ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for FOXN3

Gene summary

Gene information	Gene symbol	FOXN3
	Gene ID	1112
	Gene name	forkhead box N3
	Synonyms	C14orf116\|CHES1\|PRO1635
	Cytomap	14q31.3-q32.11
	Type of gene	protein-coding
	Description	forkhead box protein N3checkpoint suppressor 1
	Modification date	20180519
	UniProtAcc	O00409
	Context	PubMed: FOXN3 [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
FOXN3	GO:0045892	negative regulation of transcription, DNA-templated	16102918

Top

Exon skipping events across known transcript of Ensembl for FOXN3 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.

Top

Gene isoform structures and expression levels for FOXN3

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

Top

Exon skipping events with PSIs in TCGA for FOXN3

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_114924	14	89629221:89629313:89647044:89647150:89656727:89656793	89647044:89647150	ENSG00000053254.11	ENST00000345097.4,ENST00000261302.5
exon_skip_114925	14	89629221:89629313:89647044:89647150:89747293:89747358	89647044:89647150	ENSG00000053254.11	ENST00000555353.1,ENST00000557258.1
exon_skip_114927	14	89647133:89647150:89656727:89656793:89747293:89747350	89656727:89656793	ENSG00000053254.11	ENST00000345097.4,ENST00000261302.5
exon_skip_114929	14	89647133:89647150:89656730:89656793:89747293:89747350	89656730:89656793	ENSG00000053254.11	ENST00000553840.1
exon_skip_114932	14	89647133:89647150:89747293:89747358:89817015:89817135	89747293:89747358	ENSG00000053254.11	ENST00000555353.1,ENST00000557258.1
exon_skip_114934	14	89656730:89656793:89747293:89747358:89817015:89817135	89747293:89747358	ENSG00000053254.11	ENST00000345097.4,ENST00000553840.1,ENST00000261302.5,ENST00000553353.1
exon_skip_114937	14	89747293:89747358:89750771:89750866:89817015:89817152	89750771:89750866	ENSG00000053254.11	ENST00000557718.1
exon_skip_114941	14	89747293:89747358:89799457:89799603:89817015:89817135	89799457:89799603	ENSG00000053254.11	ENST00000554005.1
exon_skip_114942	14	89747293:89747358:89817015:89817152:89878277:89878361	89817015:89817152	ENSG00000053254.11	ENST00000555353.1,ENST00000345097.4,ENST00000553840.1,ENST00000557258.1,ENST00000261302.5,ENST00000556916.1
exon_skip_114944	14	89817071:89817152:89878277:89878834:89952912:89953012	89878277:89878834	ENSG00000053254.11	ENST00000555855.1
exon_skip_114947	14	89878656:89878834:89952912:89953015:90085371:90085474	89952912:89953015	ENSG00000053254.11	ENST00000555855.1

PSI values of skipped exons in TCGA.

Top

Exon skipping events with PSIs in GTEx for FOXN3

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_114924	14	89629221:89629313:89647044:89647150:89656727:89656793	89647044:89647150	ENSG00000053254.11	ENST00000345097.4,ENST00000261302.5
exon_skip_114925	14	89629221:89629313:89647044:89647150:89747293:89747358	89647044:89647150	ENSG00000053254.11	ENST00000557258.1,ENST00000555353.1
exon_skip_114927	14	89647133:89647150:89656727:89656793:89747293:89747350	89656727:89656793	ENSG00000053254.11	ENST00000345097.4,ENST00000261302.5
exon_skip_114929	14	89647133:89647150:89656730:89656793:89747293:89747350	89656730:89656793	ENSG00000053254.11	ENST00000553840.1
exon_skip_114932	14	89647133:89647150:89747293:89747358:89817015:89817135	89747293:89747358	ENSG00000053254.11	ENST00000557258.1,ENST00000555353.1
exon_skip_114934	14	89656730:89656793:89747293:89747358:89817015:89817135	89747293:89747358	ENSG00000053254.11	ENST00000345097.4,ENST00000261302.5,ENST00000553840.1,ENST00000553353.1
exon_skip_114937	14	89747293:89747358:89750771:89750866:89817015:89817152	89750771:89750866	ENSG00000053254.11	ENST00000557718.1
exon_skip_114941	14	89747293:89747358:89799457:89799603:89817015:89817135	89799457:89799603	ENSG00000053254.11	ENST00000554005.1
exon_skip_114942	14	89747293:89747358:89817015:89817152:89878277:89878361	89817015:89817152	ENSG00000053254.11	ENST00000345097.4,ENST00000261302.5,ENST00000557258.1,ENST00000555353.1,ENST00000553840.1,ENST00000556916.1
exon_skip_114944	14	89817071:89817152:89878277:89878834:89952912:89953012	89878277:89878834	ENSG00000053254.11	ENST00000555855.1
exon_skip_114947	14	89878656:89878834:89952912:89953015:90085371:90085474	89952912:89953015	ENSG00000053254.11	ENST00000555855.1

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

Top

Open reading frame (ORF) annotation in the exon skipping event for FOXN3

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
ENST00000261302	89647044	89647150	Frame-shift
ENST00000345097	89647044	89647150	Frame-shift
ENST00000261302	89747293	89747358	Frame-shift
ENST00000345097	89747293	89747358	Frame-shift
ENST00000261302	89817015	89817152	Frame-shift
ENST00000345097	89817015	89817152	Frame-shift
ENST00000261302	89656727	89656793	In-frame
ENST00000345097	89656727	89656793	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
ENST00000261302	89647044	89647150	Frame-shift
ENST00000345097	89647044	89647150	Frame-shift
ENST00000261302	89747293	89747358	Frame-shift
ENST00000345097	89747293	89747358	Frame-shift
ENST00000261302	89817015	89817152	Frame-shift
ENST00000345097	89817015	89817152	Frame-shift
ENST00000261302	89656727	89656793	In-frame
ENST00000345097	89656727	89656793	In-frame

Top

Infer the effects of exon skipping event on protein functional features for FOXN3

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
ENST00000261302	7735	490	89656727	89656793	762	827	248	270
ENST00000345097	7849	490	89656727	89656793	863	928	248	270

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
ENST00000261302	7735	490	89656727	89656793	762	827	248	270
ENST00000345097	7849	490	89656727	89656793	863	928	248	270

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
O00409	248	270	249	271	Alternative sequence	ID=VSP_001551;Note=In isoform 2. DPDIDAASAMMLLNTPPEIQAGF->V;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
O00409	248	270	249	271	Alternative sequence	ID=VSP_001551;Note=In isoform 2. DPDIDAASAMMLLNTPPEIQAGF->V;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
O00409	248	270	1	490	Chain	ID=PRO_0000091869;Note=Forkhead box protein N3
O00409	248	270	1	490	Chain	ID=PRO_0000091869;Note=Forkhead box protein N3

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
O00409	248	270	249	271	Alternative sequence	ID=VSP_001551;Note=In isoform 2. DPDIDAASAMMLLNTPPEIQAGF->V;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
O00409	248	270	249	271	Alternative sequence	ID=VSP_001551;Note=In isoform 2. DPDIDAASAMMLLNTPPEIQAGF->V;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
O00409	248	270	1	490	Chain	ID=PRO_0000091869;Note=Forkhead box protein N3
O00409	248	270	1	490	Chain	ID=PRO_0000091869;Note=Forkhead box protein N3

Top

SNVs in the skipped exons for FOXN3

- 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.

FOXN3_LUSC_exon_skip_114927_psi_boxplot.png
boxplot

FOXN3_LUSC_exon_skip_114929_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
LIHC	TCGA-DD-A39Y-01	exon_skip_114924 exon_skip_114925	89647045	89647150	89647104	89647104	Frame_Shift_Del	C	-	p.G286fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_114924 exon_skip_114925	89647045	89647150	89647104	89647104	Frame_Shift_Del	C	-	p.G286fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_114944	89878278	89878834	89878299	89878299	Frame_Shift_Del	T	-	p.K174fs
LIHC	TCGA-DD-A39Y-01	exon_skip_114944	89878278	89878834	89878473	89878473	Frame_Shift_Del	G	-	p.P116fs
COAD	TCGA-A6-6653-01	exon_skip_114944	89878278	89878834	89878534	89878534	Frame_Shift_Del	G	-	p.P96fs
COAD	TCGA-A6-6781-01	exon_skip_114944	89878278	89878834	89878534	89878534	Frame_Shift_Del	G	-	p.P96fs
STAD	TCGA-BR-4370-01	exon_skip_114944	89878278	89878834	89878534	89878534	Frame_Shift_Del	G	-	p.P96fs
STAD	TCGA-BR-7851-01	exon_skip_114944	89878278	89878834	89878534	89878534	Frame_Shift_Del	G	-	p.P96fs
STAD	TCGA-BR-8360-01	exon_skip_114944	89878278	89878834	89878534	89878534	Frame_Shift_Del	G	-	p.P96fs
STAD	TCGA-CD-A4MG-01	exon_skip_114944	89878278	89878834	89878534	89878534	Frame_Shift_Del	G	-	p.P96fs
STAD	TCGA-D7-A4YV-01	exon_skip_114944	89878278	89878834	89878534	89878534	Frame_Shift_Del	G	-	p.P96fs
STAD	TCGA-HU-A4GT-01	exon_skip_114944	89878278	89878834	89878534	89878534	Frame_Shift_Del	G	-	p.P96fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_114944	89878278	89878834	89878634	89878634	Frame_Shift_Del	G	-	p.L63fs
COAD	TCGA-AA-3713-01	exon_skip_114944	89878278	89878834	89878533	89878534	Frame_Shift_Ins	-	G	p.P96fs
KIRC	TCGA-A3-3365-01	exon_skip_114944	89878278	89878834	89878533	89878534	Frame_Shift_Ins	-	G	p.L96fs
STAD	TCGA-CG-5721-01	exon_skip_114944	89878278	89878834	89878533	89878534	Frame_Shift_Ins	-	G	p.P96fs
STAD	TCGA-MX-A5UJ-01	exon_skip_114944	89878278	89878834	89878533	89878534	Frame_Shift_Ins	-	G	p.L96fs
STAD	TCGA-MX-A5UJ-01	exon_skip_114944	89878278	89878834	89878533	89878534	Frame_Shift_Ins	-	G	p.P96fs
BLCA	TCGA-ZF-AA51-01	exon_skip_114944	89878278	89878834	89878715	89878715	Nonsense_Mutation	G	A	p.Q36*
LUSC	TCGA-63-6202-01	exon_skip_114927 exon_skip_114929	89656728	89656793	89656795	89656795	Splice_Site	T	C	p.D249_splice
LUSC	TCGA-63-6202-01	exon_skip_114927 exon_skip_114929	89656731	89656793	89656795	89656795	Splice_Site	T	C	p.D249_splice
KICH	TCGA-KN-8428-01	exon_skip_114942	89817016	89817152	89817014	89817014	Splice_Site	A	G	p.S227_splice

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-63-6202-01
	Cancer type: LUSC
	ESID: exon_skip_114929
	Skipped exon start: 89656728
	Skipped exon end: 89656793
	Mutation start: 89656795
	Mutation end: 89656795
	Mutation type: Splice_Site
	Reference seq: T
	Mutation seq: C
	AAchange: p.D249_splice
	Sample: TCGA-63-6202-01
	Cancer type: LUSC
	ESID: exon_skip_114929
	Skipped exon start: 89656731
	Skipped exon end: 89656793
	Mutation start: 89656795
	Mutation end: 89656795
	Mutation type: Splice_Site
	Reference seq: T
	Mutation seq: C
	AAchange: p.D249_splice
exon_skip_114927_LUSC_TCGA-63-6202-01.png
exon_skip_114929_LUSC_TCGA-63-6202-01.png
exon_skip_126247_LUSC_TCGA-63-6202-01.png
	Sample: TCGA-63-6202-01
	Cancer type: LUSC
	ESID: exon_skip_114929
	Skipped exon start: 89656728
	Skipped exon end: 89656793
	Mutation start: 89656795
	Mutation end: 89656795
	Mutation type: Splice_Site
	Reference seq: T
	Mutation seq: C
	AAchange: p.D249_splice
	Sample: TCGA-63-6202-01
	Cancer type: LUSC
	ESID: exon_skip_114929
	Skipped exon start: 89656731
	Skipped exon end: 89656793
	Mutation start: 89656795
	Mutation end: 89656795
	Mutation type: Splice_Site
	Reference seq: T
	Mutation seq: C
	AAchange: p.D249_splice
exon_skip_114927_LUSC_TCGA-63-6202-01.png
exon_skip_114929_LUSC_TCGA-63-6202-01.png
exon_skip_126247_LUSC_TCGA-63-6202-01.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
CW2_LARGE_INTESTINE	89878278	89878834	89878473	89878473	Frame_Shift_Del	G	-	p.P116fs
CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	89878278	89878834	89878534	89878534	Frame_Shift_Del	G	-	p.P96fs
HEC151_ENDOMETRIUM	89878278	89878834	89878534	89878534	Frame_Shift_Del	G	-	p.P96fs
MDAPCA2B_PROSTATE	89878278	89878834	89878534	89878534	Frame_Shift_Del	G	-	p.P96fs
SNUC2A_LARGE_INTESTINE	89878278	89878834	89878534	89878534	Frame_Shift_Del	G	-	p.P96fs
GP5D_LARGE_INTESTINE	89878278	89878834	89878534	89878534	Frame_Shift_Del	G	-	p.P96fs
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	89878278	89878834	89878534	89878534	Frame_Shift_Del	G	-	p.P96fs
OCUBM_BREAST	89878278	89878834	89878534	89878534	Frame_Shift_Del	G	-	p.P96fs
DM3_FIBROBLAST	89647045	89647150	89647069	89647069	Missense_Mutation	G	T	p.P298H
SNU324_PANCREAS	89647045	89647150	89647088	89647088	Missense_Mutation	G	A	p.R292W
RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	89647045	89647150	89647121	89647121	Missense_Mutation	G	A	p.R281W
MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	89647045	89647150	89647123	89647123	Missense_Mutation	G	A	p.A280V
BICR18_UPPER_AERODIGESTIVE_TRACT	89656728	89656793	89656752	89656752	Missense_Mutation	T	A	p.T263S
BICR18_UPPER_AERODIGESTIVE_TRACT	89656731	89656793	89656752	89656752	Missense_Mutation	T	A	p.T263S
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	89656728	89656793	89656752	89656752	Missense_Mutation	T	A	p.T263S
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	89656731	89656793	89656752	89656752	Missense_Mutation	T	A	p.T263S
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	89656728	89656793	89656752	89656752	Missense_Mutation	T	A	p.T263S
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	89656731	89656793	89656752	89656752	Missense_Mutation	T	A	p.T263S
OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	89656728	89656793	89656752	89656752	Missense_Mutation	T	A	p.T263S
OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	89656731	89656793	89656752	89656752	Missense_Mutation	T	A	p.T263S
HT115_LARGE_INTESTINE	89656728	89656793	89656778	89656778	Missense_Mutation	G	T	p.A254D
HT115_LARGE_INTESTINE	89656731	89656793	89656778	89656778	Missense_Mutation	G	T	p.A254D
PATU8988T_PANCREAS	89656728	89656793	89656781	89656781	Missense_Mutation	T	C	p.D253G
PATU8988T_PANCREAS	89656731	89656793	89656781	89656781	Missense_Mutation	T	C	p.D253G
SNU81_LARGE_INTESTINE	89817016	89817152	89817081	89817081	Missense_Mutation	C	A	p.K205N
GP2D_LARGE_INTESTINE	89817016	89817152	89817110	89817110	Missense_Mutation	T	C	p.R196G
SNU1040_LARGE_INTESTINE	89878278	89878834	89878517	89878517	Missense_Mutation	C	G	p.D102H
SW13_ADRENAL_CORTEX	89878278	89878834	89878528	89878528	Missense_Mutation	G	C	p.P98R
OAW28_OVARY	89878278	89878834	89878723	89878723	Missense_Mutation	T	C	p.K33R
CA922_UPPER_AERODIGESTIVE_TRACT	89878278	89878834	89878734	89878734	Missense_Mutation	G	C	p.S29R
SKMEL5_SKIN	89878278	89878834	89878748	89878748	Missense_Mutation	A	G	p.C25R
HCC515_LUNG	89878278	89878834	89878765	89878765	Missense_Mutation	G	C	p.S19C
SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	89878278	89878834	89878559	89878559	Nonsense_Mutation	G	A	p.Q88*

Top

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for FOXN3

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

Top

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for FOXN3

Top

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for FOXN3

Top

RelatedDrugs for FOXN3

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

Top

RelatedDiseases for FOXN3

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

Home

Download

Statistics

Landscape

Help

Contact