Human Gene TNFSF11 (ENST00000398795.7_6) from GENCODE V47lift37
  Description: TNF superfamily member 11, transcript variant 1 (from RefSeq NM_003701.4)
Gencode Transcript: ENST00000398795.7_6
Gencode Gene: ENSG00000120659.16_10
Transcript (Including UTRs)
   Position: hg19 chr13:43,148,288-43,182,149 Size: 33,862 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr13:43,148,440-43,181,054 Size: 32,615 Coding Exon Count: 5 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:43,148,288-43,182,149)mRNA (may differ from genome)Protein (317 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  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.
Click here to open Exonprimer with this transcript

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: TNFSF11
Diseases sorted by gene-association score: osteopetrosis, autosomal recessive 2* (1229), autosomal recessive malignant osteopetrosis* (247), tnfsf11-related autosomal recessive osteopetrosis* (100), periapical granuloma (30), osteopetrosis (29), root resorption (26), giant cell tumor (23), cherubism (22), multicentric reticulohistiocytosis (21), multicentric carpotarsal osteolysis syndrome (20), periodontal disease (20), osteoporosis (17), dissociative disorder (17), multiple personality disorder (17), dissociative amnesia (17), periapical periodontitis (16), depersonalization disorder (16), bone cancer (16), chronic apical periodontitis (15), hyperostosis, endosteal (15), arthritis (15), osteonecrosis (14), periodontitis (13), joint disorders (12), glucocorticoid-induced osteoporosis (12), ischemic bone disease (12), osteopetrosis, autosomal dominant 2 (12), short stature, brachydactyly, intellectual developmental disability, and seizures (12), paget disease of bone 5, juvenile-onset (11), bone resorption disease (11), bone remodeling disease (11), ameloblastoma (11), rheumatoid arthritis (11), polyarticular onset juvenile idiopathic arthritis (11), pigmented villonodular synovitis (10), tooth resorption (10), osteomyelitis (10), breast leiomyosarcoma (10), synovitis (10), chondroblastoma (9), cholesteatoma (9), cholesteatoma of middle ear (9), breast adenocarcinoma (9), psoriatic arthritis (8), osteolysis, familial expansile (8), villonodular synovitis (8), keratocystic odontogenic tumor (8), paget's disease of bone (8), hemophilic arthropathy (8), arthropathy (7), aneurysmal bone cysts (7), spondyloarthropathy (7), aggressive periodontitis (6), idiopathic hypercalciuria (6), auditory agnosia (6), tooth ankylosis (6), mandibular cancer (6), dependent personality disorder (6), spondyloarthropathy 1 (5), bone inflammation disease (5), osteosarcoma, somatic (5), exhibitionism (5), jaw cancer (4), aortic valve disease 2 (4), multiple myeloma (4), osteoarthritis (4), paraphilia disorder (4), hajdu-cheney syndrome (4), prostate cancer (2), breast cancer (2), mouth disease (2)
* = 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: 5.97 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 8.00 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -68.00152-0.447 Picture PostScript Text
3' UTR -247.201095-0.226 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
IPR006052 - TNF
IPR017355 - TNF_ligand_10/11
IPR008983 - Tumour_necrosis_fac-like

Pfam Domains:
PF00229 - TNF(Tumour Necrosis Factor) family

SCOP Domains:
49842 - TNF-like

ModBase Predicted Comparative 3D Structure on Q5T9Y4
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005125 cytokine activity
GO:0005164 tumor necrosis factor receptor binding
GO:0032813 tumor necrosis factor receptor superfamily binding

Biological Process:
GO:0001503 ossification
GO:0002158 osteoclast proliferation
GO:0006955 immune response
GO:0007257 activation of JUN kinase activity
GO:0009887 animal organ morphogenesis
GO:0010469 regulation of receptor activity
GO:0010628 positive regulation of gene expression
GO:0019722 calcium-mediated signaling
GO:0030316 osteoclast differentiation
GO:0033209 tumor necrosis factor-mediated signaling pathway
GO:0033598 mammary gland epithelial cell proliferation
GO:0036035 osteoclast development
GO:0038001 paracrine signaling
GO:0042327 positive regulation of phosphorylation
GO:0043123 positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0044691 tooth eruption
GO:0045453 bone resorption
GO:0045670 regulation of osteoclast differentiation
GO:0045672 positive regulation of osteoclast differentiation
GO:0046330 positive regulation of JNK cascade
GO:0051091 positive regulation of sequence-specific DNA binding transcription factor activity
GO:0051260 protein homooligomerization
GO:0051466 positive regulation of corticotropin-releasing hormone secretion
GO:0051897 positive regulation of protein kinase B signaling
GO:0055074 calcium ion homeostasis
GO:0060348 bone development
GO:0060749 mammary gland alveolus development
GO:0070371 ERK1 and ERK2 cascade
GO:0071812 positive regulation of fever generation by positive regulation of prostaglandin secretion
GO:0071847 TNFSF11-mediated signaling pathway
GO:1990830 cellular response to leukemia inhibitory factor
GO:2001206 positive regulation of osteoclast development

Cellular Component:
GO:0005615 extracellular space
GO:0005622 intracellular
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  BC040889 - Homo sapiens, clone IMAGE:5742080, mRNA.
AB037599 - Homo sapiens mRNA for sODF/TRANCE, complete cds.
AF053712 - Homo sapiens osteoprotegerin ligand mRNA, complete cds.
JD461788 - Sequence 442812 from Patent EP1572962.
AF019047 - Homo sapiens receptor activator of nuclear factor kappa B ligand (RANKL) mRNA, complete cds.
AB064268 - Homo sapiens hRANKL 3 mRNA for receptor activator of nuclear factor kappa B ligand 3, complete cds.
AB064269 - Homo sapiens hRANKL 1 mRNA for receptor activator of nuclear factor kappa B ligand 1, complete cds.
AB064270 - Homo sapiens hRANKL 2-2 mRNA for receptor activator of nuclear factor kappa B ligand 2-2, complete cds.
JD095954 - Sequence 76978 from Patent EP1572962.
JD444002 - Sequence 425026 from Patent EP1572962.
BC117286 - Homo sapiens tumor necrosis factor (ligand) superfamily, member 11, mRNA (cDNA clone MGC:150895 IMAGE:40125837), complete cds.
BC117288 - Homo sapiens tumor necrosis factor (ligand) superfamily, member 11, mRNA (cDNA clone MGC:150897 IMAGE:40125839), complete cds.
BC074823 - Homo sapiens tumor necrosis factor (ligand) superfamily, member 11, mRNA (cDNA clone MGC:104087 IMAGE:30915538), complete cds.
BC074890 - Homo sapiens tumor necrosis factor (ligand) superfamily, member 11, mRNA (cDNA clone MGC:103863 IMAGE:30915245), complete cds.
KJ892570 - Synthetic construct Homo sapiens clone ccsbBroadEn_01964 TNFSF11 gene, encodes complete protein.
KJ897877 - Synthetic construct Homo sapiens clone ccsbBroadEn_07271 TNFSF11 gene, encodes complete protein.
HQ258604 - Synthetic construct Homo sapiens clone IMAGE:100073147 tumor necrosis factor (ligand) superfamily, member 11 (TNFSF11) gene, encodes complete protein.
AB061227 - Homo sapiens mRNA for hRANKL 2, complete cds.
AF013171 - Homo sapiens TNF-related ligand TRANCE mRNA, partial cds.
JD499510 - Sequence 480534 from Patent EP1572962.
JD043839 - Sequence 24863 from Patent EP1572962.
JD558018 - Sequence 539042 from Patent EP1572962.
JD145944 - Sequence 126968 from Patent EP1572962.
JD300187 - Sequence 281211 from Patent EP1572962.
JD289516 - Sequence 270540 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_ranklPathway - Bone Remodelling

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000398795.1, ENST00000398795.2, ENST00000398795.3, ENST00000398795.4, ENST00000398795.5, ENST00000398795.6, hCG_32838 , NM_003701, Q5T9Y4, Q5T9Y4_HUMAN, TNFSF11 , TNLG6B , uc318zyg.1, uc318zyg.2
UCSC ID: ENST00000398795.7_6
RefSeq Accession: NM_003701.4
Protein: Q5T9Y4

-  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.