ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for RAP1A

Gene summary

Gene information	Gene symbol	RAP1A
	Gene ID	5906
	Gene name	RAP1A, member of RAS oncogene family
	Synonyms	C21KG\|G-22K\|KREV-1\|KREV1\|RAP1\|SMGP21
	Cytomap	1p13.2
	Type of gene	protein-coding
	Description	ras-related protein Rap-1AGTP-binding protein smg p21ARas-related protein Krev-1
	Modification date	20180522
	UniProtAcc	P62834
	Context	PubMed: RAP1A [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID)

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

Gene	GO ID	GO term	PubMed ID
RAP1A	GO:0015031	protein transport	17916086
RAP1A	GO:0071320	cellular response to cAMP	21840392

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Exon skipping events across known transcript of Ensembl for RAP1A from UCSC genome browser

Skipped exons in TCGA and GTEx 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.

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Gene isoform structures and expression levels for RAP1A

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

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Exon skipping events with PSIs in TCGA for RAP1A

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_8892	1	112162525:112162556:112170091:112170185:112233955:112233986	112170091:112170185	ENSG00000116473.10	ENST00000436150.2,ENST00000433097.1
exon_skip_8905	1	112245957:112246098:112246964:112247108:112251770:112251886	112246964:112247108	ENSG00000116473.10	ENST00000369709.3,ENST00000436150.2,ENST00000545460.1,ENST00000356415.1
exon_skip_8906	1	112246964:112247108:112249284:112249399:112251770:112251886	112249284:112249399	ENSG00000116473.10	ENST00000494982.1
exon_skip_8907	1	112246964:112247108:112251770:112251886:112255052:112255109	112251770:112251886	ENSG00000116473.10	ENST00000369709.3,ENST00000436150.2,ENST00000545460.1,ENST00000356415.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for RAP1A

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_8892	1	112162525:112162556:112170091:112170185:112233955:112233986	112170091:112170185	ENSG00000116473.10	ENST00000433097.1,ENST00000436150.2
exon_skip_8905	1	112245957:112246098:112246964:112247108:112251770:112251886	112246964:112247108	ENSG00000116473.10	ENST00000356415.1,ENST00000369709.3,ENST00000436150.2,ENST00000545460.1
exon_skip_8906	1	112246964:112247108:112249284:112249399:112251770:112251886	112249284:112249399	ENSG00000116473.10	ENST00000494982.1
exon_skip_8907	1	112246964:112247108:112251770:112251886:112255052:112255109	112251770:112251886	ENSG00000116473.10	ENST00000356415.1,ENST00000369709.3,ENST00000436150.2,ENST00000545460.1

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for RAP1A

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

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000356415	112251770	112251886	3UTR-3CDS
ENST00000369709	112251770	112251886	3UTR-3CDS
ENST00000356415	112246964	112247108	In-frame
ENST00000369709	112246964	112247108	In-frame

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

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000356415	112251770	112251886	3UTR-3CDS
ENST00000369709	112251770	112251886	3UTR-3CDS
ENST00000356415	112246964	112247108	In-frame
ENST00000369709	112246964	112247108	In-frame

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Infer the effects of exon skipping event on protein functional features for RAP1A

Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.

Loci of skipped exons in TCGA 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
ENST00000356415	1603	184	112246964	112247108	644	787	108	156
ENST00000369709	5041	184	112246964	112247108	504	647	108	156

Loci of skipped exons in GTEx 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
ENST00000356415	1603	184	112246964	112247108	644	787	108	156
ENST00000369709	5041	184	112246964	112247108	504	647	108	156

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

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
P62834	108	156	111	116	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	111	116	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	142	145	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	142	145	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	1	181	Chain	ID=PRO_0000030199;Note=Ras-related protein Rap-1A
P62834	108	156	1	181	Chain	ID=PRO_0000030199;Note=Ras-related protein Rap-1A
P62834	108	156	121	123	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	121	123	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	128	137	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	128	137	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	154	166	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	154	166	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	116	119	Nucleotide binding	Note=GTP;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:7791872,ECO:0000269\|PubMed:8756332;Dbxref=PMID:7791872,PMID:8756332
P62834	108	156	116	119	Nucleotide binding	Note=GTP;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:7791872,ECO:0000269\|PubMed:8756332;Dbxref=PMID:7791872,PMID:8756332
P62834	108	156	138	140	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1GUA
P62834	108	156	138	140	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1GUA
P62834	108	156	148	150	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	148	150	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG

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

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
P62834	108	156	111	116	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	111	116	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	142	145	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	142	145	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	1	181	Chain	ID=PRO_0000030199;Note=Ras-related protein Rap-1A
P62834	108	156	1	181	Chain	ID=PRO_0000030199;Note=Ras-related protein Rap-1A
P62834	108	156	121	123	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	121	123	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	128	137	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	128	137	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	154	166	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	154	166	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	116	119	Nucleotide binding	Note=GTP;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:7791872,ECO:0000269\|PubMed:8756332;Dbxref=PMID:7791872,PMID:8756332
P62834	108	156	116	119	Nucleotide binding	Note=GTP;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:7791872,ECO:0000269\|PubMed:8756332;Dbxref=PMID:7791872,PMID:8756332
P62834	108	156	138	140	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1GUA
P62834	108	156	138	140	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1GUA
P62834	108	156	148	150	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG
P62834	108	156	148	150	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4KVG

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SNVs in the skipped exons for RAP1A

- Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.

- Differential PSIs between mutated versus non-mutated samples.

- Non-synonymous mutations located in the skipped exons in TCGA.

Cancer type	Sample	ESID	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
KIRC	TCGA-BP-4162-01	exon_skip_8905	112246965	112247108	112247019	112247019	Frame_Shift_Del	G	-	p.V126fs
STAD	TCGA-BR-6452-01	exon_skip_8905	112246965	112247108	112247110	112247110	Splice_Site	T	A	p.E156_splice

- Depth of coverage in the three exons composing exon skipping event

Depth of coverage in three exons

Mutation description

- 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
NCIH2106_LUNG	112246965	112247108	112247039	112247039	Missense_Mutation	T	A	p.N133K
SEKI_SKIN	112246965	112247108	112247100	112247100	Missense_Mutation	G	A	p.V154I
LU134A_LUNG	112251771	112251886	112251824	112251824	Missense_Mutation	G	T	p.K174N

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAP1A

sQTL information located at the skipped exons.

Exon skip ID	Chromosome	Three exons	Skippped exon	ENST	Cancer type	SNP id	Location	DNA change (ref/var)	P-value
exon_skip_8892	1	112162525:112162556:112170091:112170185:112233955:112233986	112170091:112170185	ENST00000436150.2,ENST00000433097.1	CESC	rs72695278	chr1:112170151	A/G	6.44e-04
exon_skip_8892	1	112162525:112162556:112170091:112170185:112233955:112233986	112170091:112170185	ENST00000436150.2,ENST00000433097.1	BLCA	rs72695278	chr1:112170151	A/G	1.45e-04
exon_skip_8892	1	112162525:112162556:112170091:112170185:112233955:112233986	112170091:112170185	ENST00000436150.2,ENST00000433097.1	ESCA	rs72695278	chr1:112170151	A/G	2.30e-04
exon_skip_8892	1	112162525:112162556:112170091:112170185:112233955:112233986	112170091:112170185	ENST00000436150.2,ENST00000433097.1	HNSC	rs72695278	chr1:112170151	A/G	4.58e-05
exon_skip_8892	1	112162525:112162556:112170091:112170185:112233955:112233986	112170091:112170185	ENST00000436150.2,ENST00000433097.1	LGG	rs72695278	chr1:112170151	A/G	1.62e-07
exon_skip_8892	1	112162525:112162556:112170091:112170185:112233955:112233986	112170091:112170185	ENST00000436150.2,ENST00000433097.1	KIRC	rs72695278	chr1:112170151	A/G	1.71e-05
exon_skip_8892	1	112162525:112162556:112170091:112170185:112233955:112233986	112170091:112170185	ENST00000436150.2,ENST00000433097.1	KIRC	rs72695278	chr1:112170151	A/G	9.37e-05
exon_skip_8892	1	112162525:112162556:112170091:112170185:112233955:112233986	112170091:112170185	ENST00000436150.2,ENST00000433097.1	KIRC	rs72695278	chr1:112170151	A/G	2.59e-03
exon_skip_8892	1	112162525:112162556:112170091:112170185:112233955:112233986	112170091:112170185	ENST00000436150.2,ENST00000433097.1	LUAD	rs72695278	chr1:112170151	A/G	8.96e-04
exon_skip_8892	1	112162525:112162556:112170091:112170185:112233955:112233986	112170091:112170185	ENST00000436150.2,ENST00000433097.1	LUSC	rs72695278	chr1:112170151	A/G	1.41e-03
exon_skip_8892	1	112162525:112162556:112170091:112170185:112233955:112233986	112170091:112170185	ENST00000436150.2,ENST00000433097.1	PRAD	rs72695278	chr1:112170151	A/G	7.12e-07
exon_skip_8892	1	112162525:112162556:112170091:112170185:112233955:112233986	112170091:112170185	ENST00000436150.2,ENST00000433097.1	SARC	rs72695278	chr1:112170151	A/G	5.08e-04
exon_skip_8892	1	112162525:112162556:112170091:112170185:112233955:112233986	112170091:112170185	ENST00000436150.2,ENST00000433097.1	THCA	rs72695278	chr1:112170151	A/G	5.05e-09

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAP1A

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAP1A

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RelatedDrugs for RAP1A

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

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for RAP1A

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 TCGA
	Exon skipping events with PSIs in GTEx
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	SNVs in the skipped exons with depth of coverage
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Splicing Quantitative Trait Methylation (sQTM) in the skipped exon
	Related drugs with this gene
	Related diseases with this gene

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