ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for PACSIN2

Gene summary

Gene information	Gene symbol	PACSIN2
	Gene ID	11252
	Gene name	protein kinase C and casein kinase substrate in neurons 2
	Synonyms	SDPII
	Cytomap	22q13.2
	Type of gene	protein-coding
	Description	protein kinase C and casein kinase substrate in neurons protein 2cytoplasmic phosphoprotein PACSIN2syndapin-2syndapin-IIsyndapin2
	Modification date	20180523
	UniProtAcc	Q9UNF0
	Context	PubMed: PACSIN2 [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
PACSIN2	GO:0097320	plasma membrane tubulation	23596323

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Exon skipping events across known transcript of Ensembl for PACSIN2 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 PACSIN2

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 PACSIN2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_370162	22	43272142:43272339:43272893:43273016:43275053:43275172	43272893:43273016	ENSG00000100266.13	ENST00000402229.1,ENST00000263246.3,ENST00000403744.3
exon_skip_370166	22	43275053:43275175:43278189:43278310:43280391:43280567	43278189:43278310	ENSG00000100266.13	ENST00000337959.4,ENST00000402229.1,ENST00000263246.3,ENST00000407585.1,ENST00000403744.3
exon_skip_370168	22	43284648:43284804:43286952:43287188:43289462:43289619	43286952:43287188	ENSG00000100266.13	ENST00000337959.4,ENST00000402229.1,ENST00000263246.3,ENST00000407585.1,ENST00000403744.3
exon_skip_370171	22	43289579:43289619:43305432:43305571:43308026:43308097	43305432:43305571	ENSG00000100266.13	ENST00000445706.1
exon_skip_370178	22	43289579:43289619:43308026:43308163:43342902:43343047	43308026:43308163	ENSG00000100266.13	ENST00000403744.3
exon_skip_370179	22	43289579:43289619:43308026:43308163:43355577:43355905	43308026:43308163	ENSG00000100266.13	ENST00000453079.1
exon_skip_370180	22	43289579:43289619:43308026:43308163:43355768:43355884	43308026:43308163	ENSG00000100266.13	ENST00000402229.1
exon_skip_370181	22	43289579:43289619:43308026:43308163:43355804:43355887	43308026:43308163	ENSG00000100266.13	ENST00000407585.1
exon_skip_370185	22	43289579:43289619:43308026:43308163:43411026:43411104	43308026:43308163	ENSG00000100266.13	ENST00000337959.4,ENST00000263246.3
exon_skip_370199	22	43308026:43308163:43389625:43389786:43411026:43411104	43389625:43389786	ENSG00000100266.13	ENST00000453643.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for PACSIN2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_370162	22	43272142:43272339:43272893:43273016:43275053:43275172	43272893:43273016	ENSG00000100266.13	ENST00000263246.3,ENST00000403744.3,ENST00000402229.1
exon_skip_370166	22	43275053:43275175:43278189:43278310:43280391:43280567	43278189:43278310	ENSG00000100266.13	ENST00000263246.3,ENST00000337959.4,ENST00000407585.1,ENST00000403744.3,ENST00000402229.1
exon_skip_370168	22	43284648:43284804:43286952:43287188:43289462:43289619	43286952:43287188	ENSG00000100266.13	ENST00000263246.3,ENST00000337959.4,ENST00000407585.1,ENST00000403744.3,ENST00000402229.1
exon_skip_370171	22	43289579:43289619:43305432:43305571:43308026:43308097	43305432:43305571	ENSG00000100266.13	ENST00000445706.1
exon_skip_370178	22	43289579:43289619:43308026:43308163:43342902:43343047	43308026:43308163	ENSG00000100266.13	ENST00000403744.3
exon_skip_370179	22	43289579:43289619:43308026:43308163:43355577:43355905	43308026:43308163	ENSG00000100266.13	ENST00000453079.1
exon_skip_370180	22	43289579:43289619:43308026:43308163:43355768:43355884	43308026:43308163	ENSG00000100266.13	ENST00000402229.1
exon_skip_370181	22	43289579:43289619:43308026:43308163:43355804:43355887	43308026:43308163	ENSG00000100266.13	ENST00000407585.1
exon_skip_370185	22	43289579:43289619:43308026:43308163:43411026:43411104	43308026:43308163	ENSG00000100266.13	ENST00000263246.3,ENST00000337959.4
exon_skip_370199	22	43308026:43308163:43389625:43389786:43411026:43411104	43389625:43389786	ENSG00000100266.13	ENST00000453643.1

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 PACSIN2

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
ENST00000263246	43308026	43308163	3UTR-3CDS
ENST00000402229	43308026	43308163	3UTR-3CDS
ENST00000403744	43308026	43308163	3UTR-3CDS
ENST00000263246	43278189	43278310	Frame-shift
ENST00000402229	43278189	43278310	Frame-shift
ENST00000403744	43278189	43278310	Frame-shift
ENST00000263246	43286952	43287188	Frame-shift
ENST00000402229	43286952	43287188	Frame-shift
ENST00000403744	43286952	43287188	Frame-shift
ENST00000263246	43272893	43273016	In-frame
ENST00000402229	43272893	43273016	In-frame
ENST00000403744	43272893	43273016	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
ENST00000263246	43308026	43308163	3UTR-3CDS
ENST00000402229	43308026	43308163	3UTR-3CDS
ENST00000403744	43308026	43308163	3UTR-3CDS
ENST00000263246	43278189	43278310	Frame-shift
ENST00000402229	43278189	43278310	Frame-shift
ENST00000403744	43278189	43278310	Frame-shift
ENST00000263246	43286952	43287188	Frame-shift
ENST00000402229	43286952	43287188	Frame-shift
ENST00000403744	43286952	43287188	Frame-shift
ENST00000263246	43272893	43273016	In-frame
ENST00000402229	43272893	43273016	In-frame
ENST00000403744	43272893	43273016	In-frame

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Infer the effects of exon skipping event on protein functional features for PACSIN2

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
ENST00000263246	3266	486	43272893	43273016	1231	1353	343	383
ENST00000402229	1900	486	43272893	43273016	1222	1344	343	383
ENST00000403744	2127	486	43272893	43273016	1251	1373	343	383

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
ENST00000263246	3266	486	43272893	43273016	1231	1353	343	383
ENST00000402229	1900	486	43272893	43273016	1222	1344	343	383
ENST00000403744	2127	486	43272893	43273016	1251	1373	343	383

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
Q9UNF0	343	383	344	384	Alternative sequence	ID=VSP_004517;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11230166,ECO:0000303\|Ref.6;Dbxref=PMID:11230166
Q9UNF0	343	383	344	384	Alternative sequence	ID=VSP_004517;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11230166,ECO:0000303\|Ref.6;Dbxref=PMID:11230166
Q9UNF0	343	383	344	384	Alternative sequence	ID=VSP_004517;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11230166,ECO:0000303\|Ref.6;Dbxref=PMID:11230166
Q9UNF0	343	383	1	486	Chain	ID=PRO_0000161795;Note=Protein kinase C and casein kinase substrate in neurons protein 2
Q9UNF0	343	383	1	486	Chain	ID=PRO_0000161795;Note=Protein kinase C and casein kinase substrate in neurons protein 2
Q9UNF0	343	383	1	486	Chain	ID=PRO_0000161795;Note=Protein kinase C and casein kinase substrate in neurons protein 2
Q9UNF0	343	383	362	364	Motif	Note=NPF1
Q9UNF0	343	383	362	364	Motif	Note=NPF1
Q9UNF0	343	383	362	364	Motif	Note=NPF1
Q9UNF0	343	383	378	380	Sequence conflict	Note=DDT->EDI;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UNF0	343	383	378	380	Sequence conflict	Note=DDT->EDI;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UNF0	343	383	378	380	Sequence conflict	Note=DDT->EDI;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
Q9UNF0	343	383	344	384	Alternative sequence	ID=VSP_004517;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11230166,ECO:0000303\|Ref.6;Dbxref=PMID:11230166
Q9UNF0	343	383	344	384	Alternative sequence	ID=VSP_004517;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11230166,ECO:0000303\|Ref.6;Dbxref=PMID:11230166
Q9UNF0	343	383	344	384	Alternative sequence	ID=VSP_004517;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11230166,ECO:0000303\|Ref.6;Dbxref=PMID:11230166
Q9UNF0	343	383	1	486	Chain	ID=PRO_0000161795;Note=Protein kinase C and casein kinase substrate in neurons protein 2
Q9UNF0	343	383	1	486	Chain	ID=PRO_0000161795;Note=Protein kinase C and casein kinase substrate in neurons protein 2
Q9UNF0	343	383	1	486	Chain	ID=PRO_0000161795;Note=Protein kinase C and casein kinase substrate in neurons protein 2
Q9UNF0	343	383	362	364	Motif	Note=NPF1
Q9UNF0	343	383	362	364	Motif	Note=NPF1
Q9UNF0	343	383	362	364	Motif	Note=NPF1
Q9UNF0	343	383	378	380	Sequence conflict	Note=DDT->EDI;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UNF0	343	383	378	380	Sequence conflict	Note=DDT->EDI;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UNF0	343	383	378	380	Sequence conflict	Note=DDT->EDI;Ontology_term=ECO:0000305;evidence=ECO:0000305

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SNVs in the skipped exons for PACSIN2

- 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
UCEC	TCGA-AP-A0LE-01	exon_skip_370162	43272894	43273016	43272955	43272956	Frame_Shift_Ins	-	T	p.P363fs
UCEC	TCGA-AP-A0LE-01	exon_skip_370166	43278190	43278310	43278237	43278237	Nonsense_Mutation	G	A	p.R287*
HNSC	TCGA-CN-4723-01	exon_skip_370168	43286953	43287188	43287098	43287098	Nonsense_Mutation	G	T	p.S103*
BLCA	TCGA-GU-AATQ-01	exon_skip_370168	43286953	43287188	43287141	43287141	Nonsense_Mutation	C	A	p.E89*
HNSC	TCGA-DQ-5624-01	exon_skip_370181 exon_skip_370185 exon_skip_370179 exon_skip_370178 exon_skip_370180	43308027	43308163	43308053	43308053	Nonsense_Mutation	C	A	p.E12*

- 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
HEC59_ENDOMETRIUM	43272894	43273016	43273010	43273010	Frame_Shift_Del	A	-	p.L345fs
HS229T_FIBROBLAST	43272894	43273016	43272907	43272907	Missense_Mutation	T	C	p.T380A
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	43272894	43273016	43272936	43272936	Missense_Mutation	G	A	p.T370M
CROAP3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	43278190	43278310	43278216	43278216	Missense_Mutation	T	C	p.M294V
GMEL_SKIN	43278190	43278310	43278272	43278272	Missense_Mutation	C	T	p.R275K
CAOV4_OVARY	43286953	43287188	43287046	43287046	Missense_Mutation	A	C	p.F120L
MM386_SKIN	43308027	43308163	43308035	43308035	Missense_Mutation	A	G	p.F18L
IGR1_SKIN	43308027	43308163	43308074	43308074	Missense_Mutation	A	G	p.Y5H
LS411N_LARGE_INTESTINE	43278190	43278310	43278202	43278202	Nonsense_Mutation	C	T	p.W298*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PACSIN2

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
exon_skip_370166	22	43275053:43275175:43278189:43278310:43280391:43280567	43278189:43278310	ENST00000337959.4,ENST00000402229.1,ENST00000263246.3,ENST00000407585.1,ENST00000403744.3	CESC	rs2899365	chr22:43278220	C/T	9.69e-05
exon_skip_370166	22	43275053:43275175:43278189:43278310:43280391:43280567	43278189:43278310	ENST00000337959.4,ENST00000402229.1,ENST00000263246.3,ENST00000407585.1,ENST00000403744.3	COAD	rs2899365	chr22:43278220	C/T	7.63e-07
exon_skip_370166	22	43275053:43275175:43278189:43278310:43280391:43280567	43278189:43278310	ENST00000337959.4,ENST00000402229.1,ENST00000263246.3,ENST00000407585.1,ENST00000403744.3	BLCA	rs2899365	chr22:43278220	C/T	6.96e-11
exon_skip_370166	22	43275053:43275175:43278189:43278310:43280391:43280567	43278189:43278310	ENST00000337959.4,ENST00000402229.1,ENST00000263246.3,ENST00000407585.1,ENST00000403744.3	HNSC	rs2899365	chr22:43278220	C/T	4.33e-16
exon_skip_370166	22	43275053:43275175:43278189:43278310:43280391:43280567	43278189:43278310	ENST00000337959.4,ENST00000402229.1,ENST00000263246.3,ENST00000407585.1,ENST00000403744.3	LGG	rs2899365	chr22:43278220	C/T	5.78e-04
exon_skip_370166	22	43275053:43275175:43278189:43278310:43280391:43280567	43278189:43278310	ENST00000337959.4,ENST00000402229.1,ENST00000263246.3,ENST00000407585.1,ENST00000403744.3	LGG	rs2899365	chr22:43278220	C/T	3.56e-03
exon_skip_370166	22	43275053:43275175:43278189:43278310:43280391:43280567	43278189:43278310	ENST00000337959.4,ENST00000402229.1,ENST00000263246.3,ENST00000407585.1,ENST00000403744.3	KIRC	rs2899365	chr22:43278220	C/T	4.73e-05
exon_skip_370166	22	43275053:43275175:43278189:43278310:43280391:43280567	43278189:43278310	ENST00000337959.4,ENST00000402229.1,ENST00000263246.3,ENST00000407585.1,ENST00000403744.3	LUSC	rs2899365	chr22:43278220	C/T	9.57e-08
exon_skip_370166	22	43275053:43275175:43278189:43278310:43280391:43280567	43278189:43278310	ENST00000337959.4,ENST00000402229.1,ENST00000263246.3,ENST00000407585.1,ENST00000403744.3	READ	rs2899365	chr22:43278220	C/T	4.03e-05
exon_skip_370166	22	43275053:43275175:43278189:43278310:43280391:43280567	43278189:43278310	ENST00000337959.4,ENST00000402229.1,ENST00000263246.3,ENST00000407585.1,ENST00000403744.3	PCPG	rs2899365	chr22:43278220	C/T	1.94e-09
exon_skip_370166	22	43275053:43275175:43278189:43278310:43280391:43280567	43278189:43278310	ENST00000337959.4,ENST00000402229.1,ENST00000263246.3,ENST00000407585.1,ENST00000403744.3	PAAD	rs2899365	chr22:43278220	C/T	6.08e-04
exon_skip_370166	22	43275053:43275175:43278189:43278310:43280391:43280567	43278189:43278310	ENST00000337959.4,ENST00000402229.1,ENST00000263246.3,ENST00000407585.1,ENST00000403744.3	PRAD	rs2899365	chr22:43278220	C/T	5.78e-05
exon_skip_370166	22	43275053:43275175:43278189:43278310:43280391:43280567	43278189:43278310	ENST00000337959.4,ENST00000402229.1,ENST00000263246.3,ENST00000407585.1,ENST00000403744.3	SARC	rs2899365	chr22:43278220	C/T	5.03e-04
exon_skip_370166	22	43275053:43275175:43278189:43278310:43280391:43280567	43278189:43278310	ENST00000337959.4,ENST00000402229.1,ENST00000263246.3,ENST00000407585.1,ENST00000403744.3	THCA	rs2899365	chr22:43278220	C/T	1.54e-19
exon_skip_370166	22	43275053:43275175:43278189:43278310:43280391:43280567	43278189:43278310	ENST00000337959.4,ENST00000402229.1,ENST00000263246.3,ENST00000407585.1,ENST00000403744.3	UCEC	rs2899365	chr22:43278220	C/T	8.14e-05

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PACSIN2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PACSIN2

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RelatedDrugs for PACSIN2

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 PACSIN2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
PACSIN2	C3495559	Juvenile arthritis	1	CTD_human

	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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