ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for SYTL2

Gene summary

Gene information	Gene symbol	SYTL2
	Gene ID	54843
	Gene name	synaptotagmin like 2
	Synonyms	CHR11SYT\|EXO4\|PPP1R151\|SGA72M\|SLP2\|SLP2A
	Cytomap	11q14.1
	Type of gene	protein-coding
	Description	synaptotagmin-like protein 2breast cancer-associated antigen SGA-72Mchromosome 11 synaptotagminexophilin-4protein phosphatase 1, regulatory subunit 151
	Modification date	20200320
	UniProtAcc	A0A024R5N9, A0A0U1RQH1, A0A0U1RQP0, A0A0U1RR07, A0A0U1RRJ3, A0A1Y8EH08, E9PIB5, E9PK22, E9PPL3, E9PQL8, E9PRW5, E9PS29, E9PS39, Q9HCH5,
	Context

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

Gene	GO ID	GO term	PubMed ID
SYTL2	GO:0006887	exocytosis	18812475
SYTL2	GO:0006904	vesicle docking involved in exocytosis	18812475
SYTL2	GO:0010923	negative regulation of phosphatase activity	19389623

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Gene structures and expression levels for SYTL2

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.

ENSG00000137501

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	DOWN	ENST00000529581.5	SYTL2-220:protein_coding:SYTL2	1.147776e+01	-1.452029e+00	5.306165e-04	1.714133e-02
PG	UP	ENST00000359152.9	SYTL2-203:protein_coding:SYTL2	1.964613e+01	6.164822e+00	1.287535e-03	1.748865e-02
CB	DOWN	ENST00000532995.5	SYTL2-225:nonsense_mediated_decay:SYTL2	1.323668e+02	-8.695432e-01	5.687505e-10	2.750511e-08
CB	DOWN	ENST00000525702.5	SYTL2-213:protein_coding:SYTL2	1.699600e+02	-8.606685e-01	7.083005e-09	2.253062e-07
TC	DOWN	ENST00000525702.5	SYTL2-213:protein_coding:SYTL2	3.073087e+02	-9.994985e-01	2.002766e-15	1.732657e-12
TC	DOWN	ENST00000532995.5	SYTL2-225:nonsense_mediated_decay:SYTL2	1.741866e+02	-1.528177e+00	1.227884e-13	5.968298e-11

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 SYTL2

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_10943	chr11	85714479:85714507:85717483:85717530:85718790:85718843	85717483:85717530
exon_skip_116769	chr11	85709467:85709500:85711113:85711232:85718790:85718842	85711113:85711232
exon_skip_121107	chr11	85714413:85714449:85717483:85717530:85718790:85718842	85717483:85717530
exon_skip_1217	chr11	85718790:85718843:85720858:85720959:85724032:85724713	85720858:85720959
exon_skip_137230	chr11	85709467:85709500:85711113:85711232:85718790:85718843	85711113:85711232
exon_skip_146780	chr11	85748272:85748423:85757625:85758114:85810954:85811129	85757625:85758114
exon_skip_153070	chr11	85720858:85720959:85724032:85727967:85733939:85734742	85724032:85727967
exon_skip_156173	chr11	85714479:85714507:85717483:85717726:85718790:85718843	85717483:85717726
exon_skip_15935	chr11	85711113:85711232:85714413:85714507:85717483:85717530	85714413:85714507
exon_skip_165394	chr11	85733939:85734742:85736501:85736615:85737575:85737656	85736501:85736615
exon_skip_16594	chr11	85714479:85714507:85716281:85716428:85718790:85719168	85716281:85716428
exon_skip_169452	chr11	85714413:85714449:85717483:85717530:85718790:85718843	85717483:85717530
exon_skip_18935	chr11	85714479:85714507:85717483:85717726:85718790:85718842	85717483:85717726
exon_skip_196682	chr11	85748411:85748423:85757625:85758114:85810954:85811141	85757625:85758114
exon_skip_202823	chr11	85707429:85707531:85708038:85708150:85709331:85709377	85708038:85708150
exon_skip_235200	chr11	85711113:85711232:85714413:85714507:85718790:85718843	85714413:85714507
exon_skip_243480	chr11	85704992:85705028:85707429:85707531:85709331:85709377	85707429:85707531
exon_skip_258715	chr11	85711113:85711232:85714413:85714507:85718790:85718842	85714413:85714507
exon_skip_282083	chr11	85720858:85720959:85727896:85727967:85733939:85734742	85727896:85727967
exon_skip_28578	chr11	85714479:85714507:85717483:85717530:85718790:85718842	85717483:85717530
exon_skip_293987	chr11	85700515:85700593:85704858:85705028:85707429:85707531	85704858:85705028
exon_skip_49272	chr11	85709467:85709500:85711113:85711232:85714413:85714449	85711113:85711232
exon_skip_58384	chr11	85733939:85734742:85736501:85736612:85737575:85737656	85736501:85736612
exon_skip_71571	chr11	85707429:85707531:85708038:85708150:85709331:85709375	85708038:85708150
exon_skip_97195	chr11	85748272:85748423:85757625:85758114:85810954:85811141	85757625:85758114

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 SYTL2

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
ENST00000528231	85714413	85714507	Frame-shift
ENST00000528231	85704858	85705028	In-frame
ENST00000528231	85711113	85711232	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
ENST00000528231	85714413	85714507	Frame-shift
ENST00000528231	85704858	85705028	In-frame
ENST00000528231	85711113	85711232	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
ENST00000528231	85707429	85707531	Frame-shift
ENST00000528231	85714413	85714507	Frame-shift
ENST00000528231	85736501	85736612	Frame-shift
ENST00000528231	85704858	85705028	In-frame
ENST00000528231	85711113	85711232	In-frame
ENST00000528231	85727896	85727967	In-frame

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Infer the effects of exon skipping event on protein functional features for SYTL2

p-ENSG00000137501_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
ENST00000528231	3553	934	85711113	85711232	1989	2107	570	609
ENST00000528231	3553	934	85704858	85705028	2382	2551	701	757

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
ENST00000528231	3553	934	85711113	85711232	1989	2107	570	609
ENST00000528231	3553	934	85704858	85705028	2382	2551	701	757

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
ENST00000528231	3553	934	85727896	85727967	1666	1736	462	486
ENST00000528231	3553	934	85711113	85711232	1989	2107	570	609
ENST00000528231	3553	934	85704858	85705028	2382	2551	701	757

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
Q9HCH5	570	609	570	570	Alternative sequence	ID=VSP_037906;Note=In isoform 7. E->M;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q9HCH5	570	609	571	610	Alternative sequence	ID=VSP_019004;Note=In isoform 3%2C isoform 4%2C isoform 8 and isoform 12. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10997877,ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334;Dbxref=PMID:10997877,PMID:1470
Q9HCH5	570	609	1	934	Chain	ID=PRO_0000190213;Note=Synaptotagmin-like protein 2
Q9HCH5	570	609	579	619	Compositional bias	Note=Ser-rich
Q9HCH5	570	609	603	603	Sequence conflict	Note=S->P;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9HCH5	701	757	1	934	Chain	ID=PRO_0000190213;Note=Synaptotagmin-like protein 2
Q9HCH5	701	757	629	733	Domain	Note=C2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00041
Q9HCH5	701	757	718	718	Sequence conflict	Note=I->V;Ontology_term=ECO:0000305;evidence=ECO:0000305

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
Q9HCH5	570	609	570	570	Alternative sequence	ID=VSP_037906;Note=In isoform 7. E->M;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q9HCH5	570	609	571	610	Alternative sequence	ID=VSP_019004;Note=In isoform 3%2C isoform 4%2C isoform 8 and isoform 12. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10997877,ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334;Dbxref=PMID:10997877,PMID:1470
Q9HCH5	570	609	1	934	Chain	ID=PRO_0000190213;Note=Synaptotagmin-like protein 2
Q9HCH5	570	609	579	619	Compositional bias	Note=Ser-rich
Q9HCH5	570	609	603	603	Sequence conflict	Note=S->P;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9HCH5	701	757	1	934	Chain	ID=PRO_0000190213;Note=Synaptotagmin-like protein 2
Q9HCH5	701	757	629	733	Domain	Note=C2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00041
Q9HCH5	701	757	718	718	Sequence conflict	Note=I->V;Ontology_term=ECO:0000305;evidence=ECO:0000305

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
Q9HCH5	462	486	1	569	Alternative sequence	ID=VSP_037896;Note=In isoform 7. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q9HCH5	462	486	1	558	Alternative sequence	ID=VSP_007885;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334
Q9HCH5	462	486	1	487	Alternative sequence	ID=VSP_037900;Note=In isoform 5%2C isoform 6 and isoform 8. MIDLSFLTEEEQEAIMKVLQRDAALKRAEEERVRHLPEKIKDDQQLKNMSGQWFYEAKAKRHRDKIHGADIIRASMRKKRPQIAAEQSKDRENGAKESWVNNVNKDAFLPPELAGVVEEPEEDAAPASPSSSVVNPASSVIDMSQENTRKPNVSPEKRKNPFNSSKLPEGHSSQQTKNEQSKNGRTGLFQTSKED
Q9HCH5	462	486	1	487	Alternative sequence	ID=VSP_037899;Note=In isoform 9. MIDLSFLTEEEQEAIMKVLQRDAALKRAEEERVRHLPEKIKDDQQLKNMSGQWFYEAKAKRHRDKIHGADIIRASMRKKRPQIAAEQSKDRENGAKESWVNNVNKDAFLPPELAGVVEEPEEDAAPASPSSSVVNPASSVIDMSQENTRKPNVSPEKRKNPFNSSKLPEGHSSQQTKNEQSKNGRTGLFQTSKEDELSESKEKSTVADTSIQKLEKSKQTLP
Q9HCH5	462	486	1	934	Chain	ID=PRO_0000190213;Note=Synaptotagmin-like protein 2
Q9HCH5	570	609	570	570	Alternative sequence	ID=VSP_037906;Note=In isoform 7. E->M;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q9HCH5	570	609	571	610	Alternative sequence	ID=VSP_019004;Note=In isoform 3%2C isoform 4%2C isoform 8 and isoform 12. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10997877,ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334;Dbxref=PMID:10997877,PMID:1470
Q9HCH5	570	609	1	934	Chain	ID=PRO_0000190213;Note=Synaptotagmin-like protein 2
Q9HCH5	570	609	579	619	Compositional bias	Note=Ser-rich
Q9HCH5	570	609	603	603	Sequence conflict	Note=S->P;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9HCH5	701	757	1	934	Chain	ID=PRO_0000190213;Note=Synaptotagmin-like protein 2
Q9HCH5	701	757	629	733	Domain	Note=C2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00041
Q9HCH5	701	757	718	718	Sequence conflict	Note=I->V;Ontology_term=ECO:0000305;evidence=ECO:0000305

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3'-UTR located exon skipping events that lost miRNA binding sites in SYTL2

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 SYTL2

- 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 SYTL2

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

ADstage

MSBB

IFG

exon_skip_10943

4.759445e-01

1.046534e-02

chr11

85714479

85714507

85717483

85717530

85718790

85718843

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SYTL2

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 SYTL2

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	RBM6	exon_skip_49272	-4.273881e-01	1.387179e-06
CB	NUP42	exon_skip_49272	4.243480e-01	1.677496e-06
IFG	NOVA1	exon_skip_10943	-4.304725e-01	2.221574e-02
STG	MSI1	exon_skip_10943	4.243297e-01	7.884934e-05
TC	RBM24	exon_skip_49272	4.569891e-01	1.583338e-09
TC	RALYL	exon_skip_49272	5.389869e-01	2.757964e-13

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RelatedDrugs for SYTL2

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 SYTL2

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 SYTL2

Gene structures and expression levels for SYTL2

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SYTL2

Open reading frame (ORF) annotation in the exon skipping event for SYTL2

Infer the effects of exon skipping event on protein functional features for SYTL2

3'-UTR located exon skipping events that lost miRNA binding sites in SYTL2

SNVs in the skipped exons for SYTL2

AD stage-associated exon skippint events for SYTL2

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SYTL2

Correlation with RNA binding proteins (RBPs) for SYTL2

RelatedDrugs for SYTL2

RelatedDiseases for SYTL2