ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for CRTC2

Gene summary

Gene information	Gene symbol	CRTC2
	Gene ID	200186
	Gene name	CREB regulated transcription coactivator 2
	Synonyms	TORC-2\|TORC2
	Cytomap	1q21.3
	Type of gene	protein-coding
	Description	CREB-regulated transcription coactivator 2transducer of regulated cAMP response element-binding protein (CREB) 2
	Modification date	20180523
	UniProtAcc	Q53ET0
	Context	PubMed: CRTC2 [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

Top

Exon skipping events across known transcript of Ensembl for CRTC2 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.

Top

Gene isoform structures and expression levels for CRTC2

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

Top

Exon skipping events with PSIs in TCGA for CRTC2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_31808	1	153920153:153920805:153920933:153921120:153921590:153921860	153920933:153921120	ENSG00000160741.12	ENST00000368630.3,ENST00000487235.1,ENST00000368633.1,ENST00000303569.6
exon_skip_31812	1	153920933:153921120:153921309:153921376:153921590:153921693	153921309:153921376	ENSG00000160741.12	ENST00000461638.2
exon_skip_31813	1	153920933:153921120:153921590:153921860:153923735:153924080	153921590:153921860	ENSG00000160741.12	ENST00000368630.3,ENST00000368633.1,ENST00000303569.6
exon_skip_31823	1	153921741:153921860:153923735:153924142:153924493:153924738	153923735:153924142	ENSG00000160741.12	ENST00000368633.1,ENST00000303569.6,ENST00000461638.2
exon_skip_31828	1	153921647:153921860:153924493:153924738:153924872:153924922	153924493:153924738	ENSG00000160741.12	ENST00000487235.1
exon_skip_31833	1	153923735:153924142:153924493:153924738:153924872:153924922	153924493:153924738	ENSG00000160741.12	ENST00000368633.1,ENST00000303569.6,ENST00000461638.2
exon_skip_31840	1	153925280:153925310:153925741:153925845:153926013:153926053	153925741:153925845	ENSG00000160741.12	ENST00000487235.1,ENST00000368633.1,ENST00000461638.2
exon_skip_31842	1	153925791:153925845:153926013:153926082:153926730:153926792	153926013:153926082	ENSG00000160741.12	ENST00000487235.1,ENST00000368633.1,ENST00000476883.1,ENST00000461638.2
exon_skip_31848	1	153927348:153927465:153927540:153927642:153930536:153930599	153927540:153927642	ENSG00000160741.12	ENST00000476883.1
exon_skip_31849	1	153927348:153927465:153927540:153927642:153930621:153930680	153927540:153927642	ENSG00000160741.12	ENST00000492073.1
exon_skip_31850	1	153927348:153927465:153927540:153927642:153930820:153931040	153927540:153927642	ENSG00000160741.12	ENST00000368633.1

PSI values of skipped exons in TCGA.

Top

Exon skipping events with PSIs in GTEx for CRTC2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_31808	1	153920153:153920805:153920933:153921120:153921590:153921860	153920933:153921120	ENSG00000160741.12	ENST00000303569.6,ENST00000368630.3,ENST00000368633.1,ENST00000487235.1
exon_skip_31812	1	153920933:153921120:153921309:153921376:153921590:153921693	153921309:153921376	ENSG00000160741.12	ENST00000461638.2
exon_skip_31813	1	153920933:153921120:153921590:153921860:153923735:153924080	153921590:153921860	ENSG00000160741.12	ENST00000303569.6,ENST00000368630.3,ENST00000368633.1
exon_skip_31823	1	153921741:153921860:153923735:153924142:153924493:153924738	153923735:153924142	ENSG00000160741.12	ENST00000303569.6,ENST00000461638.2,ENST00000368633.1
exon_skip_31828	1	153921647:153921860:153924493:153924738:153924872:153924922	153924493:153924738	ENSG00000160741.12	ENST00000487235.1
exon_skip_31833	1	153923735:153924142:153924493:153924738:153924872:153924922	153924493:153924738	ENSG00000160741.12	ENST00000303569.6,ENST00000461638.2,ENST00000368633.1
exon_skip_31840	1	153925280:153925310:153925741:153925845:153926013:153926053	153925741:153925845	ENSG00000160741.12	ENST00000461638.2,ENST00000368633.1,ENST00000487235.1
exon_skip_31842	1	153925791:153925845:153926013:153926082:153926730:153926792	153926013:153926082	ENSG00000160741.12	ENST00000461638.2,ENST00000368633.1,ENST00000487235.1,ENST00000476883.1
exon_skip_31848	1	153927348:153927465:153927540:153927642:153930536:153930599	153927540:153927642	ENSG00000160741.12	ENST00000476883.1
exon_skip_31849	1	153927348:153927465:153927540:153927642:153930621:153930680	153927540:153927642	ENSG00000160741.12	ENST00000492073.1
exon_skip_31850	1	153927348:153927465:153927540:153927642:153930820:153931040	153927540:153927642	ENSG00000160741.12	ENST00000368633.1

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

Top

Open reading frame (ORF) annotation in the exon skipping event for CRTC2

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
ENST00000368633	153920933	153921120	Frame-shift
ENST00000368633	153923735	153924142	Frame-shift
ENST00000368633	153924493	153924738	Frame-shift
ENST00000368633	153925741	153925845	Frame-shift
ENST00000368633	153921590	153921860	In-frame
ENST00000368633	153926013	153926082	In-frame
ENST00000368633	153927540	153927642	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
ENST00000368633	153920933	153921120	Frame-shift
ENST00000368633	153923735	153924142	Frame-shift
ENST00000368633	153924493	153924738	Frame-shift
ENST00000368633	153925741	153925845	Frame-shift
ENST00000368633	153921590	153921860	In-frame
ENST00000368633	153926013	153926082	In-frame
ENST00000368633	153927540	153927642	In-frame

Top

Infer the effects of exon skipping event on protein functional features for CRTC2

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
ENST00000368633	2661	693	153927540	153927642	282	383	51	85
ENST00000368633	2661	693	153926013	153926082	563	631	145	167
ENST00000368633	2661	693	153921590	153921860	1533	1802	468	558

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
ENST00000368633	2661	693	153927540	153927642	282	383	51	85
ENST00000368633	2661	693	153926013	153926082	563	631	145	167
ENST00000368633	2661	693	153921590	153921860	1533	1802	468	558

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
Q53ET0	51	85	2	693	Chain	ID=PRO_0000318528;Note=CREB-regulated transcription coactivator 2
Q53ET0	51	85	51	51	Modified residue	Note=Asymmetric dimethylarginine%3B by PRMT6;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q3U182
Q53ET0	51	85	70	70	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:19690332,ECO:0000269\|PubMed:15454081;Dbxref=PMID:18669648,PMID:19690332,PMID:15454081
Q53ET0	51	85	70	70	Mutagenesis	Note=No effect on cAMP- and calcium-regulated phosphorylation. S->A
Q53ET0	145	167	2	693	Chain	ID=PRO_0000318528;Note=CREB-regulated transcription coactivator 2
Q53ET0	145	167	161	161	Modified residue	Note=Asymmetric dimethylarginine%3B by PRMT6;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q3U182
Q53ET0	145	167	147	147	Natural variant	ID=VAR_038756;Note=M->V;Dbxref=dbSNP:rs11264680
Q53ET0	468	558	2	693	Chain	ID=PRO_0000318528;Note=CREB-regulated transcription coactivator 2
Q53ET0	468	558	488	488	Modified residue	Note=Phosphotyrosine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19690332;Dbxref=PMID:19690332
Q53ET0	468	558	489	489	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15454081;Dbxref=PMID:15454081
Q53ET0	468	558	490	490	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19690332;Dbxref=PMID:19690332
Q53ET0	468	558	492	492	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15454081;Dbxref=PMID:15454081
Q53ET0	468	558	501	501	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231
Q53ET0	468	558	499	499	Sequence conflict	Note=P->S;Ontology_term=ECO:0000305;evidence=ECO:0000305

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
Q53ET0	51	85	2	693	Chain	ID=PRO_0000318528;Note=CREB-regulated transcription coactivator 2
Q53ET0	51	85	51	51	Modified residue	Note=Asymmetric dimethylarginine%3B by PRMT6;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q3U182
Q53ET0	51	85	70	70	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:19690332,ECO:0000269\|PubMed:15454081;Dbxref=PMID:18669648,PMID:19690332,PMID:15454081
Q53ET0	51	85	70	70	Mutagenesis	Note=No effect on cAMP- and calcium-regulated phosphorylation. S->A
Q53ET0	145	167	2	693	Chain	ID=PRO_0000318528;Note=CREB-regulated transcription coactivator 2
Q53ET0	145	167	161	161	Modified residue	Note=Asymmetric dimethylarginine%3B by PRMT6;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q3U182
Q53ET0	145	167	147	147	Natural variant	ID=VAR_038756;Note=M->V;Dbxref=dbSNP:rs11264680
Q53ET0	468	558	2	693	Chain	ID=PRO_0000318528;Note=CREB-regulated transcription coactivator 2
Q53ET0	468	558	488	488	Modified residue	Note=Phosphotyrosine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19690332;Dbxref=PMID:19690332
Q53ET0	468	558	489	489	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15454081;Dbxref=PMID:15454081
Q53ET0	468	558	490	490	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19690332;Dbxref=PMID:19690332
Q53ET0	468	558	492	492	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15454081;Dbxref=PMID:15454081
Q53ET0	468	558	501	501	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231
Q53ET0	468	558	499	499	Sequence conflict	Note=P->S;Ontology_term=ECO:0000305;evidence=ECO:0000305

Top

SNVs in the skipped exons for CRTC2

- 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_31808	153920934	153921120	153921068	153921068	Frame_Shift_Del	G	-	p.P576fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_31813	153921591	153921860	153921811	153921811	Frame_Shift_Del	G	-	p.P485fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_31823	153923736	153924142	153923864	153923864	Frame_Shift_Del	G	-	p.H427fs
UCEC	TCGA-D1-A0ZS-01	exon_skip_31823	153923736	153924142	153923864	153923864	Frame_Shift_Del	G	-	p.H426fs
LIHC	TCGA-BC-A3KG-01	exon_skip_31823	153923736	153924142	153923873	153923873	Frame_Shift_Del	C	-	p.A423fs
LIHC	TCGA-DD-A39Y-01	exon_skip_31823	153923736	153924142	153924090	153924090	Frame_Shift_Del	G	-	p.P350fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_31823	153923736	153924142	153924113	153924113	Frame_Shift_Del	G	-	p.L343fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_31833 exon_skip_31828	153924494	153924738	153924620	153924620	Frame_Shift_Del	G	-	p.L291fs
STAD	TCGA-BR-6452-01	exon_skip_31833 exon_skip_31828	153924494	153924738	153924673	153924673	Frame_Shift_Del	C	-	p.G273fs
LIHC	TCGA-DD-A1EG-01	exon_skip_31842	153926014	153926082	153926037	153926037	Frame_Shift_Del	A	-	p.F160fs
LIHC	TCGA-BC-A112-01	exon_skip_31808	153920934	153921120	153921040	153921041	Frame_Shift_Ins	-	A	p.W585fs
UCS	TCGA-N7-A4Y0-01	exon_skip_31823	153923736	153924142	153923897	153923898	Frame_Shift_Ins	-	G	p.PL414fs
UCS	TCGA-N7-A4Y0-01	exon_skip_31823	153923736	153924142	153923897	153923898	Frame_Shift_Ins	-	G	p.S415fs
LIHC	TCGA-BC-A112-01	exon_skip_31823	153923736	153924142	153923907	153923908	Frame_Shift_Ins	-	A	p.W411fs
THYM	TCGA-ZB-A96M-01	exon_skip_31813	153921591	153921860	153921713	153921713	Nonsense_Mutation	G	A	p.Q518X
OV	TCGA-61-1998-01	exon_skip_31840	153925742	153925845	153925751	153925751	Nonsense_Mutation	G	A	p.R200*

- 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
SISO_CERVIX	153921591	153921860	153921691	153921691	Frame_Shift_Del	G	-	p.P525fs
GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	153921591	153921860	153921691	153921691	Frame_Shift_Del	G	-	p.P525fs
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	153924494	153924738	153924673	153924673	Frame_Shift_Del	C	-	p.G273fs
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	153924494	153924738	153924619	153924620	Frame_Shift_Ins	-	G	p.L291fs
RKO_LARGE_INTESTINE	153924494	153924738	153924672	153924673	Frame_Shift_Ins	-	C	p.G273fs
SKMEL30_SKIN	153923736	153924142	153923924	153923925	In_Frame_Ins	-	GGAGGAGGAGGAAGA	p.404_405insSSSSS
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	153920934	153921120	153920969	153920969	Missense_Mutation	G	A	p.S609F
639V_URINARY_TRACT	153920934	153921120	153921086	153921086	Missense_Mutation	C	T	p.S570N
ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	153921591	153921860	153921603	153921604	Missense_Mutation	GA	AG	p.F554S
SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	153921591	153921860	153921733	153921733	Missense_Mutation	G	A	p.P511L
NCIH446_LUNG	153921591	153921860	153921737	153921737	Missense_Mutation	G	T	p.L510M
COLO679_SKIN	153921591	153921860	153921751	153921751	Missense_Mutation	A	T	p.L505Q
AN3CA_ENDOMETRIUM	153921591	153921860	153921812	153921812	Missense_Mutation	G	T	p.P485T
HCT116_LARGE_INTESTINE	153921591	153921860	153921815	153921815	Missense_Mutation	G	T	p.P484T
SNU1040_LARGE_INTESTINE	153921591	153921860	153921856	153921856	Missense_Mutation	A	G	p.V470A
HCC2998_LARGE_INTESTINE	153923736	153924142	153923813	153923813	Missense_Mutation	C	T	p.D443N
BT549_BREAST	153923736	153924142	153923816	153923816	Missense_Mutation	C	T	p.A442T
SNU1040_LARGE_INTESTINE	153923736	153924142	153923825	153923825	Missense_Mutation	C	T	p.A439T
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	153923736	153924142	153923827	153923827	Missense_Mutation	A	G	p.L438P
BICR18_UPPER_AERODIGESTIVE_TRACT	153923736	153924142	153923827	153923827	Missense_Mutation	A	G	p.L438P
MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	153923736	153924142	153923864	153923864	Missense_Mutation	G	T	p.H426N
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	153923736	153924142	153923975	153923975	Missense_Mutation	G	T	p.H389N
LB1047EBV_MATCHED_NORMAL_TISSUE	153923736	153924142	153924034	153924034	Missense_Mutation	T	G	p.H369P
MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	153923736	153924142	153924092	153924092	Missense_Mutation	G	A	p.P350S
SNU1040_LARGE_INTESTINE	153924494	153924738	153924572	153924572	Missense_Mutation	T	C	p.T307A
HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	153924494	153924738	153924577	153924577	Missense_Mutation	T	C	p.N305S
HCC2450_LUNG	153924494	153924738	153924583	153924583	Missense_Mutation	C	A	p.G303V
JEG3_PLACENTA	153924494	153924738	153924584	153924584	Missense_Mutation	C	T	p.G303R
HCT15_LARGE_INTESTINE	153924494	153924738	153924677	153924677	Missense_Mutation	C	A	p.G272W
HDMYZ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	153925742	153925845	153925745	153925745	Missense_Mutation	C	T	p.G202R
HCT15_LARGE_INTESTINE	153923736	153924142	153923795	153923795	Nonsense_Mutation	G	A	p.Q449*
HEC251_ENDOMETRIUM	153926014	153926082	153926036	153926036	Nonsense_Mutation	G	A	p.R161*
DU145_PROSTATE	153920934	153921120	153920935	153920935	Splice_Site	T	A	p.T620T

Top

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CRTC2

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

Top

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CRTC2

Top

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CRTC2

Top

RelatedDrugs for CRTC2

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

Top

RelatedDiseases for CRTC2

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

Home

Download

Statistics

Landscape

Help

Contact

Gene summary for CRTC2

Exon skipping events across known transcript of Ensembl for CRTC2 from UCSC genome browser

Gene isoform structures and expression levels for CRTC2

Exon skipping events with PSIs in TCGA for CRTC2

Exon skipping events with PSIs in GTEx for CRTC2

Open reading frame (ORF) annotation in the exon skipping event for CRTC2

Infer the effects of exon skipping event on protein functional features for CRTC2

SNVs in the skipped exons for CRTC2

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CRTC2

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CRTC2

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CRTC2

RelatedDrugs for CRTC2

RelatedDiseases for CRTC2