2293685Bmd21Bone mineral density QTL 214.20.0003femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)74765143992651439Rat
1300151Bp181Blood pressure QTL 1813.36arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)753612714103945643Rat
2317035Aia16Adjuvant induced arthritis QTL 162.71joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)759238038104238038Rat
1298528Bp169Blood pressure QTL 1690.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)761074194106074194Rat
1559283Emca4Estrogen-induced mammary cancer QTL 43.7mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)762004452101773158Rat
1576303Ept7Estrogen-induced pituitary tumorigenesis QTL 73.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)762004452101773158Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)768938720113886318Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)768938720113886318Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)768938720113886318Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)769736226117455174Rat
1357338Stl17Serum triglyceride level QTL 173.23blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)769736356112729554Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
724537Niddm52Non-insulin dependent diabetes mellitus QTL 520.02blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)78022129993595843Rat
1641908Teswt1Testicular weight QTL 13.28testis mass (VT:1000644)both testes wet weight (CMO:0000175)78022129994811326Rat
631529Tls2T-lymphoma susceptibility QTL 200.001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)780221299109401111Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)780221299112308525Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)780221299124373579Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)780221299125221299Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)781737938126737938Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)783153392128153392Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)784257275129257275Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)784257275129257275Rat

Markers in Region
D7Hmgc3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2785,567,754 - 85,567,922 (+)MAPPERmRatBN7.2
Rnor_6.0793,799,815 - 93,799,982NCBIRnor6.0
Rnor_5.0794,437,847 - 94,438,014UniSTSRnor5.0
RGSC_v3.4790,607,659 - 90,607,826UniSTSRGSC3.4
Celera782,389,831 - 82,389,998UniSTS
RH 3.4 Map7592.1UniSTS
RH 3.4 Map7592.1RGD
Cytogenetic Map7q31UniSTS


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 1 6 3 3 3 14 7 20 11
Low 2 37 54 38 19 38 8 10 60 28 18 8
Below cutoff 1 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000011344   ⟹   ENSRNOP00000011344
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl785,566,520 - 85,594,519 (-)Ensembl
Rnor_6.0 Ensembl793,798,545 - 93,826,665 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096742   ⟹   ENSRNOP00000094946
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl785,566,523 - 85,594,538 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102998   ⟹   ENSRNOP00000086232
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl785,566,520 - 85,576,400 (-)Ensembl
RefSeq Acc Id: NM_012870   ⟹   NP_037002
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2785,566,520 - 85,594,526 (-)NCBI
Rnor_6.0793,798,580 - 93,826,586 (-)NCBI
Rnor_5.0794,436,612 - 94,464,618 (-)NCBI
RGSC_v3.4790,606,424 - 90,634,431 (-)RGD
Celera782,388,596 - 82,416,602 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_037002 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB53707 (Get FASTA)   NCBI Sequence Viewer  
  AAH81830 (Get FASTA)   NCBI Sequence Viewer  
  EDM16265 (Get FASTA)   NCBI Sequence Viewer  
  O08727 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_037002   ⟸   NM_012870
- Peptide Label: precursor
- UniProtKB: O08727 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000011344   ⟸   ENSRNOT00000011344
RefSeq Acc Id: ENSRNOP00000086232   ⟸   ENSRNOT00000102998
RefSeq Acc Id: ENSRNOP00000094946   ⟸   ENSRNOT00000096742
Protein Domains
Death   TNFR-Cys

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O08727-F1-model_v2 AlphaFold O08727 1-401 view protein structure

Transcriptome

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

Promoters
RGD ID:13695327
Promoter ID:EPDNEW_R5852
Type:multiple initiation site
Name:Tnfrsf11b_1
Description:TNF receptor superfamily member 11B
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_6.0793,826,539 - 93,826,599EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619802 AgrOrtholog
BioCyc Gene G2FUF-33397 BioCyc
Ensembl Genes ENSRNOG00000008336 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000011344 ENTREZGENE
  ENSRNOP00000011344.3 UniProtKB/Swiss-Prot
  ENSRNOP00000086232.1 UniProtKB/TrEMBL
  ENSRNOP00000094946.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011344 ENTREZGENE
  ENSRNOT00000011344.6 UniProtKB/Swiss-Prot
  ENSRNOT00000096742.1 UniProtKB/TrEMBL
  ENSRNOT00000102998.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.533.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tumor Necrosis Factor Receptor, subunit A, domain 2 UniProtKB/Swiss-Prot, 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_11 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR_11B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25341 UniProtKB/Swiss-Prot
NCBI Gene 25341 ENTREZGENE
PANTHER TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 11B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Death UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR_c6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tnfrsf11b PhenoGen
PIRSF TNFR_11B UniProtKB/Swiss-Prot
PRINTS TNFACTORR11 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFACTORR11B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE TNFR_NGFR_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR_NGFR_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART DEATH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ephrin_rec_like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47986 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNF receptor-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6A1T0_RAT UniProtKB/TrEMBL
  A0A8I6AM34_RAT UniProtKB/TrEMBL
  O08727 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-05 Tnfrsf11b  TNF receptor superfamily member 11B  Tnfrsf11b  tumor necrosis factor receptor superfamily, member 11b  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-12-15 Tnfrsf11b  tumor necrosis factor receptor superfamily, member 11b  Tnfrsf11b  tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Tnfrsf11b  tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)    tumor necrosis factor receptor superfamily, member 11b  Symbol and Name updated 625702 APPROVED
2003-04-09 Tnfrsf11b  tumor necrosis factor receptor superfamily, member 11b      Symbol and Name updated 629477 APPROVED
2003-03-12 Tnfrsf11b  tumor necrosis factor receptor superfamily, member 11b  Opg  Osteoprotegerin  Data Merged 628472 PROVISIONAL
2002-08-07 Tnfrsf11b        Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Opg  Osteoprotegerin      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease prevents ovariectomy-induced bone loss 730033
gene_expression expressed as dimeric forms of 112 kDa and 56 kDa in osteoblasts, osteocytes, and osteoprogenitor cells 70599
gene_function binds to the receptor activator of NF-KB ligand [RANKL] thus preventing the interaction with receptor activator of NF-KB [RANK] 70599
gene_process may play a role in preventing excess bone resorption during dental follicle development 730196
gene_regulation phorbol myristate acetate [PMA], an activator of protein kinase C [PKC], increased expression in a time and concentration dependent manner and this increase was blocked by bisindolyl maleimide [BIM], a protein kinase C inhibitor 70599