ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for PRCC

Gene summary

Gene information	Gene symbol	PRCC
	Gene ID	5546
	Gene name	papillary renal cell carcinoma (translocation-associated)
	Synonyms	RCCP1\|TPRC
	Cytomap	1q23.1
	Type of gene	protein-coding
	Description	proline-rich protein PRCCpapillary renal cell carcinoma translocation-associated gene protein
	Modification date	20180522
	UniProtAcc	Q92733
	Context	PubMed: PRCC [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
PRCC	GO:0007093	mitotic cell cycle checkpoint	11717438

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Exon skipping events across known transcript of Ensembl for PRCC 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 PRCC

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 PRCC

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_12451	1	156737345:156738031:156752073:156752121:156756399:156756772	156752073:156752121	ENSG00000143294.10	ENST00000353233.3,ENST00000271526.4
exon_skip_12460	1	156752077:156752121:156756399:156756966:156761488:156761584	156756399:156756966	ENSG00000143294.10	ENST00000271526.4,ENST00000491853.1
exon_skip_12461	1	156752077:156752121:156756399:156756966:156764456:156764596	156756399:156756966	ENSG00000143294.10	ENST00000353233.3
exon_skip_12468	1	156756784:156756966:156760858:156760954:156761488:156761584	156760858:156760954	ENSG00000143294.10	ENST00000454659.1
exon_skip_12474	1	156756784:156756966:156761488:156761584:156764456:156764596	156761488:156761584	ENSG00000143294.10	ENST00000271526.4

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for PRCC

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_12451	1	156737345:156738031:156752073:156752121:156756399:156756772	156752073:156752121	ENSG00000143294.10	ENST00000271526.4,ENST00000353233.3
exon_skip_12460	1	156752077:156752121:156756399:156756966:156761488:156761584	156756399:156756966	ENSG00000143294.10	ENST00000491853.1,ENST00000271526.4
exon_skip_12461	1	156752077:156752121:156756399:156756966:156764456:156764596	156756399:156756966	ENSG00000143294.10	ENST00000353233.3
exon_skip_12468	1	156756784:156756966:156760858:156760954:156761488:156761584	156760858:156760954	ENSG00000143294.10	ENST00000454659.1
exon_skip_12474	1	156756784:156756966:156761488:156761584:156764456:156764596	156761488:156761584	ENSG00000143294.10	ENST00000271526.4

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 PRCC

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
ENST00000271526	156752073	156752121	In-frame
ENST00000271526	156756399	156756966	In-frame
ENST00000271526	156761488	156761584	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
ENST00000271526	156752073	156752121	In-frame
ENST00000271526	156756399	156756966	In-frame
ENST00000271526	156761488	156761584	In-frame

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

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
ENST00000271526	2120	491	156752073	156752121	741	788	156	172
ENST00000271526	2120	491	156756399	156756966	789	1355	172	361
ENST00000271526	2120	491	156761488	156761584	1356	1451	361	393

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
ENST00000271526	2120	491	156752073	156752121	741	788	156	172
ENST00000271526	2120	491	156756399	156756966	789	1355	172	361
ENST00000271526	2120	491	156761488	156761584	1356	1451	361	393

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
Q92733	156	172	1	491	Chain	ID=PRO_0000058568;Note=Proline-rich protein PRCC
Q92733	156	172	157	157	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:23186163,ECO:0000244\|PubMed:24275569;Dbxref=PMID:1
Q92733	156	172	159	159	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:23186163,ECO:0000244\|PubMed:24275569;Dbxref=PMID:1
Q92733	172	361	1	491	Chain	ID=PRO_0000058568;Note=Proline-rich protein PRCC
Q92733	172	361	235	239	Compositional bias	Note=Poly-Thr
Q92733	172	361	212	212	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:20068231;Dbxref=PMID:20068231
Q92733	172	361	218	218	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:17081983;Dbxref=PMID:17081983
Q92733	172	361	239	239	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:20068231;Dbxref=PMID:20068231
Q92733	172	361	241	241	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:23186163;Dbxref=PMID:20068231,PMID:23186163
Q92733	172	361	267	267	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q92733	361	393	1	491	Chain	ID=PRO_0000058568;Note=Proline-rich protein PRCC

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
Q92733	156	172	1	491	Chain	ID=PRO_0000058568;Note=Proline-rich protein PRCC
Q92733	156	172	157	157	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:23186163,ECO:0000244\|PubMed:24275569;Dbxref=PMID:1
Q92733	156	172	159	159	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:23186163,ECO:0000244\|PubMed:24275569;Dbxref=PMID:1
Q92733	172	361	1	491	Chain	ID=PRO_0000058568;Note=Proline-rich protein PRCC
Q92733	172	361	235	239	Compositional bias	Note=Poly-Thr
Q92733	172	361	212	212	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:20068231;Dbxref=PMID:20068231
Q92733	172	361	218	218	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:17081983;Dbxref=PMID:17081983
Q92733	172	361	239	239	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:20068231;Dbxref=PMID:20068231
Q92733	172	361	241	241	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:23186163;Dbxref=PMID:20068231,PMID:23186163
Q92733	172	361	267	267	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q92733	361	393	1	491	Chain	ID=PRO_0000058568;Note=Proline-rich protein PRCC

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SNVs in the skipped exons for PRCC

- 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
LUAD	TCGA-17-Z028-01		156756400	156756966	156756484	156756484	Frame_Shift_Del	C	-	p.P201fs
LIHC	TCGA-DD-A3A0-01		156756400	156756966	156756497	156756497	Frame_Shift_Del	C	-	p.S205fs
HNSC	TCGA-F7-A624-01	exon_skip_12474	156761489	156761584	156761536	156761536	Frame_Shift_Del	C	-	p.V377fs
LIHC	TCGA-DD-A3A0-01	exon_skip_12474	156761489	156761584	156761553	156761553	Frame_Shift_Del	C	-	p.A383fs
KIRC	TCGA-A3-3378-01	exon_skip_12474	156761489	156761584	156761535	156761536	Frame_Shift_Ins	-	C	p.A377fs
LUAD	TCGA-44-2655-01	exon_skip_12474	156761489	156761584	156761535	156761536	Frame_Shift_Ins	-	C	p.A377fs
LUAD	TCGA-44-2656-01	exon_skip_12474	156761489	156761584	156761535	156761536	Frame_Shift_Ins	-	C	p.A377fs
LUAD	TCGA-44-2656-01	exon_skip_12474	156761489	156761584	156761535	156761536	Frame_Shift_Ins	-	C	p.V377fs
LUAD	TCGA-44-2659-01	exon_skip_12474	156761489	156761584	156761535	156761536	Frame_Shift_Ins	-	C	p.A377fs
PAAD	TCGA-IB-7887-01	exon_skip_12474	156761489	156761584	156761535	156761536	Frame_Shift_Ins	-	C	p.A377fs
STAD	TCGA-HF-A5NB-01	exon_skip_12474	156761489	156761584	156761535	156761536	Frame_Shift_Ins	-	C	p.A377fs
UCEC	TCGA-BG-A0M0-01	exon_skip_12474	156761489	156761584	156761535	156761536	Frame_Shift_Ins	-	C	p.V377fs
UCEC	TCGA-BG-A0M3-01	exon_skip_12474	156761489	156761584	156761535	156761536	Frame_Shift_Ins	-	C	p.V377fs
UCEC	TCGA-D1-A0ZS-01	exon_skip_12474	156761489	156761584	156761535	156761536	Frame_Shift_Ins	-	C	p.V377fs
UCS	TCGA-N7-A4Y0-01	exon_skip_12474	156761489	156761584	156761535	156761536	Frame_Shift_Ins	-	C	p.A377fs
STAD	TCGA-HU-A4GQ-01	exon_skip_12474	156761489	156761584	156761536	156761537	Frame_Shift_Ins	-	C	p.V377fs

- 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
RKO_LARGE_INTESTINE	156761489	156761584	156761536	156761536	Frame_Shift_Del	C	-	p.V377fs
GP2D_LARGE_INTESTINE	156761489	156761584	156761536	156761536	Frame_Shift_Del	C	-	p.V377fs
GP5D_LARGE_INTESTINE	156761489	156761584	156761536	156761536	Frame_Shift_Del	C	-	p.V377fs
OVK18_OVARY	156761489	156761584	156761536	156761536	Frame_Shift_Del	C	-	p.V377fs
WSUNHL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	156761489	156761584	156761536	156761536	Frame_Shift_Del	C	-	p.V377fs
GIMEN_AUTONOMIC_GANGLIA	156756400	156756966	156756715	156756716	In_Frame_Ins	-	CCCTCC	p.280_281insLP
LOVO_LARGE_INTESTINE	156756400	156756966	156756509	156756509	Missense_Mutation	C	T	p.S209L
HCT116_LARGE_INTESTINE	156756400	156756966	156756509	156756509	Missense_Mutation	C	T	p.S209L
KS1_CENTRAL_NERVOUS_SYSTEM	156756400	156756966	156756523	156756523	Missense_Mutation	G	C	p.D214H
AU565_BREAST	156756400	156756966	156756548	156756548	Missense_Mutation	C	G	p.S222C
SKBR3_BREAST	156756400	156756966	156756548	156756548	Missense_Mutation	C	G	p.S222C
PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	156756400	156756966	156756566	156756566	Missense_Mutation	C	G	p.S228C
UBLC1_URINARY_TRACT	156756400	156756966	156756575	156756575	Missense_Mutation	C	T	p.P231L
ESS1_ENDOMETRIUM	156756400	156756966	156756663	156756663	Missense_Mutation	C	G	p.I260M
SNU1040_LARGE_INTESTINE	156756400	156756966	156756665	156756665	Missense_Mutation	C	T	p.T261M
BICR18_UPPER_AERODIGESTIVE_TRACT	156756400	156756966	156756726	156756726	Missense_Mutation	A	C	p.E281D
BICR18_UPPER_AERODIGESTIVE_TRACT	156756400	156756966	156756765	156756766	Missense_Mutation	CA	TG	p.I295V
HCC1419_BREAST	156756400	156756966	156756772	156756772	Missense_Mutation	A	G	p.T297A
OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	156756400	156756966	156756842	156756842	Missense_Mutation	C	A	p.P320H
SNU489_CENTRAL_NERVOUS_SYSTEM	156756400	156756966	156756902	156756902	Missense_Mutation	A	G	p.D340G
HEC108_ENDOMETRIUM	156756400	156756966	156756907	156756907	Missense_Mutation	T	C	p.Y342H
NO11_CENTRAL_NERVOUS_SYSTEM	156756400	156756966	156756929	156756929	Missense_Mutation	C	T	p.T349I
KE39_STOMACH	156756400	156756966	156756949	156756949	Missense_Mutation	G	A	p.A356T
KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	156761489	156761584	156761558	156761558	Missense_Mutation	G	A	p.D385N

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

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 PRCC

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

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RelatedDrugs for PRCC

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 PRCC

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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