ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for TNS1

Gene summary

Gene information	Gene symbol	TNS1
	Gene ID	7145
	Gene name	tensin 1
	Synonyms	MST091\|MST122\|MST127\|MSTP091\|MSTP122\|MSTP127\|MXRA6\|PPP1R155\|TNS
	Cytomap	2q35
	Type of gene	protein-coding
	Description	tensin-1Matrix-remodelling-associated protein 6matrix-remodelling associated 6protein phosphatase 1, regulatory subunit 155
	Modification date	20200313
	UniProtAcc	A0A087WWW7, A0A2R8Y4T1, A0A3B3IRK7, A0A494C067, A1L0S7, B2RU35, C9J8K5, C9JFT7, C9JI43, C9JZT0, E7EMG1, E7ERH1, E9PF55, E9PGF5, H0Y4U1, H7C3Z4, Q0VG54, Q0VG55, Q6PJM3, Q86VB0, Q9HBL0,
	Context

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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Gene structures and expression levels for TNS1

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.

ENSG00000079308

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
PCC	UP	ENST00000413554.5	TNS1-204:protein_coding:TNS1	5.411479e+00	1.811552e+00	4.957752e-06	7.865068e-04
PCC	UP	ENST00000490566.1	TNS1-217:retained_intron:TNS1	8.452375e+00	8.151323e-01	2.231642e-03	4.183066e-02
HCC	UP	ENST00000413554.5	TNS1-204:protein_coding:TNS1	9.785474e+00	1.037300e+00	4.311818e-05	3.942349e-03
STG	UP	ENST00000611415.4	TNS1-220:protein_coding:TNS1	7.711385e+00	3.688222e+00	2.390457e-04	1.830728e-02
STG	UP	ENST00000446688.5	TNS1-209:protein_coding:TNS1	1.270227e+01	3.291997e+00	2.599120e-04	1.921450e-02
PG	UP	ENST00000490566.1	TNS1-217:retained_intron:TNS1	1.925165e+01	1.536016e+00	3.471132e-06	2.285782e-04
PG	UP	ENST00000492338.2	TNS1-218:retained_intron:TNS1	1.031209e+01	8.090313e-01	9.562913e-06	4.877020e-04
PG	UP	ENST00000171887.8	TNS1-201:protein_coding:TNS1	1.121773e+03	8.163560e-01	1.010520e-05	5.092189e-04
PG	UP	ENST00000439083.5	TNS1-208:protein_coding:TNS1	4.511954e+00	1.010386e+00	1.175867e-04	3.096553e-03
PG	UP	ENST00000310858.10	TNS1-202:protein_coding:TNS1	1.176854e+01	8.018415e-01	2.549784e-04	5.442962e-03
PG	UP	ENST00000413554.5	TNS1-204:protein_coding:TNS1	1.268077e+01	1.259188e+00	8.650616e-04	1.312495e-02
PG	UP	ENST00000446903.5	TNS1-210:protein_coding:TNS1	2.740097e+01	9.853685e-01	2.776588e-03	3.015470e-02
CB	UP	ENST00000413554.5	TNS1-204:protein_coding:TNS1	2.553161e+00	2.261209e+00	2.958681e-05	2.635074e-04
CB	UP	ENST00000446688.5	TNS1-209:protein_coding:TNS1	5.542676e+01	1.438536e+00	4.956756e-03	1.953388e-02
CB	UP	ENST00000449814.1	TNS1-211:protein_coding:TNS1	1.207103e+00	1.063939e+00	9.988679e-03	3.472622e-02
TC	UP	ENST00000413280.5	TNS1-203:protein_coding:TNS1	4.160132e+00	1.285054e+00	1.887509e-08	1.525489e-06
TC	UP	ENST00000446903.5	TNS1-210:protein_coding:TNS1	8.001510e+00	9.995383e-01	3.517787e-05	7.019648e-04
TC	UP	ENST00000449814.1	TNS1-211:protein_coding:TNS1	3.031886e+00	9.264242e-01	2.717241e-03	2.114817e-02

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 TNS1

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_153321	chr2	217882346:217882411:217885035:217885164:217885744:217885810	217885035:217885164
exon_skip_218602	chr2	217892948:217893012:217893439:217893561:217895006:217895056	217893439:217893561
exon_skip_234888	chr2	217821740:217821938:217829844:217829882:217831455:217831547	217829844:217829882
exon_skip_259357	chr2	217900463:217900512:217901710:217901823:217906335:217906385	217901710:217901823
exon_skip_30923	chr2	217906335:217906385:217907210:217907251:217920195:217920209	217907210:217907251
exon_skip_32250	chr2	217848884:217849087:217880898:217881014:217882346:217882411	217880898:217881014
exon_skip_33141	chr2	217821740:217821938:217830367:217830390:217831455:217831547	217830367:217830390
exon_skip_36485	chr2	217812368:217812445:217813215:217813307:217813685:217813816	217813215:217813307
exon_skip_40819	chr2	217907210:217907251:217920195:217920236:217943865:217944005	217920195:217920236
exon_skip_5120	chr2	217821740:217821938:217829844:217829882:217830367:217830390	217829844:217829882
exon_skip_65479	chr2	217829844:217829882:217830367:217830390:217831455:217831547	217830367:217830390
exon_skip_7712	chr2	217812368:217812445:217813215:217813304:217813685:217813816	217813215:217813304
exon_skip_94270	chr2	217803866:217804603:217808075:217808107:217808603:217808671	217808075:217808107

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 TNS1

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
ENST00000171887	217907210	217907251	3UTR-3UTR
ENST00000171887	217920195	217920236	3UTR-3UTR
ENST00000171887	217808075	217808107	In-frame
ENST00000171887	217813215	217813307	In-frame
ENST00000171887	217829844	217829882	In-frame
ENST00000171887	217830367	217830390	In-frame
ENST00000171887	217880898	217881014	In-frame
ENST00000171887	217893439	217893561	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
ENST00000171887	217920195	217920236	3UTR-3UTR
ENST00000171887	217829844	217829882	In-frame
ENST00000171887	217830367	217830390	In-frame
ENST00000171887	217893439	217893561	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
ENST00000171887	217907210	217907251	3UTR-3UTR
ENST00000171887	217920195	217920236	3UTR-3UTR
ENST00000171887	217885035	217885164	Frame-shift
ENST00000171887	217808075	217808107	In-frame
ENST00000171887	217813215	217813307	In-frame
ENST00000171887	217829844	217829882	In-frame
ENST00000171887	217830367	217830390	In-frame
ENST00000171887	217880898	217881014	In-frame
ENST00000171887	217893439	217893561	In-frame

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Infer the effects of exon skipping event on protein functional features for TNS1

p-ENSG00000079308_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
ENST00000171887	10348	1735	217893439	217893561	673	794	73	113
ENST00000171887	10348	1735	217880898	217881014	1391	1506	312	351
ENST00000171887	10348	1735	217829844	217829882	3476	3513	1007	1020
ENST00000171887	10348	1735	217813215	217813307	5003	5094	1516	1547
ENST00000171887	10348	1735	217808075	217808107	5484	5515	1677	1687

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
ENST00000171887	10348	1735	217893439	217893561	673	794	73	113
ENST00000171887	10348	1735	217829844	217829882	3476	3513	1007	1020

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
ENST00000171887	10348	1735	217893439	217893561	673	794	73	113
ENST00000171887	10348	1735	217880898	217881014	1391	1506	312	351
ENST00000171887	10348	1735	217829844	217829882	3476	3513	1007	1020
ENST00000171887	10348	1735	217813215	217813307	5003	5094	1516	1547
ENST00000171887	10348	1735	217808075	217808107	5484	5515	1677	1687

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
Q9HBL0	73	113	1	1735	Chain	ID=PRO_0000215900;Note=Tensin-1
Q9HBL0	73	113	4	176	Domain	Note=Phosphatase tensin-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00590
Q9HBL0	312	351	1	1735	Chain	ID=PRO_0000215900;Note=Tensin-1
Q9HBL0	312	351	338	338	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:24275569;Dbxref=PMID:24275569
Q9HBL0	1007	1020	386	1735	Alternative sequence	ID=VSP_056337;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9HBL0	1007	1020	1	1735	Chain	ID=PRO_0000215900;Note=Tensin-1
Q9HBL0	1516	1547	386	1735	Alternative sequence	ID=VSP_056337;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9HBL0	1516	1547	1	1735	Chain	ID=PRO_0000215900;Note=Tensin-1
Q9HBL0	1516	1547	1463	1572	Domain	Note=SH2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00191
Q9HBL0	1677	1687	386	1735	Alternative sequence	ID=VSP_056337;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9HBL0	1677	1687	1	1735	Chain	ID=PRO_0000215900;Note=Tensin-1

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
Q9HBL0	73	113	1	1735	Chain	ID=PRO_0000215900;Note=Tensin-1
Q9HBL0	73	113	4	176	Domain	Note=Phosphatase tensin-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00590
Q9HBL0	1007	1020	386	1735	Alternative sequence	ID=VSP_056337;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9HBL0	1007	1020	1	1735	Chain	ID=PRO_0000215900;Note=Tensin-1

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
Q9HBL0	73	113	1	1735	Chain	ID=PRO_0000215900;Note=Tensin-1
Q9HBL0	73	113	4	176	Domain	Note=Phosphatase tensin-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00590
Q9HBL0	312	351	1	1735	Chain	ID=PRO_0000215900;Note=Tensin-1
Q9HBL0	312	351	338	338	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:24275569;Dbxref=PMID:24275569
Q9HBL0	1007	1020	386	1735	Alternative sequence	ID=VSP_056337;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9HBL0	1007	1020	1	1735	Chain	ID=PRO_0000215900;Note=Tensin-1
Q9HBL0	1516	1547	386	1735	Alternative sequence	ID=VSP_056337;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9HBL0	1516	1547	1	1735	Chain	ID=PRO_0000215900;Note=Tensin-1
Q9HBL0	1516	1547	1463	1572	Domain	Note=SH2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00191
Q9HBL0	1677	1687	386	1735	Alternative sequence	ID=VSP_056337;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9HBL0	1677	1687	1	1735	Chain	ID=PRO_0000215900;Note=Tensin-1

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3'-UTR located exon skipping events that lost miRNA binding sites in TNS1

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	ENST00000171887	217920195	217920236	hsa-miR-4691-5p	chr2:217920213-217920220	8mer-1a	chr2:217920196-217920220	175.00	-34.22
Mayo	ENST00000171887	217920195	217920236	hsa-miR-4313	chr2:217920224-217920231	8mer-1a	chr2:217920212-217920233	168.00	-29.48
Mayo	ENST00000171887	217920195	217920236	hsa-miR-6792-3p	chr2:217920213-217920220	8mer-1a	chr2:217920196-217920220	175.00	-34.22
MSBB	ENST00000171887	217920195	217920236	hsa-miR-4691-5p	chr2:217920213-217920220	8mer-1a	chr2:217920196-217920220	175.00	-34.22
MSBB	ENST00000171887	217920195	217920236	hsa-miR-4313	chr2:217920224-217920231	8mer-1a	chr2:217920212-217920233	168.00	-29.48
MSBB	ENST00000171887	217920195	217920236	hsa-miR-6792-3p	chr2:217920213-217920220	8mer-1a	chr2:217920196-217920220	175.00	-34.22
ROSMAP	ENST00000171887	217920195	217920236	hsa-miR-4691-5p	chr2:217920213-217920220	8mer-1a	chr2:217920196-217920220	175.00	-34.22
ROSMAP	ENST00000171887	217920195	217920236	hsa-miR-4313	chr2:217920224-217920231	8mer-1a	chr2:217920212-217920233	168.00	-29.48
ROSMAP	ENST00000171887	217920195	217920236	hsa-miR-6792-3p	chr2:217920213-217920220	8mer-1a	chr2:217920196-217920220	175.00	-34.22

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SNVs in the skipped exons for TNS1

- 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 TNS1

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 TNS1

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
HCC	exon_skip_234888	rs11677276	chr2:217832226	2.767350e-04	2.114236e-02

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Correlation with RNA binding proteins (RBPs) for TNS1

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
IFG	EWSR1	exon_skip_234888	5.570063e-01	4.693946e-03
IFG	SRSF9	exon_skip_234888	4.560296e-01	2.511007e-02
IFG	HNRNPF	exon_skip_234888	4.499567e-01	2.737078e-02
IFG	HNRNPK	exon_skip_33141	4.597308e-01	4.140990e-02
IFG	LIN28A	exon_skip_33141	5.194615e-01	1.890848e-02

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RelatedDrugs for TNS1

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 TNS1

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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