ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for TESPA1

Gene summary

Gene information	Gene symbol	TESPA1
	Gene ID	9840
	Gene name	thymocyte expressed, positive selection associated 1
	Synonyms	HSPC257\|ITPRID3\|KIAA0748
	Cytomap	12q13.2
	Type of gene	protein-coding
	Description	protein TESPA1thymocyte-expressed positive selection-associated protein 1
	Modification date	20200313
	UniProtAcc	A2RU30, E9PHY9, E9PIN8, E9PIT9, E9PM24, E9PN46, E9PPW8, H0YDP3, H0YEX3,
	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 TESPA1

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.

ENSG00000135426

Differentially expressed gene analysis across multiple brain tissues between AD and control.

***cutpoints = c(0, 0.0001, 0.001, 0.01, 1), symbols = c("****", "***", "**", "ns")

Tissue type	DEG direction	Base mean exp.	log2FC(AD/control)	P-value	Adj. p-value
PG	DOWN	4.461105e+02	-8.366939e-01	3.545560e-09	2.647615e-07

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	ENST00000528240.1	TESPA1-209:protein_coding:TESPA1	1.041005e+01	8.716899e-01	2.063847e-03	3.994829e-02
PG	DOWN	ENST00000532804.5	TESPA1-212:protein_coding:TESPA1	5.193054e+01	-1.002534e+00	3.237707e-04	6.479262e-03
PG	DOWN	ENST00000532757.5	TESPA1-211:protein_coding:TESPA1	1.763325e+01	-1.524064e+00	5.069768e-04	8.915360e-03
PG	DOWN	ENST00000524622.5	TESPA1-203:protein_coding:TESPA1	2.367579e+02	-8.093189e-01	3.440183e-03	3.512399e-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 TESPA1

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_125364	chr12	54967183:54967236:54967843:54967892:54973477:54973519	54967843:54967892
exon_skip_146437	chr12	54967183:54967236:54967843:54968013:54973477:54973519	54967843:54968013
exon_skip_15096	chr12	54963742:54963950:54966053:54966151:54966388:54966424	54966053:54966151
exon_skip_179115	chr12	54950354:54950390:54961168:54961267:54962431:54962697	54961168:54961267
exon_skip_236297	chr12	54950366:54950390:54961168:54961267:54962431:54962697	54961168:54961267
exon_skip_278750	chr12	54950078:54950390:54961168:54961267:54962431:54962697	54961168:54961267
exon_skip_284247	chr12	54950364:54950390:54961168:54961267:54962431:54962697	54961168:54961267
exon_skip_30673	chr12	54967183:54967236:54967843:54967946:54973477:54973554	54967843:54967946
exon_skip_32753	chr12	54963859:54963950:54966053:54966151:54966388:54966424	54966053:54966151
exon_skip_38141	chr12	54966388:54966424:54967183:54967236:54967843:54967892	54967183:54967236
exon_skip_96660	chr12	54967183:54967236:54967843:54967946:54973477:54973519	54967843:54967946

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
exon_skip_35615	Mayo_TC	3.532927e-01	4.613333e-01	-1.080407e-01	9.207769e-06

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Open reading frame (ORF) annotation in the exon skipping event for TESPA1

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
ENST00000316577	54961168	54961267	5CDS-5UTR
ENST00000449076	54961168	54961267	5CDS-5UTR
ENST00000316577	54967843	54967892	Frame-shift
ENST00000449076	54967843	54967892	Frame-shift
ENST00000316577	54966053	54966151	In-frame
ENST00000449076	54966053	54966151	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
ENST00000316577	54961168	54961267	5CDS-5UTR
ENST00000449076	54961168	54961267	5CDS-5UTR
ENST00000316577	54966053	54966151	In-frame
ENST00000449076	54966053	54966151	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
ENST00000316577	54961168	54961267	5CDS-5UTR
ENST00000449076	54961168	54961267	5CDS-5UTR
ENST00000316577	54967843	54967892	Frame-shift
ENST00000449076	54967843	54967892	Frame-shift
ENST00000316577	54966053	54966151	In-frame
ENST00000449076	54966053	54966151	In-frame
ENST00000316577	54967183	54967236	In-frame
ENST00000449076	54967183	54967236	In-frame

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Infer the effects of exon skipping event on protein functional features for TESPA1

p-ENSG00000135426_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
ENST00000316577	1915	521	54966053	54966151	458	555	116	148
ENST00000449076	2027	521	54966053	54966151	481	578	116	148

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
ENST00000316577	1915	521	54966053	54966151	458	555	116	148
ENST00000449076	2027	521	54966053	54966151	481	578	116	148

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
ENST00000316577	1915	521	54967183	54967236	367	419	85	103
ENST00000449076	2027	521	54967183	54967236	390	442	85	103
ENST00000316577	1915	521	54966053	54966151	458	555	116	148
ENST00000449076	2027	521	54966053	54966151	481	578	116	148

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
A2RU30	116	148	1	138	Alternative sequence	ID=VSP_030488;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:9872452;Dbxref=PMID:14702039,PMID:15489334,PMID:9872452
A2RU30	116	148	1	138	Alternative sequence	ID=VSP_030488;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:9872452;Dbxref=PMID:14702039,PMID:15489334,PMID:9872452
A2RU30	116	148	1	521	Chain	ID=PRO_0000315219;Note=Protein TESPA1
A2RU30	116	148	1	521	Chain	ID=PRO_0000315219;Note=Protein TESPA1

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
A2RU30	116	148	1	138	Alternative sequence	ID=VSP_030488;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:9872452;Dbxref=PMID:14702039,PMID:15489334,PMID:9872452
A2RU30	116	148	1	138	Alternative sequence	ID=VSP_030488;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:9872452;Dbxref=PMID:14702039,PMID:15489334,PMID:9872452
A2RU30	116	148	1	521	Chain	ID=PRO_0000315219;Note=Protein TESPA1
A2RU30	116	148	1	521	Chain	ID=PRO_0000315219;Note=Protein TESPA1

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
A2RU30	85	103	1	138	Alternative sequence	ID=VSP_030488;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:9872452;Dbxref=PMID:14702039,PMID:15489334,PMID:9872452
A2RU30	85	103	1	138	Alternative sequence	ID=VSP_030488;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:9872452;Dbxref=PMID:14702039,PMID:15489334,PMID:9872452
A2RU30	85	103	1	521	Chain	ID=PRO_0000315219;Note=Protein TESPA1
A2RU30	85	103	1	521	Chain	ID=PRO_0000315219;Note=Protein TESPA1
A2RU30	116	148	1	138	Alternative sequence	ID=VSP_030488;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:9872452;Dbxref=PMID:14702039,PMID:15489334,PMID:9872452
A2RU30	116	148	1	138	Alternative sequence	ID=VSP_030488;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:9872452;Dbxref=PMID:14702039,PMID:15489334,PMID:9872452
A2RU30	116	148	1	521	Chain	ID=PRO_0000315219;Note=Protein TESPA1
A2RU30	116	148	1	521	Chain	ID=PRO_0000315219;Note=Protein TESPA1

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3'-UTR located exon skipping events that lost miRNA binding sites in TESPA1

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 TESPA1

- 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 TESPA1

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 TESPA1

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 TESPA1

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for TESPA1

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 TESPA1

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 TESPA1

Gene structures and expression levels for TESPA1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for TESPA1

Open reading frame (ORF) annotation in the exon skipping event for TESPA1

Infer the effects of exon skipping event on protein functional features for TESPA1

3'-UTR located exon skipping events that lost miRNA binding sites in TESPA1

SNVs in the skipped exons for TESPA1

AD stage-associated exon skippint events for TESPA1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TESPA1

Correlation with RNA binding proteins (RBPs) for TESPA1

RelatedDrugs for TESPA1

RelatedDiseases for TESPA1