ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for PLEKHA1

Gene summary

Gene information	Gene symbol	PLEKHA1
	Gene ID	59338
	Gene name	pleckstrin homology domain containing A1
	Synonyms	TAPP1
	Cytomap	10q26.13
	Type of gene	protein-coding
	Description	pleckstrin homology domain-containing family A member 1pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1tandem PH domain-containing protein 1
	Modification date	20180523
	UniProtAcc	Q9HB21
	Context	PubMed: PLEKHA1 [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
PLEKHA1	GO:0014065	phosphatidylinositol 3-kinase signaling	12101241
PLEKHA1	GO:0031529	ruffle organization	15485858
PLEKHA1	GO:0045184	establishment of protein localization	14516276
PLEKHA1	GO:0050853	B cell receptor signaling pathway	12101241
PLEKHA1	GO:0070301	cellular response to hydrogen peroxide	14516276

Top

Exon skipping events across known transcript of Ensembl for PLEKHA1 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.

Top

Gene isoform structures and expression levels for PLEKHA1

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

Top

Exon skipping events with PSIs in TCGA for PLEKHA1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_45652	10	124157433:124157490:124159858:124159904:124166091:124166156	124159858:124159904	ENSG00000107679.10	ENST00000368990.3,ENST00000433307.1,ENST00000368989.2,ENST00000392799.3,ENST00000368988.1,ENST00000463663.2,ENST00000538022.1
exon_skip_45658	10	124159858:124159904:124166091:124166189:124172435:124172492	124166091:124166189	ENSG00000107679.10	ENST00000368990.3,ENST00000433307.1,ENST00000368989.2,ENST00000392799.3,ENST00000368988.1,ENST00000463663.2,ENST00000538022.1
exon_skip_45662	10	124175374:124175518:124177415:124177484:124183714:124183779	124177415:124177484	ENSG00000107679.10	ENST00000368990.3,ENST00000433307.1,ENST00000368989.2,ENST00000392799.3,ENST00000368988.1,ENST00000538022.1
exon_skip_45663	10	124183714:124183779:124184411:124184475:124186457:124186547	124184411:124184475	ENSG00000107679.10	ENST00000368990.3,ENST00000433307.1,ENST00000368989.2,ENST00000392799.3,ENST00000368988.1,ENST00000538022.1
exon_skip_45664	10	124184411:124184475:124186457:124186547:124189139:124189638	124186457:124186547	ENSG00000107679.10	ENST00000368990.3,ENST00000433307.1,ENST00000392799.3
exon_skip_45669	10	124186457:124186547:124187791:124187832:124189139:124189638	124187791:124187832	ENSG00000107679.10	ENST00000368989.2,ENST00000368988.1
exon_skip_45671	10	124186457:124186547:124187791:124187936:124189139:124189638	124187791:124187936	ENSG00000107679.10	ENST00000538022.1

PSI values of skipped exons in TCGA.

Top

Exon skipping events with PSIs in GTEx for PLEKHA1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_45637	10	124134349:124134477:124151818:124151888:124152696:124152857	124151818:124151888	ENSG00000107679.10	ENST00000463663.2
exon_skip_45652	10	124157433:124157490:124159858:124159904:124166091:124166156	124159858:124159904	ENSG00000107679.10	ENST00000368990.3,ENST00000368988.1,ENST00000368989.2,ENST00000463663.2,ENST00000538022.1,ENST00000392799.3,ENST00000433307.1
exon_skip_45658	10	124159858:124159904:124166091:124166189:124172435:124172492	124166091:124166189	ENSG00000107679.10	ENST00000368990.3,ENST00000368988.1,ENST00000368989.2,ENST00000463663.2,ENST00000538022.1,ENST00000392799.3,ENST00000433307.1
exon_skip_45662	10	124175374:124175518:124177415:124177484:124183714:124183779	124177415:124177484	ENSG00000107679.10	ENST00000368990.3,ENST00000368988.1,ENST00000368989.2,ENST00000538022.1,ENST00000392799.3,ENST00000433307.1
exon_skip_45663	10	124183714:124183779:124184411:124184475:124186457:124186547	124184411:124184475	ENSG00000107679.10	ENST00000368990.3,ENST00000368988.1,ENST00000368989.2,ENST00000538022.1,ENST00000392799.3,ENST00000433307.1
exon_skip_45664	10	124184411:124184475:124186457:124186547:124189139:124189638	124186457:124186547	ENSG00000107679.10	ENST00000368990.3,ENST00000392799.3,ENST00000433307.1
exon_skip_45669	10	124186457:124186547:124187791:124187832:124189139:124189638	124187791:124187832	ENSG00000107679.10	ENST00000368988.1,ENST00000368989.2
exon_skip_45671	10	124186457:124186547:124187791:124187936:124189139:124189638	124187791:124187936	ENSG00000107679.10	ENST00000538022.1

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

Top

Open reading frame (ORF) annotation in the exon skipping event for PLEKHA1

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
ENST00000368990	124159858	124159904	Frame-shift
ENST00000433307	124159858	124159904	Frame-shift
ENST00000368990	124166091	124166189	Frame-shift
ENST00000433307	124166091	124166189	Frame-shift
ENST00000368990	124184411	124184475	Frame-shift
ENST00000433307	124184411	124184475	Frame-shift
ENST00000368990	124177415	124177484	In-frame
ENST00000433307	124177415	124177484	In-frame
ENST00000368990	124186457	124186547	In-frame
ENST00000433307	124186457	124186547	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
ENST00000368990	124159858	124159904	Frame-shift
ENST00000433307	124159858	124159904	Frame-shift
ENST00000368990	124166091	124166189	Frame-shift
ENST00000433307	124166091	124166189	Frame-shift
ENST00000368990	124184411	124184475	Frame-shift
ENST00000433307	124184411	124184475	Frame-shift
ENST00000368990	124177415	124177484	In-frame
ENST00000433307	124177415	124177484	In-frame
ENST00000368990	124186457	124186547	In-frame
ENST00000433307	124186457	124186547	In-frame

Top

Infer the effects of exon skipping event on protein functional features for PLEKHA1

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
ENST00000368990	3776	404	124177415	124177484	744	812	204	227
ENST00000433307	3666	404	124177415	124177484	635	703	204	227
ENST00000368990	3776	404	124186457	124186547	942	1031	270	300
ENST00000433307	3666	404	124186457	124186547	833	922	270	300

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
ENST00000368990	3776	404	124177415	124177484	744	812	204	227
ENST00000433307	3666	404	124177415	124177484	635	703	204	227
ENST00000368990	3776	404	124186457	124186547	942	1031	270	300
ENST00000433307	3666	404	124186457	124186547	833	922	270	300

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
Q9HB21	204	227	208	215	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ
Q9HB21	204	227	208	215	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ
Q9HB21	204	227	217	225	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ
Q9HB21	204	227	217	225	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ
Q9HB21	204	227	1	404	Chain	ID=PRO_0000053873;Note=Pleckstrin homology domain-containing family A member 1
Q9HB21	204	227	1	404	Chain	ID=PRO_0000053873;Note=Pleckstrin homology domain-containing family A member 1
Q9HB21	204	227	191	289	Domain	Note=PH 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00145
Q9HB21	204	227	191	289	Domain	Note=PH 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00145
Q9HB21	204	227	203	205	Mutagenesis	Note=Abolishes phosphatidylinositide binding. AVM->GGG
Q9HB21	204	227	203	205	Mutagenesis	Note=Abolishes phosphatidylinositide binding. AVM->GGG
Q9HB21	204	227	203	205	Mutagenesis	Note=Binds both PtdIns3%2C4P2 and PtdIns3%2C4%2C5P3. AVM->GLV
Q9HB21	204	227	203	205	Mutagenesis	Note=Binds both PtdIns3%2C4P2 and PtdIns3%2C4%2C5P3. AVM->GLV
Q9HB21	204	227	203	204	Mutagenesis	Note=Binds both PtdIns3%2C4P2 and PtdIns3%2C4%2C5P3. AV->GG
Q9HB21	204	227	203	204	Mutagenesis	Note=Binds both PtdIns3%2C4P2 and PtdIns3%2C4%2C5P3. AV->GG
Q9HB21	204	227	204	204	Mutagenesis	Note=No effect. V->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11513726;Dbxref=PMID:11513726
Q9HB21	204	227	204	204	Mutagenesis	Note=No effect. V->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11513726;Dbxref=PMID:11513726
Q9HB21	204	227	205	205	Mutagenesis	Note=No effect. M->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11513726;Dbxref=PMID:11513726
Q9HB21	204	227	205	205	Mutagenesis	Note=No effect. M->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11513726;Dbxref=PMID:11513726
Q9HB21	204	227	207	207	Mutagenesis	Note=No effect. N->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11513726;Dbxref=PMID:11513726
Q9HB21	204	227	207	207	Mutagenesis	Note=No effect. N->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11513726;Dbxref=PMID:11513726
Q9HB21	204	227	211	211	Mutagenesis	Note=Abolishes phosphatidylinositide binding. R->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11001876;Dbxref=PMID:11001876
Q9HB21	204	227	211	211	Mutagenesis	Note=Abolishes phosphatidylinositide binding. R->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11001876;Dbxref=PMID:11001876
Q9HB21	204	227	203	205	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ
Q9HB21	204	227	203	205	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ
Q9HB21	270	300	266	270	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ
Q9HB21	270	300	266	270	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ
Q9HB21	270	300	1	404	Chain	ID=PRO_0000053873;Note=Pleckstrin homology domain-containing family A member 1
Q9HB21	270	300	1	404	Chain	ID=PRO_0000053873;Note=Pleckstrin homology domain-containing family A member 1
Q9HB21	270	300	191	289	Domain	Note=PH 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00145
Q9HB21	270	300	191	289	Domain	Note=PH 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00145
Q9HB21	270	300	274	290	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ
Q9HB21	270	300	274	290	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ

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
Q9HB21	204	227	208	215	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ
Q9HB21	204	227	208	215	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ
Q9HB21	204	227	217	225	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ
Q9HB21	204	227	217	225	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ
Q9HB21	204	227	1	404	Chain	ID=PRO_0000053873;Note=Pleckstrin homology domain-containing family A member 1
Q9HB21	204	227	1	404	Chain	ID=PRO_0000053873;Note=Pleckstrin homology domain-containing family A member 1
Q9HB21	204	227	191	289	Domain	Note=PH 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00145
Q9HB21	204	227	191	289	Domain	Note=PH 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00145
Q9HB21	204	227	203	205	Mutagenesis	Note=Abolishes phosphatidylinositide binding. AVM->GGG
Q9HB21	204	227	203	205	Mutagenesis	Note=Abolishes phosphatidylinositide binding. AVM->GGG
Q9HB21	204	227	203	205	Mutagenesis	Note=Binds both PtdIns3%2C4P2 and PtdIns3%2C4%2C5P3. AVM->GLV
Q9HB21	204	227	203	205	Mutagenesis	Note=Binds both PtdIns3%2C4P2 and PtdIns3%2C4%2C5P3. AVM->GLV
Q9HB21	204	227	203	204	Mutagenesis	Note=Binds both PtdIns3%2C4P2 and PtdIns3%2C4%2C5P3. AV->GG
Q9HB21	204	227	203	204	Mutagenesis	Note=Binds both PtdIns3%2C4P2 and PtdIns3%2C4%2C5P3. AV->GG
Q9HB21	204	227	204	204	Mutagenesis	Note=No effect. V->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11513726;Dbxref=PMID:11513726
Q9HB21	204	227	204	204	Mutagenesis	Note=No effect. V->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11513726;Dbxref=PMID:11513726
Q9HB21	204	227	205	205	Mutagenesis	Note=No effect. M->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11513726;Dbxref=PMID:11513726
Q9HB21	204	227	205	205	Mutagenesis	Note=No effect. M->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11513726;Dbxref=PMID:11513726
Q9HB21	204	227	207	207	Mutagenesis	Note=No effect. N->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11513726;Dbxref=PMID:11513726
Q9HB21	204	227	207	207	Mutagenesis	Note=No effect. N->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11513726;Dbxref=PMID:11513726
Q9HB21	204	227	211	211	Mutagenesis	Note=Abolishes phosphatidylinositide binding. R->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11001876;Dbxref=PMID:11001876
Q9HB21	204	227	211	211	Mutagenesis	Note=Abolishes phosphatidylinositide binding. R->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11001876;Dbxref=PMID:11001876
Q9HB21	204	227	203	205	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ
Q9HB21	204	227	203	205	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ
Q9HB21	270	300	266	270	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ
Q9HB21	270	300	266	270	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ
Q9HB21	270	300	1	404	Chain	ID=PRO_0000053873;Note=Pleckstrin homology domain-containing family A member 1
Q9HB21	270	300	1	404	Chain	ID=PRO_0000053873;Note=Pleckstrin homology domain-containing family A member 1
Q9HB21	270	300	191	289	Domain	Note=PH 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00145
Q9HB21	270	300	191	289	Domain	Note=PH 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00145
Q9HB21	270	300	274	290	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ
Q9HB21	270	300	274	290	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1EAZ

Top

SNVs in the skipped exons for PLEKHA1

- 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
LUSC	TCGA-37-4135-01	exon_skip_45662	124177416	124177484	124177426	124177426	Nonsense_Mutation	G	A	p.W208*
UCEC	TCGA-AP-A051-01	exon_skip_45663	124184412	124184475	124184473	124184473	Nonsense_Mutation	C	T	p.Q270*
CESC	TCGA-C5-A1MH-01	exon_skip_45663	124184412	124184475	124184411	124184411	Splice_Site	G	A	e9-1

- 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
HCC1569_BREAST	124177416	124177484	124177453	124177453	Missense_Mutation	A	G	p.E217G
NKL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	124186458	124186547	124186506	124186506	Missense_Mutation	G	A	p.A287T
FARAGE_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	124186458	124186547	124186540	124186540	Missense_Mutation	C	T	p.A298V
EOL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	124166092	124166189	124166189	124166189	Splice_Site	A	G	p.T114T
CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	124184412	124184475	124184412	124184412	Splice_Site	C	T	p.S249S

Top

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PLEKHA1

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

Top

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PLEKHA1

Top

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PLEKHA1

Top

RelatedDrugs for PLEKHA1

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
	Q9HB21	DB04272	Citric Acid	Pleckstrin homology domain-containing family A member 1	small molecule	approved\|nutraceutical\|vet_approved

Top

RelatedDiseases for PLEKHA1

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 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

Home

Download

Statistics

Landscape

Help

Contact