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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in TCGA

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Exon skipping events with PSIs in GTEx

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Open reading frame (ORF) annotation in the exon skipping event

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Exon skipping events in the canonical protein sequence

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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for TFEB

check button Gene summary
Gene informationGene symbol

TFEB

Gene ID

7942

Gene nametranscription factor EB
SynonymsALPHATFEB|BHLHE35|TCFEB
Cytomap

6p21.1

Type of geneprotein-coding
Descriptiontranscription factor EBT-cell transcription factor EBclass E basic helix-loop-helix protein 35
Modification date20180522
UniProtAcc

P19484

ContextPubMed: TFEB [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
TFEB

GO:0045944

positive regulation of transcription by RNA polymerase II

19556463


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Exon skipping events across known transcript of Ensembl for TFEB from UCSC genome browser

check buttonSkipped 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.
all structure

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Gene isoform structures and expression levels for TFEB

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


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Exon skipping events with PSIs in TCGA for TFEB

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_459371641653827:41653975:41654831:41654907:41655490:4165554741654831:41654907ENSG00000112561.13ENST00000406563.2,ENST00000230323.4,ENST00000358871.2,ENST00000420312.1,ENST00000403298.4,ENST00000343317.6,ENST00000373033.1
exon_skip_459372641657468:41657549:41658400:41658655:41658738:4165878041658400:41658655ENSG00000112561.13ENST00000416140.1,ENST00000230323.4,ENST00000358871.2,ENST00000403298.4,ENST00000419396.1,ENST00000419574.1,ENST00000394283.1,ENST00000343317.6,ENST00000373033.1
exon_skip_459375641658915:41658973:41673384:41673490:41673654:4167367841673384:41673490ENSG00000112561.13ENST00000445214.1
exon_skip_459377641658915:41658973:41700386:41700477:41701401:4170142841700386:41700477ENSG00000112561.13ENST00000424495.1
exon_skip_459380641658915:41658973:41700386:41700505:41702637:4170279841700386:41700505ENSG00000112561.13ENST00000230323.4,ENST00000420312.1

check button PSI values of skipped exons in TCGA.
psi tcga

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Exon skipping events with PSIs in GTEx for TFEB

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_459371641653827:41653975:41654831:41654907:41655490:4165554741654831:41654907ENSG00000112561.13ENST00000406563.2,ENST00000343317.6,ENST00000230323.4,ENST00000358871.2,ENST00000403298.4,ENST00000420312.1,ENST00000373033.1
exon_skip_459372641657468:41657549:41658400:41658655:41658738:4165878041658400:41658655ENSG00000112561.13ENST00000343317.6,ENST00000230323.4,ENST00000358871.2,ENST00000403298.4,ENST00000373033.1,ENST00000394283.1,ENST00000419396.1,ENST00000416140.1,ENST00000419574.1
exon_skip_459375641658915:41658973:41673384:41673490:41673654:4167367841673384:41673490ENSG00000112561.13ENST00000445214.1
exon_skip_459377641658915:41658973:41700386:41700477:41701401:4170142841700386:41700477ENSG00000112561.13ENST00000424495.1
exon_skip_459380641658915:41658973:41700386:41700505:41702637:4170279841700386:41700505ENSG00000112561.13ENST00000230323.4,ENST00000420312.1

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for TFEB

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST0000023032341700386417005053UTR-3UTR
ENST000002303234165483141654907Frame-shift
ENST000003730334165483141654907Frame-shift
ENST000004032984165483141654907Frame-shift
ENST000002303234165840041658655In-frame
ENST000003730334165840041658655In-frame
ENST000004032984165840041658655In-frame

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST0000023032341700386417005053UTR-3UTR
ENST000002303234165483141654907Frame-shift
ENST000003730334165483141654907Frame-shift
ENST000004032984165483141654907Frame-shift
ENST000002303234165840041658655In-frame
ENST000003730334165840041658655In-frame
ENST000004032984165840041658655In-frame

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Infer the effects of exon skipping event on protein functional features for TFEB

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000002303232371476416584004165865551677071156
ENST000003730332348476416584004165865549574971156
ENST000004032982204476416584004165865535060471156

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000002303232371476416584004165865551677071156
ENST000003730332348476416584004165865549574971156
ENST000004032982204476416584004165865535060471156

check button 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 featureDescription of feature
P194847115672156Alternative sequenceID=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
P194847115672156Alternative sequenceID=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
P194847115672156Alternative sequenceID=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
P19484711561476ChainID=PRO_0000127473;Note=Transcription factor EB
P19484711561476ChainID=PRO_0000127473;Note=Transcription factor EB
P19484711561476ChainID=PRO_0000127473;Note=Transcription factor EB
P1948471156109109Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210
P1948471156109109Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210
P1948471156109109Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210
P1948471156114114Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210
P1948471156114114Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210
P1948471156114114Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210
P1948471156122122Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:23186163;Dbxref=PMID:20068231,PMID:23186163
P1948471156122122Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:23186163;Dbxref=PMID:20068231,PMID:23186163
P1948471156122122Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:23186163;Dbxref=PMID:20068231,PMID:23186163
P1948471156138138Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231
P1948471156138138Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231
P1948471156138138Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231
P1948471156142142Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231
P1948471156142142Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231
P1948471156142142Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231
P1948471156156165RegionNote=Strong transcription activation domain;Ontology_term=ECO:0000255;evidence=ECO:0000255
P1948471156156165RegionNote=Strong transcription activation domain;Ontology_term=ECO:0000255;evidence=ECO:0000255
P1948471156156165RegionNote=Strong transcription activation domain;Ontology_term=ECO:0000255;evidence=ECO:0000255
P1948471156106106Sequence conflictNote=A->AA;Ontology_term=ECO:0000305;evidence=ECO:0000305
P1948471156106106Sequence conflictNote=A->AA;Ontology_term=ECO:0000305;evidence=ECO:0000305
P1948471156106106Sequence conflictNote=A->AA;Ontology_term=ECO:0000305;evidence=ECO:0000305
P1948471156113141Sequence conflictNote=GSPKPPPAASPGVRAGHVLSSSAGNSAPN->ALRNPHQPPPQGCELDTCCPPPLATVLPI;Ontology_term=ECO:0000305;evidence=ECO:0000305
P1948471156113141Sequence conflictNote=GSPKPPPAASPGVRAGHVLSSSAGNSAPN->ALRNPHQPPPQGCELDTCCPPPLATVLPI;Ontology_term=ECO:0000305;evidence=ECO:0000305
P1948471156113141Sequence conflictNote=GSPKPPPAASPGVRAGHVLSSSAGNSAPN->ALRNPHQPPPQGCELDTCCPPPLATVLPI;Ontology_term=ECO:0000305;evidence=ECO:0000305


check button 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 featureDescription of feature
P194847115672156Alternative sequenceID=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
P194847115672156Alternative sequenceID=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
P194847115672156Alternative sequenceID=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
P19484711561476ChainID=PRO_0000127473;Note=Transcription factor EB
P19484711561476ChainID=PRO_0000127473;Note=Transcription factor EB
P19484711561476ChainID=PRO_0000127473;Note=Transcription factor EB
P1948471156109109Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210
P1948471156109109Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210
P1948471156109109Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210
P1948471156114114Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210
P1948471156114114Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210
P1948471156114114Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9R210
P1948471156122122Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:23186163;Dbxref=PMID:20068231,PMID:23186163
P1948471156122122Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:23186163;Dbxref=PMID:20068231,PMID:23186163
P1948471156122122Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:23186163;Dbxref=PMID:20068231,PMID:23186163
P1948471156138138Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231
P1948471156138138Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231
P1948471156138138Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231
P1948471156142142Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231
P1948471156142142Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231
P1948471156142142Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231
P1948471156156165RegionNote=Strong transcription activation domain;Ontology_term=ECO:0000255;evidence=ECO:0000255
P1948471156156165RegionNote=Strong transcription activation domain;Ontology_term=ECO:0000255;evidence=ECO:0000255
P1948471156156165RegionNote=Strong transcription activation domain;Ontology_term=ECO:0000255;evidence=ECO:0000255
P1948471156106106Sequence conflictNote=A->AA;Ontology_term=ECO:0000305;evidence=ECO:0000305
P1948471156106106Sequence conflictNote=A->AA;Ontology_term=ECO:0000305;evidence=ECO:0000305
P1948471156106106Sequence conflictNote=A->AA;Ontology_term=ECO:0000305;evidence=ECO:0000305
P1948471156113141Sequence conflictNote=GSPKPPPAASPGVRAGHVLSSSAGNSAPN->ALRNPHQPPPQGCELDTCCPPPLATVLPI;Ontology_term=ECO:0000305;evidence=ECO:0000305
P1948471156113141Sequence conflictNote=GSPKPPPAASPGVRAGHVLSSSAGNSAPN->ALRNPHQPPPQGCELDTCCPPPLATVLPI;Ontology_term=ECO:0000305;evidence=ECO:0000305
P1948471156113141Sequence conflictNote=GSPKPPPAASPGVRAGHVLSSSAGNSAPN->ALRNPHQPPPQGCELDTCCPPPLATVLPI;Ontology_term=ECO:0000305;evidence=ECO:0000305


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SNVs in the skipped exons for TFEB

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

check button - Differential PSIs between mutated versus non-mutated samples.
TFEB_LIHC_exon_skip_459372_psi_boxplot.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
COADTCGA-A6-2676-01exon_skip_459371
41654832416549074165489641654896Nonsense_MutationGAp.R247X
LIHCTCGA-RC-A6M6-01exon_skip_459372
41658401416586554165840041658400Splice_SiteCT.

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
TFEB_41657468_41657549_41658400_41658655_41658738_41658780_TCGA-RC-A6M6-01Sample: TCGA-RC-A6M6-01
Cancer type: LIHC
ESID: exon_skip_459372
Skipped exon start: 41658401
Skipped exon end: 41658655
Mutation start: 41658400
Mutation end: 41658400
Mutation type: Splice_Site
Reference seq: C
Mutation seq: T
AAchange: .
exon_skip_363591_LIHC_TCGA-RC-A6M6-01.png
boxplot
exon_skip_459372_LIHC_TCGA-RC-A6M6-01.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
KATOIII_STOMACH41654832416549074165488441654884Missense_MutationTCp.I251V
CW2_LARGE_INTESTINE41658401416586554165845341658453Missense_MutationGAp.A139V
CPCN_LUNG41658401416586554165846641658466Missense_MutationCTp.A135T
MHHPREB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE41658401416586554165846641658466Missense_MutationCTp.A135T

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TFEB

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value
exon_skip_459372641657468:41657549:41658400:41658655:41658738:4165878041658400:41658655ENST00000416140.1,ENST00000230323.4,ENST00000358871.2,ENST00000403298.4,ENST00000419396.1,ENST00000419574.1,ENST00000394283.1,ENST00000343317.6,ENST00000373033.1BRCArs2273068chr6:41658566A/G2.99e-04
exon_skip_459372641657468:41657549:41658400:41658655:41658738:4165878041658400:41658655ENST00000416140.1,ENST00000230323.4,ENST00000358871.2,ENST00000403298.4,ENST00000419396.1,ENST00000419574.1,ENST00000394283.1,ENST00000343317.6,ENST00000373033.1BRCArs2273068chr6:41658566A/G1.25e-03
exon_skip_459372641657468:41657549:41658400:41658655:41658738:4165878041658400:41658655ENST00000416140.1,ENST00000230323.4,ENST00000358871.2,ENST00000403298.4,ENST00000419396.1,ENST00000419574.1,ENST00000394283.1,ENST00000343317.6,ENST00000373033.1LGGrs2273068chr6:41658566A/G2.40e-06
exon_skip_459372641657468:41657549:41658400:41658655:41658738:4165878041658400:41658655ENST00000416140.1,ENST00000230323.4,ENST00000358871.2,ENST00000403298.4,ENST00000419396.1,ENST00000419574.1,ENST00000394283.1,ENST00000343317.6,ENST00000373033.1OVrs2273068chr6:41658566A/G9.20e-04
exon_skip_459372641657468:41657549:41658400:41658655:41658738:4165878041658400:41658655ENST00000416140.1,ENST00000230323.4,ENST00000358871.2,ENST00000403298.4,ENST00000419396.1,ENST00000419574.1,ENST00000394283.1,ENST00000343317.6,ENST00000373033.1OVrs2273068chr6:41658566A/G1.77e-03
exon_skip_459372641657468:41657549:41658400:41658655:41658738:4165878041658400:41658655ENST00000416140.1,ENST00000230323.4,ENST00000358871.2,ENST00000403298.4,ENST00000419396.1,ENST00000419574.1,ENST00000394283.1,ENST00000343317.6,ENST00000373033.1THCArs2273068chr6:41658566A/G3.53e-03

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TFEB


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TFEB


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RelatedDrugs for TFEB

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for TFEB

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource