ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for RAB7A

Gene summary

Gene information	Gene symbol	RAB7A
	Gene ID	7879
	Gene name	RAB7A, member RAS oncogene family
	Synonyms	PRO2706\|RAB7
	Cytomap	3q21.3
	Type of gene	protein-coding
	Description	ras-related protein Rab-7aRAB7, member RAS oncogene familyRas-associated protein RAB7
	Modification date	20180527
	UniProtAcc	P51149
	Context	PubMed: RAB7A [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
RAB7A	GO:0022615	protein to membrane docking	24344282

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Exon skipping events across known transcript of Ensembl for RAB7A 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 RAB7A

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 RAB7A

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_377390	3	128445194:128445202:128514202:128514263:128516785:128516879	128514202:128514263	ENSG00000075785.8	ENST00000491681.1,ENST00000482525.1
exon_skip_377395	3	128514202:128514263:128516785:128516912:128525214:128525292	128516785:128516912	ENSG00000075785.8	ENST00000490093.1,ENST00000482525.1,ENST00000464496.1,ENST00000265062.3
exon_skip_377401	3	128516785:128516912:128525214:128525292:128526385:128526437	128525214:128525292	ENSG00000075785.8	ENST00000482525.1
exon_skip_377402	3	128516785:128516912:128525214:128525433:128526385:128526437	128525214:128525433	ENSG00000075785.8	ENST00000464496.1,ENST00000265062.3
exon_skip_377404	3	128516785:128516912:128526385:128526514:128532169:128532288	128526385:128526514	ENSG00000075785.8	ENST00000483906.1
exon_skip_377406	3	128525214:128525433:128526385:128526514:128532169:128532288	128526385:128526514	ENSG00000075785.8	ENST00000265062.3

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for RAB7A

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_377390	3	128445194:128445202:128514202:128514263:128516785:128516879	128514202:128514263	ENSG00000075785.8	ENST00000482525.1,ENST00000491681.1
exon_skip_377395	3	128514202:128514263:128516785:128516912:128525214:128525292	128516785:128516912	ENSG00000075785.8	ENST00000265062.3,ENST00000482525.1,ENST00000464496.1,ENST00000490093.1
exon_skip_377401	3	128516785:128516912:128525214:128525292:128526385:128526437	128525214:128525292	ENSG00000075785.8	ENST00000482525.1
exon_skip_377402	3	128516785:128516912:128525214:128525433:128526385:128526437	128525214:128525433	ENSG00000075785.8	ENST00000265062.3,ENST00000464496.1
exon_skip_377404	3	128516785:128516912:128526385:128526514:128532169:128532288	128526385:128526514	ENSG00000075785.8	ENST00000483906.1
exon_skip_377406	3	128525214:128525433:128526385:128526514:128532169:128532288	128526385:128526514	ENSG00000075785.8	ENST00000265062.3

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 RAB7A

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
ENST00000265062	128516785	128516912	Frame-shift
ENST00000265062	128525214	128525433	In-frame
ENST00000265062	128526385	128526514	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
ENST00000265062	128516785	128516912	Frame-shift
ENST00000265062	128525214	128525433	In-frame
ENST00000265062	128526385	128526514	In-frame

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Infer the effects of exon skipping event on protein functional features for RAB7A

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
ENST00000265062	2261	207	128525214	128525433	427	645	60	133
ENST00000265062	2261	207	128526385	128526514	646	774	133	176

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
ENST00000265062	2261	207	128525214	128525433	427	645	60	133
ENST00000265062	2261	207	128526385	128526514	646	774	133	176

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
P51149	60	133	56	64	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	60	133	82	89	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	60	133	120	125	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	60	133	2	207	Chain	ID=PRO_0000121121;Note=Ras-related protein Rab-7a
P51149	60	133	68	70	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	60	133	93	97	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	60	133	99	110	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	60	133	115	117	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	60	133	72	72	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18669648,PMID:20068231,PMID:23186163
P51149	60	133	67	67	Mutagenesis	Note=Does not abolish localization on late endosomes%2C lysosomes and phagosomes and does not reduce phagosomal fusions. No loss of interaction with CLN5. Q->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12944476,ECO:0000269\|PubMed:2
P51149	60	133	129	129	Natural variant	ID=VAR_018722;Note=In CMT2B%3B increases GTP hydrolysis%3B decreases affinity for GTP and GDP%3B does not affect interaction with NTRK1%3B results in higher levels of NTRK1 and MAPK1/MAPK3 phosphorylation after NGF stimulation consistent with enhanced MAP
P51149	60	133	63	67	Nucleotide binding	Note=GTP;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15933719,ECO:0000269\|PubMed:20028791;Dbxref=PMID:15933719,PMID:20028791
P51149	60	133	125	128	Nucleotide binding	Note=GTP;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15933719,ECO:0000269\|PubMed:20028791;Dbxref=PMID:15933719,PMID:20028791
P51149	60	133	108	108	Sequence conflict	Note=I->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
P51149	60	133	127	127	Sequence conflict	Note=I->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
P51149	133	176	151	153	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	133	176	2	207	Chain	ID=PRO_0000121121;Note=Ras-related protein Rab-7a
P51149	133	176	136	145	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	133	176	162	181	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	133	176	157	157	Natural variant	ID=VAR_037887;Note=In CMT2B%3B does not affect interaction with NTRK1%3B results in higher levels of NTRK1 and MAPK1/MAPK3 phosphorylation after NGF stimulation consistent with enhanced MAPK signaling. K->N;Ontology_term=ECO:0000269,ECO:0000269;evidence=E
P51149	133	176	161	161	Natural variant	ID=VAR_037888;Note=In CMT2B%3B does not affect interaction with NTRK1%3B results in higher levels of NTRK1 and MAPK1/MAPK3 phosphorylation after NGF stimulation consistent with enhanced MAPK signaling. N->T;Ontology_term=ECO:0000269,ECO:0000269;evidence=E
P51149	133	176	162	162	Natural variant	ID=VAR_018723;Note=In CMT2B%3B increases GTP hydrolysis%3B decreases affinity for GTP and GDP%3B does not affect interaction with NTRK1%3B results in higher levels of NTRK1 and MAPK1/MAPK3 phosphorylation after NGF stimulation consistent with enhanced MAP
P51149	133	176	156	157	Nucleotide binding	Note=GTP;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15933719,ECO:0000269\|PubMed:20028791;Dbxref=PMID:15933719,PMID:20028791
P51149	133	176	156	159	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91

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
P51149	60	133	56	64	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	60	133	82	89	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	60	133	120	125	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	60	133	2	207	Chain	ID=PRO_0000121121;Note=Ras-related protein Rab-7a
P51149	60	133	68	70	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	60	133	93	97	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	60	133	99	110	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	60	133	115	117	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	60	133	72	72	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18669648,PMID:20068231,PMID:23186163
P51149	60	133	67	67	Mutagenesis	Note=Does not abolish localization on late endosomes%2C lysosomes and phagosomes and does not reduce phagosomal fusions. No loss of interaction with CLN5. Q->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12944476,ECO:0000269\|PubMed:2
P51149	60	133	129	129	Natural variant	ID=VAR_018722;Note=In CMT2B%3B increases GTP hydrolysis%3B decreases affinity for GTP and GDP%3B does not affect interaction with NTRK1%3B results in higher levels of NTRK1 and MAPK1/MAPK3 phosphorylation after NGF stimulation consistent with enhanced MAP
P51149	60	133	63	67	Nucleotide binding	Note=GTP;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15933719,ECO:0000269\|PubMed:20028791;Dbxref=PMID:15933719,PMID:20028791
P51149	60	133	125	128	Nucleotide binding	Note=GTP;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15933719,ECO:0000269\|PubMed:20028791;Dbxref=PMID:15933719,PMID:20028791
P51149	60	133	108	108	Sequence conflict	Note=I->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
P51149	60	133	127	127	Sequence conflict	Note=I->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
P51149	133	176	151	153	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	133	176	2	207	Chain	ID=PRO_0000121121;Note=Ras-related protein Rab-7a
P51149	133	176	136	145	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	133	176	162	181	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91
P51149	133	176	157	157	Natural variant	ID=VAR_037887;Note=In CMT2B%3B does not affect interaction with NTRK1%3B results in higher levels of NTRK1 and MAPK1/MAPK3 phosphorylation after NGF stimulation consistent with enhanced MAPK signaling. K->N;Ontology_term=ECO:0000269,ECO:0000269;evidence=E
P51149	133	176	161	161	Natural variant	ID=VAR_037888;Note=In CMT2B%3B does not affect interaction with NTRK1%3B results in higher levels of NTRK1 and MAPK1/MAPK3 phosphorylation after NGF stimulation consistent with enhanced MAPK signaling. N->T;Ontology_term=ECO:0000269,ECO:0000269;evidence=E
P51149	133	176	162	162	Natural variant	ID=VAR_018723;Note=In CMT2B%3B increases GTP hydrolysis%3B decreases affinity for GTP and GDP%3B does not affect interaction with NTRK1%3B results in higher levels of NTRK1 and MAPK1/MAPK3 phosphorylation after NGF stimulation consistent with enhanced MAP
P51149	133	176	156	157	Nucleotide binding	Note=GTP;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15933719,ECO:0000269\|PubMed:20028791;Dbxref=PMID:15933719,PMID:20028791
P51149	133	176	156	159	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1T91

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SNVs in the skipped exons for RAB7A

- 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_377402	128525215	128525433	128525368	128525368	Frame_Shift_Del	C	-	p.P112fs
STAD	TCGA-F1-6177-01	exon_skip_377395	128516786	128516912	128516847	128516848	Frame_Shift_Ins	-	CC	p.A39fs
STAD	TCGA-F1-6177-01	exon_skip_377395	128516786	128516912	128516848	128516849	Frame_Shift_Ins	-	CC	p.A39fs
PAAD	TCGA-IB-7651-01	exon_skip_377390	128514203	128514263	128514202	128514202	Splice_Site	G	A	.

- 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
LS411N_LARGE_INTESTINE	128525215	128525433	128525309	128525309	Frame_Shift_Del	C	-	p.A92fs
NCIH2342_LUNG	128514203	128514263	128514256	128514256	Missense_Mutation	G	C	p.D16H
FARAGE_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	128516786	128516912	128516835	128516835	Missense_Mutation	A	T	p.N35Y
HCC2998_LARGE_INTESTINE	128525215	128525433	128525422	128525422	Missense_Mutation	G	A	p.E130K
SNU520_STOMACH	128526386	128526514	128526399	128526399	Missense_Mutation	G	A	p.R138Q
IGROV1_OVARY	128526386	128526514	128526483	128526483	Missense_Mutation	T	C	p.F166S

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAB7A

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 RAB7A

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAB7A

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RelatedDrugs for RAB7A

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 RAB7A

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
RAB7A	C0151744	Myocardial Ischemia	1	CTD_human
RAB7A	C1833219	CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2B (disorder)	1	CTD_human;ORPHANET;UNIPROT

	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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