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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 RPSMAP, MSBB, and Mayo

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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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3'-UTR located exon skipping events lost miRNA binding sites

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SNVs in the skipped exons with depth of coverage

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AD stage-associated exon skipping events

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Correlation with RNA binding proteins (RBPs)

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Related drugs with this gene

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Related diseases with this gene

Gene summary for TSC1

check button Gene summary
Gene informationGene symbol

TSC1

Gene ID

7248

Gene nameTSC complex subunit 1
SynonymsLAM|TSC
Cytomap

9q34.13

Type of geneprotein-coding
Descriptionhamartintruncated hemartintuberous sclerosis 1 protein
Modification date20200313
UniProtAcc

A0A1V1FGH6,

A0A1V1FM02,

A0A2R8Y419,

A0A2R8Y5F8,

A0A2R8Y5J1,

A0A2R8Y5M3,

A0A2R8Y5N2,

A0A2R8Y5Q4,

A0A2R8Y5S3,

A0A2R8Y5U8,

A0A2R8Y6N1,

A0A2R8Y6S1,

A0A2R8Y6S8,

A0A2R8Y6T5,

A0A2R8Y6W1,

A0A2R8Y756,

A0A2R8Y7E9,

A0A2R8YD74,

A0A2R8YEH9,

A0A2R8YFV7,

A0A2R8YGL0,

A0A2R8YGX7,

A0A2Z3J316,

A0A2Z3J3Z0,

A7L806,

Q0VAM5,

Q32NF0,

Q59IT9,

Q86WV8,

Q92574,

Q96RT3,

Q96RT4,

Q96RT5,

X5D9D2,

Context

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
TSC1

GO:0006417

regulation of translation

17308101

TSC1

GO:0032780

negative regulation of ATPase activity

29127155

TSC1

GO:0032868

response to insulin

16996505

TSC1

GO:0050821

protein stabilization

11175345

TSC1

GO:0051492

regulation of stress fiber assembly

10806479

TSC1

GO:0051894

positive regulation of focal adhesion assembly

10806479

TSC1

GO:0090630

activation of GTPase activity

10806479


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Gene structures and expression levels for TSC1

check buttonSkipped 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.
all structure

ENSG00000165699
check button Differentially expressed gene analysis across multiple brain tissues between AD and control.
Tissue typeDEG directionBase mean exp.log2FC(AD/control)P-valueAdj. p-value

check button Differentially expressed isoform analysis across multiple brain tissues between AD and control.
gencode gene structure
Tissue typeDEG directionENSTTranscript info.Base mean exp.log2FC(AD/control)P-valueAdjc. p-value
STGUPENST00000647534.1TSC1-247:retained_intron:TSC11.016379e+016.501490e+001.487260e-034.710991e-02
CBUPENST00000647279.1TSC1-244:nonsense_mediated_decay:TSC11.529869e+011.616617e+001.305612e-051.319416e-04
CBUPENST00000644255.1TSC1-227:nonsense_mediated_decay:TSC11.307565e+011.381501e+009.708707e-057.219542e-04
CBUPENST00000298552.8TSC1-201:protein_coding:TSC19.885062e+028.112806e-012.263862e-031.020967e-02
CBUPENST00000647534.1TSC1-247:retained_intron:TSC12.884502e+028.127409e-013.583103e-031.493115e-02
CBDOWNENST00000644184.1TSC1-226:protein_coding:TSC13.041673e+02-8.309929e-017.386800e-032.711770e-02

check button Landscape of isoform expressions across multiple brain tissues between AD and control.
gencode gene structure

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for TSC1

check button Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).
boxplot

check button All exon skipping events in AD cohorts.
Exon skip IDchrExons involved in exon skippingSkipped exon
exon_skip_101704chr9132928767:132928952:132935033:132935095:132944543:132944553132935033:132935095
exon_skip_104580chr9132923480:132923492:132924815:132924906:132925587:132925739132924815:132924906
exon_skip_106909chr9132928767:132928952:132935033:132935095:132944547:132944558132935033:132935095
exon_skip_108567chr9132902731:132902787:132903651:132903817:132904411:132904454132903651:132903817
exon_skip_110517chr9132897428:132897610:132900715:132900837:132901589:132901699132900715:132900837
exon_skip_136391chr9132923480:132923492:132925587:132925739:132927201:132927304132925587:132925739
exon_skip_146645chr9132925735:132925739:132928767:132928952:132935033:132935090132928767:132928952
exon_skip_158002chr9132928767:132928952:132931209:132931304:132935033:132935095132931209:132931304
exon_skip_166215chr9132923480:132923492:132924815:132924939:132925587:132925739132924815:132924939
exon_skip_168928chr9132896542:132896754:132897184:132897345:132897423:132897610132897184:132897345
exon_skip_177700chr9132903651:132903817:132904411:132904454:132905581:132905621132904411:132904454
exon_skip_202029chr9132912282:132912457:132921363:132921436:132921819:132921858132921363:132921436
exon_skip_210698chr9132907301:132907370:132910571:132910692:132911002:132911113132910571:132910692
exon_skip_216663chr9132925735:132925739:132927201:132927304:132928767:132928952132927201:132927304
exon_skip_218335chr9132907301:132907370:132910571:132910689:132911002:132911113132910571:132910689
exon_skip_22742chr9132902605:132902787:132903651:132903802:132904411:132904454132903651:132903802
exon_skip_251134chr9132925587:132925739:132928767:132928952:132935033:132935095132928767:132928952
exon_skip_279322chr9132902605:132902787:132903651:132903817:132904411:132904454132903651:132903817
exon_skip_289978chr9132902731:132902787:132903651:132903802:132904411:132904454132903651:132903802
exon_skip_44169chr9132923348:132923492:132924815:132924906:132925587:132925739132924815:132924906
exon_skip_58415chr9132910637:132910689:132911002:132911113:132911453:132911568132911002:132911113
exon_skip_65243chr9132903651:132903817:132904411:132904454:132905581:132906095132904411:132904454
exon_skip_65838chr9132912282:132912457:132921363:132921436:132921819:132921973132921363:132921436
exon_skip_67602chr9132897428:132897610:132900715:132900837:132901631:132901699132900715:132900837
exon_skip_7779chr9132910571:132910692:132911002:132911113:132911453:132911568132911002:132911113

check button Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.
Exon skipping informationTissue typeAvg(PSIs) in ADAvg(PSIs) in controlDifference (PSI)Adj. p-value


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Open reading frame (ORF) annotation in the exon skipping event for TSC1

check button Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000006438751329350331329350953UTR-3UTR
ENST00000298552132903651132903817Frame-shift
ENST00000440111132903651132903817Frame-shift
ENST00000643875132903651132903817Frame-shift
ENST00000646625132903651132903817Frame-shift
ENST00000298552132904411132904454Frame-shift
ENST00000440111132904411132904454Frame-shift
ENST00000643875132904411132904454Frame-shift
ENST00000646625132904411132904454Frame-shift
ENST00000298552132921363132921436Frame-shift
ENST00000440111132921363132921436Frame-shift
ENST00000643875132921363132921436Frame-shift
ENST00000646625132921363132921436Frame-shift
ENST00000298552132927201132927304Frame-shift
ENST00000440111132927201132927304Frame-shift
ENST00000643875132927201132927304Frame-shift
ENST00000646625132927201132927304Frame-shift

check button Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST00000298552132921363132921436Frame-shift
ENST00000440111132921363132921436Frame-shift
ENST00000643875132921363132921436Frame-shift
ENST00000646625132921363132921436Frame-shift
ENST00000298552132927201132927304Frame-shift
ENST00000440111132927201132927304Frame-shift
ENST00000643875132927201132927304Frame-shift
ENST00000646625132927201132927304Frame-shift
ENST00000298552132925587132925739In-frame
ENST00000440111132925587132925739In-frame
ENST00000643875132925587132925739In-frame
ENST00000646625132925587132925739In-frame

check button Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000002985521329350331329350953UTR-3UTR
ENST00000298552132903651132903817Frame-shift
ENST00000440111132903651132903817Frame-shift
ENST00000643875132903651132903817Frame-shift
ENST00000646625132903651132903817Frame-shift
ENST00000298552132904411132904454Frame-shift
ENST00000440111132904411132904454Frame-shift
ENST00000643875132904411132904454Frame-shift
ENST00000646625132904411132904454Frame-shift
ENST00000298552132910571132910692Frame-shift
ENST00000440111132910571132910692Frame-shift
ENST00000643875132910571132910692Frame-shift
ENST00000646625132910571132910692Frame-shift
ENST00000298552132911002132911113Frame-shift
ENST00000440111132911002132911113Frame-shift
ENST00000643875132911002132911113Frame-shift
ENST00000646625132911002132911113Frame-shift
ENST00000298552132921363132921436Frame-shift
ENST00000440111132921363132921436Frame-shift
ENST00000643875132921363132921436Frame-shift
ENST00000646625132921363132921436Frame-shift
ENST00000298552132927201132927304Frame-shift
ENST00000440111132927201132927304Frame-shift
ENST00000643875132927201132927304Frame-shift
ENST00000646625132927201132927304Frame-shift
ENST00000298552132897184132897345In-frame
ENST00000440111132897184132897345In-frame
ENST00000643875132897184132897345In-frame
ENST00000646625132897184132897345In-frame
ENST00000298552132900715132900837In-frame
ENST00000440111132900715132900837In-frame
ENST00000643875132900715132900837In-frame
ENST00000646625132900715132900837In-frame

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Infer the effects of exon skipping event on protein functional features for TSC1

p-ENSG00000165699_img4.png
boxplot

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

check button Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000002985528633116413292558713292573944559670120
ENST000004401118480116413292558713292573929444570120
ENST000006438756608116413292558713292573942557670120
ENST000006466258599116413292558713292573941656770120

check button Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000002985528633116413290071513290083727372858834874
ENST000004401118480116413290071513290083725862707834874
ENST000006438756608116413290071513290083727172838834874
ENST000006466258599116413290071513290083727082829834874
ENST000002985528633116413289718413289734530483208938991
ENST000004401118480116413289718413289734528973057938991
ENST000006438756608116413289718413289734530283188938991
ENST000006466258599116413289718413289734530193179938991

check button 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 featureDescription of feature

check button 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 featureDescription of feature
Q925747012070120Alternative sequenceID=VSP_042890;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q925747012070120Alternative sequenceID=VSP_042890;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q925747012070120Alternative sequenceID=VSP_042890;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q925747012070120Alternative sequenceID=VSP_042890;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q925747012011164ChainID=PRO_0000065651;Note=Hamartin
Q925747012011164ChainID=PRO_0000065651;Note=Hamartin
Q925747012011164ChainID=PRO_0000065651;Note=Hamartin
Q925747012011164ChainID=PRO_0000065651;Note=Hamartin
Q92574701207272Natural variantID=VAR_054387;Note=In TSC1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10533069;Dbxref=dbSNP:rs118203354,PMID:10533069
Q92574701207272Natural variantID=VAR_054387;Note=In TSC1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10533069;Dbxref=dbSNP:rs118203354,PMID:10533069
Q92574701207272Natural variantID=VAR_054387;Note=In TSC1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10533069;Dbxref=dbSNP:rs118203354,PMID:10533069
Q92574701207272Natural variantID=VAR_054387;Note=In TSC1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10533069;Dbxref=dbSNP:rs118203354,PMID:10533069
Q9257470120117117Natural variantID=VAR_070637;Note=In TSC1%3B reduced expression%3B altered subcellular localization%3B reduced interaction with TSC2%3B reduced inhibition of TORC1 signaling. L->P;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:18830229,ECO
Q9257470120117117Natural variantID=VAR_070637;Note=In TSC1%3B reduced expression%3B altered subcellular localization%3B reduced interaction with TSC2%3B reduced inhibition of TORC1 signaling. L->P;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:18830229,ECO
Q9257470120117117Natural variantID=VAR_070637;Note=In TSC1%3B reduced expression%3B altered subcellular localization%3B reduced interaction with TSC2%3B reduced inhibition of TORC1 signaling. L->P;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:18830229,ECO
Q9257470120117117Natural variantID=VAR_070637;Note=In TSC1%3B reduced expression%3B altered subcellular localization%3B reduced interaction with TSC2%3B reduced inhibition of TORC1 signaling. L->P;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:18830229,ECO

check button 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 featureDescription of feature
Q9257483487411164ChainID=PRO_0000065651;Note=Hamartin
Q9257483487411164ChainID=PRO_0000065651;Note=Hamartin
Q9257483487411164ChainID=PRO_0000065651;Note=Hamartin
Q9257483487411164ChainID=PRO_0000065651;Note=Hamartin
Q92574834874721997Coiled coilOntology_term=ECO:0000255;evidence=ECO:0000255
Q92574834874721997Coiled coilOntology_term=ECO:0000255;evidence=ECO:0000255
Q92574834874721997Coiled coilOntology_term=ECO:0000255;evidence=ECO:0000255
Q92574834874721997Coiled coilOntology_term=ECO:0000255;evidence=ECO:0000255
Q925748348741651164Natural variantID=VAR_078845;Note=In TSC1. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11829138;Dbxref=PMID:11829138
Q925748348741651164Natural variantID=VAR_078845;Note=In TSC1. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11829138;Dbxref=PMID:11829138
Q925748348741651164Natural variantID=VAR_078845;Note=In TSC1. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11829138;Dbxref=PMID:11829138
Q925748348741651164Natural variantID=VAR_078845;Note=In TSC1. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11829138;Dbxref=PMID:11829138
Q9257493899111164ChainID=PRO_0000065651;Note=Hamartin
Q9257493899111164ChainID=PRO_0000065651;Note=Hamartin
Q9257493899111164ChainID=PRO_0000065651;Note=Hamartin
Q9257493899111164ChainID=PRO_0000065651;Note=Hamartin
Q92574938991721997Coiled coilOntology_term=ECO:0000255;evidence=ECO:0000255
Q92574938991721997Coiled coilOntology_term=ECO:0000255;evidence=ECO:0000255
Q92574938991721997Coiled coilOntology_term=ECO:0000255;evidence=ECO:0000255
Q92574938991721997Coiled coilOntology_term=ECO:0000255;evidence=ECO:0000255
Q92574938991941971HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Z6Y
Q92574938991941971HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Z6Y
Q92574938991941971HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Z6Y
Q92574938991941971HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Z6Y
Q92574938991975991HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Z6Y
Q92574938991975991HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Z6Y
Q92574938991975991HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Z6Y
Q92574938991975991HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Z6Y
Q925749389911651164Natural variantID=VAR_078845;Note=In TSC1. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11829138;Dbxref=PMID:11829138
Q925749389911651164Natural variantID=VAR_078845;Note=In TSC1. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11829138;Dbxref=PMID:11829138
Q925749389911651164Natural variantID=VAR_078845;Note=In TSC1. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11829138;Dbxref=PMID:11829138
Q925749389911651164Natural variantID=VAR_078845;Note=In TSC1. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11829138;Dbxref=PMID:11829138
Q92574938991978978Natural variantID=VAR_070661;Note=In TSC1%3B unknown pathological significance%3B no effect on expression%3B no effect on subcellular localization%3B no effect on inhibition of TORC1 signaling. L->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:22161988;Dbxref=d
Q92574938991978978Natural variantID=VAR_070661;Note=In TSC1%3B unknown pathological significance%3B no effect on expression%3B no effect on subcellular localization%3B no effect on inhibition of TORC1 signaling. L->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:22161988;Dbxref=d
Q92574938991978978Natural variantID=VAR_070661;Note=In TSC1%3B unknown pathological significance%3B no effect on expression%3B no effect on subcellular localization%3B no effect on inhibition of TORC1 signaling. L->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:22161988;Dbxref=d
Q92574938991978978Natural variantID=VAR_070661;Note=In TSC1%3B unknown pathological significance%3B no effect on expression%3B no effect on subcellular localization%3B no effect on inhibition of TORC1 signaling. L->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:22161988;Dbxref=d


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3'-UTR located exon skipping events that lost miRNA binding sites in TSC1

check button 3'-UTR exon skipping evnets lost miRNA binding.
Tissue typeENSTExon skip startExon skip endmicroRNABinding site by TargetScanBinding type by TargetScanBdinding site by miRandaScore of miRandaEnergy by miRanda
MayoENST00000298552132935033132935095hsa-miR-5585-5pchr9:132935051-1329350588mer-1achr9:132935038-132935058160.00-23.88
MayoENST00000298552132935033132935095hsa-miR-591chr9:132935088-1329350958mer-1achr9:132935076-132935095142.00-15.33
ROSMAPENST00000643875132935033132935095hsa-miR-5585-5pchr9:132935051-1329350588mer-1achr9:132935038-132935058160.00-23.88
ROSMAPENST00000643875132935033132935095hsa-miR-591chr9:132935088-1329350958mer-1achr9:132935076-132935095142.00-15.33

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SNVs in the skipped exons for TSC1

check button - Differential PSIs between mutated versus non-mutated samples.

check button - Depth of Coverage in the skipped exon of the mutated samples.

check button - Sashimi plot in the skipped exon of the mutated samples.

check button - Non-synonymous mutations located in the skipped exons.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange

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AD stage-associated exon skippint events for TSC1

check button Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).
AD stage infoCohortTissueSE idCoefficient P-valueChromosomeStrandE1 startE1 endSkipped startSkipped endE2 startE2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TSC1

check button sQTL information located at the skipped exons.
Tissue typeExon skip IDSNP idLocationP-valueFDR

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Correlation with RNA binding proteins (RBPs) for TSC1

check button Correlated RBP and related information.
Tissue typeRBP nameExon skip IDCorrelation coeifficientP-value

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RelatedDrugs for TSC1

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

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RelatedDiseases for TSC1

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