ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for CHD3

Gene summary

Gene information	Gene symbol	CHD3
	Gene ID	1107
	Gene name	chromodomain helicase DNA binding protein 3
	Synonyms	Mi-2a\|Mi2-ALPHA\|ZFH
	Cytomap	17p13.1
	Type of gene	protein-coding
	Description	chromodomain-helicase-DNA-binding protein 3ATP-dependent helicase CHD3CHD-3hZFHmi-2 autoantigen 240 kDa proteinzinc finger helicasezinc-finger helicase (Snf2-like)
	Modification date	20180522
	UniProtAcc	Q12873
	Context	PubMed: CHD3 [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
CHD3	GO:0007051	spindle organization	17626165
CHD3	GO:0007098	centrosome cycle	17626165

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Exon skipping events across known transcript of Ensembl for CHD3 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 CHD3

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 CHD3

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_148920	17	7794257:7794382:7796603:7796887:7797122:7797253	7796603:7796887	ENSG00000170004.12	ENST00000358181.4,ENST00000330494.7,ENST00000380358.4,ENST00000452447.1
exon_skip_148921	17	7797444:7797583:7797732:7797926:7798234:7798468	7797732:7797926	ENSG00000170004.12	ENST00000358181.4,ENST00000330494.7,ENST00000380358.4,ENST00000452447.1
exon_skip_148924	17	7798234:7798468:7798656:7798860:7800400:7800612	7798656:7798860	ENSG00000170004.12	ENST00000358181.4,ENST00000330494.7,ENST00000380358.4,ENST00000452447.1
exon_skip_148926	17	7800400:7800612:7801288:7801420:7801813:7801913	7801288:7801420	ENSG00000170004.12	ENST00000358181.4,ENST00000330494.7,ENST00000380358.4
exon_skip_148927	17	7802660:7802861:7803213:7803351:7803607:7803729	7803213:7803351	ENSG00000170004.12	ENST00000358181.4,ENST00000330494.7,ENST00000380358.4
exon_skip_148929	17	7804169:7804311:7804561:7804693:7805927:7806045	7804561:7804693	ENSG00000170004.12	ENST00000358181.4,ENST00000330494.7,ENST00000380358.4
exon_skip_148933	17	7805927:7806045:7806254:7806379:7806589:7806821	7806254:7806379	ENSG00000170004.12	ENST00000358181.4,ENST00000330494.7,ENST00000380358.4
exon_skip_148936	17	7807759:7807937:7808417:7808483:7808938:7808974	7808417:7808483	ENSG00000170004.12	ENST00000470531.1,ENST00000358181.4,ENST00000330494.7,ENST00000466233.1,ENST00000380358.4
exon_skip_148939	17	7808417:7808483:7808938:7809024:7809173:7809307	7808938:7809024	ENSG00000170004.12	ENST00000470531.1,ENST00000358181.4,ENST00000330494.7,ENST00000380358.4
exon_skip_148941	17	7809870:7810015:7810186:7810349:7810443:7810565	7810186:7810349	ENSG00000170004.12	ENST00000470531.1,ENST00000358181.4,ENST00000330494.7,ENST00000380358.4
exon_skip_148946	17	7810670:7810806:7810918:7811020:7811208:7811337	7810918:7811020	ENSG00000170004.12	ENST00000470531.1
exon_skip_148947	17	7810670:7810806:7810918:7811020:7811211:7811337	7810918:7811020	ENSG00000170004.12	ENST00000330494.7,ENST00000380358.4
exon_skip_148961	17	7812460:7812656:7813745:7813909:7814164:7814213	7813745:7813909	ENSG00000170004.12	ENST00000470531.1,ENST00000358181.4,ENST00000330494.7,ENST00000380358.4
exon_skip_148963	17	7812460:7812656:7813756:7813909:7814164:7814213	7813756:7813909	ENSG00000170004.12	ENST00000573936.1
exon_skip_148965	17	7812460:7812656:7814164:7814291:7814781:7815068	7814164:7814291	ENSG00000170004.12	ENST00000449744.1
exon_skip_148969	17	7812460:7812702:7813745:7813909:7814164:7814213	7813745:7813909	ENSG00000170004.12	ENST00000439235.1
exon_skip_148970	17	7813756:7813909:7814164:7814291:7814781:7815068	7814164:7814291	ENSG00000170004.12	ENST00000439235.1,ENST00000470531.1,ENST00000481999.1,ENST00000358181.4,ENST00000330494.7,ENST00000380358.4

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for CHD3

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_148920	17	7794257:7794382:7796603:7796887:7797122:7797253	7796603:7796887	ENSG00000170004.12	ENST00000380358.4,ENST00000358181.4,ENST00000330494.7,ENST00000452447.1
exon_skip_148921	17	7797444:7797583:7797732:7797926:7798234:7798468	7797732:7797926	ENSG00000170004.12	ENST00000380358.4,ENST00000358181.4,ENST00000330494.7,ENST00000452447.1
exon_skip_148924	17	7798234:7798468:7798656:7798860:7800400:7800612	7798656:7798860	ENSG00000170004.12	ENST00000380358.4,ENST00000358181.4,ENST00000330494.7,ENST00000452447.1
exon_skip_148926	17	7800400:7800612:7801288:7801420:7801813:7801913	7801288:7801420	ENSG00000170004.12	ENST00000380358.4,ENST00000358181.4,ENST00000330494.7
exon_skip_148927	17	7802660:7802861:7803213:7803351:7803607:7803729	7803213:7803351	ENSG00000170004.12	ENST00000380358.4,ENST00000358181.4,ENST00000330494.7
exon_skip_148929	17	7804169:7804311:7804561:7804693:7805927:7806045	7804561:7804693	ENSG00000170004.12	ENST00000380358.4,ENST00000358181.4,ENST00000330494.7
exon_skip_148933	17	7805927:7806045:7806254:7806379:7806589:7806821	7806254:7806379	ENSG00000170004.12	ENST00000380358.4,ENST00000358181.4,ENST00000330494.7
exon_skip_148936	17	7807759:7807937:7808417:7808483:7808938:7808974	7808417:7808483	ENSG00000170004.12	ENST00000380358.4,ENST00000358181.4,ENST00000330494.7,ENST00000470531.1,ENST00000466233.1
exon_skip_148939	17	7808417:7808483:7808938:7809024:7809173:7809307	7808938:7809024	ENSG00000170004.12	ENST00000380358.4,ENST00000358181.4,ENST00000330494.7,ENST00000470531.1
exon_skip_148941	17	7809870:7810015:7810186:7810349:7810443:7810565	7810186:7810349	ENSG00000170004.12	ENST00000380358.4,ENST00000358181.4,ENST00000330494.7,ENST00000470531.1
exon_skip_148946	17	7810670:7810806:7810918:7811020:7811208:7811337	7810918:7811020	ENSG00000170004.12	ENST00000470531.1
exon_skip_148947	17	7810670:7810806:7810918:7811020:7811211:7811337	7810918:7811020	ENSG00000170004.12	ENST00000380358.4,ENST00000330494.7
exon_skip_148961	17	7812460:7812656:7813745:7813909:7814164:7814213	7813745:7813909	ENSG00000170004.12	ENST00000380358.4,ENST00000358181.4,ENST00000330494.7,ENST00000470531.1
exon_skip_148963	17	7812460:7812656:7813756:7813909:7814164:7814213	7813756:7813909	ENSG00000170004.12	ENST00000573936.1
exon_skip_148965	17	7812460:7812656:7814164:7814291:7814781:7815068	7814164:7814291	ENSG00000170004.12	ENST00000449744.1
exon_skip_148969	17	7812460:7812702:7813745:7813909:7814164:7814213	7813745:7813909	ENSG00000170004.12	ENST00000439235.1
exon_skip_148970	17	7813756:7813909:7814164:7814291:7814781:7815068	7814164:7814291	ENSG00000170004.12	ENST00000380358.4,ENST00000358181.4,ENST00000330494.7,ENST00000470531.1,ENST00000439235.1,ENST00000481999.1

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 CHD3

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
ENST00000330494	7796603	7796887	Frame-shift
ENST00000330494	7797732	7797926	Frame-shift
ENST00000330494	7806254	7806379	Frame-shift
ENST00000330494	7808938	7809024	Frame-shift
ENST00000330494	7810186	7810349	Frame-shift
ENST00000330494	7813745	7813909	Frame-shift
ENST00000330494	7814164	7814291	Frame-shift
ENST00000330494	7798656	7798860	In-frame
ENST00000330494	7801288	7801420	In-frame
ENST00000330494	7803213	7803351	In-frame
ENST00000330494	7804561	7804693	In-frame
ENST00000330494	7808417	7808483	In-frame
ENST00000330494	7810918	7811020	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
ENST00000330494	7796603	7796887	Frame-shift
ENST00000330494	7797732	7797926	Frame-shift
ENST00000330494	7806254	7806379	Frame-shift
ENST00000330494	7808938	7809024	Frame-shift
ENST00000330494	7810186	7810349	Frame-shift
ENST00000330494	7813745	7813909	Frame-shift
ENST00000330494	7814164	7814291	Frame-shift
ENST00000330494	7798656	7798860	In-frame
ENST00000330494	7801288	7801420	In-frame
ENST00000330494	7803213	7803351	In-frame
ENST00000330494	7804561	7804693	In-frame
ENST00000330494	7808417	7808483	In-frame
ENST00000330494	7810918	7811020	In-frame

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Infer the effects of exon skipping event on protein functional features for CHD3

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
ENST00000330494	7345	2000	7798656	7798860	1654	1857	501	569
ENST00000330494	7345	2000	7801288	7801420	2070	2201	640	683
ENST00000330494	7345	2000	7803213	7803351	2695	2832	848	894
ENST00000330494	7345	2000	7804561	7804693	3271	3402	1040	1084
ENST00000330494	7345	2000	7808417	7808483	4223	4288	1357	1379

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
ENST00000330494	7345	2000	7798656	7798860	1654	1857	501	569
ENST00000330494	7345	2000	7801288	7801420	2070	2201	640	683
ENST00000330494	7345	2000	7803213	7803351	2695	2832	848	894
ENST00000330494	7345	2000	7804561	7804693	3271	3402	1040	1084
ENST00000330494	7345	2000	7808417	7808483	4223	4288	1357	1379

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
Q12873	501	569	1	2000	Chain	ID=PRO_0000080227;Note=Chromodomain-helicase-DNA-binding protein 3
Q12873	501	569	494	594	Domain	Note=Chromo 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00053
Q12873	501	569	456	503	Zinc finger	Note=PHD-type 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00146
Q12873	640	683	1	2000	Chain	ID=PRO_0000080227;Note=Chromodomain-helicase-DNA-binding protein 3
Q12873	640	683	631	673	Domain	Note=Chromo 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00053
Q12873	640	683	653	653	Sequence conflict	Note=W->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q12873	848	894	1	2000	Chain	ID=PRO_0000080227;Note=Chromodomain-helicase-DNA-binding protein 3
Q12873	848	894	748	932	Domain	Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00541
Q12873	848	894	883	886	Motif	Note=DEAH box
Q12873	1040	1084	1	2000	Chain	ID=PRO_0000080227;Note=Chromodomain-helicase-DNA-binding protein 3
Q12873	1040	1084	1064	1229	Domain	Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00542
Q12873	1357	1379	1	2000	Chain	ID=PRO_0000080227;Note=Chromodomain-helicase-DNA-binding protein 3
Q12873	1357	1379	1367	1367	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648

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
Q12873	501	569	1	2000	Chain	ID=PRO_0000080227;Note=Chromodomain-helicase-DNA-binding protein 3
Q12873	501	569	494	594	Domain	Note=Chromo 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00053
Q12873	501	569	456	503	Zinc finger	Note=PHD-type 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00146
Q12873	640	683	1	2000	Chain	ID=PRO_0000080227;Note=Chromodomain-helicase-DNA-binding protein 3
Q12873	640	683	631	673	Domain	Note=Chromo 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00053
Q12873	640	683	653	653	Sequence conflict	Note=W->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q12873	848	894	1	2000	Chain	ID=PRO_0000080227;Note=Chromodomain-helicase-DNA-binding protein 3
Q12873	848	894	748	932	Domain	Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00541
Q12873	848	894	883	886	Motif	Note=DEAH box
Q12873	1040	1084	1	2000	Chain	ID=PRO_0000080227;Note=Chromodomain-helicase-DNA-binding protein 3
Q12873	1040	1084	1064	1229	Domain	Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00542
Q12873	1357	1379	1	2000	Chain	ID=PRO_0000080227;Note=Chromodomain-helicase-DNA-binding protein 3
Q12873	1357	1379	1367	1367	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648

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SNVs in the skipped exons for CHD3

- 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.

CHD3_PAAD_exon_skip_148920_psi_boxplot.png
boxplot

CHD3_SKCM_exon_skip_148936_psi_boxplot.png
boxplot

CHD3_STAD_exon_skip_148920_psi_boxplot.png
boxplot

- 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
UCEC	TCGA-A5-A0GW-01	exon_skip_148920	7796604	7796887	7796789	7796789	Frame_Shift_Del	C	-	p.T291fs
STAD	TCGA-F1-6177-01	exon_skip_148920	7796604	7796887	7796827	7796827	Frame_Shift_Del	C	-	p.P245fs
STAD	TCGA-F1-6177-01	exon_skip_148920	7796604	7796887	7796827	7796827	Frame_Shift_Del	C	-	p.P303fs
LIHC	TCGA-DD-A3A0-01	exon_skip_148920	7796604	7796887	7796867	7796867	Frame_Shift_Del	C	-	p.A317fs
LIHC	TCGA-DD-A3A0-01	exon_skip_148920	7796604	7796887	7796884	7796884	Frame_Shift_Del	A	-	p.K323fs
COAD	TCGA-AA-3492-01	exon_skip_148921	7797733	7797926	7797756	7797756	Frame_Shift_Del	G	-	p.A366fs
KIRC	TCGA-CJ-4639-01	exon_skip_148921	7797733	7797926	7797796	7797799	Frame_Shift_Del	ATTA	-	p.439_440del
UCEC	TCGA-AX-A0J1-01	exon_skip_148921	7797733	7797926	7797818	7797818	Frame_Shift_Del	G	-	p.G447fs
COAD	TCGA-A6-6653-01	exon_skip_148924	7798657	7798860	7798703	7798703	Frame_Shift_Del	G	-	p.W517fs
LIHC	TCGA-DD-A3A1-01	exon_skip_148924	7798657	7798860	7798703	7798703	Frame_Shift_Del	G	-	p.W576fs
COAD	TCGA-A6-6653-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P537fs
COAD	TCGA-AY-6197-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P537fs
COAD	TCGA-AZ-4615-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P537fs
ESCA	TCGA-L5-A43J-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P598fs
ESCA	TCGA-L5-A43J-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.R540fs
PRAD	TCGA-V1-A8WN-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P598fs
STAD	TCGA-BR-8487-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P596fs
STAD	TCGA-CG-4305-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P596fs
STAD	TCGA-CG-5728-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P596fs
STAD	TCGA-D7-A4YY-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P596fs
STAD	TCGA-HF-A5NB-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P596fs
STAD	TCGA-HF-A5NB-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P598fs
STAD	TCGA-HU-A4G8-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P596fs
UCEC	TCGA-BG-A0VZ-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P597fs
UCEC	TCGA-BS-A0U8-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P597fs
UCEC	TCGA-D1-A0ZS-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P597fs
UCEC	TCGA-D1-A101-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P597fs
UCEC	TCGA-D1-A163-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P597fs
UCEC	TCGA-D1-A177-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P597fs
UCEC	TCGA-D1-A17D-01	exon_skip_148924	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P597fs
UCEC	TCGA-D1-A174-01	exon_skip_148939	7808939	7809024	7809010	7809010	Frame_Shift_Del	G	-	p.G1463fs
LIHC	TCGA-DD-A3A0-01	exon_skip_148947 exon_skip_148946	7810919	7811020	7810943	7810943	Frame_Shift_Del	G	-	p.R1709fs
UCEC	TCGA-AX-A06H-01	exon_skip_148947 exon_skip_148946	7810919	7811020	7810943	7810943	Frame_Shift_Del	G	-	p.R1709fs
PAAD	TCGA-HZ-8636-01	exon_skip_148920	7796604	7796887	7796799	7796800	Frame_Shift_Ins	-	C	p.L295fs
PAAD	TCGA-IB-7891-01	exon_skip_148920	7796604	7796887	7796803	7796804	Frame_Shift_Ins	-	C	p.R296fs
PAAD	TCGA-F2-A8YN-01	exon_skip_148920	7796604	7796887	7796808	7796809	Frame_Shift_Ins	-	C	p.GP297fs
PAAD	TCGA-HZ-A77P-01	exon_skip_148920	7796604	7796887	7796808	7796809	Frame_Shift_Ins	-	C	p.GP297fs
PAAD	TCGA-IB-AAUU-01	exon_skip_148920	7796604	7796887	7796808	7796809	Frame_Shift_Ins	-	C	p.GP297fs
HNSC	TCGA-CN-6024-01	exon_skip_148921	7797733	7797926	7797825	7797826	Frame_Shift_Ins	-	A	p.E390fs
HNSC	TCGA-CN-6024-01	exon_skip_148921	7797733	7797926	7797825	7797826	Frame_Shift_Ins	-	A	p.N449fs
COAD	TCGA-AA-3713-01	exon_skip_148924	7798657	7798860	7798702	7798703	Frame_Shift_Ins	-	G	p.W517fs
KIRC	TCGA-A3-3308-01	exon_skip_148924	7798657	7798860	7798764	7798765	Frame_Shift_Ins	-	C	p.PP596fs
KIRC	TCGA-A3-3313-01	exon_skip_148924	7798657	7798860	7798764	7798765	Frame_Shift_Ins	-	C	p.PP596fs
KIRC	TCGA-AK-3427-01	exon_skip_148924	7798657	7798860	7798764	7798765	Frame_Shift_Ins	-	C	p.PP596fs
KIRC	TCGA-AK-3440-01	exon_skip_148924	7798657	7798860	7798764	7798765	Frame_Shift_Ins	-	C	p.PP596fs
KIRC	TCGA-AK-3453-01	exon_skip_148924	7798657	7798860	7798764	7798765	Frame_Shift_Ins	-	C	p.PP596fs
KIRC	TCGA-AK-3465-01	exon_skip_148924	7798657	7798860	7798764	7798765	Frame_Shift_Ins	-	C	p.PP596fs
KIRC	TCGA-AS-3777-01	exon_skip_148924	7798657	7798860	7798764	7798765	Frame_Shift_Ins	-	C	p.PP596fs
KIRC	TCGA-AS-3778-01	exon_skip_148924	7798657	7798860	7798764	7798765	Frame_Shift_Ins	-	C	p.PP596fs
LUAD	TCGA-44-2655-01	exon_skip_148924	7798657	7798860	7798764	7798765	Frame_Shift_Ins	-	C	p.PP596fs
PRAD	TCGA-M7-A722-01	exon_skip_148924	7798657	7798860	7798764	7798765	Frame_Shift_Ins	-	C	p.PP596fs
UCEC	TCGA-B5-A0K2-01	exon_skip_148924	7798657	7798860	7798764	7798765	Frame_Shift_Ins	-	C	p.P596fs
UCEC	TCGA-B5-A0K7-01	exon_skip_148924	7798657	7798860	7798764	7798765	Frame_Shift_Ins	-	C	p.P596fs
UCEC	TCGA-BG-A0M3-01	exon_skip_148924	7798657	7798860	7798764	7798765	Frame_Shift_Ins	-	C	p.P596fs
PRAD	TCGA-CH-5762-01	exon_skip_148926	7801289	7801420	7801306	7801307	Frame_Shift_Ins	-	T	p.I705fs
PRAD	TCGA-CH-5762-01	exon_skip_148926	7801289	7801420	7801306	7801307	Frame_Shift_Ins	-	T	p.Y706fs
UCEC	TCGA-BG-A0M3-01	exon_skip_148947 exon_skip_148946	7810919	7811020	7810942	7810943	Frame_Shift_Ins	-	G	p.R1709fs
UCEC	TCGA-BG-A0M9-01	exon_skip_148947 exon_skip_148946	7810919	7811020	7810942	7810943	Frame_Shift_Ins	-	G	p.R1709fs
BRCA	TCGA-BH-A0BP-01	exon_skip_148924	7798657	7798860	7798780	7798780	Nonsense_Mutation	C	T	p.Q602*
COAD	TCGA-F4-6854-01	exon_skip_148965 exon_skip_148970	7814165	7814291	7814170	7814170	Nonsense_Mutation	C	A	p.Y1886X
LGG	TCGA-E1-A7YI-01	exon_skip_148965 exon_skip_148970	7814165	7814291	7814264	7814264	Nonsense_Mutation	C	T	p.Q2011*
LUAD	TCGA-73-4658-01	exon_skip_148927	7803214	7803351	7803213	7803213	Splice_Site	G	A	p.R849_splice
SKCM	TCGA-FS-A1ZC-06	exon_skip_148936	7808418	7808483	7808417	7808417	Splice_Site	G	A	.
UCEC	TCGA-AP-A056-01	exon_skip_148936	7808418	7808483	7808417	7808417	Splice_Site	G	T	e26-1

- Depth of coverage in the three exons composing exon skipping event

Depth of coverage in three exons	Mutation description
	Sample: TCGA-FS-A1ZC-06
	Cancer type: SKCM
	ESID: exon_skip_148936
	Skipped exon start: 7808418
	Skipped exon end: 7808483
	Mutation start: 7808417
	Mutation end: 7808417
	Mutation type: Splice_Site
	Reference seq: G
	Mutation seq: A
	AAchange: .
exon_skip_148936_SKCM_TCGA-FS-A1ZC-06.png
exon_skip_508428_SKCM_TCGA-FS-A1ZC-06.png
	Sample: TCGA-AP-A056-01
	Cancer type: UCEC
	ESID: exon_skip_148936
	Skipped exon start: 7808418
	Skipped exon end: 7808483
	Mutation start: 7808417
	Mutation end: 7808417
	Mutation type: Splice_Site
	Reference seq: G
	Mutation seq: T
	AAchange: e26-1
exon_skip_148936_UCEC_TCGA-AP-A056-01.png
exon_skip_331276_UCEC_TCGA-AP-A056-01.png
exon_skip_347552_UCEC_TCGA-AP-A056-01.png
exon_skip_37318_UCEC_TCGA-AP-A056-01.png
exon_skip_389380_UCEC_TCGA-AP-A056-01.png
exon_skip_445277_UCEC_TCGA-AP-A056-01.png
exon_skip_470936_UCEC_TCGA-AP-A056-01.png
exon_skip_54221_UCEC_TCGA-AP-A056-01.png
exon_skip_81411_UCEC_TCGA-AP-A056-01.png
	Sample: TCGA-HZ-8636-01
	Cancer type: PAAD
	ESID: exon_skip_148920
	Skipped exon start: 7796604
	Skipped exon end: 7796887
	Mutation start: 7796799
	Mutation end: 7796800
	Mutation type: Frame_Shift_Ins
	Reference seq: -
	Mutation seq: C
	AAchange: p.L295fs
exon_skip_148920_PAAD_TCGA-HZ-8636-01.png
	Sample: TCGA-HZ-A77P-01
	Cancer type: PAAD
	ESID: exon_skip_148920
	Skipped exon start: 7796604
	Skipped exon end: 7796887
	Mutation start: 7796808
	Mutation end: 7796809
	Mutation type: Frame_Shift_Ins
	Reference seq: -
	Mutation seq: C
	AAchange: p.GP297fs
exon_skip_148920_PAAD_TCGA-HZ-A77P-01.png
	Sample: TCGA-F2-A8YN-01
	Cancer type: PAAD
	ESID: exon_skip_148920
	Skipped exon start: 7796604
	Skipped exon end: 7796887
	Mutation start: 7796808
	Mutation end: 7796809
	Mutation type: Frame_Shift_Ins
	Reference seq: -
	Mutation seq: C
	AAchange: p.GP297fs
exon_skip_148920_PAAD_TCGA-F2-A8YN-01.png
	Sample: TCGA-IB-AAUU-01
	Cancer type: PAAD
	ESID: exon_skip_148920
	Skipped exon start: 7796604
	Skipped exon end: 7796887
	Mutation start: 7796808
	Mutation end: 7796809
	Mutation type: Frame_Shift_Ins
	Reference seq: -
	Mutation seq: C
	AAchange: p.GP297fs
exon_skip_148920_PAAD_TCGA-IB-AAUU-01.png
exon_skip_286384_PAAD_TCGA-IB-AAUU-01.png
	Sample: TCGA-IB-7891-01
	Cancer type: PAAD
	ESID: exon_skip_148920
	Skipped exon start: 7796604
	Skipped exon end: 7796887
	Mutation start: 7796803
	Mutation end: 7796804
	Mutation type: Frame_Shift_Ins
	Reference seq: -
	Mutation seq: C
	AAchange: p.R296fs
exon_skip_148920_PAAD_TCGA-IB-7891-01.png

- 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
EFO27_OVARY	7796604	7796887	7796789	7796789	Frame_Shift_Del	C	-	p.T232fs
SW48_LARGE_INTESTINE	7796604	7796887	7796809	7796809	Frame_Shift_Del	C	-	p.P240fs
MFE319_ENDOMETRIUM	7797733	7797926	7797756	7797756	Frame_Shift_Del	G	-	p.G367fs
22RV1_PROSTATE	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P539fs
HEC108_ENDOMETRIUM	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P539fs
HEC151_ENDOMETRIUM	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P539fs
SNU520_STOMACH	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P539fs
KM12_LARGE_INTESTINE	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P539fs
SKUT1_SOFT_TISSUE	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P539fs
CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P539fs
MDAPCA2B_PROSTATE	7798657	7798860	7798765	7798765	Frame_Shift_Del	C	-	p.P539fs
MDAPCA2B_PROSTATE	7798657	7798860	7798765	7798766	Frame_Shift_Ins	-	C	p.P538fs
HCT15_LARGE_INTESTINE	7796604	7796887	7796615	7796615	Missense_Mutation	C	A	p.A174D
HEC251_ENDOMETRIUM	7796604	7796887	7796723	7796723	Missense_Mutation	C	T	p.A210V
HCT116_LARGE_INTESTINE	7796604	7796887	7796831	7796831	Missense_Mutation	C	T	p.P246L
BICR18_UPPER_AERODIGESTIVE_TRACT	7796604	7796887	7796836	7796836	Missense_Mutation	G	C	p.A248P
BICR18_UPPER_AERODIGESTIVE_TRACT	7796604	7796887	7796841	7796841	Missense_Mutation	T	A	p.D249E
BICR18_UPPER_AERODIGESTIVE_TRACT	7797733	7797926	7797753	7797753	Missense_Mutation	G	A	p.A366T
A673_BONE	7797733	7797926	7797813	7797813	Missense_Mutation	C	G	p.Q386E
BICR16_UPPER_AERODIGESTIVE_TRACT	7797733	7797926	7797911	7797911	Missense_Mutation	G	C	p.W418C
CW2_LARGE_INTESTINE	7798657	7798860	7798772	7798772	Missense_Mutation	G	A	p.R540H
AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	7803214	7803351	7803262	7803262	Missense_Mutation	A	G	p.I865V
HEC251_ENDOMETRIUM	7803214	7803351	7803329	7803329	Missense_Mutation	G	A	p.R887Q
HS683_CENTRAL_NERVOUS_SYSTEM	7804562	7804693	7804650	7804650	Missense_Mutation	G	A	p.R1070Q
CAL148_BREAST	7806255	7806379	7806313	7806313	Missense_Mutation	C	G	p.I1143M
CROAP3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	7806255	7806379	7806336	7806336	Missense_Mutation	T	C	p.V1151A
DJM1_SKIN	7810187	7810349	7810208	7810208	Missense_Mutation	A	G	p.N1509D
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	7810187	7810349	7810214	7810214	Missense_Mutation	C	T	p.R1511C
GB1_CENTRAL_NERVOUS_SYSTEM	7810187	7810349	7810253	7810253	Missense_Mutation	G	A	p.D1524N
SNUC2A_LARGE_INTESTINE	7810187	7810349	7810263	7810263	Missense_Mutation	G	A	p.R1527H
SNUC2B_LARGE_INTESTINE	7810187	7810349	7810263	7810263	Missense_Mutation	G	A	p.R1527H
MCC13_SKIN	7810187	7810349	7810266	7810267	Missense_Mutation	CC	TT	p.S1528F
MCC13_SKIN	7810187	7810349	7810266	7810266	Missense_Mutation	C	T	p.S1528F
BICR18_UPPER_AERODIGESTIVE_TRACT	7810919	7811020	7810967	7810967	Missense_Mutation	G	T	p.G1658V
BICR18_UPPER_AERODIGESTIVE_TRACT	7810919	7811020	7810987	7810987	Missense_Mutation	C	A	p.P1665T
NCIH1048_LUNG	7810919	7811020	7810993	7810993	Missense_Mutation	G	A	p.G1667R
NCIH1155_LUNG	7813746	7813909	7813785	7813785	Missense_Mutation	C	T	p.A1877V
NCIH1155_LUNG	7813757	7813909	7813785	7813785	Missense_Mutation	C	T	p.A1877V
SNU1040_LARGE_INTESTINE	7813746	7813909	7813785	7813785	Missense_Mutation	C	T	p.A1877V
SNU1040_LARGE_INTESTINE	7813757	7813909	7813785	7813785	Missense_Mutation	C	T	p.A1877V
NCIH1299_LUNG	7813746	7813909	7813890	7813890	Missense_Mutation	C	T	p.T1912M
NCIH1299_LUNG	7813757	7813909	7813890	7813890	Missense_Mutation	C	T	p.T1912M
MZ1B_MATCHED_NORMAL_TISSUE	7813746	7813909	7813890	7813890	Missense_Mutation	C	T	p.T1912M
MZ1B_MATCHED_NORMAL_TISSUE	7813757	7813909	7813890	7813890	Missense_Mutation	C	T	p.T1912M
CAL72_BONE	7814165	7814291	7814172	7814172	Missense_Mutation	C	T	p.P1921L
SNU213_PANCREAS	7814165	7814291	7814196	7814196	Missense_Mutation	C	T	p.P1929L
NUGC3_STOMACH	7814165	7814291	7814196	7814196	Missense_Mutation	C	T	p.P1929L
NCIH1651_LUNG	7814165	7814291	7814244	7814244	Missense_Mutation	C	A	p.A1945D
OVK18_OVARY	7796604	7796887	7796860	7796860	Nonsense_Mutation	C	T	p.R256*
DOV13_OVARY	7798657	7798860	7798795	7798795	Nonsense_Mutation	C	T	p.R548*
SNU81_LARGE_INTESTINE	7808418	7808483	7808459	7808459	Nonsense_Mutation	G	T	p.E1372*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CHD3

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 CHD3

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CHD3

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RelatedDrugs for CHD3

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 CHD3

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
CHD3	C0036920	Sezary Syndrome	1	CTD_human

	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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