ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for PRKACA

Gene summary

Gene information	Gene symbol	PRKACA
	Gene ID	5566
	Gene name	protein kinase cAMP-activated catalytic subunit alpha
	Synonyms	PKACA\|PPNAD4
	Cytomap	19p13.12
	Type of gene	protein-coding
	Description	cAMP-dependent protein kinase catalytic subunit alphaPKA C-alphaprotein kinase A catalytic subunitprotein kinase, cAMP-dependent, alpha catalytic subunitprotein kinase, cAMP-dependent, catalytic, alpha
	Modification date	20180527
	UniProtAcc	P17612
	Context	PubMed: PRKACA [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
PRKACA	GO:0006397	mRNA processing	17594903
PRKACA	GO:0006468	protein phosphorylation	12475942
PRKACA	GO:0018105	peptidyl-serine phosphorylation	10805756\|11029056
PRKACA	GO:0034605	cellular response to heat	21085490
PRKACA	GO:0045667	regulation of osteoblast differentiation	19949837
PRKACA	GO:0061136	regulation of proteasomal protein catabolic process	17565987
PRKACA	GO:0071333	cellular response to glucose stimulus	19949837
PRKACA	GO:2000810	regulation of bicellular tight junction assembly	15905176

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Exon skipping events across known transcript of Ensembl for PRKACA 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.

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Gene isoform structures and expression levels for PRKACA

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

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Exon skipping events with PSIs in TCGA for PRKACA

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_315706	19	14203861:14204049:14204439:14204604:14208172:14208213	14204439:14204604	ENSG00000072062.9	ENST00000589994.1,ENST00000308677.4,ENST00000350356.3
exon_skip_315710	19	14208172:14208295:14208390:14208486:14208575:14208702	14208390:14208486	ENSG00000072062.9	ENST00000589994.1,ENST00000587372.1,ENST00000308677.4,ENST00000588209.1,ENST00000536649.1,ENST00000350356.3
exon_skip_315712	19	14208575:14208702:14211637:14211720:14213627:14213726	14211637:14211720	ENSG00000072062.9	ENST00000589994.1,ENST00000593092.1,ENST00000587372.1,ENST00000308677.4,ENST00000536649.1,ENST00000350356.3
exon_skip_315713	19	14211637:14211720:14213627:14213726:14217571:14217672	14213627:14213726	ENSG00000072062.9	ENST00000589994.1,ENST00000593092.1,ENST00000587372.1,ENST00000308677.4,ENST00000536649.1,ENST00000350356.3

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for PRKACA

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_315706	19	14203861:14204049:14204439:14204604:14208172:14208213	14204439:14204604	ENSG00000072062.9	ENST00000308677.4,ENST00000350356.3,ENST00000589994.1
exon_skip_315710	19	14208172:14208295:14208390:14208486:14208575:14208702	14208390:14208486	ENSG00000072062.9	ENST00000308677.4,ENST00000350356.3,ENST00000587372.1,ENST00000589994.1,ENST00000588209.1,ENST00000536649.1
exon_skip_315712	19	14208575:14208702:14211637:14211720:14213627:14213726	14211637:14211720	ENSG00000072062.9	ENST00000308677.4,ENST00000350356.3,ENST00000587372.1,ENST00000589994.1,ENST00000536649.1,ENST00000593092.1
exon_skip_315713	19	14211637:14211720:14213627:14213726:14217571:14217672	14213627:14213726	ENSG00000072062.9	ENST00000308677.4,ENST00000350356.3,ENST00000587372.1,ENST00000589994.1,ENST00000536649.1,ENST00000593092.1

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

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

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
ENST00000308677	14211637	14211720	Frame-shift
ENST00000308677	14204439	14204604	In-frame
ENST00000308677	14208390	14208486	In-frame
ENST00000308677	14213627	14213726	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
ENST00000308677	14211637	14211720	Frame-shift
ENST00000308677	14204439	14204604	In-frame
ENST00000308677	14208390	14208486	In-frame
ENST00000308677	14213627	14213726	In-frame

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

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
ENST00000308677	2694	351	14213627	14213726	435	533	79	112
ENST00000308677	2694	351	14208390	14208486	744	839	182	214
ENST00000308677	2694	351	14204439	14204604	963	1127	255	310

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
ENST00000308677	2694	351	14213627	14213726	435	533	79	112
ENST00000308677	2694	351	14208390	14208486	744	839	182	214
ENST00000308677	2694	351	14204439	14204604	963	1127	255	310

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
P17612	79	112	107	112	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	79	112	2	351	Chain	ID=PRO_0000086052;Note=cAMP-dependent protein kinase catalytic subunit alpha
P17612	79	112	44	298	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P17612	79	112	77	82	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	79	112	86	98	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	79	112	96	96	Mutagenesis	Note=Enhanced basal kinase activity%3B when associated with R-48%2C L-121%2C A-124%2C K-182 and A-184. L->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21774789;Dbxref=PMID:21774789
P17612	182	214	181	183	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	182	214	212	214	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IZJ
P17612	182	214	2	351	Chain	ID=PRO_0000086052;Note=cAMP-dependent protein kinase catalytic subunit alpha
P17612	182	214	44	298	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P17612	182	214	186	188	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4UJ2
P17612	182	214	203	205	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	182	214	208	211	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	182	214	196	196	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12372837;Dbxref=PMID:12372837
P17612	182	214	198	198	Modified residue	Note=Phosphothreonine%3B by PDPK1;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12372837,ECO:0000269\|PubMed:16765046,ECO:0000269\|PubMed:20137943,ECO:0000269\|PubMed:20481595,EC
P17612	182	214	182	182	Mutagenesis	Note=Enhanced basal kinase activity%3B when associated with R-48%2C Q-96%2C L-121%2C A-124 and A-184. Q->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21774789;Dbxref=PMID:21774789
P17612	182	214	184	184	Mutagenesis	Note=Enhanced basal kinase activity%3B when associated with R-48%2C Q-96%2C L-121%2C A-124 and K-182. T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21774789;Dbxref=PMID:21774789
P17612	182	214	195	195	Mutagenesis	Note=No phosphorylation. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12372837;Dbxref=PMID:12372837
P17612	182	214	201	201	Mutagenesis	Note=No phosphorylation. G->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12372837;Dbxref=PMID:12372837
P17612	182	214	202	202	Mutagenesis	Note=No phosphorylation. T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12372837;Dbxref=PMID:12372837
P17612	182	214	205	205	Mutagenesis	Note=Loss of allosteric regulation. Y->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18178622;Dbxref=PMID:18178622
P17612	182	214	206	206	Natural variant	ID=VAR_071707;Note=In PPNAD4%3B somatic mutation%3B the mutation results in cAMP-independent basal protein kinase activity and constitutive activation of protein kinase A. L->R;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:000
P17612	255	310	2	351	Chain	ID=PRO_0000086052;Note=cAMP-dependent protein kinase catalytic subunit alpha
P17612	255	310	44	298	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P17612	255	310	299	351	Domain	Note=AGC-kinase C-terminal
P17612	255	310	264	273	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	310	290	293	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	310	296	298	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	310	303	307	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	310	264	264	Natural variant	ID=VAR_040593;Note=S->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs35635531,PMID:17344846
P17612	255	310	278	280	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	310	282	284	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IZF
P17612	255	310	286	289	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8

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
P17612	79	112	107	112	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	79	112	2	351	Chain	ID=PRO_0000086052;Note=cAMP-dependent protein kinase catalytic subunit alpha
P17612	79	112	44	298	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P17612	79	112	77	82	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	79	112	86	98	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	79	112	96	96	Mutagenesis	Note=Enhanced basal kinase activity%3B when associated with R-48%2C L-121%2C A-124%2C K-182 and A-184. L->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21774789;Dbxref=PMID:21774789
P17612	182	214	181	183	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	182	214	212	214	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IZJ
P17612	182	214	2	351	Chain	ID=PRO_0000086052;Note=cAMP-dependent protein kinase catalytic subunit alpha
P17612	182	214	44	298	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P17612	182	214	186	188	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4UJ2
P17612	182	214	203	205	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	182	214	208	211	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	182	214	196	196	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12372837;Dbxref=PMID:12372837
P17612	182	214	198	198	Modified residue	Note=Phosphothreonine%3B by PDPK1;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12372837,ECO:0000269\|PubMed:16765046,ECO:0000269\|PubMed:20137943,ECO:0000269\|PubMed:20481595,EC
P17612	182	214	182	182	Mutagenesis	Note=Enhanced basal kinase activity%3B when associated with R-48%2C Q-96%2C L-121%2C A-124 and A-184. Q->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21774789;Dbxref=PMID:21774789
P17612	182	214	184	184	Mutagenesis	Note=Enhanced basal kinase activity%3B when associated with R-48%2C Q-96%2C L-121%2C A-124 and K-182. T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21774789;Dbxref=PMID:21774789
P17612	182	214	195	195	Mutagenesis	Note=No phosphorylation. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12372837;Dbxref=PMID:12372837
P17612	182	214	201	201	Mutagenesis	Note=No phosphorylation. G->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12372837;Dbxref=PMID:12372837
P17612	182	214	202	202	Mutagenesis	Note=No phosphorylation. T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12372837;Dbxref=PMID:12372837
P17612	182	214	205	205	Mutagenesis	Note=Loss of allosteric regulation. Y->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18178622;Dbxref=PMID:18178622
P17612	182	214	206	206	Natural variant	ID=VAR_071707;Note=In PPNAD4%3B somatic mutation%3B the mutation results in cAMP-independent basal protein kinase activity and constitutive activation of protein kinase A. L->R;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:000
P17612	255	310	2	351	Chain	ID=PRO_0000086052;Note=cAMP-dependent protein kinase catalytic subunit alpha
P17612	255	310	44	298	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P17612	255	310	299	351	Domain	Note=AGC-kinase C-terminal
P17612	255	310	264	273	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	310	290	293	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	310	296	298	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	310	303	307	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	310	264	264	Natural variant	ID=VAR_040593;Note=S->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs35635531,PMID:17344846
P17612	255	310	278	280	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	310	282	284	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IZF
P17612	255	310	286	289	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8

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SNVs in the skipped exons for PRKACA

- 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
LIHC	TCGA-DD-A1EG-01	exon_skip_315706	14204440	14204604	14204505	14204505	Frame_Shift_Del	C	-	p.V289fs
UCEC	TCGA-BG-A0LX-01	exon_skip_315710	14208391	14208486	14208459	14208459	Frame_Shift_Del	C	-	p.V192fs
LIHC	TCGA-DD-A39Y-01	exon_skip_315713	14213628	14213726	14213686	14213686	Frame_Shift_Del	T	-	p.K93fs
ESCA	TCGA-L5-A43J-01	exon_skip_315710	14208391	14208486	14208488	14208488	Splice_Site	T	C	.
ESCA	TCGA-L5-A43J-01	exon_skip_315710	14208391	14208486	14208488	14208488	Splice_Site	T	C	e7-2

- 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
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	14204440	14204604	14204457	14204457	Missense_Mutation	C	A	p.A305S
MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	14204440	14204604	14204464	14204464	Missense_Mutation	G	T	p.D302E
MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	14204440	14204604	14204474	14204474	Missense_Mutation	G	A	p.A299V
LS180_LARGE_INTESTINE	14204440	14204604	14204520	14204520	Missense_Mutation	T	C	p.N284D
SNU1040_LARGE_INTESTINE	14204440	14204604	14204559	14204559	Missense_Mutation	G	A	p.R271W
NCIH211_LUNG	14204440	14204604	14204571	14204571	Missense_Mutation	T	G	p.K267Q
NO10_CENTRAL_NERVOUS_SYSTEM	14204440	14204604	14204596	14204597	Missense_Mutation	GA	AG	p.F258S
MFE319_ENDOMETRIUM	14208391	14208486	14208458	14208458	Missense_Mutation	A	G	p.V192A
GOS3_CENTRAL_NERVOUS_SYSTEM	14211638	14211720	14211653	14211653	Missense_Mutation	C	T	p.R135Q
U343_CENTRAL_NERVOUS_SYSTEM	14211638	14211720	14211653	14211653	Missense_Mutation	C	T	p.R135Q
RERFLCAD1_LUNG	14211638	14211720	14211681	14211681	Missense_Mutation	C	A	p.G126C
LS411N_LARGE_INTESTINE	14204440	14204604	14204547	14204547	Nonsense_Mutation	G	A	p.Q275*
SNUC1_LARGE_INTESTINE	14211638	14211720	14211665	14211665	Nonsense_Mutation	G	C	p.S131*

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

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

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

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

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RelatedDrugs for PRKACA

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
	P17612	DB12010	Fostamatinib	cAMP-dependent protein kinase catalytic subunit alpha	small molecule	approved\|investigational

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RelatedDiseases for PRKACA

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
PRKACA	C0001624	Adrenal Gland Neoplasms	1	CTD_human
PRKACA	C0206698	Cholangiocarcinoma	1	CTD_human
PRKACA	C4014425	PIGMENTED NODULAR ADRENOCORTICAL DISEASE, PRIMARY, 4	1	UNIPROT

	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

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