ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for RAP1GDS1

Gene summary

Gene information	Gene symbol	RAP1GDS1
	Gene ID	5910
	Gene name	Rap1 GTPase-GDP dissociation stimulator 1
	Synonyms	GDS1\|SmgGDS
	Cytomap	4q23
	Type of gene	protein-coding
	Description	rap1 GTPase-GDP dissociation stimulator 1RAP1, GTP-GDP dissociation stimulator 1SMG GDS proteinSMG P21 stimulatory GDP/GTP exchange proteinexchange factor smgGDS
	Modification date	20200322
	UniProtAcc	D6RB97, D6RBC6, D6RC12, D6RC85, D6REZ0, D6RHH8, D6RHZ7, H0Y8M2, P52306, U3KQJ4,
	Context

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 RAP1GDS1

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.

ENSG00000138698

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
PG	UP	ENST00000339360.9	RAP1GDS1-202:protein_coding:RAP1GDS1	2.345330e+00	4.299269e+00	1.858754e-03	2.263079e-02
CB	UP	ENST00000264572.11	RAP1GDS1-201:protein_coding:RAP1GDS1	2.337096e+01	8.280436e-01	2.966773e-04	1.855831e-03
CB	UP	ENST00000514122.5	RAP1GDS1-219:protein_coding:RAP1GDS1	3.163878e+00	1.194569e+00	6.468770e-04	3.582989e-03

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 RAP1GDS1

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_101439	chr4	98293408:98293515:98343139:98343261:98352476:98352567	98343139:98343261
exon_skip_101718	chr4	98420019:98420144:98421258:98421394:98433936:98434062	98421258:98421394
exon_skip_105639	chr4	98343139:98343261:98352476:98352601:98379017:98379163	98352476:98352601
exon_skip_106208	chr4	98293408:98293515:98343139:98343319:98352476:98352567	98343139:98343319
exon_skip_107421	chr4	98433936:98434062:98436940:98437068:98441990:98442052	98436940:98437068
exon_skip_109374	chr4	98343139:98343261:98352476:98352601:98391952:98392080	98352476:98352601
exon_skip_120101	chr4	98352513:98352601:98379017:98379163:98391952:98391989	98379017:98379163
exon_skip_141887	chr4	98433936:98434062:98436940:98437068:98441990:98442117	98436940:98437068
exon_skip_159382	chr4	98343139:98343261:98352476:98352601:98379017:98379160	98352476:98352601
exon_skip_159594	chr4	98261518:98261569:98293405:98293515:98343139:98343261	98293405:98293515
exon_skip_176245	chr4	98421258:98421394:98433936:98434062:98436940:98437068	98433936:98434062
exon_skip_196502	chr4	98352513:98352601:98379017:98379163:98387436:98387503	98379017:98379163
exon_skip_200441	chr4	98379159:98379163:98387436:98387503:98391952:98391989	98387436:98387503
exon_skip_206330	chr4	98418657:98418791:98420019:98420144:98421255:98421283	98420019:98420144
exon_skip_219368	chr4	98261518:98261569:98293408:98293515:98343139:98343261	98293408:98293515
exon_skip_239641	chr4	98343139:98343261:98379017:98379163:98391952:98392080	98379017:98379163
exon_skip_240736	chr4	98379159:98379163:98391952:98392080:98404477:98404586	98391952:98392080
exon_skip_260925	chr4	98343139:98343261:98379017:98379163:98391952:98391989	98379017:98379163
exon_skip_262625	chr4	98352476:98352601:98379017:98379163:98387436:98387507	98379017:98379163
exon_skip_269124	chr4	98352513:98352601:98391952:98392080:98404477:98404586	98391952:98392080
exon_skip_289920	chr4	98293408:98293515:98296918:98296990:98343139:98343261	98296918:98296990
exon_skip_290728	chr4	98343139:98343261:98352476:98352601:98391952:98391989	98352476:98352601
exon_skip_295568	chr4	98352513:98352601:98387436:98387507:98391952:98391989	98387436:98387507
exon_skip_48275	chr4	98352476:98352601:98387436:98387507:98391952:98391989	98387436:98387507
exon_skip_55062	chr4	98391952:98392080:98404477:98404602:98416745:98416888	98404477:98404602
exon_skip_56630	chr4	98343139:98343261:98352476:98352601:98387436:98387503	98352476:98352601
exon_skip_56705	chr4	98293408:98293515:98343139:98343319:98352476:98352601	98343139:98343319
exon_skip_60963	chr4	98420019:98420144:98421255:98421394:98433936:98434062	98421255:98421394
exon_skip_78198	chr4	98418657:98418791:98420019:98420144:98421258:98421394	98420019:98420144
exon_skip_80122	chr4	98293408:98293515:98343139:98343261:98352476:98352601	98343139:98343261

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 RAP1GDS1

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
ENST00000408927	98343139	98343261	In-frame
ENST00000408927	98352476	98352601	In-frame
ENST00000408927	98379017	98379163	In-frame
ENST00000408927	98391952	98392080	In-frame
ENST00000408927	98404477	98404602	In-frame
ENST00000408927	98420019	98420144	In-frame
ENST00000408927	98436940	98437068	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
ENST00000408927	98421255	98421394	Frame-shift
ENST00000408927	98343139	98343261	In-frame
ENST00000408927	98352476	98352601	In-frame
ENST00000408927	98379017	98379163	In-frame
ENST00000408927	98391952	98392080	In-frame
ENST00000408927	98404477	98404602	In-frame
ENST00000408927	98420019	98420144	In-frame
ENST00000408927	98436940	98437068	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
ENST00000408927	98433936	98434062	Frame-shift
ENST00000408927	98293408	98293515	In-frame
ENST00000408927	98343139	98343261	In-frame
ENST00000408927	98352476	98352601	In-frame
ENST00000408927	98379017	98379163	In-frame
ENST00000408927	98391952	98392080	In-frame
ENST00000408927	98404477	98404602	In-frame
ENST00000408927	98420019	98420144	In-frame
ENST00000408927	98436940	98437068	In-frame

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Infer the effects of exon skipping event on protein functional features for RAP1GDS1

p-ENSG00000138698_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
ENST00000408927	3698	607	98343139	98343261	227	348	38	78
ENST00000408927	3698	607	98352476	98352601	350	474	79	120
ENST00000408927	3698	607	98379017	98379163	476	621	121	169
ENST00000408927	3698	607	98391952	98392080	623	750	170	212
ENST00000408927	3698	607	98404477	98404602	752	876	213	254
ENST00000408927	3698	607	98420019	98420144	1289	1413	392	433
ENST00000408927	3698	607	98436940	98437068	1682	1809	523	565

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
ENST00000408927	3698	607	98343139	98343261	227	348	38	78
ENST00000408927	3698	607	98352476	98352601	350	474	79	120
ENST00000408927	3698	607	98379017	98379163	476	621	121	169
ENST00000408927	3698	607	98391952	98392080	623	750	170	212
ENST00000408927	3698	607	98404477	98404602	752	876	213	254
ENST00000408927	3698	607	98420019	98420144	1289	1413	392	433
ENST00000408927	3698	607	98436940	98437068	1682	1809	523	565

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
ENST00000408927	3698	607	98293408	98293515	119	225	2	37
ENST00000408927	3698	607	98343139	98343261	227	348	38	78
ENST00000408927	3698	607	98352476	98352601	350	474	79	120
ENST00000408927	3698	607	98379017	98379163	476	621	121	169
ENST00000408927	3698	607	98391952	98392080	623	750	170	212
ENST00000408927	3698	607	98404477	98404602	752	876	213	254
ENST00000408927	3698	607	98420019	98420144	1289	1413	392	433
ENST00000408927	3698	607	98436940	98437068	1682	1809	523	565

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
P52306	38	78	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	38	78	56	56	Natural variant	ID=VAR_069149;Note=S->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15489334;Dbxref=dbSNP:rs17849535,PMID:15489334
P52306	38	78	77	118	Repeat	Note=ARM 1
P52306	79	120	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	79	120	88	97	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	79	120	103	115	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	79	120	77	118	Repeat	Note=ARM 1
P52306	121	169	121	213	Alternative sequence	ID=VSP_047041;Note=In isoform 6. HEGRSAVDQAGGAQIVIDHLRSLCSITDPANEKLLTVFCGMLMNYSNENDSLQAQLINMGVIPTLVKLLGIHCQNAALTEMCLVAFGNLAELE->Q;Ontology_term=ECO:0000305;evidence=ECO:0000305
P52306	121	169	122	170	Alternative sequence	ID=VSP_001658;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:1549351;Dbxref=PMID:15489334,PMID:1549351
P52306	121	169	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	121	169	169	211	Repeat	Note=ARM 2
P52306	170	212	121	213	Alternative sequence	ID=VSP_047041;Note=In isoform 6. HEGRSAVDQAGGAQIVIDHLRSLCSITDPANEKLLTVFCGMLMNYSNENDSLQAQLINMGVIPTLVKLLGIHCQNAALTEMCLVAFGNLAELE->Q;Ontology_term=ECO:0000305;evidence=ECO:0000305
P52306	170	212	122	170	Alternative sequence	ID=VSP_001658;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:1549351;Dbxref=PMID:15489334,PMID:1549351
P52306	170	212	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	170	212	171	178	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	170	212	181	191	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	170	212	196	209	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	170	212	169	211	Repeat	Note=ARM 2
P52306	170	212	192	194	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	213	254	121	213	Alternative sequence	ID=VSP_047041;Note=In isoform 6. HEGRSAVDQAGGAQIVIDHLRSLCSITDPANEKLLTVFCGMLMNYSNENDSLQAQLINMGVIPTLVKLLGIHCQNAALTEMCLVAFGNLAELE->Q;Ontology_term=ECO:0000305;evidence=ECO:0000305
P52306	213	254	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	213	254	213	219	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	213	254	224	234	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	213	254	238	251	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	213	254	230	230	Modified residue	Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19608861;Dbxref=PMID:19608861
P52306	213	254	237	237	Sequence conflict	Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
P52306	213	254	220	223	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	392	433	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	392	433	392	401	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	392	433	403	408	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	392	433	416	429	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	392	433	391	431	Repeat	Note=ARM 4
P52306	392	433	394	394	Sequence conflict	Note=N->D;Ontology_term=ECO:0000305;evidence=ECO:0000305
P52306	392	433	394	394	Sequence conflict	Note=N->D;Ontology_term=ECO:0000305;evidence=ECO:0000305
P52306	392	433	409	412	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	392	433	430	432	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	523	565	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	523	565	504	531	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	523	565	534	540	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	523	565	550	553	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	523	565	554	562	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC

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
P52306	38	78	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	38	78	56	56	Natural variant	ID=VAR_069149;Note=S->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15489334;Dbxref=dbSNP:rs17849535,PMID:15489334
P52306	38	78	77	118	Repeat	Note=ARM 1
P52306	79	120	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	79	120	88	97	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	79	120	103	115	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	79	120	77	118	Repeat	Note=ARM 1
P52306	121	169	121	213	Alternative sequence	ID=VSP_047041;Note=In isoform 6. HEGRSAVDQAGGAQIVIDHLRSLCSITDPANEKLLTVFCGMLMNYSNENDSLQAQLINMGVIPTLVKLLGIHCQNAALTEMCLVAFGNLAELE->Q;Ontology_term=ECO:0000305;evidence=ECO:0000305
P52306	121	169	122	170	Alternative sequence	ID=VSP_001658;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:1549351;Dbxref=PMID:15489334,PMID:1549351
P52306	121	169	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	121	169	169	211	Repeat	Note=ARM 2
P52306	170	212	121	213	Alternative sequence	ID=VSP_047041;Note=In isoform 6. HEGRSAVDQAGGAQIVIDHLRSLCSITDPANEKLLTVFCGMLMNYSNENDSLQAQLINMGVIPTLVKLLGIHCQNAALTEMCLVAFGNLAELE->Q;Ontology_term=ECO:0000305;evidence=ECO:0000305
P52306	170	212	122	170	Alternative sequence	ID=VSP_001658;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:1549351;Dbxref=PMID:15489334,PMID:1549351
P52306	170	212	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	170	212	171	178	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	170	212	181	191	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	170	212	196	209	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	170	212	169	211	Repeat	Note=ARM 2
P52306	170	212	192	194	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	213	254	121	213	Alternative sequence	ID=VSP_047041;Note=In isoform 6. HEGRSAVDQAGGAQIVIDHLRSLCSITDPANEKLLTVFCGMLMNYSNENDSLQAQLINMGVIPTLVKLLGIHCQNAALTEMCLVAFGNLAELE->Q;Ontology_term=ECO:0000305;evidence=ECO:0000305
P52306	213	254	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	213	254	213	219	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	213	254	224	234	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	213	254	238	251	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	213	254	230	230	Modified residue	Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19608861;Dbxref=PMID:19608861
P52306	213	254	237	237	Sequence conflict	Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
P52306	213	254	220	223	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	392	433	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	392	433	392	401	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	392	433	403	408	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	392	433	416	429	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	392	433	391	431	Repeat	Note=ARM 4
P52306	392	433	394	394	Sequence conflict	Note=N->D;Ontology_term=ECO:0000305;evidence=ECO:0000305
P52306	392	433	394	394	Sequence conflict	Note=N->D;Ontology_term=ECO:0000305;evidence=ECO:0000305
P52306	392	433	409	412	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	392	433	430	432	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	523	565	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	523	565	504	531	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	523	565	534	540	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	523	565	550	553	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	523	565	554	562	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC

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
P52306	2	37	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	38	78	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	38	78	56	56	Natural variant	ID=VAR_069149;Note=S->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15489334;Dbxref=dbSNP:rs17849535,PMID:15489334
P52306	38	78	77	118	Repeat	Note=ARM 1
P52306	79	120	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	79	120	88	97	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	79	120	103	115	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	79	120	77	118	Repeat	Note=ARM 1
P52306	121	169	121	213	Alternative sequence	ID=VSP_047041;Note=In isoform 6. HEGRSAVDQAGGAQIVIDHLRSLCSITDPANEKLLTVFCGMLMNYSNENDSLQAQLINMGVIPTLVKLLGIHCQNAALTEMCLVAFGNLAELE->Q;Ontology_term=ECO:0000305;evidence=ECO:0000305
P52306	121	169	122	170	Alternative sequence	ID=VSP_001658;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:1549351;Dbxref=PMID:15489334,PMID:1549351
P52306	121	169	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	121	169	169	211	Repeat	Note=ARM 2
P52306	170	212	121	213	Alternative sequence	ID=VSP_047041;Note=In isoform 6. HEGRSAVDQAGGAQIVIDHLRSLCSITDPANEKLLTVFCGMLMNYSNENDSLQAQLINMGVIPTLVKLLGIHCQNAALTEMCLVAFGNLAELE->Q;Ontology_term=ECO:0000305;evidence=ECO:0000305
P52306	170	212	122	170	Alternative sequence	ID=VSP_001658;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:1549351;Dbxref=PMID:15489334,PMID:1549351
P52306	170	212	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	170	212	171	178	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	170	212	181	191	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	170	212	196	209	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	170	212	169	211	Repeat	Note=ARM 2
P52306	170	212	192	194	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	213	254	121	213	Alternative sequence	ID=VSP_047041;Note=In isoform 6. HEGRSAVDQAGGAQIVIDHLRSLCSITDPANEKLLTVFCGMLMNYSNENDSLQAQLINMGVIPTLVKLLGIHCQNAALTEMCLVAFGNLAELE->Q;Ontology_term=ECO:0000305;evidence=ECO:0000305
P52306	213	254	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	213	254	213	219	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	213	254	224	234	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	213	254	238	251	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	213	254	230	230	Modified residue	Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19608861;Dbxref=PMID:19608861
P52306	213	254	237	237	Sequence conflict	Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
P52306	213	254	220	223	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	392	433	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	392	433	392	401	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	392	433	403	408	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	392	433	416	429	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	392	433	391	431	Repeat	Note=ARM 4
P52306	392	433	394	394	Sequence conflict	Note=N->D;Ontology_term=ECO:0000305;evidence=ECO:0000305
P52306	392	433	394	394	Sequence conflict	Note=N->D;Ontology_term=ECO:0000305;evidence=ECO:0000305
P52306	392	433	409	412	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	392	433	430	432	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	523	565	1	607	Chain	ID=PRO_0000056759;Note=Rap1 GTPase-GDP dissociation stimulator 1
P52306	523	565	504	531	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	523	565	534	540	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	523	565	550	553	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC
P52306	523	565	554	562	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XGC

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3'-UTR located exon skipping events that lost miRNA binding sites in RAP1GDS1

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 RAP1GDS1

- 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 RAP1GDS1

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 RAP1GDS1

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 RAP1GDS1

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	SNRPA	exon_skip_120101	-4.009791e-01	2.336275e-07
CB	RBM4	exon_skip_120101	-6.981135e-01	5.788384e-24
FL	MSI1	exon_skip_120101	4.563556e-01	1.788996e-11
FL	RALYL	exon_skip_120101	-4.662096e-01	5.717871e-12
HCC	MSI1	exon_skip_120101	5.099658e-01	2.065400e-19
HCC	UNK	exon_skip_120101	4.080327e-01	2.457060e-12
IFG	TRNAU1AP	exon_skip_120101	4.404067e-01	1.900248e-02
IFG	RBM47	exon_skip_120101	5.330775e-01	3.490884e-03
PCC	MSI1	exon_skip_120101	5.337198e-01	3.729471e-17
PCC	RBM47	exon_skip_120101	4.410511e-01	1.340284e-11
PG	RALYL	exon_skip_120101	-6.127765e-01	3.523038e-21
PG	NOVA1	exon_skip_120101	-4.279724e-01	5.942985e-10
STG	MSI1	exon_skip_120101	4.476746e-01	1.547598e-05
TC	MSI1	exon_skip_120101	4.753506e-01	2.130328e-10
TC	RALYL	exon_skip_120101	-6.782129e-01	6.733854e-23
TC	CELF1	exon_skip_120101	-4.682455e-01	4.271145e-10
TC	ESRP1	exon_skip_120101	-5.400822e-01	1.701414e-13
TC	NOVA1	exon_skip_120101	-6.051510e-01	2.340394e-17

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RelatedDrugs for RAP1GDS1

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 RAP1GDS1

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 RAP1GDS1

Gene structures and expression levels for RAP1GDS1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for RAP1GDS1

Open reading frame (ORF) annotation in the exon skipping event for RAP1GDS1

Infer the effects of exon skipping event on protein functional features for RAP1GDS1

3'-UTR located exon skipping events that lost miRNA binding sites in RAP1GDS1

SNVs in the skipped exons for RAP1GDS1

AD stage-associated exon skippint events for RAP1GDS1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAP1GDS1

Correlation with RNA binding proteins (RBPs) for RAP1GDS1

RelatedDrugs for RAP1GDS1

RelatedDiseases for RAP1GDS1