ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for FOXP3

Gene summary

Gene information	Gene symbol	FOXP3
	Gene ID	50943
	Gene name	forkhead box P3
	Synonyms	AIID\|DIETER\|IPEX\|JM2\|PIDX\|XPID
	Cytomap	Xp11.23
	Type of gene	protein-coding
	Description	forkhead box protein P3FOXP3delta7immune dysregulation, polyendocrinopathy, enteropathy, X-linkedimmunodeficiency, polyendocrinopathy, enteropathy, X-linkedscurfin
	Modification date	20180527
	UniProtAcc	Q9BZS1
	Context	PubMed: FOXP3 [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
FOXP3	GO:0002725	negative regulation of T cell cytokine production	15466453
FOXP3	GO:0008285	negative regulation of cell proliferation	15652505
FOXP3	GO:0032088	negative regulation of NF-kappaB transcription factor activity	16652169
FOXP3	GO:0032689	negative regulation of interferon-gamma production	15466453
FOXP3	GO:0032693	negative regulation of interleukin-10 production	15466453
FOXP3	GO:0032703	negative regulation of interleukin-2 production	15466453\|17360565\|17377532
FOXP3	GO:0032713	negative regulation of interleukin-4 production	15466453
FOXP3	GO:0032792	negative regulation of CREB transcription factor activity	16652169
FOXP3	GO:0042036	negative regulation of cytokine biosynthetic process	11483607
FOXP3	GO:0042110	T cell activation	15466453
FOXP3	GO:0042130	negative regulation of T cell proliferation	15466453
FOXP3	GO:0043433	negative regulation of DNA binding transcription factor activity	16873067
FOXP3	GO:0045892	negative regulation of transcription, DNA-templated	11483607\|16920951\|17360565\|22678915
FOXP3	GO:0045893	positive regulation of transcription, DNA-templated	15466453
FOXP3	GO:0050710	negative regulation of cytokine secretion	11483607
FOXP3	GO:0050777	negative regulation of immune response	15652505

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Exon skipping events across known transcript of Ensembl for FOXP3 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 FOXP3

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 FOXP3

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_514910	X	49110377:49110528:49111889:49111970:49112175:49112263	49111889:49111970	ENSG00000049768.10	ENST00000376199.2,ENST00000557224.1,ENST00000376197.1,ENST00000376207.4,ENST00000518685.1
exon_skip_514912	X	49113381:49113469:49113883:49114022:49114752:49114901	49113883:49114022	ENSG00000049768.10	ENST00000376199.2,ENST00000557224.1,ENST00000376197.1,ENST00000518685.1
exon_skip_514916	X	49113883:49114022:49114120:49114225:49114752:49114901	49114120:49114225	ENSG00000049768.10	ENST00000455775.2,ENST00000376207.4

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for FOXP3

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_514910	X	49110377:49110528:49111889:49111970:49112175:49112263	49111889:49111970	ENSG00000049768.10	ENST00000376207.4,ENST00000376199.2,ENST00000557224.1,ENST00000518685.1,ENST00000376197.1
exon_skip_514912	X	49113381:49113469:49113883:49114022:49114752:49114901	49113883:49114022	ENSG00000049768.10	ENST00000376199.2,ENST00000557224.1,ENST00000518685.1,ENST00000376197.1
exon_skip_514916	X	49113883:49114022:49114120:49114225:49114752:49114901	49114120:49114225	ENSG00000049768.10	ENST00000376207.4,ENST00000455775.2

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 FOXP3

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
ENST00000376207	49111889	49111970	In-frame
ENST00000376207	49114120	49114225	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
ENST00000376207	49111889	49111970	In-frame
ENST00000376207	49114120	49114225	In-frame

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Infer the effects of exon skipping event on protein functional features for FOXP3

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
ENST00000376207	2399	431	49114120	49114225	399	503	70	105
ENST00000376207	2399	431	49111889	49111970	924	1004	245	272

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
ENST00000376207	2399	431	49114120	49114225	399	503	70	105
ENST00000376207	2399	431	49111889	49111970	924	1004	245	272

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
Q9BZS1	70	105	72	106	Alternative sequence	ID=VSP_015796;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.4,ECO:0000303\|Ref.7;Dbxref=PMID:15489334
Q9BZS1	70	105	1	431	Chain	ID=PRO_0000091886;Note=Forkhead box protein P3
Q9BZS1	70	105	1	417	Chain	ID=PRO_0000432430;Note=Forkhead box protein P3%2C C-terminally processed;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:19117830;Dbxref=PMID:19117830
Q9BZS1	70	105	52	417	Chain	ID=PRO_0000432431;Note=Forkhead box protein P3 41 kDa form;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:19117830;Dbxref=PMID:19117830
Q9BZS1	70	105	68	76	Motif	Note=Nuclear export signal;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22678915;Dbxref=PMID:22678915
Q9BZS1	70	105	92	96	Motif	Note=LXXLL motif;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18354202;Dbxref=PMID:18354202
Q9BZS1	70	105	71	71	Mutagenesis	Note=Decrease in nuclear export%3B when associated with A-69%2C A-74 and A-76. L->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22678915;Dbxref=PMID:22678915
Q9BZS1	70	105	74	74	Mutagenesis	Note=Decrease in nuclear export%3B when associated with A-69%2C A-71 and A-76. L->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22678915;Dbxref=PMID:22678915
Q9BZS1	70	105	76	76	Mutagenesis	Note=Decrease in nuclear export%3B when associated with A-69%2C A-71 and A-74. L->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22678915;Dbxref=PMID:22678915
Q9BZS1	70	105	95	96	Mutagenesis	Note=Loss of interaction with RORA. LL->AA;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18354202;Dbxref=PMID:18354202
Q9BZS1	245	272	246	272	Alternative sequence	ID=VSP_047859;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q9BZS1	245	272	1	431	Chain	ID=PRO_0000091886;Note=Forkhead box protein P3
Q9BZS1	245	272	1	417	Chain	ID=PRO_0000432430;Note=Forkhead box protein P3%2C C-terminally processed;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:19117830;Dbxref=PMID:19117830
Q9BZS1	245	272	52	417	Chain	ID=PRO_0000432431;Note=Forkhead box protein P3 41 kDa form;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:19117830;Dbxref=PMID:19117830
Q9BZS1	245	272	250	250	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin);Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q99JB6
Q9BZS1	245	272	252	252	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin);Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q99JB6
Q9BZS1	245	272	263	263	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q99JB6
Q9BZS1	245	272	268	268	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q99JB6
Q9BZS1	245	272	263	263	Modified residue	Note=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22312127;Dbxref=PMID:22312127
Q9BZS1	245	272	268	268	Modified residue	Note=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22312127;Dbxref=PMID:22312127
Q9BZS1	245	272	239	248	Motif	Note=Nuclear export signal;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22678915;Dbxref=PMID:22678915
Q9BZS1	245	272	246	246	Mutagenesis	Note=Decrease in nuclear export%3B when associated with A-242 and A-248. L->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22678915;Dbxref=PMID:22678915
Q9BZS1	245	272	248	248	Mutagenesis	Note=Decrease in nuclear export%3B when associated with A-242 and A-246. L->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22678915;Dbxref=PMID:22678915
Q9BZS1	245	272	251	251	Natural variant	ID=VAR_011330;Note=In IPEX%3B significantly reduces dimerization. Missing;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11120765,ECO:0000269\|PubMed:21458306;Dbxref=PMID:11120765,PMID:21458306
Q9BZS1	245	272	239	260	Region	Note=Leucine-zipper

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
Q9BZS1	70	105	72	106	Alternative sequence	ID=VSP_015796;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.4,ECO:0000303\|Ref.7;Dbxref=PMID:15489334
Q9BZS1	70	105	1	431	Chain	ID=PRO_0000091886;Note=Forkhead box protein P3
Q9BZS1	70	105	1	417	Chain	ID=PRO_0000432430;Note=Forkhead box protein P3%2C C-terminally processed;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:19117830;Dbxref=PMID:19117830
Q9BZS1	70	105	52	417	Chain	ID=PRO_0000432431;Note=Forkhead box protein P3 41 kDa form;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:19117830;Dbxref=PMID:19117830
Q9BZS1	70	105	68	76	Motif	Note=Nuclear export signal;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22678915;Dbxref=PMID:22678915
Q9BZS1	70	105	92	96	Motif	Note=LXXLL motif;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18354202;Dbxref=PMID:18354202
Q9BZS1	70	105	71	71	Mutagenesis	Note=Decrease in nuclear export%3B when associated with A-69%2C A-74 and A-76. L->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22678915;Dbxref=PMID:22678915
Q9BZS1	70	105	74	74	Mutagenesis	Note=Decrease in nuclear export%3B when associated with A-69%2C A-71 and A-76. L->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22678915;Dbxref=PMID:22678915
Q9BZS1	70	105	76	76	Mutagenesis	Note=Decrease in nuclear export%3B when associated with A-69%2C A-71 and A-74. L->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22678915;Dbxref=PMID:22678915
Q9BZS1	70	105	95	96	Mutagenesis	Note=Loss of interaction with RORA. LL->AA;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18354202;Dbxref=PMID:18354202
Q9BZS1	245	272	246	272	Alternative sequence	ID=VSP_047859;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q9BZS1	245	272	1	431	Chain	ID=PRO_0000091886;Note=Forkhead box protein P3
Q9BZS1	245	272	1	417	Chain	ID=PRO_0000432430;Note=Forkhead box protein P3%2C C-terminally processed;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:19117830;Dbxref=PMID:19117830
Q9BZS1	245	272	52	417	Chain	ID=PRO_0000432431;Note=Forkhead box protein P3 41 kDa form;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:19117830;Dbxref=PMID:19117830
Q9BZS1	245	272	250	250	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin);Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q99JB6
Q9BZS1	245	272	252	252	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin);Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q99JB6
Q9BZS1	245	272	263	263	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q99JB6
Q9BZS1	245	272	268	268	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q99JB6
Q9BZS1	245	272	263	263	Modified residue	Note=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22312127;Dbxref=PMID:22312127
Q9BZS1	245	272	268	268	Modified residue	Note=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22312127;Dbxref=PMID:22312127
Q9BZS1	245	272	239	248	Motif	Note=Nuclear export signal;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22678915;Dbxref=PMID:22678915
Q9BZS1	245	272	246	246	Mutagenesis	Note=Decrease in nuclear export%3B when associated with A-242 and A-248. L->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22678915;Dbxref=PMID:22678915
Q9BZS1	245	272	248	248	Mutagenesis	Note=Decrease in nuclear export%3B when associated with A-242 and A-246. L->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22678915;Dbxref=PMID:22678915
Q9BZS1	245	272	251	251	Natural variant	ID=VAR_011330;Note=In IPEX%3B significantly reduces dimerization. Missing;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11120765,ECO:0000269\|PubMed:21458306;Dbxref=PMID:11120765,PMID:21458306
Q9BZS1	245	272	239	260	Region	Note=Leucine-zipper

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SNVs in the skipped exons for FOXP3

- 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_514912	49113884	49114022	49113920	49113920	Frame_Shift_Del	C	-	p.V140fs
KIRC	TCGA-B0-4810-01	exon_skip_514912	49113884	49114022	49113932	49113935	Frame_Shift_Del	TGGT	-	p.135_136del
LIHC	TCGA-DD-A39Y-01	exon_skip_514912	49113884	49114022	49113971	49113971	Frame_Shift_Del	G	-	p.L123fs
UCEC	TCGA-AP-A0LJ-01	exon_skip_514912	49113884	49114022	49114024	49114025	Splice_Site	-	G	p.L106_splice
BRCA	TCGA-AN-A0FL-01	exon_skip_514916	49114121	49114225	49114119	49114119	Splice_Site	A	G	e2+2

- 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
451LU_SKIN	49111890	49111970	49111943	49111943	Missense_Mutation	C	A	p.A255S
SW982_SOFT_TISSUE	49113884	49114022	49114010	49114011	Missense_Mutation	CC	TT	p.D110N
DMS273_LUNG	49114121	49114225	49114207	49114207	Missense_Mutation	C	A	p.V77F

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for FOXP3

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 FOXP3

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for FOXP3

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RelatedDrugs for FOXP3

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 FOXP3

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
FOXP3	C0342288	Insulin-dependent diabetes mellitus secretory diarrhea syndrome	3	CTD_human;ORPHANET;UNIPROT
FOXP3	C0003873	Rheumatoid Arthritis	1	CTD_human
FOXP3	C0005586	Bipolar Disorder	1	PSYGENET
FOXP3	C0023493	Adult T-Cell Lymphoma/Leukemia	1	CTD_human
FOXP3	C0032460	Polycystic Ovary Syndrome	1	CTD_human
FOXP3	C1458155	Mammary Neoplasms	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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