ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for PTPRN2

Gene summary

Gene information	Gene symbol	PTPRN2
	Gene ID	5799
	Gene name	protein tyrosine phosphatase receptor type N2
	Synonyms	IA-2beta\|IAR\|ICAAR\|PTPRP\|R-PTP-N2
	Cytomap	7q36.3
	Type of gene	protein-coding
	Description	receptor-type tyrosine-protein phosphatase N2IAR/receptor-like protein-tyrosine phosphataseislet cell autoantigen-related proteinphogrinprotein tyrosine phosphatase receptor piprotein tyrosine phosphatase, receptor type, N polypeptide 2tyrosine phos
	Modification date	20200313
	UniProtAcc	A0A0A0MSD7, A0A0J9YWV3, A0A3B3IU41, E7EM83, I6L9F8, Q92932,
	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 PTPRN2

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.

ENSG00000155093

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

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 PTPRN2

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_100163	chr7	158081298:158081377:158110829:158110915:158133677:158134059	158110829:158110915
exon_skip_108048	chr7	158136655:158136695:158138294:158138515:158166931:158167291	158138294:158138515
exon_skip_114395	chr7	157898673:157898737:158081298:158081377:158110829:158110915	158081298:158081377
exon_skip_118663	chr7	158205171:158205273:158316819:158316932:158489735:158489785	158316819:158316932
exon_skip_156523	chr7	157898673:157898737:158081298:158081377:158133677:158134059	158081298:158081377
exon_skip_184960	chr7	157578021:157578140:157595238:157595315:157604002:157604075	157595238:157595315
exon_skip_209065	chr7	157540337:157540446:157540718:157540785:157548946:157549019	157540718:157540785
exon_skip_213986	chr7	158316819:158316932:158489735:158489785:158587558:158587575	158489735:158489785
exon_skip_235631	chr7	158166931:158167291:158192327:158192495:158205171:158205273	158192327:158192495
exon_skip_74217	chr7	157595238:157595315:157604002:157604075:157621362:157621509	157604002:157604075

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 PTPRN2

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
ENST00000389418	157604002	157604075	Frame-shift
ENST00000389418	158081298	158081377	Frame-shift
ENST00000389418	158192327	158192495	Frame-shift
ENST00000389418	157595238	157595315	In-frame
ENST00000389418	158110829	158110915	In-frame
ENST00000389418	158138294	158138515	In-frame
ENST00000389418	158316819	158316932	In-frame
ENST00000389418	158489735	158489785	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
ENST00000389418	157604002	157604075	Frame-shift
ENST00000389418	158081298	158081377	Frame-shift
ENST00000389418	158192327	158192495	Frame-shift
ENST00000389418	158110829	158110915	In-frame
ENST00000389418	158138294	158138515	In-frame
ENST00000389418	158316819	158316932	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
ENST00000389418	157604002	157604075	Frame-shift
ENST00000389418	158192327	158192495	Frame-shift
ENST00000389418	157595238	157595315	In-frame
ENST00000389418	158110829	158110915	In-frame
ENST00000389418	158138294	158138515	In-frame
ENST00000389418	158316819	158316932	In-frame

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Infer the effects of exon skipping event on protein functional features for PTPRN2

p-ENSG00000155093_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
ENST00000389418	4723	1015	158489735	158489785	123	172	37	54
ENST00000389418	4723	1015	158316819	158316932	174	286	54	92
ENST00000389418	4723	1015	158138294	158138515	921	1141	303	377
ENST00000389418	4723	1015	158110829	158110915	1567	1652	519	547
ENST00000389418	4723	1015	157595238	157595315	2429	2505	806	831

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
ENST00000389418	4723	1015	158316819	158316932	174	286	54	92
ENST00000389418	4723	1015	158138294	158138515	921	1141	303	377
ENST00000389418	4723	1015	158110829	158110915	1567	1652	519	547

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
ENST00000389418	4723	1015	158316819	158316932	174	286	54	92
ENST00000389418	4723	1015	158138294	158138515	921	1141	303	377
ENST00000389418	4723	1015	158110829	158110915	1567	1652	519	547
ENST00000389418	4723	1015	157595238	157595315	2429	2505	806	831

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
Q92932	37	54	1	37	Alternative sequence	ID=VSP_035264;Note=In isoform 3. MGPPLPLLLLLLLLLPPRVLPAAPSSVPRGRQLPGRL->MAVESEYSLLRTEASFPTMKMFCVSHTLPRVEVMFVSGPQTRERTEPVDPRWQCLVQMWA;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:9205841;Dbxref=PMID:9205841
Q92932	37	54	38	54	Alternative sequence	ID=VSP_045032;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.4
Q92932	37	54	22	1015	Chain	ID=PRO_0000025454;Note=Receptor-type tyrosine-protein phosphatase N2
Q92932	37	54	1	421	Region	Note=Involved in localization to secretory granules%3B interaction with CPE;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P80560
Q92932	37	54	22	615	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q92932	54	92	38	54	Alternative sequence	ID=VSP_045032;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.4
Q92932	54	92	22	1015	Chain	ID=PRO_0000025454;Note=Receptor-type tyrosine-protein phosphatase N2
Q92932	54	92	1	421	Region	Note=Involved in localization to secretory granules%3B interaction with CPE;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P80560
Q92932	54	92	22	615	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q92932	303	377	22	1015	Chain	ID=PRO_0000025454;Note=Receptor-type tyrosine-protein phosphatase N2
Q92932	303	377	325	325	Natural variant	ID=VAR_020302;Note=S->N;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:8954911,ECO:0000269\|Ref.4;Dbxref=dbSNP:rs1130499,PMID:8954911
Q92932	303	377	343	343	Natural variant	ID=VAR_022015;Note=V->M;Dbxref=dbSNP:rs3752368
Q92932	303	377	1	421	Region	Note=Involved in localization to secretory granules%3B interaction with CPE;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P80560
Q92932	303	377	323	323	Sequence conflict	Note=G->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q92932	303	377	22	615	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q92932	519	547	519	547	Alternative sequence	ID=VSP_007779;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q92932	519	547	544	550	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4HTI
Q92932	519	547	22	1015	Chain	ID=PRO_0000025454;Note=Receptor-type tyrosine-protein phosphatase N2
Q92932	519	547	502	1015	Chain	ID=PRO_0000438088;Note=IA-2beta60;Ontology_term=ECO:0000250,ECO:0000250;evidence=ECO:0000250\|UniProtKB:P80560,ECO:0000250\|UniProtKB:Q63475
Q92932	519	547	523	536	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4HTI
Q92932	519	547	541	543	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4HTI
Q92932	519	547	22	615	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q92932	806	831	802	806	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2QEP
Q92932	806	831	811	813	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2QEP
Q92932	806	831	815	819	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2QEP
Q92932	806	831	22	1015	Chain	ID=PRO_0000025454;Note=Receptor-type tyrosine-protein phosphatase N2
Q92932	806	831	502	1015	Chain	ID=PRO_0000438088;Note=IA-2beta60;Ontology_term=ECO:0000250,ECO:0000250;evidence=ECO:0000250\|UniProtKB:P80560,ECO:0000250\|UniProtKB:Q63475
Q92932	806	831	745	1005	Domain	Note=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00160
Q92932	806	831	824	826	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2QEP
Q92932	806	831	827	836	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2QEP
Q92932	806	831	637	1015	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255

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
Q92932	54	92	38	54	Alternative sequence	ID=VSP_045032;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.4
Q92932	54	92	22	1015	Chain	ID=PRO_0000025454;Note=Receptor-type tyrosine-protein phosphatase N2
Q92932	54	92	1	421	Region	Note=Involved in localization to secretory granules%3B interaction with CPE;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P80560
Q92932	54	92	22	615	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q92932	303	377	22	1015	Chain	ID=PRO_0000025454;Note=Receptor-type tyrosine-protein phosphatase N2
Q92932	303	377	325	325	Natural variant	ID=VAR_020302;Note=S->N;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:8954911,ECO:0000269\|Ref.4;Dbxref=dbSNP:rs1130499,PMID:8954911
Q92932	303	377	343	343	Natural variant	ID=VAR_022015;Note=V->M;Dbxref=dbSNP:rs3752368
Q92932	303	377	1	421	Region	Note=Involved in localization to secretory granules%3B interaction with CPE;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P80560
Q92932	303	377	323	323	Sequence conflict	Note=G->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q92932	303	377	22	615	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q92932	519	547	519	547	Alternative sequence	ID=VSP_007779;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q92932	519	547	544	550	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4HTI
Q92932	519	547	22	1015	Chain	ID=PRO_0000025454;Note=Receptor-type tyrosine-protein phosphatase N2
Q92932	519	547	502	1015	Chain	ID=PRO_0000438088;Note=IA-2beta60;Ontology_term=ECO:0000250,ECO:0000250;evidence=ECO:0000250\|UniProtKB:P80560,ECO:0000250\|UniProtKB:Q63475
Q92932	519	547	523	536	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4HTI
Q92932	519	547	541	543	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4HTI
Q92932	519	547	22	615	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

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
Q92932	54	92	38	54	Alternative sequence	ID=VSP_045032;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.4
Q92932	54	92	22	1015	Chain	ID=PRO_0000025454;Note=Receptor-type tyrosine-protein phosphatase N2
Q92932	54	92	1	421	Region	Note=Involved in localization to secretory granules%3B interaction with CPE;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P80560
Q92932	54	92	22	615	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q92932	303	377	22	1015	Chain	ID=PRO_0000025454;Note=Receptor-type tyrosine-protein phosphatase N2
Q92932	303	377	325	325	Natural variant	ID=VAR_020302;Note=S->N;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:8954911,ECO:0000269\|Ref.4;Dbxref=dbSNP:rs1130499,PMID:8954911
Q92932	303	377	343	343	Natural variant	ID=VAR_022015;Note=V->M;Dbxref=dbSNP:rs3752368
Q92932	303	377	1	421	Region	Note=Involved in localization to secretory granules%3B interaction with CPE;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P80560
Q92932	303	377	323	323	Sequence conflict	Note=G->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q92932	303	377	22	615	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q92932	519	547	519	547	Alternative sequence	ID=VSP_007779;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q92932	519	547	544	550	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4HTI
Q92932	519	547	22	1015	Chain	ID=PRO_0000025454;Note=Receptor-type tyrosine-protein phosphatase N2
Q92932	519	547	502	1015	Chain	ID=PRO_0000438088;Note=IA-2beta60;Ontology_term=ECO:0000250,ECO:0000250;evidence=ECO:0000250\|UniProtKB:P80560,ECO:0000250\|UniProtKB:Q63475
Q92932	519	547	523	536	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4HTI
Q92932	519	547	541	543	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4HTI
Q92932	519	547	22	615	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q92932	806	831	802	806	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2QEP
Q92932	806	831	811	813	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2QEP
Q92932	806	831	815	819	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2QEP
Q92932	806	831	22	1015	Chain	ID=PRO_0000025454;Note=Receptor-type tyrosine-protein phosphatase N2
Q92932	806	831	502	1015	Chain	ID=PRO_0000438088;Note=IA-2beta60;Ontology_term=ECO:0000250,ECO:0000250;evidence=ECO:0000250\|UniProtKB:P80560,ECO:0000250\|UniProtKB:Q63475
Q92932	806	831	745	1005	Domain	Note=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00160
Q92932	806	831	824	826	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2QEP
Q92932	806	831	827	836	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2QEP
Q92932	806	831	637	1015	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255

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3'-UTR located exon skipping events that lost miRNA binding sites in PTPRN2

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 PTPRN2

- 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 PTPRN2

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 PTPRN2

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
HCC	exon_skip_100163	rs10228083	chr7:158119521	5.399209e-08	1.141351e-05
DLPFC	exon_skip_100163	rs10228083	chr7:158119521	4.574103e-05	4.280515e-03

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Correlation with RNA binding proteins (RBPs) for PTPRN2

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for PTPRN2

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 PTPRN2

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 PTPRN2

Gene structures and expression levels for PTPRN2

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PTPRN2

Open reading frame (ORF) annotation in the exon skipping event for PTPRN2

Infer the effects of exon skipping event on protein functional features for PTPRN2

3'-UTR located exon skipping events that lost miRNA binding sites in PTPRN2

SNVs in the skipped exons for PTPRN2

AD stage-associated exon skippint events for PTPRN2

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PTPRN2

Correlation with RNA binding proteins (RBPs) for PTPRN2

RelatedDrugs for PTPRN2

RelatedDiseases for PTPRN2