ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for IKZF1

Gene summary

Gene information	Gene symbol	IKZF1
	Gene ID	10320
	Gene name	IKAROS family zinc finger 1
	Synonyms	CVID13\|Hs.54452\|IK1\|IKAROS\|LYF1\|LyF-1\|PPP1R92\|PRO0758\|ZNFN1A1
	Cytomap	7p12.2
	Type of gene	protein-coding
	Description	DNA-binding protein IkarosCLL-associated antigen KW-6ikaros family zinc finger protein 1lymphoid transcription factor LyF-1protein phosphatase 1, regulatory subunit 92zinc finger protein, subfamily 1A, 1 (Ikaros)
	Modification date	20200329
	UniProtAcc	A0A087WU46, A0A0A0MRA0, A0A0A0MST1, A0A2R8Y4D3, A0A2R8Y4T7, A0A2R8YFR0, C9JTB0, Q13422, Q3T907, R9R4D9,
	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 IKZF1

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.

ENSG00000185811

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

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 IKZF1

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_135010	chr7	50382540:50382707:50387345:50387470:50391729:50391833	50387345:50387470
exon_skip_137992	chr7	50327649:50327757:50376533:50376793:50382540:50382613	50376533:50376793
exon_skip_236829	chr7	50327649:50327757:50368006:50368065:50382540:50382613	50368006:50368065
exon_skip_287558	chr7	50382540:50382707:50391729:50391863:50399918:50405098	50391729:50391863
exon_skip_289573	chr7	50382540:50382707:50387345:50387470:50391729:50391863	50387345:50387470

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

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Open reading frame (ORF) annotation in the exon skipping event for IKZF1

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
ENST00000331340	50376533	50376793	In-frame
ENST00000331340	50387345	50387470	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
ENST00000331340	50376533	50376793	In-frame
ENST00000331340	50387345	50387470	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
ENST00000331340	50376533	50376793	In-frame
ENST00000331340	50387345	50387470	In-frame

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Infer the effects of exon skipping event on protein functional features for IKZF1

p-ENSG00000185811_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
ENST00000331340	6272	519	50376533	50376793	383	642	54	140
ENST00000331340	6272	519	50387345	50387470	812	936	197	238

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
ENST00000331340	6272	519	50376533	50376793	383	642	54	140
ENST00000331340	6272	519	50387345	50387470	812	936	197	238

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
ENST00000331340	6272	519	50376533	50376793	383	642	54	140
ENST00000331340	6272	519	50387345	50387470	812	936	197	238

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
Q13422	54	140	54	283	Alternative sequence	ID=VSP_006849;Note=In isoform Ik6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13422	54	140	54	140	Alternative sequence	ID=VSP_006848;Note=In isoform Ik2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q13422	54	140	1	519	Chain	ID=PRO_0000047094;Note=DNA-binding protein Ikaros
Q13422	54	140	58	58	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO);Ontology_term=ECO:0000250;evidence=ECO:0000250
Q13422	54	140	63	63	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:23186163;Dbxref=PMID:19690332,PMID:23186163
Q13422	54	140	101	101	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q03267
Q13422	54	140	140	140	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q03267
Q13422	54	140	117	139	Zinc finger	Note=C2H2-type 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q13422	197	238	54	283	Alternative sequence	ID=VSP_006849;Note=In isoform Ik6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13422	197	238	141	283	Alternative sequence	ID=VSP_006852;Note=In isoform Ik5. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13422	197	238	197	283	Alternative sequence	ID=VSP_006850;Note=In isoform Ik3 and isoform Ik4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13422	197	238	197	238	Alternative sequence	ID=VSP_006851;Note=In isoform Ik7 and isoform Ikx. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.3,ECO:0000303\|Ref.5;Dbxref=PMID:15489334
Q13422	197	238	1	519	Chain	ID=PRO_0000047094;Note=DNA-binding protein Ikaros
Q13422	197	238	210	210	Natural variant	ID=VAR_076405;Note=In CVID13%3B decreases binding to pericentromeric heterochromatin DNA%3B has diffuse nuclear localization. Y->C;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:21548011,ECO:0000269\|PubMed:26981933;Dbxref=dbSNP:rs869312
Q13422	197	238	214	214	Sequence conflict	Note=S->T;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13422	197	238	201	224	Zinc finger	Note=C2H2-type 4;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
Q13422	54	140	54	283	Alternative sequence	ID=VSP_006849;Note=In isoform Ik6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13422	54	140	54	140	Alternative sequence	ID=VSP_006848;Note=In isoform Ik2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q13422	54	140	1	519	Chain	ID=PRO_0000047094;Note=DNA-binding protein Ikaros
Q13422	54	140	58	58	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO);Ontology_term=ECO:0000250;evidence=ECO:0000250
Q13422	54	140	63	63	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:23186163;Dbxref=PMID:19690332,PMID:23186163
Q13422	54	140	101	101	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q03267
Q13422	54	140	140	140	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q03267
Q13422	54	140	117	139	Zinc finger	Note=C2H2-type 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q13422	197	238	54	283	Alternative sequence	ID=VSP_006849;Note=In isoform Ik6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13422	197	238	141	283	Alternative sequence	ID=VSP_006852;Note=In isoform Ik5. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13422	197	238	197	283	Alternative sequence	ID=VSP_006850;Note=In isoform Ik3 and isoform Ik4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13422	197	238	197	238	Alternative sequence	ID=VSP_006851;Note=In isoform Ik7 and isoform Ikx. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.3,ECO:0000303\|Ref.5;Dbxref=PMID:15489334
Q13422	197	238	1	519	Chain	ID=PRO_0000047094;Note=DNA-binding protein Ikaros
Q13422	197	238	210	210	Natural variant	ID=VAR_076405;Note=In CVID13%3B decreases binding to pericentromeric heterochromatin DNA%3B has diffuse nuclear localization. Y->C;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:21548011,ECO:0000269\|PubMed:26981933;Dbxref=dbSNP:rs869312
Q13422	197	238	214	214	Sequence conflict	Note=S->T;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13422	197	238	201	224	Zinc finger	Note=C2H2-type 4;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
Q13422	54	140	54	283	Alternative sequence	ID=VSP_006849;Note=In isoform Ik6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13422	54	140	54	140	Alternative sequence	ID=VSP_006848;Note=In isoform Ik2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q13422	54	140	1	519	Chain	ID=PRO_0000047094;Note=DNA-binding protein Ikaros
Q13422	54	140	58	58	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO);Ontology_term=ECO:0000250;evidence=ECO:0000250
Q13422	54	140	63	63	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:23186163;Dbxref=PMID:19690332,PMID:23186163
Q13422	54	140	101	101	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q03267
Q13422	54	140	140	140	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q03267
Q13422	54	140	117	139	Zinc finger	Note=C2H2-type 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042
Q13422	197	238	54	283	Alternative sequence	ID=VSP_006849;Note=In isoform Ik6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13422	197	238	141	283	Alternative sequence	ID=VSP_006852;Note=In isoform Ik5. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13422	197	238	197	283	Alternative sequence	ID=VSP_006850;Note=In isoform Ik3 and isoform Ik4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13422	197	238	197	238	Alternative sequence	ID=VSP_006851;Note=In isoform Ik7 and isoform Ikx. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.3,ECO:0000303\|Ref.5;Dbxref=PMID:15489334
Q13422	197	238	1	519	Chain	ID=PRO_0000047094;Note=DNA-binding protein Ikaros
Q13422	197	238	210	210	Natural variant	ID=VAR_076405;Note=In CVID13%3B decreases binding to pericentromeric heterochromatin DNA%3B has diffuse nuclear localization. Y->C;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:21548011,ECO:0000269\|PubMed:26981933;Dbxref=dbSNP:rs869312
Q13422	197	238	214	214	Sequence conflict	Note=S->T;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13422	197	238	201	224	Zinc finger	Note=C2H2-type 4;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 IKZF1

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 IKZF1

- 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 IKZF1

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 IKZF1

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 IKZF1

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for IKZF1

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 IKZF1

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 IKZF1

Gene structures and expression levels for IKZF1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for IKZF1

Open reading frame (ORF) annotation in the exon skipping event for IKZF1

Infer the effects of exon skipping event on protein functional features for IKZF1

3'-UTR located exon skipping events that lost miRNA binding sites in IKZF1

SNVs in the skipped exons for IKZF1

AD stage-associated exon skippint events for IKZF1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for IKZF1

Correlation with RNA binding proteins (RBPs) for IKZF1

RelatedDrugs for IKZF1

RelatedDiseases for IKZF1