ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for RAB1A

Gene summary

Gene information	Gene symbol	RAB1A
	Gene ID	5861
	Gene name	RAB1A, member RAS oncogene family
	Synonyms	RAB1\|YPT1
	Cytomap	2p14
	Type of gene	protein-coding
	Description	ras-related protein Rab-1AGTP binding protein Rab1aRAB1, member RAS oncogene familyRab GTPase YPT1 homologYPT1-related protein
	Modification date	20180523
	UniProtAcc	P62820
	Context	PubMed: RAB1A [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

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Exon skipping events across known transcript of Ensembl for RAB1A 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 RAB1A

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 RAB1A

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_339677	2	65315430:65315824:65316072:65316204:65318116:65318212	65316072:65316204	ENSG00000138069.12	ENST00000409784.3,ENST00000409751.1
exon_skip_339678	2	65315430:65315824:65316072:65316204:65325104:65325198	65316072:65316204	ENSG00000138069.12	ENST00000356214.7
exon_skip_339679	2	65315430:65315824:65316072:65316204:65331867:65331940	65316072:65316204	ENSG00000138069.12	ENST00000409892.1
exon_skip_339691	2	65315430:65315824:65325104:65325200:65331867:65331940	65325104:65325200	ENSG00000138069.12	ENST00000260638.8,ENST00000398529.3
exon_skip_339707	2	65316072:65316204:65318116:65318212:65325104:65325198	65318116:65318212	ENSG00000138069.12	ENST00000409784.3
exon_skip_339708	2	65316072:65316204:65318116:65318212:65331867:65331940	65318116:65318212	ENSG00000138069.12	ENST00000409751.1
exon_skip_339714	2	65316072:65316204:65325104:65325200:65331867:65331940	65325104:65325200	ENSG00000138069.12	ENST00000356214.7
exon_skip_339720	2	65318116:65318212:65325104:65325200:65331867:65331940	65325104:65325200	ENSG00000138069.12	ENST00000409784.3
exon_skip_339725	2	65325104:65325200:65331867:65331940:65357026:65357220	65331867:65331940	ENSG00000138069.12	ENST00000356214.7,ENST00000409784.3,ENST00000398529.3

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for RAB1A

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_339677	2	65315430:65315824:65316072:65316204:65318116:65318212	65316072:65316204	ENSG00000138069.12	ENST00000409784.3,ENST00000409751.1
exon_skip_339678	2	65315430:65315824:65316072:65316204:65325104:65325198	65316072:65316204	ENSG00000138069.12	ENST00000356214.7
exon_skip_339679	2	65315430:65315824:65316072:65316204:65331867:65331940	65316072:65316204	ENSG00000138069.12	ENST00000409892.1
exon_skip_339691	2	65315430:65315824:65325104:65325200:65331867:65331940	65325104:65325200	ENSG00000138069.12	ENST00000398529.3,ENST00000260638.8
exon_skip_339707	2	65316072:65316204:65318116:65318212:65325104:65325198	65318116:65318212	ENSG00000138069.12	ENST00000409784.3
exon_skip_339708	2	65316072:65316204:65318116:65318212:65331867:65331940	65318116:65318212	ENSG00000138069.12	ENST00000409751.1
exon_skip_339714	2	65316072:65316204:65325104:65325200:65331867:65331940	65325104:65325200	ENSG00000138069.12	ENST00000356214.7
exon_skip_339720	2	65318116:65318212:65325104:65325200:65331867:65331940	65325104:65325200	ENSG00000138069.12	ENST00000409784.3
exon_skip_339725	2	65325104:65325200:65331867:65331940:65357026:65357220	65331867:65331940	ENSG00000138069.12	ENST00000409784.3,ENST00000398529.3,ENST00000356214.7

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 RAB1A

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
ENST00000409784	65331867	65331940	Frame-shift
ENST00000409784	65316072	65316204	In-frame
ENST00000409784	65318116	65318212	In-frame
ENST00000409784	65325104	65325200	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
ENST00000409784	65331867	65331940	Frame-shift
ENST00000409784	65316072	65316204	In-frame
ENST00000409784	65318116	65318212	In-frame
ENST00000409784	65325104	65325200	In-frame

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Infer the effects of exon skipping event on protein functional features for RAB1A

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
ENST00000409784	2464	205	65325104	65325200	288	383	32	64
ENST00000409784	2464	205	65318116	65318212	384	479	64	96
ENST00000409784	2464	205	65316072	65316204	480	611	96	140

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
ENST00000409784	2464	205	65325104	65325200	288	383	32	64
ENST00000409784	2464	205	65318116	65318212	384	479	64	96
ENST00000409784	2464	205	65316072	65316204	480	611	96	140

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
P62820	32	64	33	96	Alternative sequence	ID=VSP_005525;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P62820	32	64	30	32	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3L0I
P62820	32	64	47	55	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	32	64	58	65	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	32	64	2	205	Chain	ID=PRO_0000121056;Note=Ras-related protein Rab-1A
P62820	32	64	39	44	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	32	64	40	48	Motif	Note=Effector region;Ontology_term=ECO:0000250;evidence=ECO:0000250
P62820	32	64	36	43	Nucleotide binding	Note=GTP;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000244\|PDB:2FOL,ECO:0000244\|PDB:3SFV,ECO:0000244\|PDB:3TKL,ECO:0000244\|PDB:4FMC,ECO:000
P62820	64	96	33	96	Alternative sequence	ID=VSP_005525;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P62820	64	96	65	140	Alternative sequence	ID=VSP_005526;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11230166,ECO:0000303\|Ref.6;Dbxref=PMID:11230166
P62820	64	96	58	65	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	64	96	85	92	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	64	96	2	205	Chain	ID=PRO_0000121056;Note=Ras-related protein Rab-1A
P62820	64	96	70	72	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	64	96	78	80	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	64	96	96	112	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	64	96	79	79	Modified residue	Note=O-(2-cholinephosphoryl)serine;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:21822290,ECO:0000269\|PubMed:22158903;Dbxref=PMID:21822290,PMID:22158903
P62820	64	96	66	70	Nucleotide binding	Note=GTP;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PDB:3TKL,ECO:0000269\|PubMed:22416225;Dbxref=PMID:22416225
P62820	64	96	81	83	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3SFV
P62820	96	140	33	96	Alternative sequence	ID=VSP_005525;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P62820	96	140	65	140	Alternative sequence	ID=VSP_005526;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11230166,ECO:0000303\|Ref.6;Dbxref=PMID:11230166
P62820	96	140	117	125	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	96	140	2	205	Chain	ID=PRO_0000121056;Note=Ras-related protein Rab-1A
P62820	96	140	96	112	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	96	140	129	131	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3SFV
P62820	96	140	136	145	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	96	140	124	124	Mutagenesis	Note=Dominant negative mutant. Strongly reduces the levels of CASR present at the cell-surface. N->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:20861236;Dbxref=PMID:20861236
P62820	96	140	124	127	Nucleotide binding	Note=GTP;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000244\|PDB:2FOL,ECO:0000244\|PDB:3SFV,ECO:0000244\|PDB:3TKL,ECO:

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
P62820	32	64	33	96	Alternative sequence	ID=VSP_005525;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P62820	32	64	30	32	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3L0I
P62820	32	64	47	55	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	32	64	58	65	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	32	64	2	205	Chain	ID=PRO_0000121056;Note=Ras-related protein Rab-1A
P62820	32	64	39	44	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	32	64	40	48	Motif	Note=Effector region;Ontology_term=ECO:0000250;evidence=ECO:0000250
P62820	32	64	36	43	Nucleotide binding	Note=GTP;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000244\|PDB:2FOL,ECO:0000244\|PDB:3SFV,ECO:0000244\|PDB:3TKL,ECO:0000244\|PDB:4FMC,ECO:000
P62820	64	96	33	96	Alternative sequence	ID=VSP_005525;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P62820	64	96	65	140	Alternative sequence	ID=VSP_005526;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11230166,ECO:0000303\|Ref.6;Dbxref=PMID:11230166
P62820	64	96	58	65	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	64	96	85	92	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	64	96	2	205	Chain	ID=PRO_0000121056;Note=Ras-related protein Rab-1A
P62820	64	96	70	72	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	64	96	78	80	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	64	96	96	112	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	64	96	79	79	Modified residue	Note=O-(2-cholinephosphoryl)serine;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:21822290,ECO:0000269\|PubMed:22158903;Dbxref=PMID:21822290,PMID:22158903
P62820	64	96	66	70	Nucleotide binding	Note=GTP;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PDB:3TKL,ECO:0000269\|PubMed:22416225;Dbxref=PMID:22416225
P62820	64	96	81	83	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3SFV
P62820	96	140	33	96	Alternative sequence	ID=VSP_005525;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P62820	96	140	65	140	Alternative sequence	ID=VSP_005526;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11230166,ECO:0000303\|Ref.6;Dbxref=PMID:11230166
P62820	96	140	117	125	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	96	140	2	205	Chain	ID=PRO_0000121056;Note=Ras-related protein Rab-1A
P62820	96	140	96	112	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	96	140	129	131	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3SFV
P62820	96	140	136	145	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2WWX
P62820	96	140	124	124	Mutagenesis	Note=Dominant negative mutant. Strongly reduces the levels of CASR present at the cell-surface. N->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:20861236;Dbxref=PMID:20861236
P62820	96	140	124	127	Nucleotide binding	Note=GTP;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000244\|PDB:2FOL,ECO:0000244\|PDB:3SFV,ECO:0000244\|PDB:3TKL,ECO:

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SNVs in the skipped exons for RAB1A

- 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
LIHC	TCGA-DD-A3A0-01	exon_skip_339677 exon_skip_339679 exon_skip_339678	65316073	65316204	65316122	65316122	Frame_Shift_Del	T	-	p.N124fs
LIHC	TCGA-DD-A3A0-01	exon_skip_339677 exon_skip_339679 exon_skip_339678	65316073	65316204	65316146	65316146	Frame_Shift_Del	T	-	p.N116fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_339677 exon_skip_339679 exon_skip_339678	65316073	65316204	65316146	65316146	Frame_Shift_Del	T	-	p.N116fs
UCEC	TCGA-AP-A0LM-01	exon_skip_339708 exon_skip_339707	65318117	65318212	65318185	65318185	Nonsense_Mutation	G	A	p.R74*
UCEC	TCGA-D1-A163-01	exon_skip_339708 exon_skip_339707	65318117	65318212	65318185	65318185	Nonsense_Mutation	G	A	p.R74*
UCEC	TCGA-D1-A17Q-01	exon_skip_339708 exon_skip_339707	65318117	65318212	65318185	65318185	Nonsense_Mutation	G	A	p.R74*

- 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
HCC1569_BREAST	65316073	65316204	65316086	65316086	Missense_Mutation	T	C	p.Y136C
GP2D_LARGE_INTESTINE	65316073	65316204	65316140	65316140	Missense_Mutation	T	C	p.N118S
NCIH1048_LUNG	65316073	65316204	65316179	65316179	Missense_Mutation	C	A	p.W105L
OVCAR4_OVARY	65316073	65316204	65316181	65316181	Missense_Mutation	C	A	p.Q104H
SNU719_STOMACH	65318117	65318212	65318161	65318161	Missense_Mutation	T	C	p.R82G
MFE319_ENDOMETRIUM	65331868	65331940	65331906	65331906	Missense_Mutation	A	G	p.S20P
OC316_OVARY	65325105	65325200	65325177	65325177	Nonsense_Mutation	G	C	p.Y40*
OC314_OVARY	65325105	65325200	65325177	65325177	Nonsense_Mutation	G	C	p.Y40*
HEMCSS_BONE	65331868	65331940	65331868	65331868	Splice_Site	T	C	p.A32A

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAB1A

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

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAB1A

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAB1A

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RelatedDrugs for RAB1A

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 RAB1A

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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Gene summary for RAB1A

Exon skipping events across known transcript of Ensembl for RAB1A from UCSC genome browser

Gene isoform structures and expression levels for RAB1A

Exon skipping events with PSIs in TCGA for RAB1A

Exon skipping events with PSIs in GTEx for RAB1A

Open reading frame (ORF) annotation in the exon skipping event for RAB1A

Infer the effects of exon skipping event on protein functional features for RAB1A

SNVs in the skipped exons for RAB1A

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAB1A

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAB1A

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAB1A

RelatedDrugs for RAB1A

RelatedDiseases for RAB1A