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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for TFEB |
 Gene summary |
| Gene information | Gene symbol | TFEB | Gene ID | 7942 |
| Gene name | transcription factor EB | |
| Synonyms | ALPHATFEB|BHLHE35|TCFEB | |
| Cytomap | 6p21.1 | |
| Type of gene | protein-coding | |
| Description | transcription factor EBT-cell transcription factor EBclass E basic helix-loop-helix protein 35 | |
| Modification date | 20200329 | |
| UniProtAcc | A0A024RCY3, A0A1B0GXL9, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| TFEB | GO:0010468 | regulation of gene expression | 27278822 |
| TFEB | GO:0045893 | positive regulation of transcription, DNA-templated | 27278822|29146937 |
| TFEB | GO:0045944 | positive regulation of transcription by RNA polymerase II | 19556463 |
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Gene structures and expression levels for TFEB |
| Skipped exons in the ROSMAP, MSBB, and Mayo 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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ENSG00000112561
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| PG | UP | ENST00000416140.5 | TFEB-208:protein_coding:TFEB | 7.880411e+00 | 8.968946e-01 | 5.338645e-05 | 1.723488e-03 |
| PG | UP | ENST00000425401.1 | TFEB-213:protein_coding:TFEB | 8.204578e-01 | 1.071854e+00 | 1.404187e-03 | 1.859493e-02 |
| CB | DOWN | ENST00000406563.6 | TFEB-207:protein_coding:TFEB | 3.128478e+02 | -8.977906e-01 | 9.166603e-11 | 5.881363e-09 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for TFEB |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_101782 | chr6 | 41686090:41686237:41687094:41687169:41687753:41687809 | 41687094:41687169 |
| exon_skip_138452 | chr6 | 41691178:41691235:41732649:41732767:41734900:41735060 | 41732649:41732767 |
| exon_skip_144530 | chr6 | 41687910:41688028:41689731:41689811:41691001:41691042 | 41689731:41689811 |
| exon_skip_60369 | chr6 | 41689731:41689811:41690663:41690917:41691001:41691042 | 41690663:41690917 |
| exon_skip_8267 | chr6 | 41691178:41691235:41705647:41705752:41705917:41705940 | 41705647:41705752 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_101782 | Mayo_CB | 6.228049e-01 | 8.477922e-01 | -2.249873e-01 | 5.604914e-08 |
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Open reading frame (ORF) annotation in the exon skipping event for TFEB |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000230323 | 41687094 | 41687169 | Frame-shift |
| ENST00000373033 | 41687094 | 41687169 | Frame-shift |
| ENST00000403298 | 41687094 | 41687169 | Frame-shift |
| ENST00000230323 | 41690663 | 41690917 | In-frame |
| ENST00000373033 | 41690663 | 41690917 | In-frame |
| ENST00000403298 | 41690663 | 41690917 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000230323 | 41732649 | 41732767 | 3UTR-3UTR |
| ENST00000230323 | 41687094 | 41687169 | Frame-shift |
| ENST00000373033 | 41687094 | 41687169 | Frame-shift |
| ENST00000403298 | 41687094 | 41687169 | Frame-shift |
| ENST00000230323 | 41690663 | 41690917 | In-frame |
| ENST00000373033 | 41690663 | 41690917 | In-frame |
| ENST00000403298 | 41690663 | 41690917 | In-frame |
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Infer the effects of exon skipping event on protein functional features for TFEB |
p-ENSG00000112561_img4.png |
| Loci of skipped exons in ROSMAP 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 |
| ENST00000230323 | 2371 | 476 | 41690663 | 41690917 | 516 | 769 | 71 | 155 |
| ENST00000373033 | 2348 | 476 | 41690663 | 41690917 | 495 | 748 | 71 | 155 |
| ENST00000403298 | 2179 | 476 | 41690663 | 41690917 | 325 | 578 | 71 | 155 |
| Loci of skipped exons in MSBB 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 |
| Loci of skipped exons in Mayo 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 |
| ENST00000230323 | 2371 | 476 | 41690663 | 41690917 | 516 | 769 | 71 | 155 |
| ENST00000373033 | 2348 | 476 | 41690663 | 41690917 | 495 | 748 | 71 | 155 |
| ENST00000403298 | 2179 | 476 | 41690663 | 41690917 | 325 | 578 | 71 | 155 |
| Lost protein functional features of individual exon skipping events in ROSMAP. |
| 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 |
| P19484 | 71 | 155 | 72 | 156 | Alternative sequence | ID=VSP_002159;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:2115126;Dbxref=PMID:15489334,PMID:2115126 |
| P19484 | 71 | 155 | 72 | 156 | Alternative sequence | ID=VSP_002159;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:2115126;Dbxref=PMID:15489334,PMID:2115126 |
| P19484 | 71 | 155 | 72 | 156 | Alternative sequence | ID=VSP_002159;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:2115126;Dbxref=PMID:15489334,PMID:2115126 |
| P19484 | 71 | 155 | 1 | 476 | Chain | ID=PRO_0000127473;Note=Transcription factor EB |
| P19484 | 71 | 155 | 1 | 476 | Chain | ID=PRO_0000127473;Note=Transcription factor EB |
| P19484 | 71 | 155 | 1 | 476 | Chain | ID=PRO_0000127473;Note=Transcription factor EB |
| P19484 | 71 | 155 | 109 | 109 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210 |
| P19484 | 71 | 155 | 109 | 109 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210 |
| P19484 | 71 | 155 | 109 | 109 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210 |
| P19484 | 71 | 155 | 114 | 114 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210 |
| P19484 | 71 | 155 | 114 | 114 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210 |
| P19484 | 71 | 155 | 114 | 114 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210 |
| P19484 | 71 | 155 | 122 | 122 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:23186163;Dbxref=PMID:20068231,PMID:23186163 |
| P19484 | 71 | 155 | 122 | 122 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:23186163;Dbxref=PMID:20068231,PMID:23186163 |
| P19484 | 71 | 155 | 122 | 122 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:23186163;Dbxref=PMID:20068231,PMID:23186163 |
| P19484 | 71 | 155 | 138 | 138 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231 |
| P19484 | 71 | 155 | 138 | 138 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231 |
| P19484 | 71 | 155 | 138 | 138 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231 |
| P19484 | 71 | 155 | 142 | 142 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231 |
| P19484 | 71 | 155 | 142 | 142 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231 |
| P19484 | 71 | 155 | 142 | 142 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231 |
| P19484 | 71 | 155 | 106 | 106 | Sequence conflict | Note=A->AA;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P19484 | 71 | 155 | 106 | 106 | Sequence conflict | Note=A->AA;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P19484 | 71 | 155 | 106 | 106 | Sequence conflict | Note=A->AA;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P19484 | 71 | 155 | 113 | 141 | Sequence conflict | Note=GSPKPPPAASPGVRAGHVLSSSAGNSAPN->ALRNPHQPPPQGCELDTCCPPPLATVLPI;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P19484 | 71 | 155 | 113 | 141 | Sequence conflict | Note=GSPKPPPAASPGVRAGHVLSSSAGNSAPN->ALRNPHQPPPQGCELDTCCPPPLATVLPI;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P19484 | 71 | 155 | 113 | 141 | Sequence conflict | Note=GSPKPPPAASPGVRAGHVLSSSAGNSAPN->ALRNPHQPPPQGCELDTCCPPPLATVLPI;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Lost protein functional features of individual exon skipping events in MSBB. |
| 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 |
| Lost protein functional features of individual exon skipping events in Mayo. |
| 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 |
| P19484 | 71 | 155 | 72 | 156 | Alternative sequence | ID=VSP_002159;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:2115126;Dbxref=PMID:15489334,PMID:2115126 |
| P19484 | 71 | 155 | 72 | 156 | Alternative sequence | ID=VSP_002159;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:2115126;Dbxref=PMID:15489334,PMID:2115126 |
| P19484 | 71 | 155 | 72 | 156 | Alternative sequence | ID=VSP_002159;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:2115126;Dbxref=PMID:15489334,PMID:2115126 |
| P19484 | 71 | 155 | 1 | 476 | Chain | ID=PRO_0000127473;Note=Transcription factor EB |
| P19484 | 71 | 155 | 1 | 476 | Chain | ID=PRO_0000127473;Note=Transcription factor EB |
| P19484 | 71 | 155 | 1 | 476 | Chain | ID=PRO_0000127473;Note=Transcription factor EB |
| P19484 | 71 | 155 | 109 | 109 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210 |
| P19484 | 71 | 155 | 109 | 109 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210 |
| P19484 | 71 | 155 | 109 | 109 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210 |
| P19484 | 71 | 155 | 114 | 114 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210 |
| P19484 | 71 | 155 | 114 | 114 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210 |
| P19484 | 71 | 155 | 114 | 114 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210 |
| P19484 | 71 | 155 | 122 | 122 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:23186163;Dbxref=PMID:20068231,PMID:23186163 |
| P19484 | 71 | 155 | 122 | 122 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:23186163;Dbxref=PMID:20068231,PMID:23186163 |
| P19484 | 71 | 155 | 122 | 122 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:23186163;Dbxref=PMID:20068231,PMID:23186163 |
| P19484 | 71 | 155 | 138 | 138 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231 |
| P19484 | 71 | 155 | 138 | 138 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231 |
| P19484 | 71 | 155 | 138 | 138 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231 |
| P19484 | 71 | 155 | 142 | 142 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231 |
| P19484 | 71 | 155 | 142 | 142 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231 |
| P19484 | 71 | 155 | 142 | 142 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231 |
| P19484 | 71 | 155 | 106 | 106 | Sequence conflict | Note=A->AA;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P19484 | 71 | 155 | 106 | 106 | Sequence conflict | Note=A->AA;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P19484 | 71 | 155 | 106 | 106 | Sequence conflict | Note=A->AA;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P19484 | 71 | 155 | 113 | 141 | Sequence conflict | Note=GSPKPPPAASPGVRAGHVLSSSAGNSAPN->ALRNPHQPPPQGCELDTCCPPPLATVLPI;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P19484 | 71 | 155 | 113 | 141 | Sequence conflict | Note=GSPKPPPAASPGVRAGHVLSSSAGNSAPN->ALRNPHQPPPQGCELDTCCPPPLATVLPI;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P19484 | 71 | 155 | 113 | 141 | Sequence conflict | Note=GSPKPPPAASPGVRAGHVLSSSAGNSAPN->ALRNPHQPPPQGCELDTCCPPPLATVLPI;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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3'-UTR located exon skipping events that lost miRNA binding sites in TFEB |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
| Mayo | ENST00000230323 | 41732649 | 41732767 | hsa-miR-6072 | chr6:41732726-41732733 | 8mer-1a | chr6:41732714-41732741 | 167.00 | -34.69 |
| Mayo | ENST00000230323 | 41732649 | 41732767 | hsa-miR-6761-5p | chr6:41732720-41732727 | 8mer-1a | chr6:41732714-41732741 | 167.00 | -34.69 |
| Mayo | ENST00000230323 | 41732649 | 41732767 | hsa-miR-570-3p | chr6:41732704-41732711 | 8mer-1a | chr6:41732701-41732721 | 157.00 | -25.63 |
| Mayo | ENST00000230323 | 41732649 | 41732767 | hsa-miR-6891-3p | chr6:41732726-41732733 | 8mer-1a | chr6:41732714-41732741 | 167.00 | -34.69 |
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SNVs in the skipped exons for TFEB |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - 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 |
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AD stage-associated exon skippint events for TFEB |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TFEB |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| HCC | exon_skip_101782 | rs9471637 | chr6:41724957 | 1.505024e-04 | 1.285906e-02 |
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Correlation with RNA binding proteins (RBPs) for TFEB |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | RBM3 | exon_skip_101782 | 4.558098e-01 | 1.566024e-09 |
| CB | PCBP1 | exon_skip_101782 | -4.409218e-01 | 5.999774e-09 |
| CB | SNRPA | exon_skip_101782 | -4.151143e-01 | 5.309809e-08 |
| CB | NUP42 | exon_skip_101782 | 4.546406e-01 | 1.744345e-09 |
| DLPFC | RBM3 | exon_skip_101782 | 4.240786e-01 | 8.575360e-16 |
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RelatedDrugs for TFEB |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for TFEB |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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