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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 TBC1D20 |
 Gene summary |
| Gene information | Gene symbol | TBC1D20 | Gene ID | 128637 |
| Gene name | TBC1 domain family member 20 | |
| Synonyms | C20orf140|WARBM4 | |
| Cytomap | 20p13 | |
| Type of gene | protein-coding | |
| Description | TBC1 domain family member 20 | |
| Modification date | 20180523 | |
| UniProtAcc | Q96BZ9 | |
| Context | PubMed: TBC1D20 [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 TBC1D20 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 TBC1D20 |
| 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 TBC1D20 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_354207 | 20 | 419751:419939:420891:421033:422231:422333 | 420891:421033 | ENSG00000125875.9 | ENST00000354200.4,ENST00000494633.1,ENST00000461304.1 |
| exon_skip_354216 | 20 | 422500:422687:425693:425774:428532:428718 | 425693:425774 | ENSG00000125875.9 | ENST00000354200.4,ENST00000494633.1,ENST00000461304.1 |
| exon_skip_354219 | 20 | 425693:425774:428532:428718:442979:443175 | 428532:428718 | ENSG00000125875.9 | ENST00000354200.4,ENST00000494633.1,ENST00000461304.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for TBC1D20 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_354207 | 20 | 419751:419939:420891:421033:422231:422333 | 420891:421033 | ENSG00000125875.9 | ENST00000461304.1,ENST00000354200.4,ENST00000494633.1 |
| exon_skip_354216 | 20 | 422500:422687:425693:425774:428532:428718 | 425693:425774 | ENSG00000125875.9 | ENST00000461304.1,ENST00000354200.4,ENST00000494633.1 |
| exon_skip_354219 | 20 | 425693:425774:428532:428718:442979:443175 | 428532:428718 | ENSG00000125875.9 | ENST00000461304.1,ENST00000354200.4,ENST00000494633.1 |
| 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 TBC1D20 |
| 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 |
| ENST00000354200 | 420891 | 421033 | Frame-shift |
| ENST00000354200 | 425693 | 425774 | In-frame |
| ENST00000354200 | 428532 | 428718 | 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 |
| ENST00000354200 | 420891 | 421033 | Frame-shift |
| ENST00000354200 | 425693 | 425774 | In-frame |
| ENST00000354200 | 428532 | 428718 | In-frame |
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Infer the effects of exon skipping event on protein functional features for TBC1D20 |
| 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 |
| ENST00000354200 | 4483 | 403 | 428532 | 428718 | 219 | 404 | 23 | 85 |
| ENST00000354200 | 4483 | 403 | 425693 | 425774 | 405 | 485 | 85 | 112 |
| 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 |
| ENST00000354200 | 4483 | 403 | 428532 | 428718 | 219 | 404 | 23 | 85 |
| ENST00000354200 | 4483 | 403 | 425693 | 425774 | 405 | 485 | 85 | 112 |
| 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 |
| Q96BZ9 | 23 | 85 | 1 | 192 | Alternative sequence | ID=VSP_008100;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q96BZ9 | 23 | 85 | 42 | 44 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4HL4 |
| Q96BZ9 | 23 | 85 | 1 | 403 | Chain | ID=PRO_0000208048;Note=TBC1 domain family member 20 |
| Q96BZ9 | 23 | 85 | 60 | 246 | Domain | Note=Rab-GAP TBC;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00163 |
| Q96BZ9 | 23 | 85 | 26 | 40 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4HL4 |
| Q96BZ9 | 23 | 85 | 47 | 55 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4HL4 |
| Q96BZ9 | 23 | 85 | 63 | 73 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4HL4 |
| Q96BZ9 | 23 | 85 | 79 | 79 | Natural variant | ID=VAR_052543;Note=N->S;Dbxref=dbSNP:rs36088178 |
| Q96BZ9 | 23 | 85 | 57 | 60 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4HLQ |
| Q96BZ9 | 85 | 112 | 1 | 192 | Alternative sequence | ID=VSP_008100;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q96BZ9 | 85 | 112 | 112 | 114 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4HLQ |
| Q96BZ9 | 85 | 112 | 1 | 403 | Chain | ID=PRO_0000208048;Note=TBC1 domain family member 20 |
| Q96BZ9 | 85 | 112 | 60 | 246 | Domain | Note=Rab-GAP TBC;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00163 |
| Q96BZ9 | 85 | 112 | 89 | 92 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4HL4 |
| Q96BZ9 | 85 | 112 | 96 | 104 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4HL4 |
| Q96BZ9 | 85 | 112 | 105 | 109 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4HL4 |
| Q96BZ9 | 85 | 112 | 105 | 105 | Mutagenesis | Note=1000-fold decrease in GAP activity. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23236136;Dbxref=PMID:23236136 |
| Q96BZ9 | 85 | 112 | 105 | 105 | Site | Note=Arginine finger |
| 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 |
| Q96BZ9 | 23 | 85 | 1 | 192 | Alternative sequence | ID=VSP_008100;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q96BZ9 | 23 | 85 | 42 | 44 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4HL4 |
| Q96BZ9 | 23 | 85 | 1 | 403 | Chain | ID=PRO_0000208048;Note=TBC1 domain family member 20 |
| Q96BZ9 | 23 | 85 | 60 | 246 | Domain | Note=Rab-GAP TBC;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00163 |
| Q96BZ9 | 23 | 85 | 26 | 40 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4HL4 |
| Q96BZ9 | 23 | 85 | 47 | 55 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4HL4 |
| Q96BZ9 | 23 | 85 | 63 | 73 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4HL4 |
| Q96BZ9 | 23 | 85 | 79 | 79 | Natural variant | ID=VAR_052543;Note=N->S;Dbxref=dbSNP:rs36088178 |
| Q96BZ9 | 23 | 85 | 57 | 60 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4HLQ |
| Q96BZ9 | 85 | 112 | 1 | 192 | Alternative sequence | ID=VSP_008100;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q96BZ9 | 85 | 112 | 112 | 114 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4HLQ |
| Q96BZ9 | 85 | 112 | 1 | 403 | Chain | ID=PRO_0000208048;Note=TBC1 domain family member 20 |
| Q96BZ9 | 85 | 112 | 60 | 246 | Domain | Note=Rab-GAP TBC;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00163 |
| Q96BZ9 | 85 | 112 | 89 | 92 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4HL4 |
| Q96BZ9 | 85 | 112 | 96 | 104 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4HL4 |
| Q96BZ9 | 85 | 112 | 105 | 109 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4HL4 |
| Q96BZ9 | 85 | 112 | 105 | 105 | Mutagenesis | Note=1000-fold decrease in GAP activity. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23236136;Dbxref=PMID:23236136 |
| Q96BZ9 | 85 | 112 | 105 | 105 | Site | Note=Arginine finger |
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SNVs in the skipped exons for TBC1D20 |
| - 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_354219 | 428533 | 428718 | 428697 | 428697 | Frame_Shift_Del | T | - | p.K31fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_354219 | 428533 | 428718 | 428697 | 428697 | Frame_Shift_Del | T | - | p.K32fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_354219 | 428533 | 428718 | 428704 | 428704 | Frame_Shift_Del | T | - | p.R29fs |
| UCEC | TCGA-BS-A0U7-01 | exon_skip_354219 | 428533 | 428718 | 428590 | 428590 | Nonsense_Mutation | G | A | p.R67* |
| HNSC | TCGA-CV-6961-01 | exon_skip_354219 | 428533 | 428718 | 428599 | 428599 | Nonsense_Mutation | C | A | p.E64* |
| - 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 |
| JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 428533 | 428718 | 428615 | 428631 | Frame_Shift_Del | TCCTTCACTGATAGCCA | - | p.MAISEG53fs |
| SNU1040_LARGE_INTESTINE | 420892 | 421033 | 420977 | 420977 | Missense_Mutation | A | G | p.V228A |
| TGBC11TKB_STOMACH | 425694 | 425774 | 425766 | 425766 | Missense_Mutation | G | T | p.L89I |
| GP2D_LARGE_INTESTINE | 428533 | 428718 | 428589 | 428589 | Missense_Mutation | C | T | p.R67Q |
| GP5D_LARGE_INTESTINE | 428533 | 428718 | 428589 | 428589 | Missense_Mutation | C | T | p.R67Q |
| EW1_BONE | 428533 | 428718 | 428712 | 428712 | Missense_Mutation | T | C | p.N26S |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TBC1D20 |
| 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 TBC1D20 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TBC1D20 |
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RelatedDrugs for TBC1D20 |
| 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 TBC1D20 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
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