ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for PMS2

Gene summary

Gene information	Gene symbol	PMS2
	Gene ID	5395
	Gene name	PMS1 homolog 2, mismatch repair system component
	Synonyms	HNPCC4\|MLH4\|PMS2CL\|PMSL2
	Cytomap	7p22.1
	Type of gene	protein-coding
	Description	mismatch repair endonuclease PMS2DNA mismatch repair protein PMS2PMS1 homolog 2, mismatch repair proteinPMS1 protein homolog 2PMS2 postmeiotic segregation increased 2postmeiotic segregation increased 2 nirs variant 6
	Modification date	20200327
	UniProtAcc	A0A2R8Y6S3, A5YRY4, C9J167, P54278, Q5FBW7, Q5FBW8, Q5FBX0,
	Context

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene	GO ID	GO term	PubMed ID
PMS2	GO:0006298	mismatch repair	10871409\|23709753

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Gene structures and expression levels for PMS2

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.

ENSG00000122512

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
DLPFC	DOWN	ENST00000642456.1	PMS2-209:protein_coding:PMS2	2.556397e+01	-8.625930e-01	1.683919e-03	4.717837e-02
TC	UP	ENST00000300069.5	RBPMS2-201:protein_coding:RBPMS2	3.232206e+01	9.659685e-01	1.037210e-06	4.147512e-05

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 PMS2

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_1038	chr7	5978596:5978696:5982824:5982991:5986759:5987620	5982824:5982991
exon_skip_123120	chr7	5997326:5997423:5999108:5999275:6002453:6002636	5999108:5999275
exon_skip_123801	chr7	5977588:5977757:5978596:5978696:5982824:5982991	5978596:5978696
exon_skip_137908	chr7	5997326:5997423:5999108:5999226:6002453:6002636	5999108:5999226
exon_skip_152256	chr7	5987087:5987620:5989800:5989955:5991973:5992057	5989800:5989955
exon_skip_202443	chr7	6003972:6004058:6005892:6006031:6008997:6009097	6005892:6006031
exon_skip_237393	chr7	5999108:5999226:6002453:6002636:6003690:6003792	6002453:6002636
exon_skip_247174	chr7	5982824:5982991:5986759:5987620:5989800:5989955	5986759:5987620
exon_skip_253947	chr7	5999108:5999275:6002453:6002636:6003972:6004006	6002453:6002636
exon_skip_268625	chr7	6003972:6004058:6005892:6006026:6008997:6009097	6005892:6006026
exon_skip_287890	chr7	5987411:5987620:5989800:5989955:5991973:5992057	5989800:5989955
exon_skip_33868	chr7	5991973:5992057:5995534:5995633:5997326:5997423	5995534:5995633
exon_skip_61610	chr7	6002453:6002636:6003690:6003792:6003972:6004006	6003690:6003792

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 PMS2

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
ENST00000265849	5978596	5978696	Frame-shift
ENST00000265849	5986759	5987620	Frame-shift
ENST00000265849	5995534	5995633	Frame-shift
ENST00000265849	6003690	6003792	Frame-shift
ENST00000265849	5989800	5989955	In-frame
ENST00000265849	5999108	5999275	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
ENST00000265849	5978596	5978696	Frame-shift
ENST00000265849	5995534	5995633	Frame-shift
ENST00000265849	6003690	6003792	Frame-shift
ENST00000265849	5989800	5989955	In-frame
ENST00000265849	5999108	5999275	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
ENST00000265849	5978596	5978696	Frame-shift
ENST00000265849	5986759	5987620	Frame-shift
ENST00000265849	5995534	5995633	Frame-shift
ENST00000265849	6003690	6003792	Frame-shift
ENST00000265849	5982824	5982991	In-frame
ENST00000265849	5989800	5989955	In-frame
ENST00000265849	5999108	5999275	In-frame

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Infer the effects of exon skipping event on protein functional features for PMS2

p-ENSG00000122512_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
ENST00000265849	2872	862	5999108	5999275	644	810	179	234
ENST00000265849	2872	862	5989800	5989955	1095	1249	329	381

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
ENST00000265849	2872	862	5999108	5999275	644	810	179	234
ENST00000265849	2872	862	5989800	5989955	1095	1249	329	381

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
ENST00000265849	2872	862	5999108	5999275	644	810	179	234
ENST00000265849	2872	862	5989800	5989955	1095	1249	329	381
ENST00000265849	2872	862	5982824	5982991	2113	2279	669	724

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
P54278	179	234	180	183	Alternative sequence	ID=VSP_029384;Note=In isoform 4. EYAK->QASV;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
P54278	179	234	184	862	Alternative sequence	ID=VSP_029385;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
P54278	179	234	199	205	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	179	234	211	216	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	179	234	1	862	Chain	ID=PRO_0000178005;Note=Mismatch repair endonuclease PMS2
P54278	179	234	177	194	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	179	234	223	231	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	179	234	233	237	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	179	234	182	182	Natural variant	ID=VAR_078523;Note=In HNPCC4%3B unknown pathological significance. A->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16619239;Dbxref=dbSNP:rs587779341,PMID:16619239
P54278	179	234	205	205	Natural variant	ID=VAR_078524;Note=In MMRCS and HNPCC4%3B unknown pathological significance%3B normal DNA mismatch repair activity. Q->P;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:18602922,ECO:0000269\|PubMed:24027009,ECO:0000269\|PubMed:
P54278	179	234	207	207	Natural variant	ID=VAR_078525;Note=In HNPCC4%3B unknown pathological significance%3B normal DNA mismatch repair activity. G->E;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:19479271,ECO:0000269\|PubMed:24027009;Dbxref=dbSNP:rs374704824,PMID:19479271,PM
P54278	329	381	184	862	Alternative sequence	ID=VSP_029385;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
P54278	329	381	269	669	Alternative sequence	ID=VSP_029386;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
P54278	329	381	332	334	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	329	381	343	345	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	329	381	1	862	Chain	ID=PRO_0000178005;Note=Mismatch repair endonuclease PMS2
P54278	329	381	329	331	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	329	381	348	363	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S

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
P54278	179	234	180	183	Alternative sequence	ID=VSP_029384;Note=In isoform 4. EYAK->QASV;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
P54278	179	234	184	862	Alternative sequence	ID=VSP_029385;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
P54278	179	234	199	205	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	179	234	211	216	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	179	234	1	862	Chain	ID=PRO_0000178005;Note=Mismatch repair endonuclease PMS2
P54278	179	234	177	194	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	179	234	223	231	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	179	234	233	237	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	179	234	182	182	Natural variant	ID=VAR_078523;Note=In HNPCC4%3B unknown pathological significance. A->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16619239;Dbxref=dbSNP:rs587779341,PMID:16619239
P54278	179	234	205	205	Natural variant	ID=VAR_078524;Note=In MMRCS and HNPCC4%3B unknown pathological significance%3B normal DNA mismatch repair activity. Q->P;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:18602922,ECO:0000269\|PubMed:24027009,ECO:0000269\|PubMed:
P54278	179	234	207	207	Natural variant	ID=VAR_078525;Note=In HNPCC4%3B unknown pathological significance%3B normal DNA mismatch repair activity. G->E;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:19479271,ECO:0000269\|PubMed:24027009;Dbxref=dbSNP:rs374704824,PMID:19479271,PM
P54278	329	381	184	862	Alternative sequence	ID=VSP_029385;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
P54278	329	381	269	669	Alternative sequence	ID=VSP_029386;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
P54278	329	381	332	334	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	329	381	343	345	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	329	381	1	862	Chain	ID=PRO_0000178005;Note=Mismatch repair endonuclease PMS2
P54278	329	381	329	331	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	329	381	348	363	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S

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
P54278	179	234	180	183	Alternative sequence	ID=VSP_029384;Note=In isoform 4. EYAK->QASV;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
P54278	179	234	184	862	Alternative sequence	ID=VSP_029385;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
P54278	179	234	199	205	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	179	234	211	216	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	179	234	1	862	Chain	ID=PRO_0000178005;Note=Mismatch repair endonuclease PMS2
P54278	179	234	177	194	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	179	234	223	231	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	179	234	233	237	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	179	234	182	182	Natural variant	ID=VAR_078523;Note=In HNPCC4%3B unknown pathological significance. A->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16619239;Dbxref=dbSNP:rs587779341,PMID:16619239
P54278	179	234	205	205	Natural variant	ID=VAR_078524;Note=In MMRCS and HNPCC4%3B unknown pathological significance%3B normal DNA mismatch repair activity. Q->P;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:18602922,ECO:0000269\|PubMed:24027009,ECO:0000269\|PubMed:
P54278	179	234	207	207	Natural variant	ID=VAR_078525;Note=In HNPCC4%3B unknown pathological significance%3B normal DNA mismatch repair activity. G->E;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:19479271,ECO:0000269\|PubMed:24027009;Dbxref=dbSNP:rs374704824,PMID:19479271,PM
P54278	329	381	184	862	Alternative sequence	ID=VSP_029385;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
P54278	329	381	269	669	Alternative sequence	ID=VSP_029386;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
P54278	329	381	332	334	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	329	381	343	345	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	329	381	1	862	Chain	ID=PRO_0000178005;Note=Mismatch repair endonuclease PMS2
P54278	329	381	329	331	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	329	381	348	363	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H7S
P54278	669	724	184	862	Alternative sequence	ID=VSP_029385;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
P54278	669	724	269	669	Alternative sequence	ID=VSP_029386;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
P54278	669	724	573	862	Alternative sequence	ID=VSP_029388;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
P54278	669	724	1	862	Chain	ID=PRO_0000178005;Note=Mismatch repair endonuclease PMS2
P54278	669	724	699	699	Natural variant	ID=VAR_079819;Note=Polymorphism%3B no effect on protein levels. D->H;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28494185;Dbxref=dbSNP:rs587781317,PMID:28494185
P54278	669	724	705	705	Natural variant	ID=VAR_012974;Note=In MMRCS and HNPCC4%3B decreases DNA mismatch repair activity. E->K;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:18602922,ECO:0000269\|PubMed:24027009,ECO:0000269\|PubMed:9419979;Dbxref=dbSNP:rs267608161,P

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3'-UTR located exon skipping events that lost miRNA binding sites in PMS2

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 PMS2

- 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 PMS2

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 PMS2

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
HCC	exon_skip_202443	rs10487932	chr7:6027388	5.165038e-04	3.478650e-02
HCC	exon_skip_202443	rs10487933	chr7:6027612	5.165038e-04	3.478650e-02

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Correlation with RNA binding proteins (RBPs) for PMS2

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	CNOT4	exon_skip_61610	-5.321106e-01	1.118886e-11
CB	TRA2A	exon_skip_61610	-5.608746e-01	4.712992e-13
CB	HNRNPA2B1	exon_skip_61610	-5.214891e-01	3.347206e-11
CB	RBM45	exon_skip_61610	5.639478e-01	3.299189e-13
CB	RBM23	exon_skip_61610	-4.085018e-01	4.938991e-07
IFG	HNRNPF	exon_skip_61610	-4.197733e-01	3.276887e-02

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RelatedDrugs for PMS2

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 PMS2

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 PMS2

Gene structures and expression levels for PMS2

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PMS2

Open reading frame (ORF) annotation in the exon skipping event for PMS2

Infer the effects of exon skipping event on protein functional features for PMS2

3'-UTR located exon skipping events that lost miRNA binding sites in PMS2

SNVs in the skipped exons for PMS2

AD stage-associated exon skippint events for PMS2

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PMS2

Correlation with RNA binding proteins (RBPs) for PMS2

RelatedDrugs for PMS2

RelatedDiseases for PMS2