ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for SF1

Gene summary

Gene information	Gene symbol	SF1
	Gene ID	7536
	Gene name	splicing factor 1
	Synonyms	BBP\|D11S636\|MBBP\|ZCCHC25\|ZFM1\|ZNF162
	Cytomap	11q13.1
	Type of gene	protein-coding
	Description	splicing factor 1mammalian branch point-binding proteintranscription factor ZFM1zinc finger gene in MEN1 locuszinc finger protein 162
	Modification date	20180526
	UniProtAcc	Q15637
	Context	PubMed: SF1 [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 SF1 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 SF1

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 SF1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_73983	11	64532761:64532990:64533422:64533627:64534371:64534409	64533422:64533627	ENSG00000168066.16	ENST00000334944.5
exon_skip_73990	11	64532761:64532990:64534371:64534551:64534663:64534718	64534371:64534551	ENSG00000168066.16	ENST00000227503.9,ENST00000448404.1,ENST00000422298.2,ENST00000443908.1,ENST00000377387.1,ENST00000377394.3
exon_skip_73993	11	64533511:64533627:64534371:64534551:64534663:64534718	64534371:64534551	ENSG00000168066.16	ENST00000334944.5,ENST00000486867.1,ENST00000433274.2,ENST00000413725.1,ENST00000377390.3
exon_skip_73995	11	64534538:64534551:64534663:64534718:64535042:64535118	64534663:64534718	ENSG00000168066.16	ENST00000486867.1
exon_skip_73996	11	64534538:64534551:64534663:64534723:64535038:64535089	64534663:64534723	ENSG00000168066.16	ENST00000448404.1,ENST00000413725.1,ENST00000377394.3
exon_skip_73997	11	64534538:64534551:64534663:64534723:64535042:64535118	64534663:64534723	ENSG00000168066.16	ENST00000334944.5,ENST00000227503.9,ENST00000477596.1,ENST00000422298.2,ENST00000433274.2,ENST00000377387.1,ENST00000377390.3
exon_skip_73998	11	64534538:64534551:64534663:64534747:64535042:64535118	64534663:64534747	ENSG00000168066.16	ENST00000443908.1
exon_skip_74001	11	64536749:64536810:64536897:64537081:64537435:64537525	64536897:64537081	ENSG00000168066.16	ENST00000486960.1,ENST00000334944.5,ENST00000227503.9,ENST00000448404.1,ENST00000422298.2,ENST00000433274.2,ENST00000377387.1,ENST00000377394.3,ENST00000377390.3
exon_skip_74009	11	64537851:64537880:64540901:64540977:64543969:64544098	64540901:64540977	ENSG00000168066.16	ENST00000334944.5,ENST00000413951.1,ENST00000227503.9,ENST00000432725.1,ENST00000433274.2,ENST00000377387.1,ENST00000377394.3,ENST00000377390.3
exon_skip_74011	11	64543969:64544098:64545458:64545618:64545833:64545976	64545458:64545618	ENSG00000168066.16	ENST00000413951.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for SF1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_73983	11	64532761:64532990:64533422:64533627:64534371:64534409	64533422:64533627	ENSG00000168066.16	ENST00000334944.5
exon_skip_73990	11	64532761:64532990:64534371:64534551:64534663:64534718	64534371:64534551	ENSG00000168066.16	ENST00000377387.1,ENST00000227503.9,ENST00000448404.1,ENST00000377394.3,ENST00000422298.2,ENST00000443908.1
exon_skip_73993	11	64533511:64533627:64534371:64534551:64534663:64534718	64534371:64534551	ENSG00000168066.16	ENST00000377390.3,ENST00000334944.5,ENST00000413725.1,ENST00000433274.2,ENST00000486867.1
exon_skip_73995	11	64534538:64534551:64534663:64534718:64535042:64535118	64534663:64534718	ENSG00000168066.16	ENST00000486867.1
exon_skip_73996	11	64534538:64534551:64534663:64534723:64535038:64535089	64534663:64534723	ENSG00000168066.16	ENST00000448404.1,ENST00000377394.3,ENST00000413725.1
exon_skip_73997	11	64534538:64534551:64534663:64534723:64535042:64535118	64534663:64534723	ENSG00000168066.16	ENST00000377387.1,ENST00000377390.3,ENST00000227503.9,ENST00000334944.5,ENST00000422298.2,ENST00000433274.2,ENST00000477596.1
exon_skip_73998	11	64534538:64534551:64534663:64534747:64535042:64535118	64534663:64534747	ENSG00000168066.16	ENST00000443908.1
exon_skip_74001	11	64536749:64536810:64536897:64537081:64537435:64537525	64536897:64537081	ENSG00000168066.16	ENST00000377387.1,ENST00000377390.3,ENST00000227503.9,ENST00000448404.1,ENST00000377394.3,ENST00000334944.5,ENST00000422298.2,ENST00000433274.2,ENST00000486960.1
exon_skip_74009	11	64537851:64537880:64540901:64540977:64543969:64544098	64540901:64540977	ENSG00000168066.16	ENST00000377387.1,ENST00000377390.3,ENST00000227503.9,ENST00000377394.3,ENST00000334944.5,ENST00000433274.2,ENST00000413951.1,ENST00000432725.1
exon_skip_74011	11	64543969:64544098:64545458:64545618:64545833:64545976	64545458:64545618	ENSG00000168066.16	ENST00000413951.1

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 SF1

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
ENST00000377390	64536897	64537081	Frame-shift
ENST00000377390	64540901	64540977	Frame-shift
ENST00000377390	64534371	64534551	In-frame
ENST00000377390	64534663	64534723	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
ENST00000377390	64536897	64537081	Frame-shift
ENST00000377390	64540901	64540977	Frame-shift
ENST00000377390	64534371	64534551	In-frame
ENST00000377390	64534663	64534723	In-frame

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Infer the effects of exon skipping event on protein functional features for SF1

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
ENST00000377390	3487	639	64534663	64534723	1681	1740	447	467
ENST00000377390	3487	639	64534371	64534551	1741	1920	467	527

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
ENST00000377390	3487	639	64534663	64534723	1681	1740	447	467
ENST00000377390	3487	639	64534371	64534551	1741	1920	467	527

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

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

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SNVs in the skipped exons for SF1

- 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.

SF1_ESCA_exon_skip_73983_psi_boxplot.png
boxplot

SF1_HNSC_exon_skip_73983_psi_boxplot.png
boxplot

- 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
ESCA	TCGA-LN-A4A5-01	exon_skip_73983	64533423	64533627	64533469	64533469	Frame_Shift_Del	C	-	p.A581fs
LIHC	TCGA-DD-A3A0-01	exon_skip_73990 exon_skip_73993	64534372	64534551	64534485	64534485	Frame_Shift_Del	G	-	p.P493fs
COAD	TCGA-CM-4743-01	exon_skip_74001	64536898	64537081	64537024	64537024	Frame_Shift_Del	C	-	p.K305fs
STAD	TCGA-HU-A4G8-01	exon_skip_74001	64536898	64537081	64537024	64537024	Frame_Shift_Del	C	-	p.K180fs
STAD	TCGA-HU-A4G8-01	exon_skip_74001	64536898	64537081	64537024	64537024	Frame_Shift_Del	C	-	p.K305fs
LIHC	TCGA-DD-A3A0-01	exon_skip_74009	64540902	64540977	64540917	64540917	Frame_Shift_Del	G	-	p.P199fs
LIHC	TCGA-DD-A3A0-01	exon_skip_74009	64540902	64540977	64540917	64540917	Frame_Shift_Del	G	-	p.P74fs
STAD	TCGA-D7-A4YV-01	exon_skip_74009	64540902	64540977	64540917	64540917	Frame_Shift_Del	G	-	p.P199fs
STAD	TCGA-D7-A4YV-01	exon_skip_74009	64540902	64540977	64540917	64540917	Frame_Shift_Del	G	-	p.P74fs
HNSC	TCGA-BA-4078-01	exon_skip_73983	64533423	64533627	64533489	64533490	Frame_Shift_Ins	-	G	p.A574fs
LUAD	TCGA-64-1680-01	exon_skip_73995	64534664	64534718	64534716	64534716	Nonsense_Mutation	G	T	p.Y450*
LUAD	TCGA-64-1680-01	exon_skip_73997 exon_skip_73996	64534664	64534723	64534716	64534716	Nonsense_Mutation	G	T	p.Y450*
LUAD	TCGA-64-1680-01	exon_skip_73998	64534664	64534747	64534716	64534716	Nonsense_Mutation	G	T	p.Y450*

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-64-1680-01
	Cancer type: LUAD
	ESID: exon_skip_73998
	Skipped exon start: 64534664
	Skipped exon end: 64534747
	Mutation start: 64534716
	Mutation end: 64534716
	Mutation type: Nonsense_Mutation
	Reference seq: G
	Mutation seq: T
	AAchange: p.Y450*
	Sample: TCGA-64-1680-01
	Cancer type: LUAD
	ESID: exon_skip_73996
	Skipped exon start: 64534664
	Skipped exon end: 64534723
	Mutation start: 64534716
	Mutation end: 64534716
	Mutation type: Nonsense_Mutation
	Reference seq: G
	Mutation seq: T
	AAchange: p.Y450*
	Sample: TCGA-64-1680-01
	Cancer type: LUAD
	ESID: exon_skip_73995
	Skipped exon start: 64534664
	Skipped exon end: 64534718
	Mutation start: 64534716
	Mutation end: 64534716
	Mutation type: Nonsense_Mutation
	Reference seq: G
	Mutation seq: T
	AAchange: p.Y450*
exon_skip_346610_LUAD_TCGA-64-1680-01.png
exon_skip_73998_LUAD_TCGA-64-1680-01.png
	Sample: TCGA-LN-A4A5-01
	Cancer type: ESCA
	ESID: exon_skip_73983
	Skipped exon start: 64533423
	Skipped exon end: 64533627
	Mutation start: 64533469
	Mutation end: 64533469
	Mutation type: Frame_Shift_Del
	Reference seq: C
	Mutation seq: -
	AAchange: p.A581fs
exon_skip_73983_ESCA_TCGA-LN-A4A5-01.png
	Sample: TCGA-BA-4078-01
	Cancer type: HNSC
	ESID: exon_skip_73983
	Skipped exon start: 64533423
	Skipped exon end: 64533627
	Mutation start: 64533489
	Mutation end: 64533490
	Mutation type: Frame_Shift_Ins
	Reference seq: -
	Mutation seq: G
	AAchange: p.A574fs
exon_skip_351842_HNSC_TCGA-BA-4078-01.png
exon_skip_389812_HNSC_TCGA-BA-4078-01.png
exon_skip_73983_HNSC_TCGA-BA-4078-01.png

- 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	64533423	64533627	64533497	64533497	Frame_Shift_Del	G	-	p.P571fs
NCIH630_LARGE_INTESTINE	64534372	64534551	64534485	64534485	Frame_Shift_Del	G	-	p.P493fs
MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	64536898	64537081	64537024	64537024	Frame_Shift_Del	C	-	p.G179fs
LS411N_LARGE_INTESTINE	64536898	64537081	64537024	64537024	Frame_Shift_Del	C	-	p.G179fs
HS936T_SKIN	64533423	64533627	64533496	64533497	Frame_Shift_Ins	-	G	p.G572fs
Y79_AUTONOMIC_GANGLIA	64533423	64533627	64533427	64533427	Missense_Mutation	T	A	p.M595L
KMS12BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	64533423	64533627	64533462	64533462	Missense_Mutation	G	A	p.P583L
CCK81_LARGE_INTESTINE	64533423	64533627	64533496	64533496	Missense_Mutation	C	G	p.G572R
CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	64533423	64533627	64533537	64533537	Missense_Mutation	G	T	p.P558H
BICR18_UPPER_AERODIGESTIVE_TRACT	64533423	64533627	64533541	64533541	Missense_Mutation	C	T	p.A557T
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	64533423	64533627	64533541	64533541	Missense_Mutation	C	T	p.A557T
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	64533423	64533627	64533541	64533541	Missense_Mutation	C	T	p.A557T
OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	64533423	64533627	64533541	64533541	Missense_Mutation	C	T	p.A557T
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	64533423	64533627	64533564	64533564	Missense_Mutation	G	A	p.A549V
BICR18_UPPER_AERODIGESTIVE_TRACT	64533423	64533627	64533576	64533576	Missense_Mutation	T	C	p.Q545R
GP5D_LARGE_INTESTINE	64534372	64534551	64534410	64534410	Missense_Mutation	C	T	p.S515N
SARC9371_BONE	64534372	64534551	64534420	64534420	Missense_Mutation	G	A	p.P512S
NCIH1651_LUNG	64534372	64534551	64534459	64534459	Missense_Mutation	G	C	p.P499A
HCC15_LUNG	64534372	64534551	64534495	64534495	Missense_Mutation	C	A	p.G487W
HEC59_ENDOMETRIUM	64534372	64534551	64534515	64534515	Missense_Mutation	G	A	p.P480L
CP50EBV_MATCHED_NORMAL_TISSUE	64534372	64534551	64534515	64534515	Missense_Mutation	G	A	p.P480L
CP50MELB_SKIN	64534372	64534551	64534515	64534515	Missense_Mutation	G	A	p.P480L
MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	64534372	64534551	64534522	64534522	Missense_Mutation	T	A	p.M478L
MM426_SKIN	64536898	64537081	64536947	64536947	Missense_Mutation	G	A	p.A205V
SISO_CERVIX	64536898	64537081	64536993	64536993	Missense_Mutation	G	A	p.R190C
GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	64536898	64537081	64536993	64536993	Missense_Mutation	G	A	p.R190C
NCIH1355_LUNG	64536898	64537081	64537001	64537001	Missense_Mutation	T	G	p.K187T
HCT15_LARGE_INTESTINE	64536898	64537081	64537016	64537016	Missense_Mutation	G	T	p.S182Y
NCIH650_LUNG	64536898	64537081	64537043	64537043	Missense_Mutation	G	T	p.A173D
PCI4B_UPPER_AERODIGESTIVE_TRACT	64536898	64537081	64537071	64537071	Missense_Mutation	G	C	p.L164V
GP2D_LARGE_INTESTINE	64536898	64537081	64537074	64537074	Missense_Mutation	T	C	p.T163A
FEPD_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	64540902	64540977	64540939	64540939	Missense_Mutation	T	A	p.T67S
SNU1040_LARGE_INTESTINE	64534372	64534551	64534492	64534492	Nonsense_Mutation	G	A	p.Q488*
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	64534664	64534747	64534721	64534721	Nonsense_Mutation	G	A	p.Q449*
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	64534664	64534723	64534721	64534721	Nonsense_Mutation	G	A	p.Q449*
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	64534664	64534718	64534721	64534721	Nonsense_Mutation	G	A	p.Q449*
MFE319_ENDOMETRIUM	64536898	64537081	64536898	64536898	Splice_Site	C	T	p.Q221Q

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SF1

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 SF1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SF1

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RelatedDrugs for SF1

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 SF1

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
SF1	C0025202	melanoma	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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