ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for TCF7L2

Gene summary

Gene information	Gene symbol	TCF7L2
	Gene ID	6934
	Gene name	transcription factor 7 like 2
	Synonyms	TCF-4\|TCF4
	Cytomap	10q25.2-q25.3
	Type of gene	protein-coding
	Description	transcription factor 7-like 2HMG box transcription factor 4T-cell factor 4T-cell-specific transcription factor 4hTCF-4transcription factor 7-like 2 (T-cell specific, HMG-box)
	Modification date	20200315
	UniProtAcc	A0A0A0MTL7, A0A0D9SGH8, A0A1B0GU84, A0A1B0GUV5, A0A1B0GVE1, A0A2Z5HTM8, A0A2Z5HTN9, B5BU30, C6ZRJ6, C6ZRJ7, C6ZRK5, E2GH13, E2GH15, E2GH16, E2GH18, E2GH23, E2GH26, H0YEE5, Q5JRY3, Q5JRY4, Q5JRY5, Q5VVR5, Q5VVR7, Q5VVR8, Q6FHW4,
	Context

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene	GO ID	GO term	PubMed ID
TCF7L2	GO:0000122	negative regulation of transcription by RNA polymerase II	12799378
TCF7L2	GO:0006357	regulation of transcription by RNA polymerase II	9727977
TCF7L2	GO:0032092	positive regulation of protein binding	12799378
TCF7L2	GO:0032350	regulation of hormone metabolic process	15525634
TCF7L2	GO:0042593	glucose homeostasis	15525634
TCF7L2	GO:0043433	negative regulation of DNA-binding transcription factor activity	12799378
TCF7L2	GO:0045444	fat cell differentiation	10937998
TCF7L2	GO:0045892	negative regulation of transcription, DNA-templated	12799378\|15525634
TCF7L2	GO:0045944	positive regulation of transcription by RNA polymerase II	9065401\|19168596
TCF7L2	GO:0048625	myoblast fate commitment	10937998

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Gene structures and expression levels for TCF7L2

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.

ENSG00000148737

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.

Tissue type

DEG direction

ENST

Transcript info.

Base mean exp.

log2FC(AD/control)

P-value

Adjc. p-value

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 TCF7L2

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

All exon skipping events in AD cohorts.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon
exon_skip_108865	chr10	113159920:113159992:113160619:113160691:113161579:113161603	113160619:113160691
exon_skip_117172	chr10	113160619:113160691:113161579:113161603:113165555:113165587	113161579:113161603
exon_skip_121467	chr10	113158021:113158069:113159920:113159992:113165555:113165587	113159920:113159992
exon_skip_124419	chr10	113158667:113158717:113159920:113159992:113165555:113167678	113159920:113159992
exon_skip_130775	chr10	113040025:113040126:113089397:113089540:113141184:113141316	113089397:113089540
exon_skip_15296	chr10	113158667:113158717:113159920:113159992:113165555:113165587	113159920:113159992
exon_skip_171369	chr10	113158021:113158069:113159920:113159992:113160619:113160691	113159920:113159992
exon_skip_181849	chr10	112951491:112951607:112964556:112964624:113040025:113040126	112964556:112964624
exon_skip_201836	chr10	113159920:113159992:113161579:113161603:113165555:113165587	113161579:113161603
exon_skip_228326	chr10	113158021:113158069:113158667:113158717:113165555:113165587	113158667:113158717
exon_skip_229584	chr10	113157773:113158069:113158667:113158717:113165555:113165587	113158667:113158717
exon_skip_23750	chr10	113158021:113158069:113160619:113160691:113165555:113165587	113160619:113160691
exon_skip_238890	chr10	112951483:112951607:113040025:113040126:113141184:113141316	113040025:113040126
exon_skip_282089	chr10	113040025:113040126:113089400:113089540:113141184:113141316	113089400:113089540
exon_skip_288716	chr10	113158021:113158069:113158667:113158717:113159920:113159992	113158667:113158717
exon_skip_36145	chr10	112951483:112951607:112964556:112964624:113040025:113040126	112964556:112964624
exon_skip_61481	chr10	113143923:113144013:113146011:113146097:113150998:113151023	113146011:113146097
exon_skip_62374	chr10	113158021:113158069:113158667:113158717:113165555:113167678	113158667:113158717
exon_skip_9656	chr10	113159920:113159992:113160619:113160691:113165555:113165587	113160619:113160691

Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.

Exon skipping information

Tissue type

Avg(PSIs) in AD

Avg(PSIs) in control

Difference (PSI)

Adj. p-value

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Open reading frame (ORF) annotation in the exon skipping event for TCF7L2

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
ENST00000355995	113159920	113159992	Frame-shift
ENST00000355995	112964556	112964624	In-frame
ENST00000355995	113158667	113158717	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
ENST00000355995	113159920	113159992	Frame-shift
ENST00000355995	112964556	112964624	In-frame
ENST00000355995	113158667	113158717	In-frame

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
ENST00000355995	113159920	113159992	Frame-shift
ENST00000355995	112964556	112964624	In-frame
ENST00000355995	113158667	113158717	In-frame

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Infer the effects of exon skipping event on protein functional features for TCF7L2

p-ENSG00000148737_img4.png
boxplot

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
ENST00000355995	4090	619	112964556	112964624	890	957	127	150
ENST00000355995	4090	619	113158667	113158717	1827	1876	440	456

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
ENST00000355995	4090	619	112964556	112964624	890	957	127	150
ENST00000355995	4090	619	113158667	113158717	1827	1876	440	456

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
ENST00000355995	4090	619	112964556	112964624	890	957	127	150
ENST00000355995	4090	619	113158667	113158717	1827	1876	440	456

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
Q9NQB0	127	150	7	290	Alternative sequence	ID=VSP_053749;Note=In isoform 17. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:21256126;Dbxref=PMID:21256126
Q9NQB0	127	150	128	150	Alternative sequence	ID=VSP_006962;Note=In isoform 8%2C isoform 10%2C isoform 11%2C isoform 12%2C isoform 13%2C isoform 14%2C isoform 15 and isoform 16. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:
Q9NQB0	127	150	1	619	Chain	ID=PRO_0000048623;Note=Transcription factor 7-like 2
Q9NQB0	440	456	440	465	Alternative sequence	ID=VSP_006965;Note=In isoform 9%2C isoform 11%2C isoform 14 and isoform 15. EHSECFLNPCLSLPPITDLSAPKKCR->GEKKSAFATYKVKAAASAHPLQMEAY;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|P
Q9NQB0	440	456	440	456	Alternative sequence	ID=VSP_006964;Note=In isoform 4%2C isoform 5%2C isoform 7%2C isoform 13 and isoform 16. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:19602480,ECO:0000303\|PubMed:21256126;Dbxref=PMID:19602480,PMID:21256126
Q9NQB0	440	456	1	619	Chain	ID=PRO_0000048623;Note=Transcription factor 7-like 2

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
Q9NQB0	127	150	7	290	Alternative sequence	ID=VSP_053749;Note=In isoform 17. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:21256126;Dbxref=PMID:21256126
Q9NQB0	127	150	128	150	Alternative sequence	ID=VSP_006962;Note=In isoform 8%2C isoform 10%2C isoform 11%2C isoform 12%2C isoform 13%2C isoform 14%2C isoform 15 and isoform 16. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:
Q9NQB0	127	150	1	619	Chain	ID=PRO_0000048623;Note=Transcription factor 7-like 2
Q9NQB0	440	456	440	465	Alternative sequence	ID=VSP_006965;Note=In isoform 9%2C isoform 11%2C isoform 14 and isoform 15. EHSECFLNPCLSLPPITDLSAPKKCR->GEKKSAFATYKVKAAASAHPLQMEAY;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|P
Q9NQB0	440	456	440	456	Alternative sequence	ID=VSP_006964;Note=In isoform 4%2C isoform 5%2C isoform 7%2C isoform 13 and isoform 16. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:19602480,ECO:0000303\|PubMed:21256126;Dbxref=PMID:19602480,PMID:21256126
Q9NQB0	440	456	1	619	Chain	ID=PRO_0000048623;Note=Transcription factor 7-like 2

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
Q9NQB0	127	150	7	290	Alternative sequence	ID=VSP_053749;Note=In isoform 17. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:21256126;Dbxref=PMID:21256126
Q9NQB0	127	150	128	150	Alternative sequence	ID=VSP_006962;Note=In isoform 8%2C isoform 10%2C isoform 11%2C isoform 12%2C isoform 13%2C isoform 14%2C isoform 15 and isoform 16. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:
Q9NQB0	127	150	1	619	Chain	ID=PRO_0000048623;Note=Transcription factor 7-like 2
Q9NQB0	440	456	440	465	Alternative sequence	ID=VSP_006965;Note=In isoform 9%2C isoform 11%2C isoform 14 and isoform 15. EHSECFLNPCLSLPPITDLSAPKKCR->GEKKSAFATYKVKAAASAHPLQMEAY;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|P
Q9NQB0	440	456	440	456	Alternative sequence	ID=VSP_006964;Note=In isoform 4%2C isoform 5%2C isoform 7%2C isoform 13 and isoform 16. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:19602480,ECO:0000303\|PubMed:21256126;Dbxref=PMID:19602480,PMID:21256126
Q9NQB0	440	456	1	619	Chain	ID=PRO_0000048623;Note=Transcription factor 7-like 2

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3'-UTR located exon skipping events that lost miRNA binding sites in TCF7L2

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

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SNVs in the skipped exons for TCF7L2

- 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 TCF7L2

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 TCF7L2

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

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Correlation with RNA binding proteins (RBPs) for TCF7L2

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
PCC	RALYL	exon_skip_201836	4.066936e-01	1.612267e-08
TC	HNRNPD	exon_skip_201836	5.308948e-01	5.268257e-10
TC	RALYL	exon_skip_201836	7.532654e-01	4.986328e-23

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RelatedDrugs for TCF7L2

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 TCF7L2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in RPSMAP, MSBB, and Mayo
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	3'-UTR located exon skipping events lost miRNA binding sites
	SNVs in the skipped exons with depth of coverage
	AD stage-associated exon skipping events
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Correlation with RNA binding proteins (RBPs)
	Related drugs with this gene
	Related diseases with this gene

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Gene summary for TCF7L2

Gene structures and expression levels for TCF7L2

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for TCF7L2

Open reading frame (ORF) annotation in the exon skipping event for TCF7L2

Infer the effects of exon skipping event on protein functional features for TCF7L2

3'-UTR located exon skipping events that lost miRNA binding sites in TCF7L2

SNVs in the skipped exons for TCF7L2

AD stage-associated exon skippint events for TCF7L2

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TCF7L2

Correlation with RNA binding proteins (RBPs) for TCF7L2

RelatedDrugs for TCF7L2

RelatedDiseases for TCF7L2