ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for SEL1L3

Gene summary

Gene information	Gene symbol	SEL1L3
	Gene ID	23231
	Gene name	SEL1L family member 3
	Synonyms	Sel-1L3
	Cytomap	4p15.2
	Type of gene	protein-coding
	Description	protein sel-1 homolog 3sel-1 suppressor of lin-12-like 3suppressor of lin-12-like protein 3
	Modification date	20180519
	UniProtAcc	Q68CR1
	Context	PubMed: SEL1L3 [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

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Exon skipping events across known transcript of Ensembl for SEL1L3 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 SEL1L3

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 SEL1L3

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_428909	4	25759155:25759228:25759309:25759412:25760562:25760576	25759309:25759412	ENSG00000091490.6	ENST00000513416.1,ENST00000399878.3,ENST00000510448.1,ENST00000264868.5,ENST00000502949.1
exon_skip_428913	4	25759309:25759412:25760562:25760690:25766947:25766982	25760562:25760690	ENSG00000091490.6	ENST00000399878.3,ENST00000510448.1,ENST00000264868.5,ENST00000502949.1
exon_skip_428916	4	25769205:25769231:25769361:25769452:25777898:25777982	25769361:25769452	ENSG00000091490.6	ENST00000399878.3,ENST00000509290.1,ENST00000264868.5,ENST00000502949.1
exon_skip_428919	4	25769361:25769452:25777898:25777982:25780697:25780825	25777898:25777982	ENSG00000091490.6	ENST00000399878.3,ENST00000264868.5,ENST00000502949.1
exon_skip_428922	4	25777898:25777982:25780697:25780825:25783863:25784040	25780697:25780825	ENSG00000091490.6	ENST00000399878.3,ENST00000264868.5,ENST00000502949.1
exon_skip_428923	4	25783863:25784040:25785849:25785912:25789845:25789986	25785849:25785912	ENSG00000091490.6	ENST00000399878.3,ENST00000264868.5,ENST00000502949.1
exon_skip_428925	4	25785849:25785912:25789845:25789986:25792076:25792196	25789845:25789986	ENSG00000091490.6	ENST00000399878.3,ENST00000264868.5,ENST00000502949.1
exon_skip_428926	4	25792076:25792196:25803904:25804084:25806162:25806374	25803904:25804084	ENSG00000091490.6	ENST00000399878.3,ENST00000264868.5,ENST00000502949.1
exon_skip_428928	4	25806162:25806374:25819759:25819900:25821429:25821562	25819759:25819900	ENSG00000091490.6	ENST00000399878.3,ENST00000264868.5,ENST00000502949.1
exon_skip_428931	4	25823617:25823750:25831719:25831778:25834616:25834732	25831719:25831778	ENSG00000091490.6	ENST00000399878.3,ENST00000264868.5,ENST00000502949.1
exon_skip_428936	4	25835069:25835191:25836818:25836945:25848915:25849137	25836818:25836945	ENSG00000091490.6	ENST00000399878.3,ENST00000264868.5,ENST00000502949.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for SEL1L3

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_428909	4	25759155:25759228:25759309:25759412:25760562:25760576	25759309:25759412	ENSG00000091490.6	ENST00000399878.3,ENST00000264868.5,ENST00000513416.1,ENST00000502949.1,ENST00000510448.1
exon_skip_428913	4	25759309:25759412:25760562:25760690:25766947:25766982	25760562:25760690	ENSG00000091490.6	ENST00000399878.3,ENST00000264868.5,ENST00000502949.1,ENST00000510448.1
exon_skip_428916	4	25769205:25769231:25769361:25769452:25777898:25777982	25769361:25769452	ENSG00000091490.6	ENST00000399878.3,ENST00000264868.5,ENST00000502949.1,ENST00000509290.1
exon_skip_428919	4	25769361:25769452:25777898:25777982:25780697:25780825	25777898:25777982	ENSG00000091490.6	ENST00000399878.3,ENST00000264868.5,ENST00000502949.1
exon_skip_428922	4	25777898:25777982:25780697:25780825:25783863:25784040	25780697:25780825	ENSG00000091490.6	ENST00000399878.3,ENST00000264868.5,ENST00000502949.1
exon_skip_428923	4	25783863:25784040:25785849:25785912:25789845:25789986	25785849:25785912	ENSG00000091490.6	ENST00000399878.3,ENST00000264868.5,ENST00000502949.1
exon_skip_428925	4	25785849:25785912:25789845:25789986:25792076:25792196	25789845:25789986	ENSG00000091490.6	ENST00000399878.3,ENST00000264868.5,ENST00000502949.1
exon_skip_428926	4	25792076:25792196:25803904:25804084:25806162:25806374	25803904:25804084	ENSG00000091490.6	ENST00000399878.3,ENST00000264868.5,ENST00000502949.1
exon_skip_428931	4	25823617:25823750:25831719:25831778:25834616:25834732	25831719:25831778	ENSG00000091490.6	ENST00000399878.3,ENST00000264868.5,ENST00000502949.1
exon_skip_428936	4	25835069:25835191:25836818:25836945:25848915:25849137	25836818:25836945	ENSG00000091490.6	ENST00000399878.3,ENST00000264868.5,ENST00000502949.1

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 SEL1L3

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
ENST00000399878	25759309	25759412	Frame-shift
ENST00000399878	25760562	25760690	Frame-shift
ENST00000399878	25769361	25769452	Frame-shift
ENST00000399878	25780697	25780825	Frame-shift
ENST00000399878	25831719	25831778	Frame-shift
ENST00000399878	25836818	25836945	Frame-shift
ENST00000399878	25777898	25777982	In-frame
ENST00000399878	25785849	25785912	In-frame
ENST00000399878	25789845	25789986	In-frame
ENST00000399878	25803904	25804084	In-frame
ENST00000399878	25819759	25819900	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
ENST00000399878	25759309	25759412	Frame-shift
ENST00000399878	25760562	25760690	Frame-shift
ENST00000399878	25769361	25769452	Frame-shift
ENST00000399878	25780697	25780825	Frame-shift
ENST00000399878	25831719	25831778	Frame-shift
ENST00000399878	25836818	25836945	Frame-shift
ENST00000399878	25777898	25777982	In-frame
ENST00000399878	25785849	25785912	In-frame
ENST00000399878	25789845	25789986	In-frame
ENST00000399878	25803904	25804084	In-frame

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Infer the effects of exon skipping event on protein functional features for SEL1L3

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
ENST00000399878	4531	1132	25819759	25819900	1547	1687	474	521
ENST00000399878	4531	1132	25803904	25804084	1900	2079	592	652
ENST00000399878	4531	1132	25789845	25789986	2200	2340	692	739
ENST00000399878	4531	1132	25785849	25785912	2341	2403	739	760
ENST00000399878	4531	1132	25777898	25777982	2709	2792	862	889

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
ENST00000399878	4531	1132	25803904	25804084	1900	2079	592	652
ENST00000399878	4531	1132	25789845	25789986	2200	2340	692	739
ENST00000399878	4531	1132	25785849	25785912	2341	2403	739	760
ENST00000399878	4531	1132	25777898	25777982	2709	2792	862	889

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
Q68CR1	474	521	1	1132	Chain	ID=PRO_0000321894;Note=Protein sel-1 homolog 3
Q68CR1	592	652	1	1132	Chain	ID=PRO_0000321894;Note=Protein sel-1 homolog 3
Q68CR1	592	652	608	608	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q68CR1	592	652	575	609	Repeat	Note=Sel1-like 1
Q68CR1	592	652	611	647	Repeat	Note=Sel1-like 2
Q68CR1	692	739	1	1132	Chain	ID=PRO_0000321894;Note=Protein sel-1 homolog 3
Q68CR1	692	739	694	730	Repeat	Note=Sel1-like 3
Q68CR1	692	739	732	767	Repeat	Note=Sel1-like 4
Q68CR1	739	760	1	1132	Chain	ID=PRO_0000321894;Note=Protein sel-1 homolog 3
Q68CR1	739	760	732	767	Repeat	Note=Sel1-like 4
Q68CR1	862	889	1	1132	Chain	ID=PRO_0000321894;Note=Protein sel-1 homolog 3
Q68CR1	862	889	840	877	Repeat	Note=Sel1-like 7

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
Q68CR1	592	652	1	1132	Chain	ID=PRO_0000321894;Note=Protein sel-1 homolog 3
Q68CR1	592	652	608	608	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q68CR1	592	652	575	609	Repeat	Note=Sel1-like 1
Q68CR1	592	652	611	647	Repeat	Note=Sel1-like 2
Q68CR1	692	739	1	1132	Chain	ID=PRO_0000321894;Note=Protein sel-1 homolog 3
Q68CR1	692	739	694	730	Repeat	Note=Sel1-like 3
Q68CR1	692	739	732	767	Repeat	Note=Sel1-like 4
Q68CR1	739	760	1	1132	Chain	ID=PRO_0000321894;Note=Protein sel-1 homolog 3
Q68CR1	739	760	732	767	Repeat	Note=Sel1-like 4
Q68CR1	862	889	1	1132	Chain	ID=PRO_0000321894;Note=Protein sel-1 homolog 3
Q68CR1	862	889	840	877	Repeat	Note=Sel1-like 7

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SNVs in the skipped exons for SEL1L3

- 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-DD-A3A0-01	exon_skip_428916	25769362	25769452	25769415	25769415	Frame_Shift_Del	T	-	p.T903fs
STAD	TCGA-BR-8682-01	exon_skip_428922	25780698	25780825	25780725	25780725	Frame_Shift_Del	A	-	p.F853fs
ESCA	TCGA-LN-A8I0-01	exon_skip_428925	25789846	25789986	25789889	25789889	Frame_Shift_Del	T	-	p.E725fs
STAD	TCGA-IN-A6RO-01	exon_skip_428925	25789846	25789986	25789889	25789892	Frame_Shift_Del	TCCG	-	p.724_725del
STAD	TCGA-IN-A6RO-01	exon_skip_428925	25789846	25789986	25789889	25789892	Frame_Shift_Del	TCCG	-	p.TE724fs
UCEC	TCGA-A5-A0GB-01	exon_skip_428926	25803905	25804084	25803988	25803988	Frame_Shift_Del	G	-	p.L625fs
KIRP	TCGA-HE-A5NL-01	exon_skip_428928	25819760	25819900	25819805	25819806	Frame_Shift_Ins	-	T	p.H507fs
KIRP	TCGA-HE-A5NL-01	exon_skip_428928	25819760	25819900	25819805	25819806	Frame_Shift_Ins	-	T	p.K506fs
HNSC	TCGA-T2-A6X2-01	exon_skip_428913	25760563	25760690	25760611	25760611	Nonsense_Mutation	G	C	p.S1012*
THYM	TCGA-5V-A9RR-01	exon_skip_428922	25780698	25780825	25780763	25780763	Nonsense_Mutation	C	T	p.W840*
THYM	TCGA-5V-A9RR-01	exon_skip_428922	25780698	25780825	25780763	25780763	Nonsense_Mutation	C	T	p.W840X
SKCM	TCGA-GN-A26C-01	exon_skip_428922	25780698	25780825	25780821	25780821	Nonsense_Mutation	A	T	p.L821*
SKCM	TCGA-EE-A2GC-06	exon_skip_428926	25803905	25804084	25803907	25803907	Nonsense_Mutation	G	A	p.Q652*
SKCM	TCGA-EE-A2GC-06	exon_skip_428926	25803905	25804084	25803907	25803907	Nonsense_Mutation	G	A	p.Q652X

- 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
697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	25760563	25760690	25760666	25760666	Frame_Shift_Del	T	-	p.I994fs
SISO_CERVIX	25785850	25785912	25785854	25785855	Frame_Shift_Ins	-	A	p.S759fs
GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	25785850	25785912	25785854	25785855	Frame_Shift_Ins	-	A	p.S759fs
IGROV1_OVARY	25831720	25831778	25831757	25831758	Frame_Shift_Ins	-	A	p.G374fs
JHOC5_OVARY	25760563	25760690	25760567	25760567	Missense_Mutation	C	T	p.E1027K
MZ2MEL_SKIN	25760563	25760690	25760576	25760576	Missense_Mutation	C	T	p.E1024K
L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	25769362	25769452	25769400	25769400	Missense_Mutation	A	G	p.S908P
NCIH196_LUNG	25769362	25769452	25769409	25769409	Missense_Mutation	T	C	p.I905V
LNCAPCLONEFGC_PROSTATE	25777899	25777982	25777921	25777921	Missense_Mutation	T	C	p.N883D
CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	25777899	25777982	25777932	25777932	Missense_Mutation	C	T	p.R879H
HSC4_UPPER_AERODIGESTIVE_TRACT	25777899	25777982	25777934	25777934	Missense_Mutation	G	C	p.I878M
VCAP_PROSTATE	25777899	25777982	25777938	25777938	Missense_Mutation	A	G	p.V877A
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	25785850	25785912	25785887	25785887	Missense_Mutation	C	A	p.R748L
BT474_BREAST	25785850	25785912	25785893	25785893	Missense_Mutation	T	G	p.N746T
NB1643_AUTONOMIC_GANGLIA	25785850	25785912	25785905	25785905	Missense_Mutation	C	T	p.G742E
EN_ENDOMETRIUM	25789846	25789986	25789865	25789865	Missense_Mutation	T	C	p.Y733C
SW1783_CENTRAL_NERVOUS_SYSTEM	25789846	25789986	25789892	25789892	Missense_Mutation	G	A	p.T724M
LS180_LARGE_INTESTINE	25789846	25789986	25789902	25789902	Missense_Mutation	C	T	p.A721T
GOTO_AUTONOMIC_GANGLIA	25789846	25789986	25789902	25789902	Missense_Mutation	C	T	p.A721T
MFE319_ENDOMETRIUM	25789846	25789986	25789917	25789917	Missense_Mutation	A	G	p.W716R
PC9_LUNG	25819760	25819900	25819769	25819769	Missense_Mutation	G	T	p.L519M
PC14_LUNG	25819760	25819900	25819769	25819769	Missense_Mutation	G	T	p.L519M
CW2_LARGE_INTESTINE	25819760	25819900	25819843	25819843	Missense_Mutation	C	T	p.C494Y
JHUEM7_ENDOMETRIUM	25819760	25819900	25819867	25819867	Missense_Mutation	C	T	p.R486H
NEC8_TESTIS	25831720	25831778	25831733	25831733	Missense_Mutation	T	G	p.N382H
MHHPREB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	25831720	25831778	25831741	25831741	Missense_Mutation	C	T	p.S379N
OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	25831720	25831778	25831768	25831768	Missense_Mutation	G	A	p.T370I
OPM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	25831720	25831778	25831768	25831768	Missense_Mutation	G	A	p.T370I
SNU1040_LARGE_INTESTINE	25836819	25836945	25836840	25836840	Missense_Mutation	C	T	p.R280H
EN_ENDOMETRIUM	25836819	25836945	25836862	25836862	Nonsense_Mutation	G	A	p.R273*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SEL1L3

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 SEL1L3

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SEL1L3

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RelatedDrugs for SEL1L3

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 SEL1L3

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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Gene summary for SEL1L3

Exon skipping events across known transcript of Ensembl for SEL1L3 from UCSC genome browser

Gene isoform structures and expression levels for SEL1L3

Exon skipping events with PSIs in TCGA for SEL1L3

Exon skipping events with PSIs in GTEx for SEL1L3

Open reading frame (ORF) annotation in the exon skipping event for SEL1L3

Infer the effects of exon skipping event on protein functional features for SEL1L3

SNVs in the skipped exons for SEL1L3

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SEL1L3

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SEL1L3

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SEL1L3

RelatedDrugs for SEL1L3

RelatedDiseases for SEL1L3