ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for RAP1GAP

Gene summary

Gene information	Gene symbol	RAP1GAP
	Gene ID	5909
	Gene name	RAP1 GTPase activating protein
	Synonyms	RAP1GA1\|RAP1GAP1\|RAP1GAPII\|RAPGAP
	Cytomap	1p36.12
	Type of gene	protein-coding
	Description	rap1 GTPase-activating protein 1
	Modification date	20200313
	UniProtAcc	A0A0A0MQY8, A0A0B6XK13, F2Z357, J3KPC5, P47736, Q49AP2, Q5T3T0, Q5T3T1, X6R8W7,
	Context

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

Gene	GO ID	GO term	PubMed ID
RAP1GAP	GO:0043087	regulation of GTPase activity	18309292
RAP1GAP	GO:0043547	positive regulation of GTPase activity	15141215

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Gene structures and expression levels for RAP1GAP

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.

ENSG00000076864

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
CB	UP	ENST00000317967.11	RAP1GAP-202:protein_coding:RAP1GAP	1.157721e+01	1.603976e+00	6.585859e-14	1.661900e-11
TC	DOWN	ENST00000495204.5	RAP1GAP-211:protein_coding:RAP1GAP	2.649238e+01	-1.269658e+00	7.935957e-03	4.723663e-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 RAP1GAP

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_105099	chr1	21609575:21609646:21610120:21610275:21611452:21611581	21610120:21610275
exon_skip_117566	chr1	21602818:21602913:21603658:21603912:21606066:21606197	21603658:21603912
exon_skip_120815	chr1	21606134:21606197:21608213:21608350:21608850:21608936	21608213:21608350
exon_skip_124129	chr1	21597243:21597264:21597686:21597728:21597961:21598040	21597686:21597728
exon_skip_131402	chr1	21626304:21626397:21649761:21649796:21665211:21665317	21649761:21649796
exon_skip_13301	chr1	21597008:21597264:21597686:21597728:21597961:21597980	21597686:21597728
exon_skip_137975	chr1	21619025:21619072:21620015:21620050:21626304:21626397	21620015:21620050
exon_skip_149786	chr1	21608850:21608936:21609575:21609646:21610120:21610224	21609575:21609646
exon_skip_155753	chr1	21613628:21613706:21613986:21614089:21617306:21617402	21613986:21614089
exon_skip_157107	chr1	21617307:21617491:21617934:21617972:21619025:21619072	21617934:21617972
exon_skip_166304	chr1	21597686:21597728:21597961:21598095:21598400:21598449	21597961:21598095
exon_skip_17423	chr1	21598400:21598502:21599494:21599617:21601684:21601797	21599494:21599617
exon_skip_175431	chr1	21602804:21602913:21603835:21603912:21606066:21606094	21603835:21603912
exon_skip_177823	chr1	21613628:21613706:21613986:21614089:21617306:21617491	21613986:21614089
exon_skip_185103	chr1	21602804:21602913:21603658:21603912:21606066:21606197	21603658:21603912
exon_skip_194095	chr1	21649761:21649796:21665211:21665317:21667598:21667681	21665211:21665317
exon_skip_19476	chr1	21608850:21608936:21609575:21609646:21610120:21610275	21609575:21609646
exon_skip_194993	chr1	21602804:21602913:21606066:21606197:21608213:21608350	21606066:21606197
exon_skip_196167	chr1	21606066:21606197:21608213:21608350:21608850:21608936	21608213:21608350
exon_skip_201361	chr1	21599581:21599617:21601684:21601797:21602804:21602839	21601684:21601797
exon_skip_203999	chr1	21626304:21626397:21649761:21649796:21669254:21669283	21649761:21649796
exon_skip_210455	chr1	21611786:21611816:21612026:21612109:21613176:21613229	21612026:21612109
exon_skip_211985	chr1	21665211:21665317:21668511:21668593:21669254:21669283	21668511:21668593
exon_skip_221829	chr1	21597686:21597728:21597961:21598064:21598400:21598449	21597961:21598064
exon_skip_227041	chr1	21626388:21626397:21649761:21649796:21669254:21669283	21649761:21649796
exon_skip_229239	chr1	21617363:21617491:21617934:21617972:21619025:21619072	21617934:21617972
exon_skip_242665	chr1	21649761:21649796:21665211:21665317:21669254:21669283	21665211:21665317
exon_skip_24489	chr1	21608213:21608350:21608850:21608936:21609575:21609646	21608850:21608936
exon_skip_245277	chr1	21602818:21602913:21603835:21603912:21606066:21606197	21603835:21603912
exon_skip_247784	chr1	21599581:21599617:21601684:21601797:21602804:21602913	21601684:21601797
exon_skip_254544	chr1	21602804:21602913:21603658:21603912:21606066:21606094	21603658:21603912
exon_skip_258195	chr1	21597686:21597728:21597961:21598040:21598400:21598449	21597961:21598040
exon_skip_265385	chr1	21602804:21602913:21603835:21603912:21606066:21606197	21603835:21603912
exon_skip_268865	chr1	21649761:21649796:21665211:21665317:21668511:21668593	21665211:21665317
exon_skip_283009	chr1	21608850:21608936:21609575:21609646:21610120:21610269	21609575:21609646
exon_skip_288708	chr1	21597238:21597264:21597686:21597728:21597961:21598040	21597686:21597728
exon_skip_3032	chr1	21597008:21597264:21597686:21597728:21597961:21598040	21597686:21597728
exon_skip_58307	chr1	21599581:21599617:21601684:21601797:21602804:21602892	21601684:21601797
exon_skip_60025	chr1	21626388:21626397:21649761:21649796:21665211:21665317	21649761:21649796
exon_skip_76904	chr1	21611716:21611816:21612026:21612109:21613176:21613229	21612026:21612109
exon_skip_80469	chr1	21597215:21597264:21597686:21597728:21597961:21598040	21597686:21597728
exon_skip_86309	chr1	21620041:21620050:21626304:21626397:21649761:21649796	21626304:21626397
exon_skip_89792	chr1	21610120:21610275:21611452:21611581:21611716:21611816	21611452:21611581
exon_skip_90154	chr1	21608850:21608936:21609575:21609646:21610120:21610221	21609575:21609646

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 RAP1GAP

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
ENST00000374765	21626304	21626397	3UTR-3UTR
ENST00000374765	21649761	21649796	3UTR-3UTR
ENST00000374765	21597686	21597728	5CDS-5UTR
ENST00000374765	21597961	21598064	Frame-shift
ENST00000374765	21599494	21599617	Frame-shift
ENST00000374765	21611452	21611581	Frame-shift
ENST00000374765	21601684	21601797	In-frame
ENST00000374765	21606066	21606197	In-frame
ENST00000374765	21608213	21608350	In-frame
ENST00000374765	21608850	21608936	In-frame
ENST00000374765	21609575	21609646	In-frame
ENST00000374765	21610120	21610275	In-frame
ENST00000374765	21612026	21612109	In-frame
ENST00000374765	21617934	21617972	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
ENST00000374765	21649761	21649796	3UTR-3UTR
ENST00000374765	21597686	21597728	5CDS-5UTR
ENST00000374765	21611452	21611581	Frame-shift
ENST00000374765	21601684	21601797	In-frame
ENST00000374765	21608850	21608936	In-frame
ENST00000374765	21609575	21609646	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
ENST00000374765	21620015	21620050	3UTR-3CDS
ENST00000374765	21626304	21626397	3UTR-3UTR
ENST00000374765	21649761	21649796	3UTR-3UTR
ENST00000374765	21597686	21597728	5CDS-5UTR
ENST00000374765	21597961	21598064	Frame-shift
ENST00000374765	21599494	21599617	Frame-shift
ENST00000374765	21611452	21611581	Frame-shift
ENST00000374765	21613986	21614089	Frame-shift
ENST00000374765	21601684	21601797	In-frame
ENST00000374765	21606066	21606197	In-frame
ENST00000374765	21608213	21608350	In-frame
ENST00000374765	21609575	21609646	In-frame
ENST00000374765	21610120	21610275	In-frame
ENST00000374765	21612026	21612109	In-frame
ENST00000374765	21617934	21617972	In-frame

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Infer the effects of exon skipping event on protein functional features for RAP1GAP

p-ENSG00000076864_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
ENST00000374765	3288	663	21617934	21617972	268	305	22	34
ENST00000374765	3288	663	21612026	21612109	730	812	176	203
ENST00000374765	3288	663	21610120	21610275	1045	1199	281	332
ENST00000374765	3288	663	21609575	21609646	1201	1271	333	356
ENST00000374765	3288	663	21608850	21608936	1273	1358	357	385
ENST00000374765	3288	663	21608213	21608350	1360	1496	386	431
ENST00000374765	3288	663	21606066	21606197	1498	1628	432	475
ENST00000374765	3288	663	21601684	21601797	1740	1852	513	550

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
ENST00000374765	3288	663	21609575	21609646	1201	1271	333	356
ENST00000374765	3288	663	21608850	21608936	1273	1358	357	385
ENST00000374765	3288	663	21601684	21601797	1740	1852	513	550

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
ENST00000374765	3288	663	21617934	21617972	268	305	22	34
ENST00000374765	3288	663	21612026	21612109	730	812	176	203
ENST00000374765	3288	663	21610120	21610275	1045	1199	281	332
ENST00000374765	3288	663	21609575	21609646	1201	1271	333	356
ENST00000374765	3288	663	21608213	21608350	1360	1496	386	431
ENST00000374765	3288	663	21606066	21606197	1498	1628	432	475
ENST00000374765	3288	663	21601684	21601797	1740	1852	513	550

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
P47736	22	34	1	663	Chain	ID=PRO_0000056743;Note=Rap1 GTPase-activating protein 1
P47736	176	203	192	200	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	176	203	1	663	Chain	ID=PRO_0000056743;Note=Rap1 GTPase-activating protein 1
P47736	176	203	181	397	Domain	Note=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00165
P47736	176	203	177	186	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	281	332	292	300	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	281	332	316	323	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	281	332	327	329	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BRW
P47736	281	332	331	338	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	281	332	1	663	Chain	ID=PRO_0000056743;Note=Rap1 GTPase-activating protein 1
P47736	281	332	181	397	Domain	Note=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00165
P47736	281	332	282	288	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	281	332	306	308	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	281	332	286	286	Mutagenesis	Note=Reduces GTPase activation. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15141215;Dbxref=PMID:15141215
P47736	281	332	287	287	Mutagenesis	Note=Abolishes GTPase activation. H->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15141215;Dbxref=PMID:15141215
P47736	281	332	290	290	Mutagenesis	Note=Abolishes GTPase activation. N->A%2CK;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15141215;Dbxref=PMID:15141215
P47736	281	332	291	291	Mutagenesis	Note=Abolishes GTPase activation. D->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15141215;Dbxref=PMID:15141215
P47736	281	332	304	304	Sequence conflict	Note=F->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
P47736	333	356	331	338	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	333	356	354	358	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	333	356	1	663	Chain	ID=PRO_0000056743;Note=Rap1 GTPase-activating protein 1
P47736	333	356	181	397	Domain	Note=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00165
P47736	357	385	354	358	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	357	385	1	663	Chain	ID=PRO_0000056743;Note=Rap1 GTPase-activating protein 1
P47736	357	385	181	397	Domain	Note=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00165
P47736	357	385	359	376	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	357	385	380	409	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	386	431	1	663	Chain	ID=PRO_0000056743;Note=Rap1 GTPase-activating protein 1
P47736	386	431	181	397	Domain	Note=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00165
P47736	386	431	380	409	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	386	431	388	388	Mutagenesis	Note=Reduces GTPase activation. R->A%2CP;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15141215;Dbxref=PMID:15141215
P47736	432	475	1	663	Chain	ID=PRO_0000056743;Note=Rap1 GTPase-activating protein 1
P47736	432	475	441	441	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
P47736	513	550	1	663	Chain	ID=PRO_0000056743;Note=Rap1 GTPase-activating protein 1
P47736	513	550	515	515	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
P47736	513	550	541	541	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:A2ALS5
P47736	513	550	542	542	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:A2ALS5

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
P47736	333	356	331	338	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	333	356	354	358	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	333	356	1	663	Chain	ID=PRO_0000056743;Note=Rap1 GTPase-activating protein 1
P47736	333	356	181	397	Domain	Note=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00165
P47736	357	385	354	358	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	357	385	1	663	Chain	ID=PRO_0000056743;Note=Rap1 GTPase-activating protein 1
P47736	357	385	181	397	Domain	Note=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00165
P47736	357	385	359	376	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	357	385	380	409	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	513	550	1	663	Chain	ID=PRO_0000056743;Note=Rap1 GTPase-activating protein 1
P47736	513	550	515	515	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
P47736	513	550	541	541	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:A2ALS5
P47736	513	550	542	542	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:A2ALS5

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
P47736	22	34	1	663	Chain	ID=PRO_0000056743;Note=Rap1 GTPase-activating protein 1
P47736	176	203	192	200	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	176	203	1	663	Chain	ID=PRO_0000056743;Note=Rap1 GTPase-activating protein 1
P47736	176	203	181	397	Domain	Note=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00165
P47736	176	203	177	186	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	281	332	292	300	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	281	332	316	323	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	281	332	327	329	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BRW
P47736	281	332	331	338	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	281	332	1	663	Chain	ID=PRO_0000056743;Note=Rap1 GTPase-activating protein 1
P47736	281	332	181	397	Domain	Note=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00165
P47736	281	332	282	288	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	281	332	306	308	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	281	332	286	286	Mutagenesis	Note=Reduces GTPase activation. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15141215;Dbxref=PMID:15141215
P47736	281	332	287	287	Mutagenesis	Note=Abolishes GTPase activation. H->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15141215;Dbxref=PMID:15141215
P47736	281	332	290	290	Mutagenesis	Note=Abolishes GTPase activation. N->A%2CK;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15141215;Dbxref=PMID:15141215
P47736	281	332	291	291	Mutagenesis	Note=Abolishes GTPase activation. D->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15141215;Dbxref=PMID:15141215
P47736	281	332	304	304	Sequence conflict	Note=F->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
P47736	333	356	331	338	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	333	356	354	358	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	333	356	1	663	Chain	ID=PRO_0000056743;Note=Rap1 GTPase-activating protein 1
P47736	333	356	181	397	Domain	Note=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00165
P47736	386	431	1	663	Chain	ID=PRO_0000056743;Note=Rap1 GTPase-activating protein 1
P47736	386	431	181	397	Domain	Note=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00165
P47736	386	431	380	409	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1SRQ
P47736	386	431	388	388	Mutagenesis	Note=Reduces GTPase activation. R->A%2CP;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15141215;Dbxref=PMID:15141215
P47736	432	475	1	663	Chain	ID=PRO_0000056743;Note=Rap1 GTPase-activating protein 1
P47736	432	475	441	441	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
P47736	513	550	1	663	Chain	ID=PRO_0000056743;Note=Rap1 GTPase-activating protein 1
P47736	513	550	515	515	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
P47736	513	550	541	541	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:A2ALS5
P47736	513	550	542	542	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:A2ALS5

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3'-UTR located exon skipping events that lost miRNA binding sites in RAP1GAP

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	ENST00000374765	21626304	21626397	hsa-miR-6715b-5p	chr1:21626360-21626367	8mer-1a	chr1:21626346-21626367	151.00	-21.99
Mayo	ENST00000374765	21626304	21626397	hsa-miR-4269	chr1:21626360-21626367	8mer-1a	chr1:21626346-21626367	151.00	-21.99
Mayo	ENST00000374765	21626304	21626397	hsa-miR-4667-3p	chr1:21626327-21626334	8mer-1a	chr1:21626313-21626334	146.00	-23.16
ROSMAP	ENST00000374765	21626304	21626397	hsa-miR-6715b-5p	chr1:21626360-21626367	8mer-1a	chr1:21626346-21626367	151.00	-21.99
ROSMAP	ENST00000374765	21626304	21626397	hsa-miR-4269	chr1:21626360-21626367	8mer-1a	chr1:21626346-21626367	151.00	-21.99
ROSMAP	ENST00000374765	21626304	21626397	hsa-miR-4667-3p	chr1:21626327-21626334	8mer-1a	chr1:21626313-21626334	146.00	-23.16

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SNVs in the skipped exons for RAP1GAP

- 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 RAP1GAP

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

ADstage

MSBB

IFG

exon_skip_3032

-4.693843e-01

1.173762e-02

chr1

21597008

21597264

21597686

21597728

21597961

21598040

CDR

MSBB

IFG

exon_skip_265385

-4.330874e-01

2.132975e-02

chr1

21602804

21602913

21603835

21603912

21606066

21606197

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAP1GAP

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 RAP1GAP

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	RBM6	exon_skip_247784	-4.671571e-01	5.382630e-10
CB	SAMD4A	exon_skip_247784	-5.593911e-01	1.798580e-14
CB	CNOT4	exon_skip_247784	-5.095397e-01	6.923889e-12
CB	PCBP1	exon_skip_247784	-4.619852e-01	8.800186e-10
CB	TRA2A	exon_skip_247784	-5.173669e-01	2.896521e-12
CB	RBM23	exon_skip_247784	-4.742186e-01	2.714432e-10
DLPFC	SAMD4A	exon_skip_247784	-4.056740e-01	5.086348e-15
DLPFC	ELAVL4	exon_skip_265385	4.400350e-01	2.161871e-17
HCC	SAMD4A	exon_skip_247784	-4.220563e-01	4.349866e-13
HCC	MSI1	exon_skip_185103	-5.099295e-01	3.825732e-19
HCC	ELAVL4	exon_skip_185103	-4.059215e-01	4.708048e-12
HCC	SFPQ	exon_skip_185103	-5.148364e-01	1.530434e-19
HCC	RBM28	exon_skip_185103	-4.354093e-01	7.977717e-14
HCC	RBM6	exon_skip_185103	-5.266887e-01	1.573137e-20
HCC	RBM5	exon_skip_185103	-4.831617e-01	4.406281e-17
HCC	EIF4G2	exon_skip_185103	-5.298183e-01	8.498642e-21
HCC	EIF4B	exon_skip_185103	4.068940e-01	4.141435e-12
HCC	RBM4	exon_skip_185103	-5.130011e-01	2.159688e-19
HCC	RBM4B	exon_skip_185103	-5.431623e-01	5.720783e-22
HCC	MSI1	exon_skip_265385	-4.814838e-01	5.120479e-17
HCC	SFPQ	exon_skip_265385	-4.659595e-01	6.648536e-16
HCC	EIF4G2	exon_skip_265385	-4.871707e-01	1.936846e-17
HCC	SFPQ	exon_skip_211985	4.390919e-01	1.113964e-13
HCC	CNOT4	exon_skip_211985	4.329746e-01	2.641042e-13
HCC	RBM4B	exon_skip_211985	4.294343e-01	4.318406e-13
IFG	EIF4B	exon_skip_185103	4.065297e-01	3.181144e-02
IFG	ESRP2	exon_skip_265385	-5.324820e-01	3.534544e-03
IFG	HNRNPA2B1	exon_skip_131402	5.332496e-01	8.788061e-03
IFG	PCBP2	exon_skip_242665	5.081109e-01	5.770531e-03
IFG	RBM23	exon_skip_242665	4.449062e-01	1.767845e-02
STG	RBM25	exon_skip_242665	-4.590165e-01	4.416746e-05
STG	SRSF11	exon_skip_242665	-4.881971e-01	1.178852e-05
STG	RBM5	exon_skip_242665	-4.193000e-01	2.221756e-04
STG	RC3H1	exon_skip_242665	-4.450157e-01	7.986707e-05
TC	SAMD4A	exon_skip_201361	-4.446601e-01	3.847141e-09
TC	RALYL	exon_skip_117566	4.632753e-01	7.790572e-10
TC	HNRNPH2	exon_skip_117566	4.077423e-01	9.578647e-08
TC	ELAVL4	exon_skip_245277	6.137440e-01	7.863749e-18
TC	ILF2	exon_skip_245277	4.399109e-01	6.557460e-09
TC	NOVA1	exon_skip_245277	5.027174e-01	1.453666e-11

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RelatedDrugs for RAP1GAP

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 RAP1GAP

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 RAP1GAP

Gene structures and expression levels for RAP1GAP

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for RAP1GAP

Open reading frame (ORF) annotation in the exon skipping event for RAP1GAP

Infer the effects of exon skipping event on protein functional features for RAP1GAP

3'-UTR located exon skipping events that lost miRNA binding sites in RAP1GAP

SNVs in the skipped exons for RAP1GAP

AD stage-associated exon skippint events for RAP1GAP

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAP1GAP

Correlation with RNA binding proteins (RBPs) for RAP1GAP

RelatedDrugs for RAP1GAP

RelatedDiseases for RAP1GAP