ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for SRPK2

Gene summary

Gene information	Gene symbol	SRPK2
	Gene ID	6733
	Gene name	SRSF protein kinase 2
	Synonyms	SFRSK2
	Cytomap	7q22.3
	Type of gene	protein-coding
	Description	SRSF protein kinase 2SFRS protein kinase 2SR protein kinase 2SR-protein-specific kinase 2serine kinase SRPK2serine/arginine-rich protein-specific kinase 2serine/arginine-rich splicing factor kinase 2serine/threonine-protein kinase SRPK2
	Modification date	20180523
	UniProtAcc	P78362
	Context	PubMed: SRPK2 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID)

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

Gene	GO ID	GO term	PubMed ID
SRPK2	GO:0000245	spliceosomal complex assembly	9472028
SRPK2	GO:0006468	protein phosphorylation	9472028
SRPK2	GO:0008284	positive regulation of cell proliferation	18559500
SRPK2	GO:0008380	RNA splicing	9472028
SRPK2	GO:0035556	intracellular signal transduction	9472028
SRPK2	GO:0045070	positive regulation of viral genome replication	20498328
SRPK2	GO:0045071	negative regulation of viral genome replication	12417631

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Exon skipping events across known transcript of Ensembl for SRPK2 from UCSC genome browser

Skipped exons in TCGA and GTEx 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.

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Gene isoform structures and expression levels for SRPK2

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

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Exon skipping events with PSIs in TCGA for SRPK2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_478714	7	104758408:104758469:104766228:104766321:104766694:104766787	104766228:104766321	ENSG00000135250.12	ENST00000465072.1,ENST00000474770.1
exon_skip_478715	7	104758154:104758469:104766228:104766321:104767439:104767509	104766228:104766321	ENSG00000135250.12	ENST00000477925.1
exon_skip_478716	7	104758154:104758469:104766694:104766787:104767439:104767509	104766694:104766787	ENSG00000135250.12	ENST00000357311.3,ENST00000489828.1,ENST00000393651.3,ENST00000466917.1
exon_skip_478721	7	104766228:104766321:104766694:104766787:104767439:104767509	104766694:104766787	ENSG00000135250.12	ENST00000465072.1,ENST00000474770.1
exon_skip_478723	7	104783530:104783777:104785729:104785755:104786939:104787105	104785729:104785755	ENSG00000135250.12	ENST00000357311.3,ENST00000489828.1,ENST00000393651.3
exon_skip_478726	7	104785729:104785755:104786939:104787105:104800953:104801060	104786939:104787105	ENSG00000135250.12	ENST00000357311.3,ENST00000489828.1,ENST00000393651.3
exon_skip_478730	7	104809603:104809712:104844074:104844232:104909252:104909316	104844074:104844232	ENSG00000135250.12	ENST00000357311.3,ENST00000460391.1,ENST00000489828.1
exon_skip_478731	7	104809603:104809712:104844074:104844232:105029094:105029149	104844074:104844232	ENSG00000135250.12	ENST00000393651.3,ENST00000482897.1
exon_skip_478733	7	104844073:104844232:104846847:104846976:104909252:104909316	104846847:104846976	ENSG00000135250.12	ENST00000462282.1
exon_skip_478734	7	104844169:104844232:104909252:104909316:104937867:104937980	104909252:104909316	ENSG00000135250.12	ENST00000489828.1,ENST00000465112.1
exon_skip_478736	7	104844169:104844232:104909252:104909316:105029094:105029149	104909252:104909316	ENSG00000135250.12	ENST00000460391.1,ENST00000482862.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for SRPK2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_478714	7	104758408:104758469:104766228:104766321:104766694:104766787	104766228:104766321	ENSG00000135250.12	ENST00000465072.1,ENST00000474770.1
exon_skip_478715	7	104758154:104758469:104766228:104766321:104767439:104767509	104766228:104766321	ENSG00000135250.12	ENST00000477925.1
exon_skip_478716	7	104758154:104758469:104766694:104766787:104767439:104767509	104766694:104766787	ENSG00000135250.12	ENST00000393651.3,ENST00000357311.3,ENST00000466917.1,ENST00000489828.1
exon_skip_478721	7	104766228:104766321:104766694:104766787:104767439:104767509	104766694:104766787	ENSG00000135250.12	ENST00000465072.1,ENST00000474770.1
exon_skip_478723	7	104783530:104783777:104785729:104785755:104786939:104787105	104785729:104785755	ENSG00000135250.12	ENST00000393651.3,ENST00000357311.3,ENST00000489828.1
exon_skip_478726	7	104785729:104785755:104786939:104787105:104800953:104801060	104786939:104787105	ENSG00000135250.12	ENST00000393651.3,ENST00000357311.3,ENST00000489828.1
exon_skip_478730	7	104809603:104809712:104844074:104844232:104909252:104909316	104844074:104844232	ENSG00000135250.12	ENST00000357311.3,ENST00000489828.1,ENST00000460391.1
exon_skip_478731	7	104809603:104809712:104844074:104844232:105029094:105029149	104844074:104844232	ENSG00000135250.12	ENST00000393651.3,ENST00000482897.1
exon_skip_478733	7	104844073:104844232:104846847:104846976:104909252:104909316	104846847:104846976	ENSG00000135250.12	ENST00000462282.1
exon_skip_478734	7	104844169:104844232:104909252:104909316:104937867:104937980	104909252:104909316	ENSG00000135250.12	ENST00000489828.1,ENST00000465112.1
exon_skip_478736	7	104844169:104844232:104909252:104909316:105029094:105029149	104909252:104909316	ENSG00000135250.12	ENST00000460391.1,ENST00000482862.1
exon_skip_478740	7	104844169:104844232:105029094:105029149:105029237:105029341	105029094:105029149	ENSG00000135250.12	ENST00000393651.3
exon_skip_478741	7	104909252:104909316:104937867:104937980:104946882:104947018	104937867:104937980	ENSG00000135250.12	ENST00000465112.1
exon_skip_478744	7	104937867:104937980:104946882:104947018:105029094:105029149	104946882:104947018	ENSG00000135250.12	ENST00000465112.1

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for SRPK2

Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000489828	104909252	104909316	3UTR-3CDS
ENST00000357311	104785729	104785755	Frame-shift
ENST00000489828	104785729	104785755	Frame-shift
ENST00000357311	104786939	104787105	Frame-shift
ENST00000489828	104786939	104787105	Frame-shift
ENST00000357311	104844074	104844232	Frame-shift
ENST00000489828	104844074	104844232	Frame-shift
ENST00000357311	104766694	104766787	In-frame
ENST00000489828	104766694	104766787	In-frame

Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000489828	104909252	104909316	3UTR-3CDS
ENST00000357311	104785729	104785755	Frame-shift
ENST00000489828	104785729	104785755	Frame-shift
ENST00000357311	104786939	104787105	Frame-shift
ENST00000489828	104786939	104787105	Frame-shift
ENST00000357311	104844074	104844232	Frame-shift
ENST00000489828	104844074	104844232	Frame-shift
ENST00000357311	104766694	104766787	In-frame
ENST00000489828	104766694	104766787	In-frame

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Infer the effects of exon skipping event on protein functional features for SRPK2

Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.

Loci of skipped exons in TCGA 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
ENST00000357311	3717	688	104766694	104766787	1962	2054	596	627
ENST00000489828	2577	688	104766694	104766787	1971	2063	596	627

Loci of skipped exons in GTEx 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
ENST00000357311	3717	688	104766694	104766787	1962	2054	596	627
ENST00000489828	2577	688	104766694	104766787	1971	2063	596	627

Lost protein functional features of individual exon skipping events in TCGA.

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
P78362	596	627	1	688	Chain	ID=PRO_0000086677;Note=SRSF protein kinase 2
P78362	596	627	1	688	Chain	ID=PRO_0000086677;Note=SRSF protein kinase 2
P78362	596	627	140	688	Chain	ID=PRO_0000414752;Note=SRSF protein kinase 2 C-terminal
P78362	596	627	140	688	Chain	ID=PRO_0000414752;Note=SRSF protein kinase 2 C-terminal
P78362	596	627	81	684	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P78362	596	627	81	684	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P78362	596	627	594	606	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2X7G
P78362	596	627	594	606	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2X7G
P78362	596	627	611	614	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2X7G
P78362	596	627	611	614	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2X7G
P78362	596	627	620	623	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2X7G
P78362	596	627	620	623	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2X7G
P78362	596	627	608	608	Natural variant	ID=VAR_060390;Note=S->N;Dbxref=dbSNP:rs1050413
P78362	596	627	608	608	Natural variant	ID=VAR_060390;Note=S->N;Dbxref=dbSNP:rs1050413
P78362	596	627	615	615	Natural variant	ID=VAR_057111;Note=L->I;Dbxref=dbSNP:rs1050418
P78362	596	627	615	615	Natural variant	ID=VAR_057111;Note=L->I;Dbxref=dbSNP:rs1050418
P78362	596	627	601	601	Sequence conflict	Note=H->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
P78362	596	627	601	601	Sequence conflict	Note=H->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
P78362	596	627	608	609	Sequence conflict	Note=SI->KV;Ontology_term=ECO:0000305;evidence=ECO:0000305
P78362	596	627	608	609	Sequence conflict	Note=SI->KV;Ontology_term=ECO:0000305;evidence=ECO:0000305
P78362	596	627	612	616	Sequence conflict	Note=HFALS->KYAML;Ontology_term=ECO:0000305;evidence=ECO:0000305
P78362	596	627	612	616	Sequence conflict	Note=HFALS->KYAML;Ontology_term=ECO:0000305;evidence=ECO:0000305
P78362	596	627	621	621	Sequence conflict	Note=R->K;Ontology_term=ECO:0000305;evidence=ECO:0000305
P78362	596	627	621	621	Sequence conflict	Note=R->K;Ontology_term=ECO:0000305;evidence=ECO:0000305
P78362	596	627	625	627	Sequence conflict	Note=NRR->TRK;Ontology_term=ECO:0000305;evidence=ECO:0000305
P78362	596	627	625	627	Sequence conflict	Note=NRR->TRK;Ontology_term=ECO:0000305;evidence=ECO:0000305

Lost protein functional features of individual exon skipping events in GTEx.

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
P78362	596	627	1	688	Chain	ID=PRO_0000086677;Note=SRSF protein kinase 2
P78362	596	627	1	688	Chain	ID=PRO_0000086677;Note=SRSF protein kinase 2
P78362	596	627	140	688	Chain	ID=PRO_0000414752;Note=SRSF protein kinase 2 C-terminal
P78362	596	627	140	688	Chain	ID=PRO_0000414752;Note=SRSF protein kinase 2 C-terminal
P78362	596	627	81	684	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P78362	596	627	81	684	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P78362	596	627	594	606	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2X7G
P78362	596	627	594	606	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2X7G
P78362	596	627	611	614	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2X7G
P78362	596	627	611	614	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2X7G
P78362	596	627	620	623	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2X7G
P78362	596	627	620	623	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2X7G
P78362	596	627	608	608	Natural variant	ID=VAR_060390;Note=S->N;Dbxref=dbSNP:rs1050413
P78362	596	627	608	608	Natural variant	ID=VAR_060390;Note=S->N;Dbxref=dbSNP:rs1050413
P78362	596	627	615	615	Natural variant	ID=VAR_057111;Note=L->I;Dbxref=dbSNP:rs1050418
P78362	596	627	615	615	Natural variant	ID=VAR_057111;Note=L->I;Dbxref=dbSNP:rs1050418
P78362	596	627	601	601	Sequence conflict	Note=H->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
P78362	596	627	601	601	Sequence conflict	Note=H->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
P78362	596	627	608	609	Sequence conflict	Note=SI->KV;Ontology_term=ECO:0000305;evidence=ECO:0000305
P78362	596	627	608	609	Sequence conflict	Note=SI->KV;Ontology_term=ECO:0000305;evidence=ECO:0000305
P78362	596	627	612	616	Sequence conflict	Note=HFALS->KYAML;Ontology_term=ECO:0000305;evidence=ECO:0000305
P78362	596	627	612	616	Sequence conflict	Note=HFALS->KYAML;Ontology_term=ECO:0000305;evidence=ECO:0000305
P78362	596	627	621	621	Sequence conflict	Note=R->K;Ontology_term=ECO:0000305;evidence=ECO:0000305
P78362	596	627	621	621	Sequence conflict	Note=R->K;Ontology_term=ECO:0000305;evidence=ECO:0000305
P78362	596	627	625	627	Sequence conflict	Note=NRR->TRK;Ontology_term=ECO:0000305;evidence=ECO:0000305
P78362	596	627	625	627	Sequence conflict	Note=NRR->TRK;Ontology_term=ECO:0000305;evidence=ECO:0000305

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SNVs in the skipped exons for SRPK2

- Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.

- Differential PSIs between mutated versus non-mutated samples.

- Non-synonymous mutations located in the skipped exons in TCGA.

Cancer type	Sample	ESID	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
LIHC	TCGA-G3-A3CJ-01	exon_skip_478730 exon_skip_478731	104844075	104844232	104844151	104844151	Frame_Shift_Del	G	-	p.P40fs

- Depth of coverage in the three exons composing exon skipping event

Depth of coverage in three exons

Mutation description

- 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
HCC2450_LUNG	104786940	104787105	104786974	104786974	Missense_Mutation	C	G	p.Q251H
HOP92_LUNG	104786940	104787105	104787044	104787044	Missense_Mutation	G	T	p.P228Q
BHT101_THYROID	104786940	104787105	104787050	104787050	Missense_Mutation	A	G	p.I226T
R262_CENTRAL_NERVOUS_SYSTEM	104844075	104844232	104844080	104844080	Missense_Mutation	C	T	p.C75Y
T24_URINARY_TRACT	104844075	104844232	104844110	104844110	Missense_Mutation	T	G	p.D65A
SLR20_KIDNEY	104844075	104844232	104844110	104844110	Missense_Mutation	T	G	p.D65A
ACCS_URINARY_TRACT	104844075	104844232	104844110	104844110	Missense_Mutation	T	G	p.D65A
KNS62_LUNG	104844075	104844232	104844230	104844230	Missense_Mutation	G	A	p.P25L
NCIH2110_LUNG	104785730	104785755	104785741	104785741	Nonsense_Mutation	G	A	p.Q268*
OMC1_CERVIX	104785730	104785755	104785754	104785754	Splice_Site	C	T	p.V263V

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SRPK2

sQTL information located at the skipped exons.

Exon skip ID

Chromosome

Three exons

Skippped exon

ENST

Cancer type

SNP id

Location

DNA change (ref/var)

P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SRPK2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SRPK2

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RelatedDrugs for SRPK2

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for SRPK2

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 TCGA
	Exon skipping events with PSIs in GTEx
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	SNVs in the skipped exons with depth of coverage
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Splicing Quantitative Trait Methylation (sQTM) in the skipped exon
	Related drugs with this gene
	Related diseases with this gene

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