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Aliases for TNFRSF11B Gene

Aliases for TNFRSF11B Gene

  • TNF Receptor Superfamily Member 11b 2 3 5
  • Osteoprotegerin 2 3 4
  • Tumor Necrosis Factor Receptor Superfamily, Member 11b 2 3
  • Osteoclastogenesis Inhibitory Factor 3 4
  • OCIF 3 4
  • OPG 3 4
  • Tumor Necrosis Factor Receptor Superfamily Member 11B 3
  • PDB5 3
  • TR1 3

External Ids for TNFRSF11B Gene

Previous HGNC Symbols for TNFRSF11B Gene

  • OPG

Previous GeneCards Identifiers for TNFRSF11B Gene

  • GC08M119997
  • GC08M119604
  • GC08M119892
  • GC08M120004
  • GC08M119935
  • GC08M115263

Summaries for TNFRSF11B Gene

Entrez Gene Summary for TNFRSF11B Gene

  • The protein encoded by this gene is a member of the TNF-receptor superfamily. This protein is an osteoblast-secreted decoy receptor that functions as a negative regulator of bone resorption. This protein specifically binds to its ligand, osteoprotegerin ligand, both of which are key extracellular regulators of osteoclast development. Studies of the mouse counterpart also suggest that this protein and its ligand play a role in lymph-node organogenesis and vascular calcification. Alternatively spliced transcript variants of this gene have been reported, but their full length nature has not been determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for TNFRSF11B Gene

TNFRSF11B (TNF Receptor Superfamily Member 11b) is a Protein Coding gene. Diseases associated with TNFRSF11B include Paget Disease Of Bone 5, Juvenile-Onset and Chronic Apical Periodontitis. Among its related pathways are Ectoderm Differentiation and RANK Signaling in Osteoclasts. Gene Ontology (GO) annotations related to this gene include receptor activity and cytokine activity. An important paralog of this gene is TNFRSF6B.

UniProtKB/Swiss-Prot for TNFRSF11B Gene

  • 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.

Gene Wiki entry for TNFRSF11B Gene

Additional gene information for TNFRSF11B Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TNFRSF11B Gene

Genomics for TNFRSF11B Gene

GeneHancer (GH) Regulatory Elements for TNFRSF11B Gene

Promoters and enhancers for TNFRSF11B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH08I118950 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 550.8 +0.5 498 2.6 BACH1 SIN3A EBF1 ZIC2 KLF5 ETS1 ZNF335 POLR2A ZNF207 PRDM10 COLEC10 TNFRSF11B RNU6-12P LOC100286746 LOC105375723
GH08I118896 Enhancer 1 Ensembl ENCODE 5.8 +54.3 54254 2.8 PKNOX1 FOXA2 JUN BMI1 BATF CTBP1 GATA3 ARID3A NFATC1 ATF7 COLEC10 SAMD12 TNFRSF11B LOC105375723
GH08I118876 Enhancer 1 ENCODE dbSUPER 5.4 +74.0 74002 3.6 PKNOX1 CLOCK NFIB NEUROD1 RAD21 RFX5 E2F8 FOS RCOR1 SMARCA5 COLEC10 TNFRSF11B LOC105375723
GH08I118743 Enhancer 0.9 Ensembl ENCODE 6 +208.0 208047 1.8 CTCF CEBPG KLF5 RAD21 RFX5 ZKSCAN1 TEAD3 ZNF143 SMC3 ZNF444 TNFRSF11B RPS26P35 SAMD12 SAMD12-AS1
GH08I118908 Enhancer 0.8 FANTOM5 ENCODE 6.4 +40.2 40178 6.2 PKNOX1 NFYA NR2F1 ATF2 FOXA1 GATA3 POLR2A ZNF24 ATF7 COLEC10 RNU6-12P LOC100286746 TNFRSF11B LOC105375723
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TNFRSF11B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TNFRSF11B gene promoter:

Genomic Locations for TNFRSF11B Gene

Genomic Locations for TNFRSF11B Gene
chr8:118,923,557-118,952,200
(GRCh38/hg38)
Size:
28,644 bases
Orientation:
Minus strand
chr8:119,935,796-119,964,439
(GRCh37/hg19)

Genomic View for TNFRSF11B Gene

Genes around TNFRSF11B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TNFRSF11B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TNFRSF11B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TNFRSF11B Gene

Proteins for TNFRSF11B Gene

  • Protein details for TNFRSF11B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O00300-TR11B_HUMAN
    Recommended name:
    Tumor necrosis factor receptor superfamily member 11B
    Protein Accession:
    O00300
    Secondary Accessions:
    • B2R9A8
    • O60236
    • Q53FX6
    • Q9UHP4

    Protein attributes for TNFRSF11B Gene

    Size:
    401 amino acids
    Molecular mass:
    46026 Da
    Quaternary structure:
    • Homodimer. Interacts with TNFSF10 and TNFSF11.

    Three dimensional structures from OCA and Proteopedia for TNFRSF11B Gene

neXtProt entry for TNFRSF11B Gene

Post-translational modifications for TNFRSF11B Gene

  • N-glycosylated. Contains sialic acid residues.
  • The N-terminus is blocked.
  • Glycosylation at posLast=9898, posLast=152152, isoforms=165, isoforms=178, and posLast=289289
  • Modification sites at PhosphoSitePlus

Other Protein References for TNFRSF11B Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TNFRSF11B Gene

Domains & Families for TNFRSF11B Gene

Gene Families for TNFRSF11B Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Candidate cardiovascular disease genes
  • Disease related genes
  • Plasma proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for TNFRSF11B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with TNFRSF11B: view

No data available for UniProtKB/Swiss-Prot for TNFRSF11B Gene

Function for TNFRSF11B Gene

Molecular function for TNFRSF11B Gene

GENATLAS Biochemistry:
tumor necrosis factor receptor superfamily,member 11B,expressed in lymphoid cells and up-regulated by CD40 (TNFRSF5) stimulation,involved in osteoclastogenesis,secreted form down-regulating osteoclast differentiation by binding the osteoprotegerin ligand (TNFSF11)
UniProtKB/Swiss-Prot 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.
UniProtKB/Swiss-Prot Induction:
Up-regulated by increasing calcium-concentration in the medium and estrogens. Down-regulated by glucocorticoids.

Phenotypes From GWAS Catalog for TNFRSF11B Gene

Gene Ontology (GO) - Molecular Function for TNFRSF11B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004872 receptor activity TAS 9108485
GO:0005031 tumor necrosis factor-activated receptor activity IBA --
GO:0005125 cytokine activity TAS 9168977
GO:0005515 protein binding IPI 22664871
genes like me logo Genes that share ontologies with TNFRSF11B: view
genes like me logo Genes that share phenotypes with TNFRSF11B: view

Human Phenotype Ontology for TNFRSF11B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TNFRSF11B Gene

MGI Knock Outs for TNFRSF11B:

Animal Model Products

CRISPR Products

miRNA for TNFRSF11B Gene

Inhibitory RNA Products

Clone Products

  • R&D Systems cDNA Clones for TNFRSF11B (Osteoprotegerin/TNFRSF11B)

Cell Line Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for TNFRSF11B Gene

Localization for TNFRSF11B Gene

Subcellular locations from UniProtKB/Swiss-Prot for TNFRSF11B Gene

Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TNFRSF11B gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytoskeleton 2
nucleus 2
cytosol 2
mitochondrion 1
lysosome 1

Gene Ontology (GO) - Cellular Components for TNFRSF11B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS 9108485
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005615 extracellular space IDA,IEA 15516325
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IBA --
genes like me logo Genes that share ontologies with TNFRSF11B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TNFRSF11B Gene

Pathways & Interactions for TNFRSF11B Gene

genes like me logo Genes that share pathways with TNFRSF11B: view

SIGNOR curated interactions for TNFRSF11B Gene

Is activated by:

Gene Ontology (GO) - Biological Process for TNFRSF11B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development TAS 9108485
GO:0006915 apoptotic process IEA --
GO:0006954 inflammatory response IBA --
GO:0006955 immune response IBA --
GO:0007165 signal transduction TAS 9168977
genes like me logo Genes that share ontologies with TNFRSF11B: view

Drugs & Compounds for TNFRSF11B Gene

(69) Drugs for TNFRSF11B Gene - From: PharmGKB, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
Anastrozole Approved, Investigational Pharma Aromatase inhibitor, Potent aromatase (CYP19) inhibitor, Aromatase Inhibitors, Hormone therapy 297
Letrozole Approved, Investigational Pharma Non-steroidal aromatase inhibitor, Aromatase Inhibitors 424

(40) Additional Compounds for TNFRSF11B Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with TNFRSF11B: view

Transcripts for TNFRSF11B Gene

mRNA/cDNA for TNFRSF11B Gene

Unigene Clusters for TNFRSF11B Gene

Tumor necrosis factor receptor superfamily, member 11b:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • R&D Systems cDNA Clones for TNFRSF11B (Osteoprotegerin/TNFRSF11B)

Alternative Splicing Database (ASD) splice patterns (SP) for TNFRSF11B Gene

No ASD Table

Relevant External Links for TNFRSF11B Gene

GeneLoc Exon Structure for
TNFRSF11B
ECgene alternative splicing isoforms for
TNFRSF11B

Expression for TNFRSF11B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TNFRSF11B Gene

mRNA differential expression in normal tissues according to GTEx for TNFRSF11B Gene

This gene is overexpressed in Artery - Aorta (x17.4) and Artery - Coronary (x14.9).

Protein differential expression in normal tissues from HIPED for TNFRSF11B Gene

This gene is overexpressed in Milk (40.9), Heart (12.3), and Pancreatic juice (7.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for TNFRSF11B Gene



NURSA nuclear receptor signaling pathways regulating expression of TNFRSF11B Gene:

TNFRSF11B

SOURCE GeneReport for Unigene cluster for TNFRSF11B Gene:

Hs.81791

mRNA Expression by UniProt/SwissProt for TNFRSF11B Gene:

O00300-TR11B_HUMAN
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.

Evidence on tissue expression from TISSUES for TNFRSF11B Gene

  • Kidney(4.5)
  • Lung(4.3)
  • Eye(4)
  • Bone(3.8)
  • Bone marrow(2.8)
  • Heart(2.8)
  • Blood(2.5)
  • Thyroid gland(2.5)
  • Muscle(2.1)
  • Nervous system(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TNFRSF11B Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • cardiovascular
  • nervous
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • face
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
  • tooth
Thorax:
  • chest wall
  • clavicle
  • heart
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • kidney
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood vessel
  • peripheral nervous system
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with TNFRSF11B: view

No data available for Protein tissue co-expression partners for TNFRSF11B Gene

Orthologs for TNFRSF11B Gene

This gene was present in the common ancestor of chordates.

Orthologs for TNFRSF11B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TNFRSF11B 33 34
  • 99.42 (n)
dog
(Canis familiaris)
Mammalia TNFRSF11B 33 34
  • 89.19 (n)
cow
(Bos Taurus)
Mammalia TNFRSF11B 33 34
  • 87.61 (n)
rat
(Rattus norvegicus)
Mammalia Tnfrsf11b 33
  • 84 (n)
mouse
(Mus musculus)
Mammalia Tnfrsf11b 33 16 34
  • 83.96 (n)
oppossum
(Monodelphis domestica)
Mammalia TNFRSF11B 34
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TNFRSF11B 34
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves TNFRSF11B 33 34
  • 71.74 (n)
lizard
(Anolis carolinensis)
Reptilia TNFRSF11B 34
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tnfrsf11b 33
  • 58.27 (n)
zebrafish
(Danio rerio)
Actinopterygii CABZ01053483.1 34
  • 19 (a)
ManyToMany
Species where no ortholog for TNFRSF11B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for TNFRSF11B Gene

ENSEMBL:
Gene Tree for TNFRSF11B (if available)
TreeFam:
Gene Tree for TNFRSF11B (if available)

Paralogs for TNFRSF11B Gene

Paralogs for TNFRSF11B Gene

(1) SIMAP similar genes for TNFRSF11B Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with TNFRSF11B: view

Variants for TNFRSF11B Gene

Sequence variations from dbSNP and Humsavar for TNFRSF11B Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs1005633209 uncertain-significance, Hyperphosphatasemia with bone disease 118,951,920(-) C/T 5_prime_UTR_variant
rs104894091 pathogenic, Hyperphosphatasemia with bone disease 118,933,071(-) C/T coding_sequence_variant, missense_variant
rs104894092 pathogenic, Hyperphosphatasemia with bone disease 118,932,982(-) A/G coding_sequence_variant, missense_variant
rs10505344 likely-benign, Hyperphosphatasemia with bone disease 118,933,307(-) G/A intron_variant
rs11573930 likely-benign, Hyperphosphatasemia with bone disease 118,926,597(-) C/T coding_sequence_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for TNFRSF11B Gene

Variant ID Type Subtype PubMed ID
esv2005767 CNV deletion 18987734
esv2737483 CNV deletion 23290073
esv2737484 CNV deletion 23290073
esv2737486 CNV deletion 23290073
esv2737487 CNV deletion 23290073
esv2759639 CNV gain 17122850

Variation tolerance for TNFRSF11B Gene

Residual Variation Intolerance Score: 52.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.03; 37.33% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TNFRSF11B Gene

Human Gene Mutation Database (HGMD)
TNFRSF11B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TNFRSF11B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TNFRSF11B Gene

Disorders for TNFRSF11B Gene

MalaCards: The human disease database

(65) MalaCards diseases for TNFRSF11B Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
paget disease of bone 5, juvenile-onset
  • jpd
chronic apical periodontitis
  • chronic apical periodontitis nos
root resorption
osteoporosis
  • bone mineral density quantitative trait locus; bmnd
multicentric carpotarsal osteolysis syndrome
  • mcto
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

TR11B_HUMAN
  • Paget disease of bone 5, juvenile-onset (PDB5) [MIM:239000]: An autosomal recessive, juvenile-onset form of Paget disease, a disorder of bone remodeling characterized by increased bone turnover affecting one or more sites throughout the skeleton, primarily the axial skeleton. Osteoclastic overactivity followed by compensatory osteoblastic activity leads to a structurally disorganized mosaic of bone (woven bone), which is mechanically weaker, larger, less compact, more vascular, and more susceptible to fracture than normal adult lamellar bone. PDB5 clinical manifestations include short stature, progressive long bone deformities, fractures, vertebral collapse, skull enlargement, and hyperostosis with progressive deafness. {ECO:0000269 PubMed:12189164}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TNFRSF11B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with TNFRSF11B: view

No data available for Genatlas for TNFRSF11B Gene

Publications for TNFRSF11B Gene

  1. [Osteoprotegerin gene polymorphism and therapeutic response to alendronate in postmenopausal women with osteoporosis]. (PMID: 20137703) Wang C … Zhang ZL (Zhonghua yi xue za zhi 2009) 3 22 44 58
  2. The combinations of polymorphisms in vitamin D receptor, osteoprotegerin and tumour necrosis factor superfamily member 11 genes are associated with bone mineral density. (PMID: 19131500) Mencej-Bedrac S … Marc J (Journal of molecular endocrinology 2009) 3 22 44 58
  3. Multiple genetic loci for bone mineral density and fractures. (PMID: 18445777) Styrkarsdottir U … Stefansson K (The New England journal of medicine 2008) 3 22 44 58
  4. Polymorphisms at the osteoprotegerin and interleukin-6 genes in relation to first-ever stroke. (PMID: 17878722) Strand M … Olsson T (Cerebrovascular diseases (Basel, Switzerland) 2007) 3 22 44 58
  5. Serum levels of osteoprotegerin and osteoprotegerin polymorphisms in Gaucher disease. (PMID: 16512834) Magal I … Elstein D (British journal of haematology 2006) 3 22 44 58

Products for TNFRSF11B Gene

Sources for TNFRSF11B Gene

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