ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for FER

Gene summary

Gene information	Gene symbol	FER
	Gene ID	2241
	Gene name	FER tyrosine kinase
	Synonyms	PPP1R74\|TYK3\|p94-Fer
	Cytomap	5q21.3
	Type of gene	protein-coding
	Description	tyrosine-protein kinase Ferfeline encephalitis virus-related kinase FERfer (fps/fes related) tyrosine kinasefujinami poultry sarcoma/Feline sarcoma-related protein Ferphosphoprotein NCP94protein phosphatase 1, regulatory subunit 74proto-oncogene c-F
	Modification date	20200320
	UniProtAcc	A0A0D9SEV4, D6RAF9, P16591, Q05DA5, Q6PEJ9, W0S4B9,
	Context

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

Gene	GO ID	GO term	PubMed ID
FER	GO:0007260	tyrosine phosphorylation of STAT protein	19147545
FER	GO:0010591	regulation of lamellipodium assembly	19738202
FER	GO:0018108	peptidyl-tyrosine phosphorylation	12972546\|19738202
FER	GO:0046777	protein autophosphorylation	7623846

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Gene structures and expression levels for FER

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.

ENSG00000151422

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

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 FER

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_145340	chr5	108867767:108867950:108871365:108871502:108872093:108872212	108871365:108871502
exon_skip_199534	chr5	108768093:108768238:108782663:108782755:108798124:108798389	108782663:108782755
exon_skip_222611	chr5	108798124:108798389:108832770:108832943:108835708:108835807	108832770:108832943
exon_skip_224450	chr5	108946130:108946222:108954729:108954932:108959225:108959347	108954729:108954932
exon_skip_277812	chr5	108747841:108748000:108768093:108768238:108798124:108798389	108768093:108768238
exon_skip_291025	chr5	109047104:109047198:109100396:109100519:109180747:109180901	109100396:109100519
exon_skip_36751	chr5	108748967:108748993:108768093:108768238:108782663:108782755	108768093:108768238

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 FER

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
ENST00000281092	108768093	108768238	5UTR-5UTR
ENST00000281092	109100396	109100519	Frame-shift
ENST00000281092	108832770	108832943	In-frame
ENST00000281092	108954729	108954932	In-frame

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
ENST00000281092	108768093	108768238	5UTR-5UTR
ENST00000281092	108832770	108832943	In-frame
ENST00000281092	108954729	108954932	In-frame

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
ENST00000281092	109100396	109100519	Frame-shift
ENST00000281092	108832770	108832943	In-frame
ENST00000281092	108871365	108871502	In-frame
ENST00000281092	108954729	108954932	In-frame

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

p-ENSG00000151422_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
ENST00000281092	12136	822	108832770	108832943	593	765	69	127
ENST00000281092	12136	822	108954729	108954932	1715	1917	443	511

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
ENST00000281092	12136	822	108832770	108832943	593	765	69	127
ENST00000281092	12136	822	108954729	108954932	1715	1917	443	511

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
ENST00000281092	12136	822	108832770	108832943	593	765	69	127
ENST00000281092	12136	822	108871365	108871502	1051	1187	222	267
ENST00000281092	12136	822	108954729	108954932	1715	1917	443	511

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
P16591	69	127	1	369	Alternative sequence	ID=VSP_043846;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22223638;Dbxref=PMID:22223638
P16591	69	127	1	175	Alternative sequence	ID=VSP_041765;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P16591	69	127	1	822	Chain	ID=PRO_0000088084;Note=Tyrosine-protein kinase Fer
P16591	69	127	123	185	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
P16591	69	127	1	259	Domain	Note=F-BAR;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01077
P16591	69	127	1	300	Region	Note=Important for interaction with membranes containing phosphoinositides
P16591	443	511	461	464	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KK6
P16591	443	511	480	484	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KK6
P16591	443	511	492	498	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KK6
P16591	443	511	501	510	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KK6
P16591	443	511	1	822	Chain	ID=PRO_0000088084;Note=Tyrosine-protein kinase Fer
P16591	443	511	460	550	Domain	Note=SH2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00191
P16591	443	511	467	472	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KK6
P16591	443	511	483	483	Mutagenesis	Note=Abolishes kinase activity. Abolishes location at microtubules. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12972546;Dbxref=PMID:12972546
P16591	443	511	443	443	Natural variant	ID=VAR_041694;Note=A->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs34259824,PMID:17344846
P16591	443	511	460	460	Natural variant	ID=VAR_041695;Note=In a lung small cell carcinoma sample%3B somatic mutation. W->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=PMID:17344846
P16591	443	511	507	507	Natural variant	ID=VAR_051695;Note=I->T;Dbxref=dbSNP:rs34204308
P16591	443	511	447	447	Sequence conflict	Note=M->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
P16591	443	511	485	485	Sequence conflict	Note=S->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
P16591	443	511	492	492	Sequence conflict	Note=Y->H;Ontology_term=ECO:0000305;evidence=ECO:0000305
P16591	443	511	505	505	Sequence conflict	Note=F->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
P16591	443	511	455	457	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KK6

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
P16591	69	127	1	369	Alternative sequence	ID=VSP_043846;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22223638;Dbxref=PMID:22223638
P16591	69	127	1	175	Alternative sequence	ID=VSP_041765;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P16591	69	127	1	822	Chain	ID=PRO_0000088084;Note=Tyrosine-protein kinase Fer
P16591	69	127	123	185	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
P16591	69	127	1	259	Domain	Note=F-BAR;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01077
P16591	69	127	1	300	Region	Note=Important for interaction with membranes containing phosphoinositides
P16591	443	511	461	464	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KK6
P16591	443	511	480	484	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KK6
P16591	443	511	492	498	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KK6
P16591	443	511	501	510	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KK6
P16591	443	511	1	822	Chain	ID=PRO_0000088084;Note=Tyrosine-protein kinase Fer
P16591	443	511	460	550	Domain	Note=SH2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00191
P16591	443	511	467	472	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KK6
P16591	443	511	483	483	Mutagenesis	Note=Abolishes kinase activity. Abolishes location at microtubules. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12972546;Dbxref=PMID:12972546
P16591	443	511	443	443	Natural variant	ID=VAR_041694;Note=A->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs34259824,PMID:17344846
P16591	443	511	460	460	Natural variant	ID=VAR_041695;Note=In a lung small cell carcinoma sample%3B somatic mutation. W->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=PMID:17344846
P16591	443	511	507	507	Natural variant	ID=VAR_051695;Note=I->T;Dbxref=dbSNP:rs34204308
P16591	443	511	447	447	Sequence conflict	Note=M->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
P16591	443	511	485	485	Sequence conflict	Note=S->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
P16591	443	511	492	492	Sequence conflict	Note=Y->H;Ontology_term=ECO:0000305;evidence=ECO:0000305
P16591	443	511	505	505	Sequence conflict	Note=F->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
P16591	443	511	455	457	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KK6

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
P16591	69	127	1	369	Alternative sequence	ID=VSP_043846;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22223638;Dbxref=PMID:22223638
P16591	69	127	1	175	Alternative sequence	ID=VSP_041765;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P16591	69	127	1	822	Chain	ID=PRO_0000088084;Note=Tyrosine-protein kinase Fer
P16591	69	127	123	185	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
P16591	69	127	1	259	Domain	Note=F-BAR;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01077
P16591	69	127	1	300	Region	Note=Important for interaction with membranes containing phosphoinositides
P16591	222	267	1	369	Alternative sequence	ID=VSP_043846;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22223638;Dbxref=PMID:22223638
P16591	222	267	1	822	Chain	ID=PRO_0000088084;Note=Tyrosine-protein kinase Fer
P16591	222	267	1	259	Domain	Note=F-BAR;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01077
P16591	222	267	1	300	Region	Note=Important for interaction with membranes containing phosphoinositides
P16591	222	267	234	234	Sequence conflict	Note=S->N;Ontology_term=ECO:0000305;evidence=ECO:0000305
P16591	443	511	461	464	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KK6
P16591	443	511	480	484	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KK6
P16591	443	511	492	498	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KK6
P16591	443	511	501	510	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KK6
P16591	443	511	1	822	Chain	ID=PRO_0000088084;Note=Tyrosine-protein kinase Fer
P16591	443	511	460	550	Domain	Note=SH2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00191
P16591	443	511	467	472	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KK6
P16591	443	511	483	483	Mutagenesis	Note=Abolishes kinase activity. Abolishes location at microtubules. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12972546;Dbxref=PMID:12972546
P16591	443	511	443	443	Natural variant	ID=VAR_041694;Note=A->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs34259824,PMID:17344846
P16591	443	511	460	460	Natural variant	ID=VAR_041695;Note=In a lung small cell carcinoma sample%3B somatic mutation. W->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=PMID:17344846
P16591	443	511	507	507	Natural variant	ID=VAR_051695;Note=I->T;Dbxref=dbSNP:rs34204308
P16591	443	511	447	447	Sequence conflict	Note=M->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
P16591	443	511	485	485	Sequence conflict	Note=S->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
P16591	443	511	492	492	Sequence conflict	Note=Y->H;Ontology_term=ECO:0000305;evidence=ECO:0000305
P16591	443	511	505	505	Sequence conflict	Note=F->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
P16591	443	511	455	457	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KK6

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

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

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SNVs in the skipped exons for FER

- 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 FER

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

CDR

MSBB

IFG

exon_skip_222611

-4.516265e-01

1.584323e-02

chr5

108798124

108798389

108832770

108832943

108835708

108835807

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

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 FER

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for FER

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

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
P16591	approved\|investigational	DB12010	Fostamatinib	small molecule	P16591

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RelatedDiseases for FER

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 FER

Gene structures and expression levels for FER

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

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

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

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

SNVs in the skipped exons for FER

AD stage-associated exon skippint events for FER

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

Correlation with RNA binding proteins (RBPs) for FER

RelatedDrugs for FER

RelatedDiseases for FER