Human Gene TNFRSF11B (ENST00000297350.9_7) from GENCODE V47lift37
  Description: TNF receptor superfamily member 11b (from RefSeq NM_002546.4)
Gencode Transcript: ENST00000297350.9_7
Gencode Gene: ENSG00000164761.9_9
Transcript (Including UTRs)
   Position: hg19 chr8:119,935,796-119,964,124 Size: 28,329 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr8:119,936,613-119,964,060 Size: 27,448 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:119,935,796-119,964,124)mRNA (may differ from genome)Protein (401 aa)
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-  Comments and Description Text from UniProtKB
  ID: TR11B_HUMAN
DESCRIPTION: RecName: Full=Tumor necrosis factor receptor superfamily member 11B; AltName: Full=Osteoclastogenesis inhibitory factor; AltName: Full=Osteoprotegerin; Flags: Precursor;
FUNCTION: Acts as decoy receptor for TNFSF11/RANKL and thereby neutralizes its function in osteoclastogenesis. Inhibits the activation of osteoclasts and promotes osteoclast apoptosis in vitro. Bone homeostasis seems to depend on the local ratio between TNFSF11 and TNFRSF11B. May also play a role in preventing arterial calcification. May act as decoy receptor for TNFSF10/TRAIL and protect against apoptosis. TNFSF10/TRAIL binding blocks the inhibition of osteoclastogenesis.
SUBUNIT: Homodimer. Interacts with TNFSF10 and TNFSF11.
SUBCELLULAR LOCATION: Secreted.
TISSUE SPECIFICITY: Highly expressed in adult lung, heart, kidney, liver, spleen, thymus, prostate, ovary, small intestine, thyroid, lymph node, trachea, adrenal gland, testis, and bone marrow. Detected at very low levels in brain, placenta and skeletal muscle. Highly expressed in fetal kidney, liver and lung.
INDUCTION: Up-regulated by increasing calcium-concentration in the medium and estrogens. Down-regulated by glucocorticoids.
PTM: N-glycosylated. Contains sialic acid residues.
PTM: The N-terminus is blocked.
DISEASE: Defects in TNFRSF11B are the cause of juvenile Paget disease (JPD) [MIM:239000]; also known as hyperostosis corticalis deformans juvenilis or hereditary hyperphosphatasia or chronic congenital idiopathic hyperphosphatasia. JPD is a rare autosomal recessive osteopathy that presents in infancy or early childhood. The disorder is characterized by rapidly remodeling woven bone, osteopenia, debilitating fractures, and deformities due to a markedly accelerated rate of bone remodeling throughout the skeleton. Approximately 40 cases of JPD have been reported worldwide. Unless it is treated with drugs that block osteoclast- mediated skeletal resorption, the disease can be fatal.
SIMILARITY: Contains 2 death domains.
SIMILARITY: Contains 4 TNFR-Cys repeats.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/TNFRSF11BID42610ch8q24.html";
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/tnfrsf11b/";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
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To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: TNFRSF11B
Diseases sorted by gene-association score: paget disease of bone 5, juvenile-onset* (1280), chronic apical periodontitis (22), paget disease of bone 5, juvenile (19), root resorption (18), osteoporosis (17), renal osteodystrophy (16), otosclerosis (15), short stature, brachydactyly, intellectual developmental disability, and seizures (15), glucocorticoid-induced osteoporosis (14), osteolysis, familial expansile (14), paget's disease of bone (14), polyarticular onset juvenile idiopathic arthritis (13), periodontal disease (12), hyperostosis, endosteal (12), osteonecrosis (12), periapical periodontitis (11), fibrogenesis imperfecta ossium (10), uremia (10), multicentric carpotarsal osteolysis syndrome (10), osteoporotic fracture (9), hyperostosis (9), secondary hyperparathyroidism of renal origin (9), bone resorption disease (8), giant cell tumor (8), bone remodeling disease (8), carotid stenosis (8), periodontitis (8), peripheral artery disease (8), multicentric reticulohistiocytosis (8), prosthetic joint infection (8), chondrocalcinosis (8), tooth resorption (8), cystoisosporiasis (8), hyperparathyroidism (8), shwachman-diamond syndrome (7), diabetic angiopathy (7), hemophilic arthropathy (7), periostitis (7), cholesteatoma (7), psoriatic arthritis (7), ankylosis (6), arthropathy (6), ischemic bone disease (6), trichorhinophalangeal syndrome, type ii (6), abdominal aortic aneurysm (6), osteopathia striata with cranial sclerosis (6), synovitis (6), optic nerve glioma (6), spondyloarthropathy 1 (5), aortic valve disease 2 (5), osteosarcoma, somatic (5), trichorhinophalangeal syndrome, type i (4), osteoarthritis (4), osteogenesis imperfecta, type i (3), vascular disease (3), rheumatoid arthritis (3), differentiated thyroid carcinoma (3), multiple myeloma (2), rheumatic disease (2), prostate cancer (2), myelofibrosis with myeloid metaplasia, somatic (1), mouth disease (1), bone inflammation disease (1), aortic valve disease 1 (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 95.78 RPKM in Artery - Aorta
Total median expression: 247.77 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -18.9064-0.295 Picture PostScript Text
3' UTR -165.40817-0.202 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000488 - Death
IPR011029 - DEATH-like
IPR001368 - TNFR/NGFR_Cys_rich_reg
IPR022323 - TNFR_11
IPR017371 - TNFR_11B

Pfam Domains:
PF00020 - TNFR/NGFR cysteine-rich region
PF00531 - Death domain

SCOP Domains:
47986 - DEATH domain
57586 - TNF receptor-like
57184 - Growth factor receptor domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3URF - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O00300
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005031 tumor necrosis factor-activated receptor activity
GO:0005125 cytokine activity
GO:0005515 protein binding
GO:0038023 signaling receptor activity

Biological Process:
GO:0001501 skeletal system development
GO:0006915 apoptotic process
GO:0006954 inflammatory response
GO:0006955 immune response
GO:0007165 signal transduction
GO:0007584 response to nutrient
GO:0010035 response to inorganic substance
GO:0010469 regulation of receptor activity
GO:0030198 extracellular matrix organization
GO:0032026 response to magnesium ion
GO:0032496 response to lipopolysaccharide
GO:0033209 tumor necrosis factor-mediated signaling pathway
GO:0042127 regulation of cell proliferation
GO:0042489 negative regulation of odontogenesis of dentin-containing tooth
GO:0042493 response to drug
GO:0042981 regulation of apoptotic process
GO:0043627 response to estrogen
GO:0045779 negative regulation of bone resorption
GO:0046685 response to arsenic-containing substance
GO:0097190 apoptotic signaling pathway

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane


-  Descriptions from all associated GenBank mRNAs
  AK223155 - Homo sapiens mRNA for osteoprotegerin precursor variant, clone: LNF00675.
BC030155 - Homo sapiens tumor necrosis factor receptor superfamily, member 11b, mRNA (cDNA clone MGC:29565 IMAGE:4875170), complete cds.
JD524999 - Sequence 506023 from Patent EP1572962.
JD202039 - Sequence 183063 from Patent EP1572962.
U94332 - Human osteoprotegerin (OPG) mRNA, complete cds.
JD305476 - Sequence 286500 from Patent EP1572962.
AF134187 - Homo sapiens osteoprotegerin mRNA, partial cds.
KJ891726 - Synthetic construct Homo sapiens clone ccsbBroadEn_01120 TNFRSF11B gene, encodes complete protein.
KR711157 - Synthetic construct Homo sapiens clone CCSBHm_00020863 TNFRSF11B (TNFRSF11B) mRNA, encodes complete protein.
KR711158 - Synthetic construct Homo sapiens clone CCSBHm_00020864 TNFRSF11B (TNFRSF11B) mRNA, encodes complete protein.
KR711159 - Synthetic construct Homo sapiens clone CCSBHm_00020865 TNFRSF11B (TNFRSF11B) mRNA, encodes complete protein.
AB002146 - Homo sapiens mRNA for osteoclastogenesis inhibitory factor (OCIF), complete cds.
AK313710 - Homo sapiens cDNA, FLJ94303, Homo sapiens tumor necrosis factor receptor superfamily, member 11b(osteoprotegerin) (TNFRSF11B), mRNA.
DQ892264 - Synthetic construct clone IMAGE:100004894; FLH184695.01X; RZPDo839A11146D tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin) (TNFRSF11B) gene, encodes complete protein.
DQ895466 - Synthetic construct Homo sapiens clone IMAGE:100009926; FLH184691.01L; RZPDo839A11145D tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin) (TNFRSF11B) gene, encodes complete protein.
AB528441 - Synthetic construct DNA, clone: pF1KB6574, Homo sapiens TNFRSF11B gene for tumor necrosis factor receptor superfamily, member 11b, without stop codon, in Flexi system.
BC011023 - Homo sapiens tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin), mRNA (cDNA clone IMAGE:4042608), with apparent retained intron.
CU688830 - Synthetic construct Homo sapiens gateway clone IMAGE:100021925 5' read TNFRSF11B mRNA.
AK308524 - Homo sapiens cDNA, FLJ98565.
JD458620 - Sequence 439644 from Patent EP1572962.
JD129031 - Sequence 110055 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O00300 (Reactome details) participates in the following event(s):

R-HSA-5669035 TNFSF11 binds TNFRSF11A, B
R-HSA-5669034 TNFs bind their physiological receptors
R-HSA-5668541 TNFR2 non-canonical NF-kB pathway
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: B2R9A8, ENST00000297350.1, ENST00000297350.2, ENST00000297350.3, ENST00000297350.4, ENST00000297350.5, ENST00000297350.6, ENST00000297350.7, ENST00000297350.8, NM_002546, O00300, O60236, OCIF, OPG, Q53FX6, Q9UHP4, TR11B_HUMAN, uc317lzr.1, uc317lzr.2
UCSC ID: ENST00000297350.9_7
RefSeq Accession: NM_002546.4
Protein: O00300 (aka TR11B_HUMAN or T11B_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.