ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for QKI

Gene summary

Gene information	Gene symbol	QKI
	Gene ID	9444
	Gene name	QKI, KH domain containing RNA binding
	Synonyms	Hqk\|QK\|QK1\|QK3\|hqkI
	Cytomap	6q26
	Type of gene	protein-coding
	Description	protein quakingQKI/LOC100132735 fusionRNA binding protein HQKhomolog of mouse quaking QKI (KH domain RNA binding protein)quaking homolog, KH domain RNA binding
	Modification date	20200327
	UniProtAcc	F5GXS8, F5GYM3, F5GYT7, F5H5U6, F5H8C8, H0YFB7, H0YG47, H0YGD6, Q96PU8,
	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 QKI

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.

ENSG00000112531

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
PG	UP	ENST00000540719.1	QKI-211:retained_intron:QKI	5.104399e+01	8.543495e-01	1.396281e-05	6.453676e-04
CB	UP	ENST00000537883.5	QKI-210:protein_coding:QKI	3.419574e+00	1.004857e+00	1.143473e-02	3.880198e-02
TC	UP	ENST00000540719.1	QKI-211:retained_intron:QKI	1.295959e+01	9.716473e-01	5.016540e-07	2.310195e-05
TC	UP	ENST00000544823.5	QKI-215:protein_coding:QKI	1.443783e+01	8.965659e-01	2.553466e-04	3.389984e-03

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 QKI

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_156466	chr6	163415238:163415335:163455279:163455421:163478780:163478802	163455279:163455421
exon_skip_163647	chr6	163478780:163478896:163534982:163535125:163561982:163562069	163534982:163535125
exon_skip_169099	chr6	163455331:163455421:163534982:163535125:163561982:163562069	163534982:163535125
exon_skip_205386	chr6	163561982:163562069:163563420:163563719:163565946:163566795	163563420:163563719
exon_skip_23887	chr6	163455340:163455421:163478780:163478896:163534982:163534984	163478780:163478896
exon_skip_242806	chr6	163563444:163563719:163566721:163566795:163570694:163570741	163566721:163566795
exon_skip_255185	chr6	163455331:163455421:163457381:163457551:163478780:163478802	163457381:163457551
exon_skip_255831	chr6	163563444:163563719:163565946:163566795:163570694:163570741	163565946:163566795
exon_skip_42494	chr6	163455331:163455421:163478780:163478896:163534982:163534984	163478780:163478896
exon_skip_96502	chr6	163561982:163562069:163563420:163563719:163565946:163566067	163563420:163563719
exon_skip_982	chr6	163415238:163415335:163478780:163478896:163534982:163534984	163478780:163478896

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 QKI

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
ENST00000361752	163455279	163455421	Frame-shift
ENST00000361752	163478780	163478896	In-frame
ENST00000361752	163534982	163535125	In-frame
ENST00000361752	163566721	163566795	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
ENST00000361752	163455279	163455421	Frame-shift
ENST00000361752	163478780	163478896	In-frame
ENST00000361752	163534982	163535125	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
ENST00000361752	163455279	163455421	Frame-shift
ENST00000361752	163478780	163478896	In-frame
ENST00000361752	163534982	163535125	In-frame
ENST00000361752	163566721	163566795	In-frame

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

p-ENSG00000112531_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
ENST00000361752	9480	341	163478780	163478896	838	953	95	134
ENST00000361752	9480	341	163534982	163535125	955	1097	134	182
ENST00000361752	9480	341	163566721	163566795	1487	1560	312	336

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
ENST00000361752	9480	341	163478780	163478896	838	953	95	134
ENST00000361752	9480	341	163534982	163535125	955	1097	134	182

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
ENST00000361752	9480	341	163478780	163478896	838	953	95	134
ENST00000361752	9480	341	163534982	163535125	955	1097	134	182
ENST00000361752	9480	341	163566721	163566795	1487	1560	312	336

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
Q96PU8	95	134	1	341	Chain	ID=PRO_0000239373;Note=Protein quaking
Q96PU8	95	134	87	153	Domain	Note=KH
Q96PU8	95	134	97	97	Mutagenesis	Note=Decrease in target mRNA abundance and 10-fold decrease in RNA binding affinity%3B when associated with A-130. N->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	120	120	Mutagenesis	Note=Decrease in target mRNA abundance and 20-fold decrease in RNA binding affinity%3B when associated with A-124. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	124	124	Mutagenesis	Note=Decrease in target mRNA abundance and 20-fold decrease in RNA binding affinity%3B when associated with A-120. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	130	130	Mutagenesis	Note=Decrease in target mRNA abundance and 10-fold decrease in RNA binding affinity%3B when associated with A-97. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	97	97	Site	Note=Involved in RNA binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	120	120	Site	Note=Involved in RNA binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	124	124	Site	Note=Involved in RNA binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	130	130	Site	Note=Involved in RNA binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	134	182	1	341	Chain	ID=PRO_0000239373;Note=Protein quaking
Q96PU8	134	182	87	153	Domain	Note=KH
Q96PU8	134	182	182	213	Region	Note=Qua2 domain%3B involved in RNA binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	312	336	312	341	Alternative sequence	ID=VSP_019190;Note=In isoform 3 and isoform 4. GAVATKVRRHDMRVHPYQRIVTADRAATGN->EWIEMPVMPDISAH;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11856480,ECO:0000303\|Ref.2,ECO:0000303\|Ref.3;Dbxref=PMID:11856480
Q96PU8	312	336	312	341	Alternative sequence	ID=VSP_019191;Note=In isoform 5. GAVATKVRRHDMRVHPYQRIVTADRAATGN->GKFFSPWG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11856480;Dbxref=PMID:11856480
Q96PU8	312	336	312	341	Alternative sequence	ID=VSP_019189;Note=In isoform 6. GAVATKVRRHDMRVHPYQRIVTADRAATGN->GMAFPTKG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
Q96PU8	312	336	1	341	Chain	ID=PRO_0000239373;Note=Protein quaking
Q96PU8	312	336	324	330	Motif	Note=Nuclear localization signal;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q96PU8	312	336	336	336	Natural variant	ID=VAR_036051;Note=In a colorectal cancer sample%3B somatic mutation. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16959974;Dbxref=PMID:16959974

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
Q96PU8	95	134	1	341	Chain	ID=PRO_0000239373;Note=Protein quaking
Q96PU8	95	134	87	153	Domain	Note=KH
Q96PU8	95	134	97	97	Mutagenesis	Note=Decrease in target mRNA abundance and 10-fold decrease in RNA binding affinity%3B when associated with A-130. N->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	120	120	Mutagenesis	Note=Decrease in target mRNA abundance and 20-fold decrease in RNA binding affinity%3B when associated with A-124. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	124	124	Mutagenesis	Note=Decrease in target mRNA abundance and 20-fold decrease in RNA binding affinity%3B when associated with A-120. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	130	130	Mutagenesis	Note=Decrease in target mRNA abundance and 10-fold decrease in RNA binding affinity%3B when associated with A-97. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	97	97	Site	Note=Involved in RNA binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	120	120	Site	Note=Involved in RNA binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	124	124	Site	Note=Involved in RNA binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	130	130	Site	Note=Involved in RNA binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	134	182	1	341	Chain	ID=PRO_0000239373;Note=Protein quaking
Q96PU8	134	182	87	153	Domain	Note=KH
Q96PU8	134	182	182	213	Region	Note=Qua2 domain%3B involved in RNA binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077

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
Q96PU8	95	134	1	341	Chain	ID=PRO_0000239373;Note=Protein quaking
Q96PU8	95	134	87	153	Domain	Note=KH
Q96PU8	95	134	97	97	Mutagenesis	Note=Decrease in target mRNA abundance and 10-fold decrease in RNA binding affinity%3B when associated with A-130. N->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	120	120	Mutagenesis	Note=Decrease in target mRNA abundance and 20-fold decrease in RNA binding affinity%3B when associated with A-124. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	124	124	Mutagenesis	Note=Decrease in target mRNA abundance and 20-fold decrease in RNA binding affinity%3B when associated with A-120. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	130	130	Mutagenesis	Note=Decrease in target mRNA abundance and 10-fold decrease in RNA binding affinity%3B when associated with A-97. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	97	97	Site	Note=Involved in RNA binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	120	120	Site	Note=Involved in RNA binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	124	124	Site	Note=Involved in RNA binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	95	134	130	130	Site	Note=Involved in RNA binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	134	182	1	341	Chain	ID=PRO_0000239373;Note=Protein quaking
Q96PU8	134	182	87	153	Domain	Note=KH
Q96PU8	134	182	182	213	Region	Note=Qua2 domain%3B involved in RNA binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23630077;Dbxref=PMID:23630077
Q96PU8	312	336	312	341	Alternative sequence	ID=VSP_019190;Note=In isoform 3 and isoform 4. GAVATKVRRHDMRVHPYQRIVTADRAATGN->EWIEMPVMPDISAH;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11856480,ECO:0000303\|Ref.2,ECO:0000303\|Ref.3;Dbxref=PMID:11856480
Q96PU8	312	336	312	341	Alternative sequence	ID=VSP_019191;Note=In isoform 5. GAVATKVRRHDMRVHPYQRIVTADRAATGN->GKFFSPWG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11856480;Dbxref=PMID:11856480
Q96PU8	312	336	312	341	Alternative sequence	ID=VSP_019189;Note=In isoform 6. GAVATKVRRHDMRVHPYQRIVTADRAATGN->GMAFPTKG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
Q96PU8	312	336	1	341	Chain	ID=PRO_0000239373;Note=Protein quaking
Q96PU8	312	336	324	330	Motif	Note=Nuclear localization signal;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q96PU8	312	336	336	336	Natural variant	ID=VAR_036051;Note=In a colorectal cancer sample%3B somatic mutation. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16959974;Dbxref=PMID:16959974

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

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 QKI

- 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 QKI

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 QKI

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 QKI

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
PG	PUM1	exon_skip_255185	-4.262955e-01	1.229513e-10
PG	SNRNP70	exon_skip_255185	-4.146311e-01	4.333246e-10
PG	EWSR1	exon_skip_255185	-5.848870e-01	1.420649e-20

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RelatedDrugs for QKI

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 QKI

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 QKI

Gene structures and expression levels for QKI

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

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

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

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

SNVs in the skipped exons for QKI

AD stage-associated exon skippint events for QKI

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

Correlation with RNA binding proteins (RBPs) for QKI

RelatedDrugs for QKI

RelatedDiseases for QKI