ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for POLA1

Gene summary

Gene information	Gene symbol	POLA1
	Gene ID	5422
	Gene name	DNA polymerase alpha 1, catalytic subunit
	Synonyms	NSX\|POLA\|p180
	Cytomap	Xp22.11-p21.3
	Type of gene	protein-coding
	Description	DNA polymerase alpha catalytic subunitDNA polymerase alpha catalytic subunit p180polymerase (DNA directed), alpha 1, catalytic subunitpolymerase (DNA) alpha 1, catalytic subunitpolymerase (DNA-directed), alpha (70kD)
	Modification date	20180523
	UniProtAcc	P09884
	Context	PubMed: POLA1 [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
POLA1	GO:0006269	DNA replication, synthesis of RNA primer	2175912
POLA1	GO:0006270	DNA replication initiation	2175912
POLA1	GO:0006272	leading strand elongation	2175912\|7910375
POLA1	GO:0006273	lagging strand elongation	2175912\|7910375
POLA1	GO:0006281	DNA repair	3335506
POLA1	GO:0008283	cell proliferation	3359994

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Exon skipping events across known transcript of Ensembl for POLA1 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 POLA1

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 POLA1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_509688	X	24717541:24717666:24721367:24721464:24722505:24722586	24721367:24721464	ENSG00000101868.6	ENST00000379059.3,ENST00000379068.3
exon_skip_509689	X	24734478:24734571:24735000:24735088:24735406:24735608	24735000:24735088	ENSG00000101868.6	ENST00000379059.3,ENST00000379068.3
exon_skip_509691	X	24742451:24742568:24744097:24744172:24745049:24745188	24744097:24744172	ENSG00000101868.6	ENST00000379059.3,ENST00000379068.3
exon_skip_509692	X	24755741:24755858:24757491:24757667:24759491:24759621	24757491:24757667	ENSG00000101868.6	ENST00000379059.3,ENST00000379068.3
exon_skip_509693	X	24759491:24759621:24760118:24760238:24761346:24761446	24760118:24760238	ENSG00000101868.6	ENST00000379059.3,ENST00000379068.3
exon_skip_509694	X	24761346:24761446:24763534:24763659:24766427:24766577	24763534:24763659	ENSG00000101868.6	ENST00000379059.3,ENST00000379068.3
exon_skip_509696	X	24766986:24767109:24793313:24793473:24828014:24828047	24793313:24793473	ENSG00000101868.6	ENST00000480125.1
exon_skip_509697	X	24861662:24861794:24906122:24906239:24948569:24948666	24906122:24906239	ENSG00000101868.6	ENST00000379059.3,ENST00000379068.3
exon_skip_509698	X	24906122:24906239:24948569:24948666:25013921:25015103	24948569:24948666	ENSG00000101868.6	ENST00000379059.3,ENST00000379068.3

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for POLA1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_509688	X	24717541:24717666:24721367:24721464:24722505:24722586	24721367:24721464	ENSG00000101868.6	ENST00000379068.3,ENST00000379059.3
exon_skip_509689	X	24734478:24734571:24735000:24735088:24735406:24735608	24735000:24735088	ENSG00000101868.6	ENST00000379068.3,ENST00000379059.3
exon_skip_509691	X	24742451:24742568:24744097:24744172:24745049:24745188	24744097:24744172	ENSG00000101868.6	ENST00000379068.3,ENST00000379059.3
exon_skip_509692	X	24755741:24755858:24757491:24757667:24759491:24759621	24757491:24757667	ENSG00000101868.6	ENST00000379068.3,ENST00000379059.3
exon_skip_509693	X	24759491:24759621:24760118:24760238:24761346:24761446	24760118:24760238	ENSG00000101868.6	ENST00000379068.3,ENST00000379059.3
exon_skip_509694	X	24761346:24761446:24763534:24763659:24766427:24766577	24763534:24763659	ENSG00000101868.6	ENST00000379068.3,ENST00000379059.3
exon_skip_509696	X	24766986:24767109:24793313:24793473:24828014:24828047	24793313:24793473	ENSG00000101868.6	ENST00000480125.1
exon_skip_509697	X	24861662:24861794:24906122:24906239:24948569:24948666	24906122:24906239	ENSG00000101868.6	ENST00000379068.3,ENST00000379059.3
exon_skip_509698	X	24906122:24906239:24948569:24948666:25013921:25015103	24948569:24948666	ENSG00000101868.6	ENST00000379068.3,ENST00000379059.3

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 POLA1

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
ENST00000379059	24721367	24721464	Frame-shift
ENST00000379059	24735000	24735088	Frame-shift
ENST00000379059	24757491	24757667	Frame-shift
ENST00000379059	24763534	24763659	Frame-shift
ENST00000379059	24948569	24948666	Frame-shift
ENST00000379059	24744097	24744172	In-frame
ENST00000379059	24760118	24760238	In-frame
ENST00000379059	24906122	24906239	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
ENST00000379059	24721367	24721464	Frame-shift
ENST00000379059	24735000	24735088	Frame-shift
ENST00000379059	24757491	24757667	Frame-shift
ENST00000379059	24763534	24763659	Frame-shift
ENST00000379059	24948569	24948666	Frame-shift
ENST00000379059	24744097	24744172	In-frame
ENST00000379059	24760118	24760238	In-frame
ENST00000379059	24906122	24906239	In-frame

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Infer the effects of exon skipping event on protein functional features for POLA1

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
ENST00000379059	5457	1462	24744097	24744172	1315	1389	433	458
ENST00000379059	5457	1462	24760118	24760238	2344	2463	776	816
ENST00000379059	5457	1462	24906122	24906239	4045	4161	1343	1382

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
ENST00000379059	5457	1462	24744097	24744172	1315	1389	433	458
ENST00000379059	5457	1462	24760118	24760238	2344	2463	776	816
ENST00000379059	5457	1462	24906122	24906239	4045	4161	1343	1382

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
P09884	433	458	431	438	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4QCL
P09884	433	458	441	445	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IUD
P09884	433	458	448	457	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4QCL
P09884	433	458	1	1462	Chain	ID=PRO_0000046428;Note=DNA polymerase alpha catalytic subunit
P09884	776	816	1	1462	Chain	ID=PRO_0000046428;Note=DNA polymerase alpha catalytic subunit
P09884	776	816	776	779	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4QCL
P09884	776	816	785	798	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4QCL
P09884	1343	1382	1346	1349	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4Y97
P09884	1343	1382	1356	1358	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4Y97
P09884	1343	1382	1359	1362	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1K18
P09884	1343	1382	1364	1367	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1N5G
P09884	1343	1382	1368	1370	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4Y97
P09884	1343	1382	1372	1383	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4Y97
P09884	1343	1382	1	1462	Chain	ID=PRO_0000046428;Note=DNA polymerase alpha catalytic subunit
P09884	1343	1382	1348	1348	Metal binding	Note=Iron-sulfur (4Fe-4S);Ontology_term=ECO:0000250;evidence=ECO:0000250
P09884	1343	1382	1353	1353	Metal binding	Note=Iron-sulfur (4Fe-4S);Ontology_term=ECO:0000250;evidence=ECO:0000250
P09884	1343	1382	1371	1371	Metal binding	Note=Iron-sulfur (4Fe-4S);Ontology_term=ECO:0000250;evidence=ECO:0000250
P09884	1343	1382	1374	1374	Metal binding	Note=Iron-sulfur (4Fe-4S);Ontology_term=ECO:0000250;evidence=ECO:0000250
P09884	1343	1382	1348	1374	Motif	Note=CysB motif
P09884	1343	1382	1245	1376	Region	Note=DNA-binding region;Ontology_term=ECO:0000255;evidence=ECO:0000255
P09884	1343	1382	1351	1353	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4Y97

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
P09884	433	458	431	438	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4QCL
P09884	433	458	441	445	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IUD
P09884	433	458	448	457	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4QCL
P09884	433	458	1	1462	Chain	ID=PRO_0000046428;Note=DNA polymerase alpha catalytic subunit
P09884	776	816	1	1462	Chain	ID=PRO_0000046428;Note=DNA polymerase alpha catalytic subunit
P09884	776	816	776	779	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4QCL
P09884	776	816	785	798	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4QCL
P09884	1343	1382	1346	1349	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4Y97
P09884	1343	1382	1356	1358	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4Y97
P09884	1343	1382	1359	1362	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1K18
P09884	1343	1382	1364	1367	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1N5G
P09884	1343	1382	1368	1370	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4Y97
P09884	1343	1382	1372	1383	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4Y97
P09884	1343	1382	1	1462	Chain	ID=PRO_0000046428;Note=DNA polymerase alpha catalytic subunit
P09884	1343	1382	1348	1348	Metal binding	Note=Iron-sulfur (4Fe-4S);Ontology_term=ECO:0000250;evidence=ECO:0000250
P09884	1343	1382	1353	1353	Metal binding	Note=Iron-sulfur (4Fe-4S);Ontology_term=ECO:0000250;evidence=ECO:0000250
P09884	1343	1382	1371	1371	Metal binding	Note=Iron-sulfur (4Fe-4S);Ontology_term=ECO:0000250;evidence=ECO:0000250
P09884	1343	1382	1374	1374	Metal binding	Note=Iron-sulfur (4Fe-4S);Ontology_term=ECO:0000250;evidence=ECO:0000250
P09884	1343	1382	1348	1374	Motif	Note=CysB motif
P09884	1343	1382	1245	1376	Region	Note=DNA-binding region;Ontology_term=ECO:0000255;evidence=ECO:0000255
P09884	1343	1382	1351	1353	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4Y97

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SNVs in the skipped exons for POLA1

- 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-A3A0-01	exon_skip_509692	24757492	24757667	24757563	24757563	Frame_Shift_Del	G	-	p.K704fs
LIHC	TCGA-DD-A3A0-01	exon_skip_509693	24760119	24760238	24760176	24760176	Frame_Shift_Del	T	-	p.F802fs
LIHC	TCGA-DD-A3A0-01	exon_skip_509693	24760119	24760238	24760224	24760224	Frame_Shift_Del	C	-	p.P818fs
PAAD	TCGA-IB-A7LX-01	exon_skip_509693	24760119	24760238	24760146	24760146	Nonsense_Mutation	G	T	p.E786X
LUAD	TCGA-55-8299-01	exon_skip_509698	24948570	24948666	24948614	24948614	Nonsense_Mutation	C	A	p.Y1403*
LUSC	TCGA-21-5784-01	exon_skip_509693	24760119	24760238	24760118	24760118	Splice_Site	G	C	p.S777_splice

- 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
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	24948570	24948666	24948651	24948653	In_Frame_Del	ACC	-	p.T1410del
BICR18_UPPER_AERODIGESTIVE_TRACT	24948570	24948666	24948651	24948653	In_Frame_Del	ACC	-	p.T1410del
MZ7MEL_SKIN	24721368	24721464	24721401	24721401	Missense_Mutation	G	A	p.D62N
HCC2998_LARGE_INTESTINE	24744098	24744172	24744109	24744109	Missense_Mutation	G	T	p.K437N
NCIH1963_LUNG	24757492	24757667	24757519	24757519	Missense_Mutation	G	A	p.A684T
PC9_LUNG	24757492	24757667	24757608	24757608	Missense_Mutation	G	C	p.Q713H
GP2D_LARGE_INTESTINE	24760119	24760238	24760191	24760191	Missense_Mutation	T	C	p.Y801H
GP5D_LARGE_INTESTINE	24760119	24760238	24760191	24760191	Missense_Mutation	T	C	p.Y801H
FTC238_THYROID	24760119	24760238	24760203	24760203	Missense_Mutation	G	T	p.D805Y
SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	24763535	24763659	24763549	24763549	Missense_Mutation	T	C	p.F855L
CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	24763535	24763659	24763649	24763649	Missense_Mutation	A	C	p.K888T
SNU175_LARGE_INTESTINE	24906123	24906239	24906154	24906154	Missense_Mutation	G	A	p.R1354H
HCC2998_LARGE_INTESTINE	24906123	24906239	24906160	24906160	Missense_Mutation	G	A	p.R1356Q
SNGM_ENDOMETRIUM	24948570	24948666	24948609	24948609	Missense_Mutation	C	T	p.R1396W
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	24948570	24948666	24948629	24948629	Missense_Mutation	G	C	p.E1402D
BICR18_UPPER_AERODIGESTIVE_TRACT	24948570	24948666	24948629	24948629	Missense_Mutation	G	C	p.E1402D
MDAMB361_BREAST	24948570	24948666	24948648	24948648	Missense_Mutation	A	G	p.T1409A
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	24744098	24744172	24744099	24744099	Splice_Site	C	T	p.P434L
BICR18_UPPER_AERODIGESTIVE_TRACT	24757492	24757667	24757492	24757492	Splice_Site	G	A	p.G675S

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for POLA1

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 POLA1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for POLA1

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RelatedDrugs for POLA1

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
	P09884	DB01073	Fludarabine	DNA polymerase alpha catalytic subunit	small molecule	approved
	P09884	DB00242	Cladribine	DNA polymerase alpha catalytic subunit	small molecule	approved\|investigational
	P09884	DB00631	Clofarabine	DNA polymerase alpha catalytic subunit	small molecule	approved\|investigational
	P09884	DB01280	Nelarabine	DNA polymerase alpha catalytic subunit	small molecule	approved\|investigational

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RelatedDiseases for POLA1

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

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