ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for RPH3A

Gene summary

Gene information	Gene symbol	RPH3A
	Gene ID	22895
	Gene name	rabphilin 3A
	Synonyms	-
	Cytomap	12q24.13
	Type of gene	protein-coding
	Description	rabphilin-3Aexophilin-1rabphilin 3A homolog
	Modification date	20180519
	UniProtAcc	Q9Y2J0
	Context	PubMed: RPH3A [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 RPH3A 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 RPH3A

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 RPH3A

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_87223	12	113013068:113013123:113055528:113055646:113087218:113087268	113055528:113055646	ENSG00000089169.10	ENST00000546426.1
exon_skip_87224	12	113013068:113013123:113055528:113055646:113229947:113230068	113055528:113055646	ENSG00000089169.10	ENST00000546703.1
exon_skip_87226	12	113013068:113013123:113229947:113230068:113266105:113266160	113229947:113230068	ENSG00000089169.10	ENST00000543106.2
exon_skip_87228	12	113087218:113087268:113089571:113089632:113229947:113230068	113089571:113089632	ENSG00000089169.10	ENST00000546426.1,ENST00000549736.1
exon_skip_87231	12	113089571:113089632:113229947:113230068:113266105:113266194	113229947:113230068	ENSG00000089169.10	ENST00000546426.1,ENST00000549736.1
exon_skip_87234	12	113229989:113230068:113251126:113251190:113266105:113266194	113251126:113251190	ENSG00000089169.10	ENST00000553114.1
exon_skip_87235	12	113229947:113230068:113266105:113266194:113274295:113274307	113266105:113266194	ENSG00000089169.10	ENST00000548197.1,ENST00000546703.1,ENST00000543106.2,ENST00000552667.1,ENST00000389385.4,ENST00000547840.1,ENST00000548866.1,ENST00000549769.1,ENST00000547728.1,ENST00000549736.1,ENST00000415485.3,ENST00000551198.1
exon_skip_87236	12	113230051:113230068:113266105:113266194:113285500:113285536	113266105:113266194	ENSG00000089169.10	ENST00000551052.1
exon_skip_87237	12	113229947:113230068:113274295:113274307:113285500:113285536	113274295:113274307	ENSG00000089169.10	ENST00000550901.1
exon_skip_87239	12	113266123:113266194:113274295:113274307:113285500:113285536	113274295:113274307	ENSG00000089169.10	ENST00000548197.1,ENST00000551593.1,ENST00000546703.1,ENST00000543106.2,ENST00000552667.1,ENST00000547686.1,ENST00000389385.4,ENST00000547840.1,ENST00000549769.1,ENST00000547728.1,ENST00000420983.2,ENST00000549736.1,ENST00000553114.1,ENST00000551748.1,ENS
exon_skip_87241	12	113266105:113266194:113274303:113274307:113285500:113285536	113274303:113274307	ENSG00000089169.10	ENST00000552679.2
exon_skip_87242	12	113266123:113266194:113285500:113285647:113303218:113303237	113285500:113285647	ENSG00000089169.10	ENST00000551052.1
exon_skip_87244	12	113274295:113274307:113285500:113285647:113303218:113303348	113285500:113285647	ENSG00000089169.10	ENST00000548197.1,ENST00000551593.1,ENST00000546703.1,ENST00000543106.2,ENST00000547099.1,ENST00000552667.1,ENST00000547686.1,ENST00000389385.4,ENST00000547840.1,ENST00000549769.1,ENST00000552679.2,ENST00000547728.1,ENST00000420983.2,ENST00000550901.1,ENS

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for RPH3A

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_87223	12	113013068:113013123:113055528:113055646:113087218:113087268	113055528:113055646	ENSG00000089169.10	ENST00000546426.1
exon_skip_87224	12	113013068:113013123:113055528:113055646:113229947:113230068	113055528:113055646	ENSG00000089169.10	ENST00000546703.1
exon_skip_87226	12	113013068:113013123:113229947:113230068:113266105:113266160	113229947:113230068	ENSG00000089169.10	ENST00000543106.2
exon_skip_87228	12	113087218:113087268:113089571:113089632:113229947:113230068	113089571:113089632	ENSG00000089169.10	ENST00000549736.1,ENST00000546426.1
exon_skip_87230	12	113089571:113089632:113155810:113155892:113266105:113266194	113155810:113155892	ENSG00000089169.10	ENST00000547686.1
exon_skip_87231	12	113089571:113089632:113229947:113230068:113266105:113266194	113229947:113230068	ENSG00000089169.10	ENST00000549736.1,ENST00000546426.1
exon_skip_87234	12	113229989:113230068:113251126:113251190:113266105:113266194	113251126:113251190	ENSG00000089169.10	ENST00000553114.1
exon_skip_87235	12	113229947:113230068:113266105:113266194:113274295:113274307	113266105:113266194	ENSG00000089169.10	ENST00000549736.1,ENST00000548197.1,ENST00000543106.2,ENST00000546703.1,ENST00000547840.1,ENST00000547728.1,ENST00000549769.1,ENST00000552667.1,ENST00000389385.4,ENST00000551198.1,ENST00000415485.3,ENST00000548866.1
exon_skip_87236	12	113230051:113230068:113266105:113266194:113285500:113285536	113266105:113266194	ENSG00000089169.10	ENST00000551052.1
exon_skip_87237	12	113229947:113230068:113274295:113274307:113285500:113285536	113274295:113274307	ENSG00000089169.10	ENST00000550901.1
exon_skip_87239	12	113266123:113266194:113274295:113274307:113285500:113285536	113274295:113274307	ENSG00000089169.10	ENST00000549736.1,ENST00000548197.1,ENST00000547686.1,ENST00000543106.2,ENST00000551593.1,ENST00000551748.1,ENST00000546703.1,ENST00000547840.1,ENST00000547728.1,ENST00000549769.1,ENST00000552667.1,ENST00000389385.4,ENST00000551198.1,ENST00000415485.3,ENS
exon_skip_87244	12	113274295:113274307:113285500:113285647:113303218:113303348	113285500:113285647	ENSG00000089169.10	ENST00000548197.1,ENST00000547686.1,ENST00000543106.2,ENST00000551593.1,ENST00000551748.1,ENST00000546703.1,ENST00000547840.1,ENST00000547728.1,ENST00000549769.1,ENST00000552667.1,ENST00000389385.4,ENST00000550901.1,ENST00000551198.1,ENST00000415485.3,ENS

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 RPH3A

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
ENST00000389385	113266105	113266194	5CDS-5UTR
ENST00000415485	113266105	113266194	5CDS-5UTR
ENST00000543106	113266105	113266194	5CDS-5UTR
ENST00000543106	113229947	113230068	5UTR-5UTR
ENST00000389385	113274295	113274307	In-frame
ENST00000415485	113274295	113274307	In-frame
ENST00000543106	113274295	113274307	In-frame
ENST00000389385	113285500	113285647	In-frame
ENST00000415485	113285500	113285647	In-frame
ENST00000543106	113285500	113285647	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
ENST00000389385	113266105	113266194	5CDS-5UTR
ENST00000415485	113266105	113266194	5CDS-5UTR
ENST00000543106	113266105	113266194	5CDS-5UTR
ENST00000543106	113229947	113230068	5UTR-5UTR
ENST00000389385	113274295	113274307	In-frame
ENST00000415485	113274295	113274307	In-frame
ENST00000543106	113274295	113274307	In-frame
ENST00000389385	113285500	113285647	In-frame
ENST00000415485	113285500	113285647	In-frame
ENST00000543106	113285500	113285647	In-frame

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Infer the effects of exon skipping event on protein functional features for RPH3A

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
ENST00000389385	4696	694	113285500	113285647	581	727	28	76
ENST00000415485	4469	694	113285500	113285647	350	496	28	76
ENST00000543106	2598	694	113285500	113285647	446	592	28	76

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
ENST00000389385	4696	694	113285500	113285647	581	727	28	76
ENST00000415485	4469	694	113285500	113285647	350	496	28	76
ENST00000543106	2598	694	113285500	113285647	446	592	28	76

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
Q9Y2J0	28	76	24	28	Alternative sequence	ID=VSP_021016;Note=In isoform 2. NDKEQ->K;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2J0	28	76	24	28	Alternative sequence	ID=VSP_021016;Note=In isoform 2. NDKEQ->K;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2J0	28	76	24	28	Alternative sequence	ID=VSP_021016;Note=In isoform 2. NDKEQ->K;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2J0	28	76	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	28	76	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	28	76	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	28	76	44	160	Domain	Note=RabBD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00234
Q9Y2J0	28	76	44	160	Domain	Note=RabBD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00234
Q9Y2J0	28	76	44	160	Domain	Note=RabBD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00234

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
Q9Y2J0	28	76	24	28	Alternative sequence	ID=VSP_021016;Note=In isoform 2. NDKEQ->K;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2J0	28	76	24	28	Alternative sequence	ID=VSP_021016;Note=In isoform 2. NDKEQ->K;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2J0	28	76	24	28	Alternative sequence	ID=VSP_021016;Note=In isoform 2. NDKEQ->K;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2J0	28	76	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	28	76	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	28	76	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	28	76	44	160	Domain	Note=RabBD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00234
Q9Y2J0	28	76	44	160	Domain	Note=RabBD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00234
Q9Y2J0	28	76	44	160	Domain	Note=RabBD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00234

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SNVs in the skipped exons for RPH3A

- 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-A1EG-01	exon_skip_87236 exon_skip_87235	113266106	113266194	113266168	113266168	Frame_Shift_Del	C	-	p.Y15fs
UCS	TCGA-N9-A4Q8-01	exon_skip_87244 exon_skip_87242	113285501	113285647	113285511	113285515	Frame_Shift_Del	GGCTG	-	p.31_33del
UCS	TCGA-N9-A4Q8-01	exon_skip_87244 exon_skip_87242	113285501	113285647	113285511	113285515	Frame_Shift_Del	GGCTG	-	p.GW32fs
LIHC	TCGA-BC-A3KG-01	exon_skip_87244 exon_skip_87242	113285501	113285647	113285525	113285525	Frame_Shift_Del	C	-	p.H36fs
LIHC	TCGA-DD-A3A0-01	exon_skip_87244 exon_skip_87242	113285501	113285647	113285584	113285584	Frame_Shift_Del	A	-	p.E56fs
SKCM	TCGA-DA-A1IC-06	exon_skip_87236 exon_skip_87235	113266106	113266194	113266161	113266161	Nonsense_Mutation	G	A	p.W13*
SKCM	TCGA-DA-A1IC-06	exon_skip_87236 exon_skip_87235	113266106	113266194	113266161	113266161	Nonsense_Mutation	G	A	p.W13X
SKCM	TCGA-DA-A1IC-06	exon_skip_87236 exon_skip_87235	113266106	113266194	113266162	113266162	Nonsense_Mutation	G	A	p.W13*
SKCM	TCGA-DA-A1IC-06	exon_skip_87236 exon_skip_87235	113266106	113266194	113266162	113266162	Nonsense_Mutation	G	A	p.W13X
BLCA	TCGA-GU-A42Q-01	exon_skip_87236 exon_skip_87235	113266106	113266194	113266187	113266187	Nonsense_Mutation	C	T	p.Q22*
SKCM	TCGA-D3-A8GI-06	exon_skip_87244 exon_skip_87242	113285501	113285647	113285505	113285505	Nonsense_Mutation	C	T	p.Q30*
UCEC	TCGA-B5-A0JY-01	exon_skip_87244 exon_skip_87242	113285501	113285647	113285583	113285583	Nonsense_Mutation	G	T	p.E56*

- 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
SNU1040_LARGE_INTESTINE	113266106	113266194	113266136	113266136	Missense_Mutation	G	A	p.V5M
MM415_SKIN	113266106	113266194	113266139	113266139	Missense_Mutation	T	A	p.F6I
HCC366_LUNG	113266106	113266194	113266144	113266144	Missense_Mutation	C	A	p.S7R
TE1_OESOPHAGUS	113266106	113266194	113266158	113266158	Missense_Mutation	G	A	p.R12H

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RPH3A

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 RPH3A

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RPH3A

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RelatedDrugs for RPH3A

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 RPH3A

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 RPH3A

Exon skipping events across known transcript of Ensembl for RPH3A from UCSC genome browser

Gene isoform structures and expression levels for RPH3A

Exon skipping events with PSIs in TCGA for RPH3A

Exon skipping events with PSIs in GTEx for RPH3A

Open reading frame (ORF) annotation in the exon skipping event for RPH3A

Infer the effects of exon skipping event on protein functional features for RPH3A

SNVs in the skipped exons for RPH3A

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RPH3A

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RPH3A

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RPH3A

RelatedDrugs for RPH3A

RelatedDiseases for RPH3A