ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for RBFOX1

Gene summary

Gene information	Gene symbol	RBFOX1
	Gene ID	54715
	Gene name	RNA binding fox-1 homolog 1
	Synonyms	2BP1\|A2BP1\|FOX-1\|FOX1\|HRNBP1
	Cytomap	16p13.3
	Type of gene	protein-coding
	Description	RNA binding protein fox-1 homolog 1RNA binding protein, fox-1 homolog 1ataxin 2-binding protein 1fox-1 homolog Afox-1-like RNA-binding protein 1hexaribonucleotide binding protein 1 isoform alphahexaribonucleotide binding protein 1 isoform betahexar
	Modification date	20200313
	UniProtAcc	A0A087X2B1, A0A286YEU2, A0A286YFF2, B7Z1U7, F5H0M1, F8VR27, F8VRS4, F8VZG9, F8VZY7, H3BM62, I3L1D4, J3KNW3, Q9NWB1, X5D7T5, X5DNY3, X5DP44,
	Context	- 30382106(Publisher Correction: Inference of RNA Decay Rate From Transcriptional Profiling Highlights the Regulatory Programs of Alzheimer's Disease)

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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Gene structures and expression levels for RBFOX1

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.

ENSG00000078328

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
STG	UP	ENST00000355637.8	RBFOX1-203:protein_coding:RBFOX1	1.512428e+01	4.603840e+00	1.517985e-03	4.741863e-02
PG	DOWN	ENST00000564850.1	RBFOX1-216:retained_intron:RBFOX1	2.920046e+00	-9.479920e-01	9.041367e-06	4.670563e-04
PG	UP	ENST00000553186.5	RBFOX1-215:protein_coding:RBFOX1	1.475010e+01	3.400737e+00	2.371374e-04	5.165284e-03
PG	DOWN	ENST00000570188.1	RBFOX1-220:retained_intron:RBFOX1	2.578313e+00	-8.391128e-01	1.453534e-03	1.903389e-02
PG	UP	ENST00000547605.5	RBFOX1-210:protein_coding:RBFOX1	1.907515e+00	3.794442e+00	2.238723e-03	2.591238e-02
CB	UP	ENST00000422070.8	RBFOX1-204:protein_coding:RBFOX1	2.123098e+01	1.164790e+00	3.679628e-09	1.299675e-07
CB	UP	ENST00000547605.5	RBFOX1-210:protein_coding:RBFOX1	2.447784e+00	9.632571e-01	5.114487e-03	2.005163e-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 RBFOX1

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_122643	chr16	7518147:7518389:7579780:7579920:7587247:7587300	7579780:7579920
exon_skip_135312	chr16	7579780:7579920:7595549:7595641:7597371:7597431	7595549:7595641
exon_skip_159759	chr16	7653815:7653947:7671557:7671599:7676774:7676838	7671557:7671599
exon_skip_165241	chr16	7587247:7587300:7597371:7597431:7607285:7607338	7597371:7597431
exon_skip_178518	chr16	7653866:7653947:7671557:7671599:7676774:7676838	7671557:7671599
exon_skip_179977	chr16	7518147:7518389:7587247:7587300:7597371:7597431	7587247:7587300
exon_skip_187814	chr16	7607303:7607338:7630603:7630683:7653815:7653846	7630603:7630683
exon_skip_195026	chr16	7587247:7587300:7595549:7595641:7597371:7597431	7595549:7595641
exon_skip_218131	chr16	7653866:7653947:7676774:7676838:7709056:7709131	7676774:7676838
exon_skip_232342	chr16	7597371:7597431:7607285:7607338:7653815:7653846	7607285:7607338
exon_skip_239431	chr16	7518147:7518389:7579777:7579920:7587247:7587300	7579777:7579920
exon_skip_259957	chr16	6654603:6654650:6983639:6983738:7052057:7052098	6983639:6983738
exon_skip_294645	chr16	7653866:7653947:7664929:7664968:7676774:7676838	7664929:7664968
exon_skip_3921	chr16	7664929:7664968:7676774:7676838:7709056:7709131	7676774:7676838
exon_skip_4362	chr16	7579780:7579920:7587247:7587300:7595549:7595641	7587247:7587300
exon_skip_72040	chr16	7676774:7676838:7693315:7693367:7709056:7709131	7693315:7693367
exon_skip_82820	chr16	7607285:7607338:7630603:7630683:7653815:7653846	7630603:7630683

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 RBFOX1

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
ENST00000547338	7664929	7664968	Frame-shift
ENST00000550418	7664929	7664968	Frame-shift
ENST00000547338	7676774	7676838	Frame-shift
ENST00000550418	7676774	7676838	Frame-shift
ENST00000547338	7579777	7579920	In-frame
ENST00000550418	7579777	7579920	In-frame
ENST00000547338	7587247	7587300	In-frame
ENST00000550418	7587247	7587300	In-frame
ENST00000547338	7595549	7595641	In-frame
ENST00000550418	7595549	7595641	In-frame
ENST00000547338	7630603	7630683	In-frame
ENST00000550418	7630603	7630683	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
ENST00000547338	7664929	7664968	Frame-shift
ENST00000550418	7664929	7664968	Frame-shift
ENST00000547338	7579777	7579920	In-frame
ENST00000550418	7579777	7579920	In-frame
ENST00000547338	7595549	7595641	In-frame
ENST00000550418	7595549	7595641	In-frame
ENST00000547338	7630603	7630683	In-frame
ENST00000550418	7630603	7630683	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
ENST00000547338	7664929	7664968	Frame-shift
ENST00000550418	7664929	7664968	Frame-shift
ENST00000547338	7676774	7676838	Frame-shift
ENST00000550418	7676774	7676838	Frame-shift
ENST00000547338	7579777	7579920	In-frame
ENST00000550418	7579777	7579920	In-frame
ENST00000547338	7587247	7587300	In-frame
ENST00000550418	7587247	7587300	In-frame
ENST00000547338	7595549	7595641	In-frame
ENST00000550418	7595549	7595641	In-frame
ENST00000547338	7630603	7630683	In-frame
ENST00000550418	7630603	7630683	In-frame

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Infer the effects of exon skipping event on protein functional features for RBFOX1

p-ENSG00000078328_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
ENST00000547338	1530	397	7579777	7579920	492	634	90	138
ENST00000550418	4792	397	7579777	7579920	1260	1402	90	138
ENST00000547338	1530	397	7587247	7587300	636	688	138	156
ENST00000550418	4792	397	7587247	7587300	1404	1456	138	156
ENST00000547338	1530	397	7595549	7595641	690	781	156	187
ENST00000550418	4792	397	7595549	7595641	1458	1549	156	187
ENST00000547338	1530	397	7630603	7630683	898	977	226	252
ENST00000550418	4792	397	7630603	7630683	1666	1745	226	252

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
ENST00000547338	1530	397	7579777	7579920	492	634	90	138
ENST00000550418	4792	397	7579777	7579920	1260	1402	90	138
ENST00000547338	1530	397	7595549	7595641	690	781	156	187
ENST00000550418	4792	397	7595549	7595641	1458	1549	156	187
ENST00000547338	1530	397	7630603	7630683	898	977	226	252
ENST00000550418	4792	397	7630603	7630683	1666	1745	226	252

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
ENST00000547338	1530	397	7579777	7579920	492	634	90	138
ENST00000550418	4792	397	7579777	7579920	1260	1402	90	138
ENST00000547338	1530	397	7587247	7587300	636	688	138	156
ENST00000550418	4792	397	7587247	7587300	1404	1456	138	156
ENST00000547338	1530	397	7595549	7595641	690	781	156	187
ENST00000550418	4792	397	7595549	7595641	1458	1549	156	187
ENST00000547338	1530	397	7630603	7630683	898	977	226	252
ENST00000550418	4792	397	7630603	7630683	1666	1745	226	252

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
Q9NWB1	90	138	117	123	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	90	138	117	123	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	90	138	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1
Q9NWB1	90	138	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1
Q9NWB1	90	138	117	193	Domain	Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9NWB1	90	138	117	193	Domain	Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9NWB1	90	138	130	138	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	90	138	130	138	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	90	138	120	120	Mutagenesis	Note=Reduces RNA-binding affinity 160-fold. H->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	120	120	Mutagenesis	Note=Reduces RNA-binding affinity 160-fold. H->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	126	126	Mutagenesis	Note=Reduces RNA-binding affinity 1500-fold. F->A%2CI%2CR;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	126	126	Mutagenesis	Note=Reduces RNA-binding affinity 1500-fold. F->A%2CI%2CR;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	126	126	Mutagenesis	Note=Reduces RNA-binding affinity 15-fold. F->H%2CW;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	126	126	Mutagenesis	Note=Reduces RNA-binding affinity 15-fold. F->H%2CW;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	126	126	Mutagenesis	Note=No effect on RNA-binding. F->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	126	126	Mutagenesis	Note=No effect on RNA-binding. F->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	92	92	Sequence conflict	Note=T->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NWB1	90	138	92	92	Sequence conflict	Note=T->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NWB1	90	138	118	118	Site	Note=Interaction with RNA
Q9NWB1	90	138	118	118	Site	Note=Interaction with RNA
Q9NWB1	90	138	126	126	Site	Note=Interaction with RNA
Q9NWB1	90	138	126	126	Site	Note=Interaction with RNA
Q9NWB1	90	138	127	127	Site	Note=Interaction with RNA
Q9NWB1	90	138	127	127	Site	Note=Interaction with RNA
Q9NWB1	90	138	110	112	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2N82
Q9NWB1	90	138	110	112	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2N82
Q9NWB1	138	156	143	151	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	138	156	143	151	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	138	156	154	165	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	138	156	154	165	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	138	156	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1
Q9NWB1	138	156	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1
Q9NWB1	138	156	117	193	Domain	Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9NWB1	138	156	117	193	Domain	Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9NWB1	138	156	130	138	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	138	156	130	138	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	138	156	151	151	Site	Note=Interaction with RNA
Q9NWB1	138	156	151	151	Site	Note=Interaction with RNA
Q9NWB1	138	156	156	156	Site	Note=Interaction with RNA
Q9NWB1	138	156	156	156	Site	Note=Interaction with RNA
Q9NWB1	156	187	154	165	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	156	187	154	165	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	156	187	187	190	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	156	187	187	190	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	156	187	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1
Q9NWB1	156	187	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1
Q9NWB1	156	187	117	193	Domain	Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9NWB1	156	187	117	193	Domain	Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9NWB1	156	187	166	176	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	156	187	166	176	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	156	187	158	158	Mutagenesis	Note=Reduces RNA-binding affinity 700-fold. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	156	187	158	158	Mutagenesis	Note=Reduces RNA-binding affinity 700-fold. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	156	187	160	160	Mutagenesis	Note=Reduces RNA-binding affinity 30'000-fold. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	156	187	160	160	Mutagenesis	Note=Reduces RNA-binding affinity 30'000-fold. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	156	187	156	156	Site	Note=Interaction with RNA
Q9NWB1	156	187	156	156	Site	Note=Interaction with RNA
Q9NWB1	156	187	160	160	Site	Note=Interaction with RNA
Q9NWB1	156	187	160	160	Site	Note=Interaction with RNA
Q9NWB1	156	187	184	184	Site	Note=Interaction with RNA
Q9NWB1	156	187	184	184	Site	Note=Interaction with RNA
Q9NWB1	226	252	226	253	Alternative sequence	ID=VSP_030875;Note=In isoform 3. GTVLLCQANQEGSSMYSAPSSLVYTSAM->V;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10814712,ECO:0000303\|PubMed:14702039,ECO:0000303\|Ref.3;Dbxref=PMID:10814712,PMID:14702039
Q9NWB1	226	252	226	253	Alternative sequence	ID=VSP_030875;Note=In isoform 3. GTVLLCQANQEGSSMYSAPSSLVYTSAM->V;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10814712,ECO:0000303\|PubMed:14702039,ECO:0000303\|Ref.3;Dbxref=PMID:10814712,PMID:14702039
Q9NWB1	226	252	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1
Q9NWB1	226	252	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1

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
Q9NWB1	90	138	117	123	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	90	138	117	123	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	90	138	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1
Q9NWB1	90	138	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1
Q9NWB1	90	138	117	193	Domain	Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9NWB1	90	138	117	193	Domain	Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9NWB1	90	138	130	138	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	90	138	130	138	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	90	138	120	120	Mutagenesis	Note=Reduces RNA-binding affinity 160-fold. H->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	120	120	Mutagenesis	Note=Reduces RNA-binding affinity 160-fold. H->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	126	126	Mutagenesis	Note=Reduces RNA-binding affinity 1500-fold. F->A%2CI%2CR;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	126	126	Mutagenesis	Note=Reduces RNA-binding affinity 1500-fold. F->A%2CI%2CR;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	126	126	Mutagenesis	Note=Reduces RNA-binding affinity 15-fold. F->H%2CW;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	126	126	Mutagenesis	Note=Reduces RNA-binding affinity 15-fold. F->H%2CW;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	126	126	Mutagenesis	Note=No effect on RNA-binding. F->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	126	126	Mutagenesis	Note=No effect on RNA-binding. F->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	92	92	Sequence conflict	Note=T->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NWB1	90	138	92	92	Sequence conflict	Note=T->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NWB1	90	138	118	118	Site	Note=Interaction with RNA
Q9NWB1	90	138	118	118	Site	Note=Interaction with RNA
Q9NWB1	90	138	126	126	Site	Note=Interaction with RNA
Q9NWB1	90	138	126	126	Site	Note=Interaction with RNA
Q9NWB1	90	138	127	127	Site	Note=Interaction with RNA
Q9NWB1	90	138	127	127	Site	Note=Interaction with RNA
Q9NWB1	90	138	110	112	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2N82
Q9NWB1	90	138	110	112	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2N82
Q9NWB1	156	187	154	165	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	156	187	154	165	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	156	187	187	190	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	156	187	187	190	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	156	187	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1
Q9NWB1	156	187	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1
Q9NWB1	156	187	117	193	Domain	Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9NWB1	156	187	117	193	Domain	Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9NWB1	156	187	166	176	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	156	187	166	176	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	156	187	158	158	Mutagenesis	Note=Reduces RNA-binding affinity 700-fold. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	156	187	158	158	Mutagenesis	Note=Reduces RNA-binding affinity 700-fold. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	156	187	160	160	Mutagenesis	Note=Reduces RNA-binding affinity 30'000-fold. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	156	187	160	160	Mutagenesis	Note=Reduces RNA-binding affinity 30'000-fold. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	156	187	156	156	Site	Note=Interaction with RNA
Q9NWB1	156	187	156	156	Site	Note=Interaction with RNA
Q9NWB1	156	187	160	160	Site	Note=Interaction with RNA
Q9NWB1	156	187	160	160	Site	Note=Interaction with RNA
Q9NWB1	156	187	184	184	Site	Note=Interaction with RNA
Q9NWB1	156	187	184	184	Site	Note=Interaction with RNA
Q9NWB1	226	252	226	253	Alternative sequence	ID=VSP_030875;Note=In isoform 3. GTVLLCQANQEGSSMYSAPSSLVYTSAM->V;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10814712,ECO:0000303\|PubMed:14702039,ECO:0000303\|Ref.3;Dbxref=PMID:10814712,PMID:14702039
Q9NWB1	226	252	226	253	Alternative sequence	ID=VSP_030875;Note=In isoform 3. GTVLLCQANQEGSSMYSAPSSLVYTSAM->V;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10814712,ECO:0000303\|PubMed:14702039,ECO:0000303\|Ref.3;Dbxref=PMID:10814712,PMID:14702039
Q9NWB1	226	252	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1
Q9NWB1	226	252	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1

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
Q9NWB1	90	138	117	123	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	90	138	117	123	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	90	138	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1
Q9NWB1	90	138	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1
Q9NWB1	90	138	117	193	Domain	Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9NWB1	90	138	117	193	Domain	Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9NWB1	90	138	130	138	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	90	138	130	138	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	90	138	120	120	Mutagenesis	Note=Reduces RNA-binding affinity 160-fold. H->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	120	120	Mutagenesis	Note=Reduces RNA-binding affinity 160-fold. H->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	126	126	Mutagenesis	Note=Reduces RNA-binding affinity 1500-fold. F->A%2CI%2CR;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	126	126	Mutagenesis	Note=Reduces RNA-binding affinity 1500-fold. F->A%2CI%2CR;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	126	126	Mutagenesis	Note=Reduces RNA-binding affinity 15-fold. F->H%2CW;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	126	126	Mutagenesis	Note=Reduces RNA-binding affinity 15-fold. F->H%2CW;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	126	126	Mutagenesis	Note=No effect on RNA-binding. F->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	126	126	Mutagenesis	Note=No effect on RNA-binding. F->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	90	138	92	92	Sequence conflict	Note=T->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NWB1	90	138	92	92	Sequence conflict	Note=T->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NWB1	90	138	118	118	Site	Note=Interaction with RNA
Q9NWB1	90	138	118	118	Site	Note=Interaction with RNA
Q9NWB1	90	138	126	126	Site	Note=Interaction with RNA
Q9NWB1	90	138	126	126	Site	Note=Interaction with RNA
Q9NWB1	90	138	127	127	Site	Note=Interaction with RNA
Q9NWB1	90	138	127	127	Site	Note=Interaction with RNA
Q9NWB1	90	138	110	112	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2N82
Q9NWB1	90	138	110	112	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2N82
Q9NWB1	138	156	143	151	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	138	156	143	151	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	138	156	154	165	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	138	156	154	165	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	138	156	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1
Q9NWB1	138	156	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1
Q9NWB1	138	156	117	193	Domain	Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9NWB1	138	156	117	193	Domain	Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9NWB1	138	156	130	138	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	138	156	130	138	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	138	156	151	151	Site	Note=Interaction with RNA
Q9NWB1	138	156	151	151	Site	Note=Interaction with RNA
Q9NWB1	138	156	156	156	Site	Note=Interaction with RNA
Q9NWB1	138	156	156	156	Site	Note=Interaction with RNA
Q9NWB1	156	187	154	165	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	156	187	154	165	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	156	187	187	190	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	156	187	187	190	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	156	187	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1
Q9NWB1	156	187	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1
Q9NWB1	156	187	117	193	Domain	Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9NWB1	156	187	117	193	Domain	Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9NWB1	156	187	166	176	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	156	187	166	176	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4ZKA
Q9NWB1	156	187	158	158	Mutagenesis	Note=Reduces RNA-binding affinity 700-fold. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	156	187	158	158	Mutagenesis	Note=Reduces RNA-binding affinity 700-fold. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	156	187	160	160	Mutagenesis	Note=Reduces RNA-binding affinity 30'000-fold. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	156	187	160	160	Mutagenesis	Note=Reduces RNA-binding affinity 30'000-fold. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16362037;Dbxref=PMID:16362037
Q9NWB1	156	187	156	156	Site	Note=Interaction with RNA
Q9NWB1	156	187	156	156	Site	Note=Interaction with RNA
Q9NWB1	156	187	160	160	Site	Note=Interaction with RNA
Q9NWB1	156	187	160	160	Site	Note=Interaction with RNA
Q9NWB1	156	187	184	184	Site	Note=Interaction with RNA
Q9NWB1	156	187	184	184	Site	Note=Interaction with RNA
Q9NWB1	226	252	226	253	Alternative sequence	ID=VSP_030875;Note=In isoform 3. GTVLLCQANQEGSSMYSAPSSLVYTSAM->V;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10814712,ECO:0000303\|PubMed:14702039,ECO:0000303\|Ref.3;Dbxref=PMID:10814712,PMID:14702039
Q9NWB1	226	252	226	253	Alternative sequence	ID=VSP_030875;Note=In isoform 3. GTVLLCQANQEGSSMYSAPSSLVYTSAM->V;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10814712,ECO:0000303\|PubMed:14702039,ECO:0000303\|Ref.3;Dbxref=PMID:10814712,PMID:14702039
Q9NWB1	226	252	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1
Q9NWB1	226	252	1	397	Chain	ID=PRO_0000081480;Note=RNA binding protein fox-1 homolog 1

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3'-UTR located exon skipping events that lost miRNA binding sites in RBFOX1

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 RBFOX1

- 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 RBFOX1

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 RBFOX1

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 RBFOX1

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	RBM45	exon_skip_195026	4.730845e-01	1.111000e-09
CB	ZNF638	exon_skip_72040	-5.446694e-01	2.367348e-13
CB	RBM6	exon_skip_72040	-4.537940e-01	3.027303e-09
CB	CNOT4	exon_skip_72040	-4.043139e-01	1.814211e-07
IFG	RBMS2	exon_skip_82820	4.385402e-01	1.957514e-02
IFG	KHSRP	exon_skip_82820	4.192197e-01	2.637866e-02
IFG	HNRNPD	exon_skip_82820	4.677396e-01	1.207606e-02

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RelatedDrugs for RBFOX1

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 RBFOX1

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 RBFOX1

Gene structures and expression levels for RBFOX1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for RBFOX1

Open reading frame (ORF) annotation in the exon skipping event for RBFOX1

Infer the effects of exon skipping event on protein functional features for RBFOX1

3'-UTR located exon skipping events that lost miRNA binding sites in RBFOX1

SNVs in the skipped exons for RBFOX1

AD stage-associated exon skippint events for RBFOX1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RBFOX1

Correlation with RNA binding proteins (RBPs) for RBFOX1

RelatedDrugs for RBFOX1

RelatedDiseases for RBFOX1