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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 TBX3 |
 Gene summary |
| Gene information | Gene symbol | TBX3 | Gene ID | 6926 |
| Gene name | T-box 3 | |
| Synonyms | TBX3-ISO|UMS|XHL | |
| Cytomap | 12q24.21 | |
| Type of gene | protein-coding | |
| Description | T-box transcription factor TBX3T-box protein 3bladder cancer related protein XHL | |
| Modification date | 20180519 | |
| UniProtAcc | O15119 | |
| Context | PubMed: TBX3 [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 |
| TBX3 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 11689487 |
| TBX3 | GO:0007569 | cell aging | 11689487|11748239 |
| TBX3 | GO:0008284 | positive regulation of cell proliferation | 11689487|11748239|12032820 |
| TBX3 | GO:0009887 | animal organ morphogenesis | 9207801 |
| TBX3 | GO:0035136 | forelimb morphogenesis | 9207801 |
| TBX3 | GO:0043066 | negative regulation of apoptotic process | 12032820 |
| TBX3 | GO:0045662 | negative regulation of myoblast differentiation | 12032820 |
| TBX3 | GO:0045787 | positive regulation of cell cycle | 12032820 |
| TBX3 | GO:0045892 | negative regulation of transcription, DNA-templated | 10468588|11689487 |
| TBX3 | GO:0090398 | cellular senescence | 22002537 |
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Exon skipping events across known transcript of Ensembl for TBX3 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 TBX3 |
| 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 TBX3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_96973 | 12 | 115111969:115112640:115114117:115114275:115115384:115115461 | 115114117:115114275 | ENSG00000135111.10 | ENST00000349155.2,ENST00000257566.3 |
| exon_skip_96977 | 12 | 115115396:115115461:115117309:115117456:115118683:115118951 | 115117309:115117456 | ENSG00000135111.10 | ENST00000349155.2 |
| exon_skip_96980 | 12 | 115117309:115117456:115117717:115117777:115118683:115118951 | 115117717:115117777 | ENSG00000135111.10 | ENST00000257566.3 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for TBX3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_96973 | 12 | 115111969:115112640:115114117:115114275:115115384:115115461 | 115114117:115114275 | ENSG00000135111.10 | ENST00000349155.2,ENST00000257566.3 |
| exon_skip_96977 | 12 | 115115396:115115461:115117309:115117456:115118683:115118951 | 115117309:115117456 | ENSG00000135111.10 | ENST00000349155.2 |
| exon_skip_96980 | 12 | 115117309:115117456:115117717:115117777:115118683:115118951 | 115117717:115117777 | ENSG00000135111.10 | ENST00000257566.3 |
| 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 TBX3 |
| 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 |
| ENST00000257566 | 115114117 | 115114275 | Frame-shift |
| ENST00000257566 | 115117717 | 115117777 | 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 |
| ENST00000257566 | 115114117 | 115114275 | Frame-shift |
| ENST00000257566 | 115117717 | 115117777 | In-frame |
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Infer the effects of exon skipping event on protein functional features for TBX3 |
| 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 |
| ENST00000257566 | 4225 | 743 | 115117717 | 115117777 | 1048 | 1107 | 219 | 239 |
| 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 |
| ENST00000257566 | 4225 | 743 | 115117717 | 115117777 | 1048 | 1107 | 219 | 239 |
| 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 |
| O15119 | 219 | 239 | 221 | 240 | Alternative sequence | ID=VSP_006384;Note=In isoform I. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10468588,ECO:0000303|PubMed:9207801;Dbxref=PMID:10468588,PMID:9207801 |
| O15119 | 219 | 239 | 1 | 743 | Chain | ID=PRO_0000184428;Note=T-box transcription factor TBX3 |
| O15119 | 219 | 239 | 107 | 220 | DNA binding | Note=T-box%3B first part;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00201 |
| 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 |
| O15119 | 219 | 239 | 221 | 240 | Alternative sequence | ID=VSP_006384;Note=In isoform I. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10468588,ECO:0000303|PubMed:9207801;Dbxref=PMID:10468588,PMID:9207801 |
| O15119 | 219 | 239 | 1 | 743 | Chain | ID=PRO_0000184428;Note=T-box transcription factor TBX3 |
| O15119 | 219 | 239 | 107 | 220 | DNA binding | Note=T-box%3B first part;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00201 |
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SNVs in the skipped exons for TBX3 |
| - 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. |
TBX3_STAD_exon_skip_96977_psi_boxplot.png |
| - 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 |
| STAD | TCGA-BR-8289-01 | exon_skip_96973 | 115114118 | 115114275 | 115114134 | 115114134 | Frame_Shift_Del | C | - | p.G361fs |
| STAD | TCGA-BR-8289-01 | exon_skip_96973 | 115114118 | 115114275 | 115114134 | 115114134 | Frame_Shift_Del | C | - | p.T362fs |
| LUAD | TCGA-05-4427-01 | exon_skip_96980 | 115117718 | 115117777 | 115117764 | 115117764 | Frame_Shift_Del | G | - | p.P224fs |
| BRCA | TCGA-B6-A0RI-01 | exon_skip_96977 | 115117310 | 115117456 | 115117430 | 115117431 | Frame_Shift_Ins | - | T | p.Y248fs |
| STAD | TCGA-CG-5721-01 | exon_skip_96977 | 115117310 | 115117456 | 115117308 | 115117308 | Splice_Site | A | G | . |
| STAD | TCGA-CG-5721-01 | exon_skip_96977 | 115117310 | 115117456 | 115117308 | 115117308 | Splice_Site | A | G | p.K288_splice |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-CG-5721-01 |
| Cancer type: STAD | |
| ESID: exon_skip_96977 | |
| Skipped exon start: 115117310 | |
| Skipped exon end: 115117456 | |
| Mutation start: 115117308 | |
| Mutation end: 115117308 | |
| Mutation type: Splice_Site | |
| Reference seq: A | |
| Mutation seq: G | |
| AAchange: . | |
| Sample: TCGA-CG-5721-01 |
| Cancer type: STAD | |
| ESID: exon_skip_96977 | |
| Skipped exon start: 115117310 | |
| Skipped exon end: 115117456 | |
| Mutation start: 115117308 | |
| Mutation end: 115117308 | |
| Mutation type: Splice_Site | |
| Reference seq: A | |
| Mutation seq: G | |
| AAchange: p.K288_splice | |
exon_skip_107493_STAD_TCGA-CG-5721-01.png | |
exon_skip_107867_STAD_TCGA-CG-5721-01.png | |
exon_skip_123973_STAD_TCGA-CG-5721-01.png | |
exon_skip_124728_STAD_TCGA-CG-5721-01.png | |
exon_skip_20583_STAD_TCGA-CG-5721-01.png | |
exon_skip_284550_STAD_TCGA-CG-5721-01.png | |
exon_skip_287086_STAD_TCGA-CG-5721-01.png | |
exon_skip_287092_STAD_TCGA-CG-5721-01.png | |
exon_skip_328008_STAD_TCGA-CG-5721-01.png | |
exon_skip_347989_STAD_TCGA-CG-5721-01.png | |
exon_skip_360357_STAD_TCGA-CG-5721-01.png | |
exon_skip_360359_STAD_TCGA-CG-5721-01.png | |
exon_skip_361242_STAD_TCGA-CG-5721-01.png | |
exon_skip_363554_STAD_TCGA-CG-5721-01.png | |
exon_skip_370065_STAD_TCGA-CG-5721-01.png | |
exon_skip_377240_STAD_TCGA-CG-5721-01.png | |
exon_skip_378735_STAD_TCGA-CG-5721-01.png | |
exon_skip_41850_STAD_TCGA-CG-5721-01.png | |
exon_skip_425098_STAD_TCGA-CG-5721-01.png | |
exon_skip_443908_STAD_TCGA-CG-5721-01.png | |
exon_skip_449553_STAD_TCGA-CG-5721-01.png | |
exon_skip_452918_STAD_TCGA-CG-5721-01.png | |
exon_skip_454809_STAD_TCGA-CG-5721-01.png | |
exon_skip_462689_STAD_TCGA-CG-5721-01.png | |
exon_skip_482821_STAD_TCGA-CG-5721-01.png | |
exon_skip_482822_STAD_TCGA-CG-5721-01.png | |
exon_skip_487878_STAD_TCGA-CG-5721-01.png | |
exon_skip_502793_STAD_TCGA-CG-5721-01.png | |
exon_skip_508189_STAD_TCGA-CG-5721-01.png | |
exon_skip_516607_STAD_TCGA-CG-5721-01.png | |
exon_skip_54935_STAD_TCGA-CG-5721-01.png | |
exon_skip_96977_STAD_TCGA-CG-5721-01.png | |
| - 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 |
| SNU1040_LARGE_INTESTINE | 115114118 | 115114275 | 115114225 | 115114225 | Frame_Shift_Del | T | - | p.K331fs |
| MDAPCA2B_PROSTATE | 115114118 | 115114275 | 115114155 | 115114157 | In_Frame_Del | AGA | - | p.S354del |
| GOTO_AUTONOMIC_GANGLIA | 115114118 | 115114275 | 115114161 | 115114163 | In_Frame_Del | AGC | - | p.A352del |
| CCK81_LARGE_INTESTINE | 115114118 | 115114275 | 115114124 | 115114124 | Missense_Mutation | G | T | p.L365I |
| HCT15_LARGE_INTESTINE | 115114118 | 115114275 | 115114126 | 115114126 | Missense_Mutation | T | G | p.N364T |
| C33A_CERVIX | 115114118 | 115114275 | 115114202 | 115114202 | Missense_Mutation | A | G | p.S339P |
| PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT | 115114118 | 115114275 | 115114205 | 115114205 | Missense_Mutation | C | T | p.E338K |
| OSC20_UPPER_AERODIGESTIVE_TRACT | 115114118 | 115114275 | 115114205 | 115114205 | Missense_Mutation | C | G | p.E338Q |
| JHUEM7_ENDOMETRIUM | 115114118 | 115114275 | 115114251 | 115114251 | Missense_Mutation | C | T | p.M322I |
| ISHIKAWAHERAKLIO02ER_ENDOMETRIUM | 115117310 | 115117456 | 115117312 | 115117312 | Missense_Mutation | T | C | p.K288E |
| NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 115117310 | 115117456 | 115117317 | 115117317 | Missense_Mutation | T | A | p.N286I |
| NB1643_AUTONOMIC_GANGLIA | 115117718 | 115117777 | 115117753 | 115117753 | Missense_Mutation | C | T | p.A228T |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TBX3 |
| 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 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TBX3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TBX3 |
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RelatedDrugs for TBX3 |
| 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 TBX3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| TBX3 | C1866994 | Ulnar-mammary syndrome | 2 | CTD_human;ORPHANET;UNIPROT |
| TBX3 | C0038356 | Stomach Neoplasms | 1 | CTD_human |
| TBX3 | C0040128 | Thyroid Diseases | 1 | CTD_human |
| TBX3 | C0040427 | Tooth Abnormalities | 1 | CTD_human |
| TBX3 | C0206762 | Limb Deformities, Congenital | 1 | CTD_human |
| TBX3 | C1458155 | Mammary Neoplasms | 1 | CTD_human |
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