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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for TNFRSF11B |
 Gene summary |
| Gene information | Gene symbol | TNFRSF11B | Gene ID | 4982 |
| Gene name | TNF receptor superfamily member 11b | |
| Synonyms | OCIF|OPG|PDB5|TR1 | |
| Cytomap | 8q24.12 | |
| Type of gene | protein-coding | |
| Description | tumor necrosis factor receptor superfamily member 11Bosteoclastogenesis inhibitory factorosteoprotegerintumor necrosis factor receptor superfamily, member 11b | |
| Modification date | 20180527 | |
| UniProtAcc | O00300 | |
| Context | PubMed: TNFRSF11B [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
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Exon skipping events across known transcript of Ensembl for TNFRSF11B from UCSC genome browser |
| Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Gene isoform structures and expression levels for TNFRSF11B |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for TNFRSF11B |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_492064 | 8 | 119936713:119937001:119938732:119938957:119940976:119941168 | 119938732:119938957 | ENSG00000164761.4 | ENST00000521597.1,ENST00000297350.4 |
| exon_skip_492066 | 8 | 119938748:119938957:119940976:119941168:119945169:119945539 | 119940976:119941168 | ENSG00000164761.4 | ENST00000297350.4 |
| exon_skip_492068 | 8 | 119940976:119941168:119942726:119943007:119945169:119945539 | 119942726:119943007 | ENSG00000164761.4 | ENST00000517352.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for TNFRSF11B |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_492064 | 8 | 119936713:119937001:119938732:119938957:119940976:119941168 | 119938732:119938957 | ENSG00000164761.4 | ENST00000297350.4,ENST00000521597.1 |
| exon_skip_492066 | 8 | 119938748:119938957:119940976:119941168:119945169:119945539 | 119940976:119941168 | ENSG00000164761.4 | ENST00000297350.4 |
| exon_skip_492068 | 8 | 119940976:119941168:119942726:119943007:119945169:119945539 | 119942726:119943007 | ENSG00000164761.4 | ENST00000517352.1 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for TNFRSF11B |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000297350 | 119938732 | 119938957 | In-frame |
| ENST00000297350 | 119940976 | 119941168 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000297350 | 119938732 | 119938957 | In-frame |
| ENST00000297350 | 119940976 | 119941168 | In-frame |
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Infer the effects of exon skipping event on protein functional features for TNFRSF11B |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000297350 | 2419 | 401 | 119940976 | 119941168 | 780 | 971 | 133 | 197 |
| ENST00000297350 | 2419 | 401 | 119938732 | 119938957 | 972 | 1196 | 197 | 272 |
| Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000297350 | 2419 | 401 | 119940976 | 119941168 | 780 | 971 | 133 | 197 |
| ENST00000297350 | 2419 | 401 | 119938732 | 119938957 | 972 | 1196 | 197 | 272 |
| Lost protein functional features of individual exon skipping events in TCGA. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| O00300 | 133 | 197 | 136 | 138 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3URF |
| O00300 | 133 | 197 | 141 | 144 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3URF |
| O00300 | 133 | 197 | 155 | 157 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3URF |
| O00300 | 133 | 197 | 167 | 171 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3URF |
| O00300 | 133 | 197 | 22 | 401 | Chain | ID=PRO_0000034587;Note=Tumor necrosis factor receptor superfamily member 11B |
| O00300 | 133 | 197 | 124 | 142 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00206,ECO:0000269|PubMed:22664871;Dbxref=PMID:22664871 |
| O00300 | 133 | 197 | 145 | 160 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00206,ECO:0000269|PubMed:22664871;Dbxref=PMID:22664871 |
| O00300 | 133 | 197 | 166 | 185 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00206,ECO:0000269|PubMed:22664871;Dbxref=PMID:22664871 |
| O00300 | 133 | 197 | 152 | 152 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O00300 | 133 | 197 | 165 | 165 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O00300 | 133 | 197 | 178 | 178 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:22664871;Dbxref=PMID:22664871 |
| O00300 | 133 | 197 | 182 | 182 | Natural variant | ID=VAR_019413;Note=In PDB5. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12189164;Dbxref=PMID:12189164 |
| O00300 | 133 | 197 | 107 | 142 | Repeat | Note=TNFR-Cys 3 |
| O00300 | 133 | 197 | 145 | 185 | Repeat | Note=TNFR-Cys 4 |
| O00300 | 197 | 272 | 22 | 401 | Chain | ID=PRO_0000034587;Note=Tumor necrosis factor receptor superfamily member 11B |
| O00300 | 197 | 272 | 198 | 269 | Domain | Note=Death 1 |
| O00300 | 197 | 272 | 270 | 365 | Domain | Note=Death 2 |
| O00300 | 197 | 272 | 263 | 263 | Sequence conflict | Note=D->A;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Lost protein functional features of individual exon skipping events in GTEx. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| O00300 | 133 | 197 | 136 | 138 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3URF |
| O00300 | 133 | 197 | 141 | 144 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3URF |
| O00300 | 133 | 197 | 155 | 157 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3URF |
| O00300 | 133 | 197 | 167 | 171 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3URF |
| O00300 | 133 | 197 | 22 | 401 | Chain | ID=PRO_0000034587;Note=Tumor necrosis factor receptor superfamily member 11B |
| O00300 | 133 | 197 | 124 | 142 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00206,ECO:0000269|PubMed:22664871;Dbxref=PMID:22664871 |
| O00300 | 133 | 197 | 145 | 160 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00206,ECO:0000269|PubMed:22664871;Dbxref=PMID:22664871 |
| O00300 | 133 | 197 | 166 | 185 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00206,ECO:0000269|PubMed:22664871;Dbxref=PMID:22664871 |
| O00300 | 133 | 197 | 152 | 152 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O00300 | 133 | 197 | 165 | 165 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O00300 | 133 | 197 | 178 | 178 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:22664871;Dbxref=PMID:22664871 |
| O00300 | 133 | 197 | 182 | 182 | Natural variant | ID=VAR_019413;Note=In PDB5. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12189164;Dbxref=PMID:12189164 |
| O00300 | 133 | 197 | 107 | 142 | Repeat | Note=TNFR-Cys 3 |
| O00300 | 133 | 197 | 145 | 185 | Repeat | Note=TNFR-Cys 4 |
| O00300 | 197 | 272 | 22 | 401 | Chain | ID=PRO_0000034587;Note=Tumor necrosis factor receptor superfamily member 11B |
| O00300 | 197 | 272 | 198 | 269 | Domain | Note=Death 1 |
| O00300 | 197 | 272 | 270 | 365 | Domain | Note=Death 2 |
| O00300 | 197 | 272 | 263 | 263 | Sequence conflict | Note=D->A;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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SNVs in the skipped exons for TNFRSF11B |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_492066 | 119940977 | 119941168 | 119940987 | 119940987 | Frame_Shift_Del | T | - | p.K194fs |
| SKCM | TCGA-D9-A3Z1-06 | exon_skip_492064 | 119938733 | 119938957 | 119938736 | 119938736 | Nonsense_Mutation | G | A | p.Q272* |
| SKCM | TCGA-D9-A3Z1-06 | exon_skip_492064 | 119938733 | 119938957 | 119938736 | 119938736 | Nonsense_Mutation | G | A | p.Q272X |
| SKCM | TCGA-W3-A824-06 | exon_skip_492064 | 119938733 | 119938957 | 119938772 | 119938772 | Nonsense_Mutation | G | A | p.Q260* |
| BRCA | TCGA-A1-A0SO-01 | exon_skip_492064 | 119938733 | 119938957 | 119938847 | 119938847 | Nonsense_Mutation | C | A | p.E235* |
| STAD | TCGA-BR-8683-01 | exon_skip_492066 | 119940977 | 119941168 | 119941043 | 119941043 | Nonsense_Mutation | T | A | p.K176* |
| STAD | TCGA-BR-8683-01 | exon_skip_492066 | 119940977 | 119941168 | 119941043 | 119941043 | Nonsense_Mutation | T | A | p.K176X |
| LGG | TCGA-DB-A75K-01 | exon_skip_492066 | 119940977 | 119941168 | 119941085 | 119941085 | Nonsense_Mutation | T | A | p.K162* |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| LAN2_AUTONOMIC_GANGLIA | 119938733 | 119938957 | 119938746 | 119938746 | Missense_Mutation | C | A | p.K268N |
| HEC251_ENDOMETRIUM | 119938733 | 119938957 | 119938757 | 119938757 | Missense_Mutation | C | A | p.D265Y |
| JHU011_UPPER_AERODIGESTIVE_TRACT | 119938733 | 119938957 | 119938801 | 119938801 | Missense_Mutation | G | A | p.T250I |
| A375_SKIN | 119938733 | 119938957 | 119938881 | 119938881 | Missense_Mutation | C | A | p.L223F |
| OC316_OVARY | 119938733 | 119938957 | 119938921 | 119938921 | Missense_Mutation | G | A | p.A210V |
| OC314_OVARY | 119938733 | 119938957 | 119938921 | 119938921 | Missense_Mutation | G | A | p.A210V |
| EPLC272H_LUNG | 119940977 | 119941168 | 119941010 | 119941010 | Missense_Mutation | C | T | p.G187R |
| L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 119940977 | 119941168 | 119941010 | 119941010 | Missense_Mutation | C | T | p.G187R |
| SNU175_LARGE_INTESTINE | 119940977 | 119941168 | 119941122 | 119941122 | Missense_Mutation | G | T | p.F149L |
| HDMYZ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 119940977 | 119941168 | 119941139 | 119941139 | Missense_Mutation | T | C | p.R144G |
| HLE_LIVER | 119940977 | 119941168 | 119941145 | 119941145 | Missense_Mutation | A | T | p.C142S |
| LN215_CENTRAL_NERVOUS_SYSTEM | 119940977 | 119941168 | 119941156 | 119941156 | Missense_Mutation | C | T | p.R138Q |
| GCT_SOFT_TISSUE | 119940977 | 119941168 | 119941156 | 119941156 | Missense_Mutation | C | T | p.R138Q |
| SH10TC_STOMACH | 119940977 | 119941168 | 119941142 | 119941142 | Nonsense_Mutation | T | A | p.K143* |
| KYSE30_OESOPHAGUS | 119940977 | 119941168 | 119941168 | 119941168 | Splice_Site | C | T | p.G134E |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TNFRSF11B |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
| exon_skip_492068 | 8 | 119940976:119941168:119942726:119943007:119945169:119945539 | 119942726:119943007 | ENST00000517352.1 | THCA | rs6469786 | chr8:119942787 | G/T | 5.44e-04 |
| exon_skip_492068 | 8 | 119940976:119941168:119942726:119943007:119945169:119945539 | 119942726:119943007 | ENST00000517352.1 | THCA | rs6469787 | chr8:119942830 | T/C | 1.58e-03 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TNFRSF11B |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TNFRSF11B |
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RelatedDrugs for TNFRSF11B |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for TNFRSF11B |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| TNFRSF11B | C0005974 | Bone Resorption | 3 | CTD_human |
| TNFRSF11B | C0003873 | Rheumatoid Arthritis | 1 | CTD_human |
| TNFRSF11B | C0020429 | Hyperalgesia | 1 | CTD_human |
| TNFRSF11B | C0020437 | Hypercalcemia | 1 | CTD_human |
| TNFRSF11B | C0021368 | Inflammation | 1 | CTD_human |
| TNFRSF11B | C0029456 | Osteoporosis | 1 | CTD_human;HPO |
| TNFRSF11B | C0041948 | Uremia | 1 | CTD_human |
| TNFRSF11B | C0221204 | Lytic lesion | 1 | CTD_human |
| TNFRSF11B | C0993582 | Arthritis, Experimental | 1 | CTD_human |
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