ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for ZC3HC1

Gene summary

Gene information	Gene symbol	ZC3HC1
	Gene ID	51530
	Gene name	zinc finger C3HC-type containing 1
	Synonyms	HSPC216\|NIPA
	Cytomap	7q32.2
	Type of gene	protein-coding
	Description	nuclear-interacting partner of ALKhematopoietic stem/progenitor cell protein 216nuclear interacting partner of anaplastic lymphoma kinase (ALK)
	Modification date	20180529
	UniProtAcc	Q86WB0
	Context	PubMed: ZC3HC1 [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 ZC3HC1 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 ZC3HC1

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 ZC3HC1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_479482	7	129662158:129662365:129663350:129663563:129664102:129664217	129663350:129663563	ENSG00000091732.11	ENST00000311873.5,ENST00000467642.1,ENST00000481503.1,ENST00000358303.4
exon_skip_479484	7	129663516:129663563:129664102:129664217:129665997:129666152	129664102:129664217	ENSG00000091732.11	ENST00000481503.1
exon_skip_479485	7	129663516:129663563:129664102:129664346:129665997:129666152	129664102:129664346	ENSG00000091732.11	ENST00000311873.5,ENST00000477578.1,ENST00000467642.1,ENST00000471022.1,ENST00000358303.4
exon_skip_479486	7	129668741:129668869:129676489:129676806:129679303:129679387	129676489:129676806	ENSG00000091732.11	ENST00000483827.1
exon_skip_479487	7	129668741:129668869:129679303:129679387:129680790:129680941	129679303:129679387	ENSG00000091732.11	ENST00000311873.5,ENST00000360708.5,ENST00000467642.1,ENST00000481503.1,ENST00000358303.4
exon_skip_479489	7	129668741:129668869:129679303:129679387:129688813:129688984	129679303:129679387	ENSG00000091732.11	ENST00000471022.1
exon_skip_479498	7	129679358:129679387:129688813:129688984:129691060:129691209	129688813:129688984	ENSG00000091732.11	ENST00000471022.1
exon_skip_479504	7	129688872:129688984:129690282:129690328:129691060:129691209	129690282:129690328	ENSG00000091732.11	ENST00000311873.5,ENST00000467642.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for ZC3HC1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_479482	7	129662158:129662365:129663350:129663563:129664102:129664217	129663350:129663563	ENSG00000091732.11	ENST00000358303.4,ENST00000467642.1,ENST00000311873.5,ENST00000481503.1
exon_skip_479484	7	129663516:129663563:129664102:129664217:129665997:129666152	129664102:129664217	ENSG00000091732.11	ENST00000481503.1
exon_skip_479485	7	129663516:129663563:129664102:129664346:129665997:129666152	129664102:129664346	ENSG00000091732.11	ENST00000358303.4,ENST00000467642.1,ENST00000311873.5,ENST00000477578.1,ENST00000471022.1
exon_skip_479486	7	129668741:129668869:129676489:129676806:129679303:129679387	129676489:129676806	ENSG00000091732.11	ENST00000483827.1
exon_skip_479487	7	129668741:129668869:129679303:129679387:129680790:129680941	129679303:129679387	ENSG00000091732.11	ENST00000358303.4,ENST00000360708.5,ENST00000467642.1,ENST00000311873.5,ENST00000481503.1
exon_skip_479489	7	129668741:129668869:129679303:129679387:129688813:129688984	129679303:129679387	ENSG00000091732.11	ENST00000471022.1
exon_skip_479498	7	129679358:129679387:129688813:129688984:129691060:129691209	129688813:129688984	ENSG00000091732.11	ENST00000471022.1
exon_skip_479504	7	129688872:129688984:129690282:129690328:129691060:129691209	129690282:129690328	ENSG00000091732.11	ENST00000467642.1,ENST00000311873.5

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 ZC3HC1

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
ENST00000358303	129664102	129664346	Frame-shift
ENST00000358303	129663350	129663563	In-frame
ENST00000358303	129679303	129679387	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
ENST00000358303	129664102	129664346	Frame-shift
ENST00000358303	129663350	129663563	In-frame
ENST00000358303	129679303	129679387	In-frame

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Infer the effects of exon skipping event on protein functional features for ZC3HC1

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
ENST00000358303	1989	502	129679303	129679387	495	578	136	164
ENST00000358303	1989	502	129663350	129663563	1106	1318	340	411

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
ENST00000358303	1989	502	129679303	129679387	495	578	136	164
ENST00000358303	1989	502	129663350	129663563	1106	1318	340	411

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

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

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SNVs in the skipped exons for ZC3HC1

- 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
KIRC	TCGA-B0-4823-01	exon_skip_479482	129663351	129663563	129663471	129663471	Frame_Shift_Del	G	-	p.P371fs
KIRC	TCGA-B0-4823-01	exon_skip_479482	129663351	129663563	129663471	129663471	Frame_Shift_Del	G	-	p.T372fs
UCEC	TCGA-AP-A0LG-01	exon_skip_479485	129664103	129664346	129664275	129664275	Frame_Shift_Del	C	-	p.G283fs
LIHC	TCGA-DD-A1EG-01	exon_skip_479487 exon_skip_479489	129679304	129679387	129679333	129679333	Frame_Shift_Del	A	-	p.F155fs
SKCM	TCGA-W3-AA1Q-06	exon_skip_479482	129663351	129663563	129663446	129663446	Nonsense_Mutation	G	A	p.R380*
BRCA	TCGA-B6-A0RE-01	exon_skip_479482	129663351	129663563	129663533	129663533	Nonsense_Mutation	G	A	p.R351*
DLBC	TCGA-G8-6906-01	exon_skip_479482	129663351	129663563	129663533	129663533	Nonsense_Mutation	G	A	p.R351X

- 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
TGW_AUTONOMIC_GANGLIA	129663351	129663563	129663383	129663383	Missense_Mutation	T	G	p.K401Q
U698M_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	129663351	129663563	129663383	129663383	Missense_Mutation	T	C	p.K401E
NCIH2110_LUNG	129663351	129663563	129663386	129663386	Missense_Mutation	C	G	p.A400P
SW900_LUNG	129663351	129663563	129663464	129663464	Missense_Mutation	T	C	p.R374G
HT115_LARGE_INTESTINE	129663351	129663563	129663518	129663518	Missense_Mutation	C	G	p.D356H
SNU1040_LARGE_INTESTINE	129664103	129664346	129664155	129664155	Missense_Mutation	C	T	p.R323Q
SNU1040_LARGE_INTESTINE	129664103	129664217	129664155	129664155	Missense_Mutation	C	T	p.R323Q
HT55_LARGE_INTESTINE	129664103	129664346	129664239	129664239	Missense_Mutation	T	A	p.D295V
MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	129688814	129688984	129688937	129688937	Missense_Mutation	G	A	p.A65V
HUPT3_PANCREAS	129688814	129688984	129688937	129688937	Missense_Mutation	G	A	p.A65V
SAS_UPPER_AERODIGESTIVE_TRACT	129688814	129688984	129688937	129688937	Missense_Mutation	G	A	p.A65V
EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	129664103	129664346	129664192	129664192	Nonsense_Mutation	G	A	p.R311*
EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	129664103	129664217	129664192	129664192	Nonsense_Mutation	G	A	p.R311*
PATU8902_PANCREAS	129679304	129679387	129679379	129679379	Nonsense_Mutation	G	A	p.R140*
HCC1569_BREAST	129679304	129679387	129679379	129679379	Nonsense_Mutation	G	A	p.R140*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ZC3HC1

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
exon_skip_479485	7	129663516:129663563:129664102:129664346:129665997:129666152	129664102:129664346	ENST00000311873.5,ENST00000477578.1,ENST00000467642.1,ENST00000471022.1,ENST00000358303.4	CESC	rs1464890	chr7:129664312	A/G	4.94e-06
exon_skip_479485	7	129663516:129663563:129664102:129664346:129665997:129666152	129664102:129664346	ENST00000311873.5,ENST00000477578.1,ENST00000467642.1,ENST00000471022.1,ENST00000358303.4	COAD	rs1464890	chr7:129664312	A/G	1.96e-03
exon_skip_479485	7	129663516:129663563:129664102:129664346:129665997:129666152	129664102:129664346	ENST00000311873.5,ENST00000477578.1,ENST00000467642.1,ENST00000471022.1,ENST00000358303.4	BLCA	rs1464890	chr7:129664312	A/G	8.36e-04
exon_skip_479485	7	129663516:129663563:129664102:129664346:129665997:129666152	129664102:129664346	ENST00000311873.5,ENST00000477578.1,ENST00000467642.1,ENST00000471022.1,ENST00000358303.4	BRCA	rs1464890	chr7:129664312	A/G	1.09e-04
exon_skip_479485	7	129663516:129663563:129664102:129664346:129665997:129666152	129664102:129664346	ENST00000311873.5,ENST00000477578.1,ENST00000467642.1,ENST00000471022.1,ENST00000358303.4	KIRP	rs1464890	chr7:129664312	A/G	2.52e-07
exon_skip_479485	7	129663516:129663563:129664102:129664346:129665997:129666152	129664102:129664346	ENST00000311873.5,ENST00000477578.1,ENST00000467642.1,ENST00000471022.1,ENST00000358303.4	LGG	rs1464890	chr7:129664312	A/G	6.95e-05
exon_skip_479485	7	129663516:129663563:129664102:129664346:129665997:129666152	129664102:129664346	ENST00000311873.5,ENST00000477578.1,ENST00000467642.1,ENST00000471022.1,ENST00000358303.4	KIRC	rs1464890	chr7:129664312	A/G	2.19e-11
exon_skip_479485	7	129663516:129663563:129664102:129664346:129665997:129666152	129664102:129664346	ENST00000311873.5,ENST00000477578.1,ENST00000467642.1,ENST00000471022.1,ENST00000358303.4	KIRC	rs1464890	chr7:129664312	A/G	7.80e-04
exon_skip_479485	7	129663516:129663563:129664102:129664346:129665997:129666152	129664102:129664346	ENST00000311873.5,ENST00000477578.1,ENST00000467642.1,ENST00000471022.1,ENST00000358303.4	LUAD	rs1464890	chr7:129664312	A/G	3.69e-05
exon_skip_479485	7	129663516:129663563:129664102:129664346:129665997:129666152	129664102:129664346	ENST00000311873.5,ENST00000477578.1,ENST00000467642.1,ENST00000471022.1,ENST00000358303.4	LIHC	rs1464890	chr7:129664312	A/G	5.95e-04
exon_skip_479485	7	129663516:129663563:129664102:129664346:129665997:129666152	129664102:129664346	ENST00000311873.5,ENST00000477578.1,ENST00000467642.1,ENST00000471022.1,ENST00000358303.4	LUSC	rs1464890	chr7:129664312	A/G	1.12e-05
exon_skip_479485	7	129663516:129663563:129664102:129664346:129665997:129666152	129664102:129664346	ENST00000311873.5,ENST00000477578.1,ENST00000467642.1,ENST00000471022.1,ENST00000358303.4	OV	rs1464890	chr7:129664312	A/G	3.63e-12
exon_skip_479485	7	129663516:129663563:129664102:129664346:129665997:129666152	129664102:129664346	ENST00000311873.5,ENST00000477578.1,ENST00000467642.1,ENST00000471022.1,ENST00000358303.4	PAAD	rs1464890	chr7:129664312	A/G	8.81e-06
exon_skip_479485	7	129663516:129663563:129664102:129664346:129665997:129666152	129664102:129664346	ENST00000311873.5,ENST00000477578.1,ENST00000467642.1,ENST00000471022.1,ENST00000358303.4	PRAD	rs1464890	chr7:129664312	A/G	6.58e-09
exon_skip_479485	7	129663516:129663563:129664102:129664346:129665997:129666152	129664102:129664346	ENST00000311873.5,ENST00000477578.1,ENST00000467642.1,ENST00000471022.1,ENST00000358303.4	STAD	rs1464890	chr7:129664312	A/G	8.23e-04
exon_skip_479485	7	129663516:129663563:129664102:129664346:129665997:129666152	129664102:129664346	ENST00000311873.5,ENST00000477578.1,ENST00000467642.1,ENST00000471022.1,ENST00000358303.4	THCA	rs1464890	chr7:129664312	A/G	8.47e-08
exon_skip_479482	7	129662158:129662365:129663350:129663563:129664102:129664217	129663350:129663563	ENST00000311873.5,ENST00000467642.1,ENST00000481503.1,ENST00000358303.4	LGG	rs11556924	chr7:129663496	C/T	2.01e-03
exon_skip_479482	7	129662158:129662365:129663350:129663563:129664102:129664217	129663350:129663563	ENST00000311873.5,ENST00000467642.1,ENST00000481503.1,ENST00000358303.4	KIRC	rs11556924	chr7:129663496	C/T	9.73e-05
exon_skip_479482	7	129662158:129662365:129663350:129663563:129664102:129664217	129663350:129663563	ENST00000311873.5,ENST00000467642.1,ENST00000481503.1,ENST00000358303.4	LUAD	rs11556924	chr7:129663496	C/T	8.00e-04
exon_skip_479482	7	129662158:129662365:129663350:129663563:129664102:129664217	129663350:129663563	ENST00000311873.5,ENST00000467642.1,ENST00000481503.1,ENST00000358303.4	LUSC	rs11556924	chr7:129663496	C/T	9.51e-06
exon_skip_479482	7	129662158:129662365:129663350:129663563:129664102:129664217	129663350:129663563	ENST00000311873.5,ENST00000467642.1,ENST00000481503.1,ENST00000358303.4	OV	rs11556924	chr7:129663496	C/T	1.27e-05
exon_skip_479482	7	129662158:129662365:129663350:129663563:129664102:129664217	129663350:129663563	ENST00000311873.5,ENST00000467642.1,ENST00000481503.1,ENST00000358303.4	PRAD	rs11556924	chr7:129663496	C/T	1.63e-05
exon_skip_479482	7	129662158:129662365:129663350:129663563:129664102:129664217	129663350:129663563	ENST00000311873.5,ENST00000467642.1,ENST00000481503.1,ENST00000358303.4	THCA	rs11556924	chr7:129663496	C/T	2.61e-04

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ZC3HC1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ZC3HC1

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RelatedDrugs for ZC3HC1

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 ZC3HC1

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
ZC3HC1	C1956346	Coronary Artery Disease	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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