ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for PIP5K1C

Gene summary

Gene information	Gene symbol	PIP5K1C
	Gene ID	23396
	Gene name	phosphatidylinositol-4-phosphate 5-kinase type 1 gamma
	Synonyms	LCCS3\|PIP5K-GAMMA\|PIP5K1-gamma\|PIP5Kgamma
	Cytomap	19p13.3
	Type of gene	protein-coding
	Description	phosphatidylinositol 4-phosphate 5-kinase type-1 gammadiphosphoinositide kinasephosphatidylinositol-4-phosphate 5-kinase, type I, gammaptdIns(4)P-5-kinase 1 gammatype I PIP kinase
	Modification date	20200313
	UniProtAcc	O60331,
	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 PIP5K1C

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.

ENSG00000186111

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	ENST00000637724.1	PIP5K1C-208:lncRNA:PIP5K1C	8.506080e-01	1.621829e+00	5.138543e-05	1.673485e-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 PIP5K1C

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_112666	chr19	3668404:3668440:3669673:3669904:3700297:3700390	3669673:3669904
exon_skip_124949	chr19	3647338:3647386:3648625:3648708:3651826:3652031	3648625:3648708
exon_skip_176063	chr19	3641705:3641809:3642907:3642939:3643243:3643381	3642907:3642939
exon_skip_187868	chr19	3661930:3662001:3664857:3664914:3667322:3667344	3664857:3664914
exon_skip_206481	chr19	3643243:3643381:3644087:3644251:3645974:3646058	3644087:3644251
exon_skip_22139	chr19	3632876:3633169:3633437:3633520:3638884:3639016	3633437:3633520
exon_skip_294421	chr19	3661930:3662001:3664822:3664914:3667322:3667344	3664822:3664914
exon_skip_42845	chr19	3633113:3633169:3633437:3633520:3638884:3639016	3633437:3633520
exon_skip_6536	chr19	3643249:3643381:3644087:3644251:3645974:3646058	3644087:3644251
exon_skip_72313	chr19	3644089:3644251:3645974:3646058:3647338:3647386	3645974:3646058

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 PIP5K1C

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
ENST00000335312	3633437	3633520	In-frame
ENST00000335312	3642907	3642939	In-frame
ENST00000335312	3644087	3644251	In-frame
ENST00000335312	3648625	3648708	In-frame
ENST00000335312	3664822	3664914	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
ENST00000335312	3633437	3633520	In-frame
ENST00000335312	3642907	3642939	In-frame
ENST00000335312	3648625	3648708	In-frame
ENST00000335312	3664822	3664914	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
ENST00000335312	3645974	3646058	Frame-shift
ENST00000335312	3633437	3633520	In-frame
ENST00000335312	3642907	3642939	In-frame
ENST00000335312	3644087	3644251	In-frame
ENST00000335312	3648625	3648708	In-frame
ENST00000335312	3664822	3664914	In-frame

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Infer the effects of exon skipping event on protein functional features for PIP5K1C

p-ENSG00000186111_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
ENST00000335312	5097	668	3664822	3664914	216	307	42	72
ENST00000335312	5097	668	3648625	3648708	1217	1299	376	403
ENST00000335312	5097	668	3644087	3644251	1435	1598	448	503
ENST00000335312	5097	668	3642907	3642939	1739	1770	550	560
ENST00000335312	5097	668	3633437	3633520	2010	2092	640	667

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
ENST00000335312	5097	668	3664822	3664914	216	307	42	72
ENST00000335312	5097	668	3648625	3648708	1217	1299	376	403
ENST00000335312	5097	668	3642907	3642939	1739	1770	550	560
ENST00000335312	5097	668	3633437	3633520	2010	2092	640	667

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
ENST00000335312	5097	668	3664822	3664914	216	307	42	72
ENST00000335312	5097	668	3648625	3648708	1217	1299	376	403
ENST00000335312	5097	668	3644087	3644251	1435	1598	448	503
ENST00000335312	5097	668	3642907	3642939	1739	1770	550	560
ENST00000335312	5097	668	3633437	3633520	2010	2092	640	667

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
O60331	42	72	1	668	Chain	ID=PRO_0000185462;Note=Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma
O60331	376	403	1	668	Chain	ID=PRO_0000185462;Note=Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma
O60331	376	403	75	443	Domain	Note=PIPK;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00781
O60331	448	503	1	668	Chain	ID=PRO_0000185462;Note=Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma
O60331	448	503	459	459	Modified residue	Note=Asymmetric dimethylarginine%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:O70161
O60331	448	503	459	459	Modified residue	Note=Omega-N-methylarginine%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:O70161
O60331	550	560	1	668	Chain	ID=PRO_0000185462;Note=Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma
O60331	550	560	555	555	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q5I6B8
O60331	640	667	640	668	Alternative sequence	ID=VSP_042078;Note=In isoform 2. FPTDERSWVYSPLHYSAQAPPASDGESDT->FWRLWGPHAPTWPWRREGRAACLCPYPPHVVTPFPGTGLCASWSPDGTGGLGAMSCCVSVS;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:19548880;Dbxref=PMID:19548880
O60331	640	667	641	668	Alternative sequence	ID=VSP_042080;Note=In isoform 3. PTDERSWVYSPLHYSAQAPPASDGESDT->FTDGRYWIYSPRHRRLRAVTLSASGTVSDRSRPPWGEGAVPLGQQGAAGPRPEAQCLTSVVFQKGFG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:19548880;Dbxref=PMID:19548880
O60331	640	667	641	668	Alternative sequence	ID=VSP_042079;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
O60331	640	667	1	668	Chain	ID=PRO_0000185462;Note=Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma
O60331	640	667	644	646	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3H1Z
O60331	640	667	649	649	Modified residue	Note=Phosphotyrosine%3B by CSK;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15738269;Dbxref=PMID:15738269
O60331	640	667	650	650	Modified residue	Note=Phosphoserine%3B by CDK5%2C MAPK1 and CDK1;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15738269;Dbxref=PMID:15738269
O60331	640	667	662	662	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:O70161
O60331	640	667	666	666	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q5I6B8
O60331	640	667	650	650	Mutagenesis	Note=Abolishes binding to TLN2. Affects localization to focal adhesions. S->D;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15738269;Dbxref=PMID:15738269
O60331	640	667	650	650	Mutagenesis	Note=Does not affect binding to TLN2 and localization to focal adhesions. S->N;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15738269;Dbxref=PMID:15738269
O60331	640	667	641	668	Region	Note=Mediates interaction with TLN2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12422219;Dbxref=PMID:12422219

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
O60331	42	72	1	668	Chain	ID=PRO_0000185462;Note=Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma
O60331	376	403	1	668	Chain	ID=PRO_0000185462;Note=Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma
O60331	376	403	75	443	Domain	Note=PIPK;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00781
O60331	550	560	1	668	Chain	ID=PRO_0000185462;Note=Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma
O60331	550	560	555	555	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q5I6B8
O60331	640	667	640	668	Alternative sequence	ID=VSP_042078;Note=In isoform 2. FPTDERSWVYSPLHYSAQAPPASDGESDT->FWRLWGPHAPTWPWRREGRAACLCPYPPHVVTPFPGTGLCASWSPDGTGGLGAMSCCVSVS;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:19548880;Dbxref=PMID:19548880
O60331	640	667	641	668	Alternative sequence	ID=VSP_042080;Note=In isoform 3. PTDERSWVYSPLHYSAQAPPASDGESDT->FTDGRYWIYSPRHRRLRAVTLSASGTVSDRSRPPWGEGAVPLGQQGAAGPRPEAQCLTSVVFQKGFG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:19548880;Dbxref=PMID:19548880
O60331	640	667	641	668	Alternative sequence	ID=VSP_042079;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
O60331	640	667	1	668	Chain	ID=PRO_0000185462;Note=Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma
O60331	640	667	644	646	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3H1Z
O60331	640	667	649	649	Modified residue	Note=Phosphotyrosine%3B by CSK;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15738269;Dbxref=PMID:15738269
O60331	640	667	650	650	Modified residue	Note=Phosphoserine%3B by CDK5%2C MAPK1 and CDK1;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15738269;Dbxref=PMID:15738269
O60331	640	667	662	662	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:O70161
O60331	640	667	666	666	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q5I6B8
O60331	640	667	650	650	Mutagenesis	Note=Abolishes binding to TLN2. Affects localization to focal adhesions. S->D;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15738269;Dbxref=PMID:15738269
O60331	640	667	650	650	Mutagenesis	Note=Does not affect binding to TLN2 and localization to focal adhesions. S->N;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15738269;Dbxref=PMID:15738269
O60331	640	667	641	668	Region	Note=Mediates interaction with TLN2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12422219;Dbxref=PMID:12422219

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
O60331	42	72	1	668	Chain	ID=PRO_0000185462;Note=Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma
O60331	376	403	1	668	Chain	ID=PRO_0000185462;Note=Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma
O60331	376	403	75	443	Domain	Note=PIPK;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00781
O60331	448	503	1	668	Chain	ID=PRO_0000185462;Note=Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma
O60331	448	503	459	459	Modified residue	Note=Asymmetric dimethylarginine%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:O70161
O60331	448	503	459	459	Modified residue	Note=Omega-N-methylarginine%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:O70161
O60331	550	560	1	668	Chain	ID=PRO_0000185462;Note=Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma
O60331	550	560	555	555	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q5I6B8
O60331	640	667	640	668	Alternative sequence	ID=VSP_042078;Note=In isoform 2. FPTDERSWVYSPLHYSAQAPPASDGESDT->FWRLWGPHAPTWPWRREGRAACLCPYPPHVVTPFPGTGLCASWSPDGTGGLGAMSCCVSVS;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:19548880;Dbxref=PMID:19548880
O60331	640	667	641	668	Alternative sequence	ID=VSP_042080;Note=In isoform 3. PTDERSWVYSPLHYSAQAPPASDGESDT->FTDGRYWIYSPRHRRLRAVTLSASGTVSDRSRPPWGEGAVPLGQQGAAGPRPEAQCLTSVVFQKGFG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:19548880;Dbxref=PMID:19548880
O60331	640	667	641	668	Alternative sequence	ID=VSP_042079;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
O60331	640	667	1	668	Chain	ID=PRO_0000185462;Note=Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma
O60331	640	667	644	646	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3H1Z
O60331	640	667	649	649	Modified residue	Note=Phosphotyrosine%3B by CSK;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15738269;Dbxref=PMID:15738269
O60331	640	667	650	650	Modified residue	Note=Phosphoserine%3B by CDK5%2C MAPK1 and CDK1;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15738269;Dbxref=PMID:15738269
O60331	640	667	662	662	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:O70161
O60331	640	667	666	666	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q5I6B8
O60331	640	667	650	650	Mutagenesis	Note=Abolishes binding to TLN2. Affects localization to focal adhesions. S->D;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15738269;Dbxref=PMID:15738269
O60331	640	667	650	650	Mutagenesis	Note=Does not affect binding to TLN2 and localization to focal adhesions. S->N;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15738269;Dbxref=PMID:15738269
O60331	640	667	641	668	Region	Note=Mediates interaction with TLN2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12422219;Dbxref=PMID:12422219

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3'-UTR located exon skipping events that lost miRNA binding sites in PIP5K1C

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 PIP5K1C

- 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 PIP5K1C

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 PIP5K1C

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
HCC	exon_skip_22139	rs8109485	chr19:3664096	1.934528e-04	1.576102e-02
PCC	exon_skip_22139	rs8109485	chr19:3664096	2.014290e-04	2.996773e-02

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Correlation with RNA binding proteins (RBPs) for PIP5K1C

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	CNOT4	exon_skip_42845	-4.879129e-01	6.877599e-11
CB	PCBP4	exon_skip_42845	5.173990e-01	2.886055e-12
CB	PTBP1	exon_skip_42845	-4.299492e-01	1.550417e-08
CB	CNOT4	exon_skip_176063	-4.684899e-01	4.735839e-10
DLPFC	ELAVL4	exon_skip_22139	4.491684e-01	4.885628e-18
HCC	RBM6	exon_skip_22139	-4.449704e-01	1.948543e-14
HCC	PTBP1	exon_skip_22139	-5.043300e-01	1.069059e-18
IFG	RBMS3	exon_skip_22139	-5.618432e-01	2.290225e-03
IFG	PCBP4	exon_skip_22139	-4.664456e-01	1.418561e-02
IFG	PTBP1	exon_skip_22139	-4.588539e-01	1.606546e-02
PCC	ELAVL4	exon_skip_22139	4.116572e-01	5.390764e-10
PCC	PTBP1	exon_skip_22139	-5.337670e-01	7.306036e-17
TC	ELAVL4	exon_skip_22139	4.517225e-01	2.279016e-09
TC	PTBP1	exon_skip_22139	-5.171398e-01	2.971632e-12

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RelatedDrugs for PIP5K1C

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 PIP5K1C

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 PIP5K1C

Gene structures and expression levels for PIP5K1C

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PIP5K1C

Open reading frame (ORF) annotation in the exon skipping event for PIP5K1C

Infer the effects of exon skipping event on protein functional features for PIP5K1C

3'-UTR located exon skipping events that lost miRNA binding sites in PIP5K1C

SNVs in the skipped exons for PIP5K1C

AD stage-associated exon skippint events for PIP5K1C

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PIP5K1C

Correlation with RNA binding proteins (RBPs) for PIP5K1C

RelatedDrugs for PIP5K1C

RelatedDiseases for PIP5K1C