ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for ZNF384

Gene summary

Gene information	Gene symbol	ZNF384
	Gene ID	171017
	Gene name	zinc finger protein 384
	Synonyms	CAGH1\|CAGH1A\|CIZ\|ERDA2\|NMP4\|NP\|TNRC1
	Cytomap	12p13.31
	Type of gene	protein-coding
	Description	zinc finger protein 384CAG repeat protein 1Cas-interacting zinc finger proteinexpanded repeat domain, CAG/CTG 2nuclear matrix transcription factor 4trinucleotide repeat-containing gene 1 protein
	Modification date	20200313
	UniProtAcc	D3DUR9, E9PHB3, F5GYZ1, F5H0D6, F5H105, F5H3Z9, F5H6N8, F5H8L7, Q8TF68, R4GMR4,
	Context

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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Gene structures and expression levels for ZNF384

Skipped exons in the ROSMAP, MSBB, and Mayo 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.

ENSG00000126746

Differentially expressed gene analysis across multiple brain tissues between AD and control.

Tissue type

DEG direction

Base mean exp.

log2FC(AD/control)

P-value

Adj. p-value

Differentially expressed isoform analysis across multiple brain tissues between AD and control.

Tissue type	DEG direction	ENST	Transcript info.	Base mean exp.	log2FC(AD/control)	P-value	Adjc. p-value
CB	UP	ENST00000436774.6	ZNF384-206:protein_coding:ZNF384	4.171698e+01	1.529636e+00	5.764979e-11	4.020266e-09

Landscape of isoform expressions across multiple brain tissues between AD and control.

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for ZNF384

Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).

All exon skipping events in AD cohorts.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon
exon_skip_129207	chr12	6679455:6679525:6688167:6688226:6689098:6689292	6688167:6688226
exon_skip_149523	chr12	6679455:6679525:6688167:6688226:6689098:6689299	6688167:6688226
exon_skip_199780	chr12	6673248:6673440:6677167:6677259:6678127:6678335	6677167:6677259
exon_skip_209253	chr12	6668017:6668115:6669031:6669189:6670760:6670838	6669031:6669189
exon_skip_239594	chr12	6678432:6678460:6678663:6678710:6678946:6679183	6678663:6678710
exon_skip_259800	chr12	6673248:6673440:6677167:6677259:6678127:6678343	6677167:6677259
exon_skip_32737	chr12	6679455:6679525:6688167:6688226:6689368:6689454	6688167:6688226
exon_skip_40317	chr12	6670760:6670838:6672350:6672532:6673216:6673395	6672350:6672532
exon_skip_4754	chr12	6668038:6668115:6669031:6669189:6670760:6670838	6669031:6669189

Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.

Exon skipping information	Tissue type	Avg(PSIs) in AD	Avg(PSIs) in control	Difference (PSI)	Adj. p-value
exon_skip_239594	Mayo_CB	4.126829e-01	5.793421e-01	-1.666592e-01	2.295353e-08

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Open reading frame (ORF) annotation in the exon skipping event for ZNF384

Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000361959	6688167	6688226	3UTR-3UTR
ENST00000361959	6669031	6669189	In-frame
ENST00000396801	6669031	6669189	In-frame
ENST00000361959	6672350	6672532	In-frame
ENST00000396801	6672350	6672532	In-frame
ENST00000361959	6678663	6678710	In-frame
ENST00000396801	6678663	6678710	In-frame

Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000361959	6672350	6672532	In-frame
ENST00000396801	6672350	6672532	In-frame
ENST00000361959	6678663	6678710	In-frame
ENST00000396801	6678663	6678710	In-frame

Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000361959	6688167	6688226	3UTR-3UTR
ENST00000396801	6688167	6688226	3UTR-3UTR
ENST00000361959	6669031	6669189	In-frame
ENST00000396801	6669031	6669189	In-frame
ENST00000361959	6672350	6672532	In-frame
ENST00000396801	6672350	6672532	In-frame
ENST00000361959	6678663	6678710	In-frame
ENST00000396801	6678663	6678710	In-frame

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Infer the effects of exon skipping event on protein functional features for ZNF384

p-ENSG00000126746_img4.png
boxplot

Loci of skipped exons in ROSMAP 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
ENST00000361959	2995	577	6678663	6678710	565	611	101	117
ENST00000396801	3025	577	6678663	6678710	513	559	101	117
ENST00000361959	2995	577	6672350	6672532	1172	1353	304	364
ENST00000396801	3025	577	6672350	6672532	1120	1301	304	364
ENST00000361959	2995	577	6669031	6669189	1434	1591	391	443
ENST00000396801	3025	577	6669031	6669189	1382	1539	391	443

Loci of skipped exons in MSBB 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
ENST00000361959	2995	577	6678663	6678710	565	611	101	117
ENST00000396801	3025	577	6678663	6678710	513	559	101	117
ENST00000361959	2995	577	6672350	6672532	1172	1353	304	364
ENST00000396801	3025	577	6672350	6672532	1120	1301	304	364

Loci of skipped exons in Mayo 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
ENST00000361959	2995	577	6678663	6678710	565	611	101	117
ENST00000396801	3025	577	6678663	6678710	513	559	101	117
ENST00000361959	2995	577	6672350	6672532	1172	1353	304	364
ENST00000396801	3025	577	6672350	6672532	1120	1301	304	364
ENST00000361959	2995	577	6669031	6669189	1434	1591	391	443
ENST00000396801	3025	577	6669031	6669189	1382	1539	391	443

Lost protein functional features of individual exon skipping events in ROSMAP.

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
Q8TF68	101	117	102	156	Alternative sequence	ID=VSP_040314;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8TF68	101	117	102	156	Alternative sequence	ID=VSP_040314;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8TF68	101	117	1	577	Chain	ID=PRO_0000047552;Note=Zinc finger protein 384
Q8TF68	101	117	1	577	Chain	ID=PRO_0000047552;Note=Zinc finger protein 384
Q8TF68	304	364	293	353	Alternative sequence	ID=VSP_040315;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8TF68	304	364	293	353	Alternative sequence	ID=VSP_040315;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8TF68	304	364	300	360	Alternative sequence	ID=VSP_006920;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8TF68	304	364	300	360	Alternative sequence	ID=VSP_006920;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8TF68	304	364	1	577	Chain	ID=PRO_0000047552;Note=Zinc finger protein 384
Q8TF68	304	364	1	577	Chain	ID=PRO_0000047552;Note=Zinc finger protein 384
Q8TF68	304	364	284	306	Zinc finger	Note=C2H2-type 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	304	364	284	306	Zinc finger	Note=C2H2-type 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	304	364	317	339	Zinc finger	Note=C2H2-type 4;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	304	364	317	339	Zinc finger	Note=C2H2-type 4;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	304	364	345	367	Zinc finger	Note=C2H2-type 5;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	304	364	345	367	Zinc finger	Note=C2H2-type 5;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	391	443	1	577	Chain	ID=PRO_0000047552;Note=Zinc finger protein 384
Q8TF68	391	443	1	577	Chain	ID=PRO_0000047552;Note=Zinc finger protein 384
Q8TF68	391	443	373	397	Zinc finger	Note=C2H2-type 6;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	391	443	373	397	Zinc finger	Note=C2H2-type 6;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	391	443	403	425	Zinc finger	Note=C2H2-type 7;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	391	443	403	425	Zinc finger	Note=C2H2-type 7;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	391	443	433	455	Zinc finger	Note=C2H2-type 8;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	391	443	433	455	Zinc finger	Note=C2H2-type 8;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042

Lost protein functional features of individual exon skipping events in MSBB.

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
Q8TF68	101	117	102	156	Alternative sequence	ID=VSP_040314;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8TF68	101	117	102	156	Alternative sequence	ID=VSP_040314;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8TF68	101	117	1	577	Chain	ID=PRO_0000047552;Note=Zinc finger protein 384
Q8TF68	101	117	1	577	Chain	ID=PRO_0000047552;Note=Zinc finger protein 384
Q8TF68	304	364	293	353	Alternative sequence	ID=VSP_040315;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8TF68	304	364	293	353	Alternative sequence	ID=VSP_040315;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8TF68	304	364	300	360	Alternative sequence	ID=VSP_006920;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8TF68	304	364	300	360	Alternative sequence	ID=VSP_006920;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8TF68	304	364	1	577	Chain	ID=PRO_0000047552;Note=Zinc finger protein 384
Q8TF68	304	364	1	577	Chain	ID=PRO_0000047552;Note=Zinc finger protein 384
Q8TF68	304	364	284	306	Zinc finger	Note=C2H2-type 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	304	364	284	306	Zinc finger	Note=C2H2-type 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	304	364	317	339	Zinc finger	Note=C2H2-type 4;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	304	364	317	339	Zinc finger	Note=C2H2-type 4;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	304	364	345	367	Zinc finger	Note=C2H2-type 5;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	304	364	345	367	Zinc finger	Note=C2H2-type 5;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042

Lost protein functional features of individual exon skipping events in Mayo.

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
Q8TF68	101	117	102	156	Alternative sequence	ID=VSP_040314;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8TF68	101	117	102	156	Alternative sequence	ID=VSP_040314;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8TF68	101	117	1	577	Chain	ID=PRO_0000047552;Note=Zinc finger protein 384
Q8TF68	101	117	1	577	Chain	ID=PRO_0000047552;Note=Zinc finger protein 384
Q8TF68	304	364	293	353	Alternative sequence	ID=VSP_040315;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8TF68	304	364	293	353	Alternative sequence	ID=VSP_040315;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8TF68	304	364	300	360	Alternative sequence	ID=VSP_006920;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8TF68	304	364	300	360	Alternative sequence	ID=VSP_006920;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8TF68	304	364	1	577	Chain	ID=PRO_0000047552;Note=Zinc finger protein 384
Q8TF68	304	364	1	577	Chain	ID=PRO_0000047552;Note=Zinc finger protein 384
Q8TF68	304	364	284	306	Zinc finger	Note=C2H2-type 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	304	364	284	306	Zinc finger	Note=C2H2-type 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	304	364	317	339	Zinc finger	Note=C2H2-type 4;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	304	364	317	339	Zinc finger	Note=C2H2-type 4;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	304	364	345	367	Zinc finger	Note=C2H2-type 5;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	304	364	345	367	Zinc finger	Note=C2H2-type 5;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	391	443	1	577	Chain	ID=PRO_0000047552;Note=Zinc finger protein 384
Q8TF68	391	443	1	577	Chain	ID=PRO_0000047552;Note=Zinc finger protein 384
Q8TF68	391	443	373	397	Zinc finger	Note=C2H2-type 6;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	391	443	373	397	Zinc finger	Note=C2H2-type 6;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	391	443	403	425	Zinc finger	Note=C2H2-type 7;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	391	443	403	425	Zinc finger	Note=C2H2-type 7;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	391	443	433	455	Zinc finger	Note=C2H2-type 8;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q8TF68	391	443	433	455	Zinc finger	Note=C2H2-type 8;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042

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3'-UTR located exon skipping events that lost miRNA binding sites in ZNF384

3'-UTR exon skipping evnets lost miRNA binding.

Tissue type

ENST

Exon skip start

Exon skip end

microRNA

Binding site by TargetScan

Binding type by TargetScan

Bdinding site by miRanda

Score of miRanda

Energy by miRanda

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SNVs in the skipped exons for ZNF384

- Differential PSIs between mutated versus non-mutated samples.

- Depth of Coverage in the skipped exon of the mutated samples.

- Sashimi plot in the skipped exon of the mutated samples.

- Non-synonymous mutations located in the skipped exons.

Cancer type

Sample

ESID

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

- 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

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AD stage-associated exon skippint events for ZNF384

Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).

AD stage info

Cohort

Tissue

SE id

Coefficient

P-value

Chromosome

Strand

E1 start

E1 end

Skipped start

Skipped end

E2 start

E2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ZNF384

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

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Correlation with RNA binding proteins (RBPs) for ZNF384

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	PCBP4	exon_skip_40317	4.390401e-01	7.077646e-09
CB	NUP42	exon_skip_40317	5.536282e-01	3.767444e-14
CB	CNOT4	exon_skip_259800	-4.010059e-01	1.622191e-07
CB	NUP42	exon_skip_259800	6.099577e-01	1.414853e-17
CB	TRA2A	exon_skip_239594	-5.986537e-01	9.773812e-17
HCC	RBM3	exon_skip_239594	4.479290e-01	9.943132e-15
PCC	ELAVL4	exon_skip_259800	4.153737e-01	2.993916e-10
PCC	RBM3	exon_skip_239594	5.514859e-01	4.156518e-18
TC	NUP42	exon_skip_40317	5.100648e-01	6.535226e-12
TC	ELAVL4	exon_skip_199780	6.020332e-01	5.926335e-17
TC	RBM24	exon_skip_199780	5.256861e-01	1.319635e-12
TC	NUP42	exon_skip_199780	4.846922e-01	1.095281e-10
TC	TRA2A	exon_skip_239594	-4.882899e-01	1.155060e-10

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RelatedDrugs for ZNF384

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for ZNF384

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 RPSMAP, MSBB, and Mayo
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	3'-UTR located exon skipping events lost miRNA binding sites
	SNVs in the skipped exons with depth of coverage
	AD stage-associated exon skipping events
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Correlation with RNA binding proteins (RBPs)
	Related drugs with this gene
	Related diseases with this gene

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Gene summary for ZNF384

Gene structures and expression levels for ZNF384

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for ZNF384

Open reading frame (ORF) annotation in the exon skipping event for ZNF384

Infer the effects of exon skipping event on protein functional features for ZNF384

3'-UTR located exon skipping events that lost miRNA binding sites in ZNF384

SNVs in the skipped exons for ZNF384

AD stage-associated exon skippint events for ZNF384

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ZNF384

Correlation with RNA binding proteins (RBPs) for ZNF384

RelatedDrugs for ZNF384

RelatedDiseases for ZNF384