ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for FOXP1

Gene summary

Gene information	Gene symbol	FOXP1
	Gene ID	27086
	Gene name	forkhead box P1
	Synonyms	12CC4\|HSPC215\|MFH\|QRF1\|hFKH1B
	Cytomap	3p13
	Type of gene	protein-coding
	Description	forkhead box protein P1fork head-related protein like Bglutamine-rich factor 1mac-1-regulated forkhead
	Modification date	20200329
	UniProtAcc	A0A087WVT2, A0A087X2G3, A0A0B4J2F3, A0A3B3IRL7, A0A3B3IRS5, A0A3B3IRW5, A0A3B3IRY1, A0A3B3IS20, A0A3B3IS87, A0A3B3ISA4, A0A3B3ISQ3, A0A3B3ISQ6, A0A3B3ISQ7, A0A3B3IST0, A0A3B3IST6, A0A3B3IT14, A0A3B3IT26, A0A3B3IT66, A0A3B3ITZ4, A0A3B3IU08, A0A3B3IU15, A0A3B3IUB6, A0A5H1ZRR8, A3KMG1, C9IYY1, C9J0F0, C9J5T4, G5E965, H0Y882, Q548T7, Q6IAJ1, Q9H334,
	Context

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene	GO ID	GO term	PubMed ID
FOXP1	GO:0002903	negative regulation of B cell apoptotic process	25267198
FOXP1	GO:0010629	negative regulation of gene expression	30111844
FOXP1	GO:0030316	osteoclast differentiation	18799727
FOXP1	GO:0032496	response to lipopolysaccharide	18799727
FOXP1	GO:0032680	regulation of tumor necrosis factor production	18799727
FOXP1	GO:0035926	chemokine (C-C motif) ligand 2 secretion	18799727
FOXP1	GO:0036035	osteoclast development	18799727
FOXP1	GO:0042116	macrophage activation	18799727
FOXP1	GO:0042117	monocyte activation	18799727
FOXP1	GO:0045655	regulation of monocyte differentiation	15286807
FOXP1	GO:0045892	negative regulation of transcription, DNA-templated	20950788
FOXP1	GO:0050706	regulation of interleukin-1 beta secretion	18799727
FOXP1	GO:0050727	regulation of inflammatory response	18799727
FOXP1	GO:0060766	negative regulation of androgen receptor signaling pathway	18640093
FOXP1	GO:1900424	regulation of defense response to bacterium	18799727
FOXP1	GO:1901256	regulation of macrophage colony-stimulating factor production	18799727
FOXP1	GO:2001182	regulation of interleukin-12 secretion	18799727

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Gene structures and expression levels for FOXP1

Skipped exons in the ROSMAP, MSBB, and Mayo 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.

ENSG00000114861

Differentially expressed gene analysis across multiple brain tissues between AD and control.

Tissue type

DEG direction

Base mean exp.

log2FC(AD/control)

P-value

Adj. p-value

Differentially expressed isoform analysis across multiple brain tissues between AD and control.

Tissue type	DEG direction	ENST	Transcript info.	Base mean exp.	log2FC(AD/control)	P-value	Adjc. p-value
PCC	UP	ENST00000648192.1	FOXP1-235:lncRNA:FOXP1	1.883325e+00	8.659902e-01	9.058006e-04	2.406103e-02
PG	UP	ENST00000649528.1	FOXP1-259:protein_coding:FOXP1	2.049173e+00	4.071635e+00	1.556194e-03	2.000140e-02
CB	DOWN	ENST00000650073.1	FOXP1-268:lncRNA:FOXP1	3.243302e+01	-1.546653e+00	4.411324e-09	1.512996e-07
CB	UP	ENST00000648384.1	FOXP1-238:nonsense_mediated_decay:FOXP1	6.373534e+00	2.146257e+00	1.588096e-06	2.221912e-05
CB	UP	ENST00000649417.1	FOXP1-255:retained_intron:FOXP1	1.879995e+00	8.351308e-01	6.667474e-04	3.676134e-03
CB	UP	ENST00000647741.1	FOXP1-228:lncRNA:FOXP1	1.356969e+00	8.434636e-01	2.348535e-03	1.052631e-02
CB	UP	ENST00000484350.5	FOXP1-210:protein_coding:FOXP1	2.233953e+00	2.111341e+00	2.643319e-03	1.161849e-02
CB	UP	ENST00000493089.7	FOXP1-214:protein_coding:FOXP1	6.407583e+00	1.896008e+00	4.428521e-03	1.781013e-02
CB	UP	ENST00000471386.3	FOXP1-207:protein_coding:FOXP1	2.237053e+00	8.023599e-01	1.057941e-02	3.640427e-02
CB	UP	ENST00000475937.5	FOXP1-209:protein_coding:FOXP1	9.432137e+01	1.098675e+00	1.551072e-02	4.957167e-02
TC	DOWN	ENST00000650073.1	FOXP1-268:lncRNA:FOXP1	1.986904e+01	-9.304561e-01	2.611630e-05	5.521755e-04
TC	UP	ENST00000649328.1	FOXP1-254:lncRNA:FOXP1	1.841003e+00	8.375791e-01	4.613659e-04	5.398405e-03
TC	UP	ENST00000648718.1	FOXP1-243:protein_coding:FOXP1	1.943249e+00	1.722416e+00	3.736709e-03	2.688601e-02

Landscape of isoform expressions across multiple brain tissues between AD and control.

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for FOXP1

Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).

All exon skipping events in AD cohorts.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon
exon_skip_115568	chr3	71299820:71299880:71335160:71335277:71359150:71359244	71335160:71335277
exon_skip_207212	chr3	71299820:71299880:71335160:71335281:71359150:71359244	71335160:71335281
exon_skip_266390	chr3	71359150:71359244:71467251:71467315:71493426:71493555	71467251:71467315
exon_skip_275662	chr3	70970736:70970805:70972555:70972676:70976941:70977042	70972555:70972676
exon_skip_37690	chr3	70965890:70966056:70970736:70970805:70976941:70977042	70970736:70970805
exon_skip_39717	chr3	70970736:70970805:70972011:70972676:70976941:70977042	70972011:70972676
exon_skip_41703	chr3	70970736:70970805:70972011:70972180:70972555:70972676	70972011:70972180
exon_skip_42996	chr3	71198202:71198392:71296433:71296445:71299820:71299880	71296433:71296445
exon_skip_47236	chr3	71359150:71359244:71493426:71493555:71581549:71581697	71493426:71493555
exon_skip_78421	chr3	70987994:70988077:71000972:71001059:71015549:71015653	71000972:71001059
exon_skip_81654	chr3	71299820:71299880:71359150:71359244:71493426:71493555	71359150:71359244

Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.

Exon skipping information

Tissue type

Avg(PSIs) in AD

Avg(PSIs) in control

Difference (PSI)

Adj. p-value

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Open reading frame (ORF) annotation in the exon skipping event for FOXP1

Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000318789	71359150	71359244	3UTR-3UTR
ENST00000475937	71359150	71359244	3UTR-3UTR
ENST00000318789	71493426	71493555	3UTR-3UTR
ENST00000318789	70972555	70972676	Frame-shift
ENST00000475937	70972555	70972676	Frame-shift
ENST00000498215	70972555	70972676	Frame-shift
ENST00000318789	71000972	71001059	Frame-shift
ENST00000475937	71000972	71001059	Frame-shift
ENST00000498215	71000972	71001059	Frame-shift

Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000318789	71359150	71359244	3UTR-3UTR
ENST00000475937	71359150	71359244	3UTR-3UTR
ENST00000318789	71493426	71493555	3UTR-3UTR
ENST00000318789	71000972	71001059	Frame-shift
ENST00000475937	71000972	71001059	Frame-shift
ENST00000498215	71000972	71001059	Frame-shift

Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000318789	71359150	71359244	3UTR-3UTR
ENST00000475937	71359150	71359244	3UTR-3UTR
ENST00000318789	71493426	71493555	3UTR-3UTR
ENST00000318789	70972555	70972676	Frame-shift
ENST00000475937	70972555	70972676	Frame-shift
ENST00000498215	70972555	70972676	Frame-shift
ENST00000318789	71000972	71001059	Frame-shift
ENST00000475937	71000972	71001059	Frame-shift
ENST00000498215	71000972	71001059	Frame-shift

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Infer the effects of exon skipping event on protein functional features for FOXP1

p-ENSG00000114861_img4.png
boxplot

Loci of skipped exons in ROSMAP 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

Loci of skipped exons in MSBB 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

Loci of skipped exons in Mayo 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

Lost protein functional features of individual exon skipping events in ROSMAP.

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 MSBB.

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 Mayo.

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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3'-UTR located exon skipping events that lost miRNA binding sites in FOXP1

3'-UTR exon skipping evnets lost miRNA binding.

Tissue type	ENST	Exon skip start	Exon skip end	microRNA	Binding site by TargetScan	Binding type by TargetScan	Bdinding site by miRanda	Score of miRanda	Energy by miRanda
Mayo	ENST00000475937	71359150	71359244	hsa-miR-2276-5p	chr3:71359235-71359242	8mer-1a	chr3:71359222-71359242	157.00	-24.65
Mayo	ENST00000475937	71359150	71359244	hsa-miR-889-5p	chr3:71359172-71359179	8mer-1a	chr3:71359170-71359191	144.00	-20.59
Mayo	ENST00000318789	71493426	71493555	hsa-miR-4710	chr3:71493494-71493501	8mer-1a	chr3:71493481-71493502	156.00	-19.19
Mayo	ENST00000318789	71493426	71493555	hsa-miR-5195-3p	chr3:71493524-71493531	8mer-1a	chr3:71493509-71493531	160.00	-16.87
Mayo	ENST00000475937	71359150	71359244	hsa-miR-4313	chr3:71359200-71359207	8mer-1a	chr3:71359195-71359215	162.00	-20.43
Mayo	ENST00000318789	71493426	71493555	hsa-miR-4721	chr3:71493491-71493498	8mer-1a	chr3:71493481-71493502	156.00	-19.19
Mayo	ENST00000475937	71359150	71359244	hsa-miR-7974	chr3:71359170-71359177	8mer-1a	chr3:71359154-71359177	150.00	-17.10
Mayo	ENST00000475937	71359150	71359244	hsa-miR-642a-5p	chr3:71359236-71359243	8mer-1a	chr3:71359226-71359243	141.00	-17.82
Mayo	ENST00000318789	71493426	71493555	hsa-miR-5088-3p	chr3:71493479-71493486	8mer-1a	chr3:71493475-71493497	156.00	-22.89
Mayo	ENST00000318789	71493426	71493555	hsa-miR-4764-5p	chr3:71493445-71493452	8mer-1a	chr3:71493440-71493461	143.00	-15.67
Mayo	ENST00000318789	71493426	71493555	hsa-miR-145-5p	chr3:71493524-71493531	8mer-1a	chr3:71493509-71493531	160.00	-16.87
Mayo	ENST00000318789	71493426	71493555	hsa-miR-29a-5p	chr3:71493472-71493479	8mer-1a	chr3:71493457-71493484	163.00	-25.68
MSBB	ENST00000475937	71359150	71359244	hsa-miR-2276-5p	chr3:71359235-71359242	8mer-1a	chr3:71359222-71359242	157.00	-24.65
MSBB	ENST00000475937	71359150	71359244	hsa-miR-889-5p	chr3:71359172-71359179	8mer-1a	chr3:71359170-71359191	144.00	-20.59
MSBB	ENST00000318789	71493426	71493555	hsa-miR-4710	chr3:71493494-71493501	8mer-1a	chr3:71493481-71493502	156.00	-19.19
MSBB	ENST00000318789	71493426	71493555	hsa-miR-5195-3p	chr3:71493524-71493531	8mer-1a	chr3:71493509-71493531	160.00	-16.87
MSBB	ENST00000475937	71359150	71359244	hsa-miR-4313	chr3:71359200-71359207	8mer-1a	chr3:71359195-71359215	162.00	-20.43
MSBB	ENST00000318789	71493426	71493555	hsa-miR-4721	chr3:71493491-71493498	8mer-1a	chr3:71493481-71493502	156.00	-19.19
MSBB	ENST00000475937	71359150	71359244	hsa-miR-7974	chr3:71359170-71359177	8mer-1a	chr3:71359154-71359177	150.00	-17.10
MSBB	ENST00000475937	71359150	71359244	hsa-miR-642a-5p	chr3:71359236-71359243	8mer-1a	chr3:71359226-71359243	141.00	-17.82
MSBB	ENST00000318789	71493426	71493555	hsa-miR-5088-3p	chr3:71493479-71493486	8mer-1a	chr3:71493475-71493497	156.00	-22.89
MSBB	ENST00000318789	71493426	71493555	hsa-miR-4764-5p	chr3:71493445-71493452	8mer-1a	chr3:71493440-71493461	143.00	-15.67
MSBB	ENST00000318789	71493426	71493555	hsa-miR-145-5p	chr3:71493524-71493531	8mer-1a	chr3:71493509-71493531	160.00	-16.87
MSBB	ENST00000318789	71493426	71493555	hsa-miR-29a-5p	chr3:71493472-71493479	8mer-1a	chr3:71493457-71493484	163.00	-25.68
ROSMAP	ENST00000475937	71359150	71359244	hsa-miR-2276-5p	chr3:71359235-71359242	8mer-1a	chr3:71359222-71359242	157.00	-24.65
ROSMAP	ENST00000475937	71359150	71359244	hsa-miR-889-5p	chr3:71359172-71359179	8mer-1a	chr3:71359170-71359191	144.00	-20.59
ROSMAP	ENST00000318789	71493426	71493555	hsa-miR-4710	chr3:71493494-71493501	8mer-1a	chr3:71493481-71493502	156.00	-19.19
ROSMAP	ENST00000318789	71493426	71493555	hsa-miR-5195-3p	chr3:71493524-71493531	8mer-1a	chr3:71493509-71493531	160.00	-16.87
ROSMAP	ENST00000475937	71359150	71359244	hsa-miR-4313	chr3:71359200-71359207	8mer-1a	chr3:71359195-71359215	162.00	-20.43
ROSMAP	ENST00000318789	71493426	71493555	hsa-miR-4721	chr3:71493491-71493498	8mer-1a	chr3:71493481-71493502	156.00	-19.19
ROSMAP	ENST00000475937	71359150	71359244	hsa-miR-7974	chr3:71359170-71359177	8mer-1a	chr3:71359154-71359177	150.00	-17.10
ROSMAP	ENST00000475937	71359150	71359244	hsa-miR-642a-5p	chr3:71359236-71359243	8mer-1a	chr3:71359226-71359243	141.00	-17.82
ROSMAP	ENST00000318789	71493426	71493555	hsa-miR-5088-3p	chr3:71493479-71493486	8mer-1a	chr3:71493475-71493497	156.00	-22.89
ROSMAP	ENST00000318789	71493426	71493555	hsa-miR-4764-5p	chr3:71493445-71493452	8mer-1a	chr3:71493440-71493461	143.00	-15.67
ROSMAP	ENST00000318789	71493426	71493555	hsa-miR-145-5p	chr3:71493524-71493531	8mer-1a	chr3:71493509-71493531	160.00	-16.87
ROSMAP	ENST00000318789	71493426	71493555	hsa-miR-29a-5p	chr3:71493472-71493479	8mer-1a	chr3:71493457-71493484	163.00	-25.68

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SNVs in the skipped exons for FOXP1

- Differential PSIs between mutated versus non-mutated samples.

- Depth of Coverage in the skipped exon of the mutated samples.

- Sashimi plot in the skipped exon of the mutated samples.

- Non-synonymous mutations located in the skipped exons.

Cancer type

Sample

ESID

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

- 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

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AD stage-associated exon skippint events for FOXP1

Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).

AD stage info

Cohort

Tissue

SE id

Coefficient

P-value

Chromosome

Strand

E1 start

E1 end

Skipped start

Skipped end

E2 start

E2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for FOXP1

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

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Correlation with RNA binding proteins (RBPs) for FOXP1

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	PCBP1	exon_skip_78421	-4.898990e-01	1.798253e-08
CB	SRSF4	exon_skip_78421	-4.815025e-01	3.394459e-08
CB	RBM4	exon_skip_78421	-4.765838e-01	4.886538e-08
IFG	MSI1	exon_skip_78421	-4.227544e-01	2.802567e-02

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RelatedDrugs for FOXP1

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for FOXP1

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 RPSMAP, MSBB, and Mayo
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	3'-UTR located exon skipping events lost miRNA binding sites
	SNVs in the skipped exons with depth of coverage
	AD stage-associated exon skipping events
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Correlation with RNA binding proteins (RBPs)
	Related drugs with this gene
	Related diseases with this gene

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Gene summary for FOXP1

Gene structures and expression levels for FOXP1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for FOXP1

Open reading frame (ORF) annotation in the exon skipping event for FOXP1

Infer the effects of exon skipping event on protein functional features for FOXP1

3'-UTR located exon skipping events that lost miRNA binding sites in FOXP1

SNVs in the skipped exons for FOXP1

AD stage-associated exon skippint events for FOXP1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for FOXP1

Correlation with RNA binding proteins (RBPs) for FOXP1

RelatedDrugs for FOXP1

RelatedDiseases for FOXP1