ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for PTPN11

Gene summary

Gene information	Gene symbol	PTPN11
	Gene ID	5781
	Gene name	protein tyrosine phosphatase non-receptor type 11
	Synonyms	BPTP3\|CFC\|JMML\|METCDS\|NS1\|PTP-1D\|PTP2C\|SH-PTP2\|SH-PTP3\|SHP2
	Cytomap	12q24.13
	Type of gene	protein-coding
	Description	tyrosine-protein phosphatase non-receptor type 11protein-tyrosine phosphatase 1Dprotein-tyrosine phosphatase 2C
	Modification date	20200329
	UniProtAcc	A0A0U1RRI0, A0A1W2PPU4, A0A3G1LBG2, B3GUD3, B3GUD4, B3GUD5, H0YF12, Q06124, Q96I26,
	Context

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

Gene	GO ID	GO term	PubMed ID
PTPN11	GO:0035335	peptidyl-tyrosine dephosphorylation	15133037
PTPN11	GO:0038127	ERBB signaling pathway	15133037
PTPN11	GO:0043254	regulation of protein complex assembly	7493946
PTPN11	GO:0046326	positive regulation of glucose import	7493946
PTPN11	GO:0046628	positive regulation of insulin receptor signaling pathway	7493946
PTPN11	GO:0048013	ephrin receptor signaling pathway	10655584

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Gene structures and expression levels for PTPN11

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.

ENSG00000179295

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 PTPN11

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_140310	chr12	112482074:112482205:112486475:112486629:112488443:112488510	112486475:112486629
exon_skip_151337	chr12	112450321:112450512:112453195:112453387:112454564:112454680	112453195:112453387
exon_skip_165089	chr12	112477932:112478015:112482074:112482205:112486475:112486629	112482074:112482205
exon_skip_173032	chr12	112502144:112502256:112504695:112504796:112505825:112509913	112504695:112504796
exon_skip_191182	chr12	112482074:112482205:112486463:112486629:112488443:112488510	112486463:112486629
exon_skip_239265	chr12	112502144:112502256:112504695:112504796:112505825:112505888	112504695:112504796
exon_skip_245462	chr12	112454564:112454680:112455950:112456063:112472944:112473040	112455950:112456063
exon_skip_288720	chr12	112446276:112446398:112450318:112450512:112453195:112453387	112450318:112450512
exon_skip_290989	chr12	112489024:112489175:112502144:112502256:112504695:112504764	112502144:112502256
exon_skip_4372	chr12	112482074:112482205:112486454:112486629:112488443:112488510	112486454:112486629
exon_skip_7367	chr12	112419112:112419125:112446276:112446398:112450318:112450512	112446276:112446398

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 PTPN11

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
ENST00000635625	112453195	112453387	Frame-shift
ENST00000635625	112486463	112486629	Frame-shift
ENST00000635625	112446276	112446398	In-frame
ENST00000635625	112450318	112450512	In-frame
ENST00000635625	112455950	112456063	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
ENST00000635625	112486463	112486629	Frame-shift
ENST00000635625	112450318	112450512	In-frame
ENST00000635625	112455950	112456063	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
ENST00000635625	112453195	112453387	Frame-shift
ENST00000635625	112486463	112486629	Frame-shift
ENST00000635625	112502144	112502256	Frame-shift
ENST00000635625	112446276	112446398	In-frame
ENST00000635625	112455950	112456063	In-frame

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Infer the effects of exon skipping event on protein functional features for PTPN11

p-ENSG00000179295_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
ENST00000635625	1811	597	112446276	112446398	16	137	5	45
ENST00000635625	1811	597	112450318	112450512	139	332	46	110
ENST00000635625	1811	597	112455950	112456063	644	756	214	252

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
ENST00000635625	1811	597	112450318	112450512	139	332	46	110
ENST00000635625	1811	597	112455950	112456063	644	756	214	252

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
ENST00000635625	1811	597	112446276	112446398	16	137	5	45
ENST00000635625	1811	597	112455950	112456063	644	756	214	252

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
Q06124	5	45	28	33	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	5	45	35	37	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	5	45	41	47	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	5	45	2	597	Chain	ID=PRO_0000094767;Note=Tyrosine-protein phosphatase non-receptor type 11
Q06124	5	45	6	102	Domain	Note=SH2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00191
Q06124	5	45	13	23	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	5	45	42	42	Natural variant	ID=VAR_015601;Note=In NS1. T->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12960218;Dbxref=dbSNP:rs397507501,PMID:11992261,PMID:12960218
Q06124	5	45	4	6	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5X7B
Q06124	46	110	41	47	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	46	110	50	57	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	46	110	59	61	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	46	110	63	65	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	46	110	70	73	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	46	110	83	85	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4OHD
Q06124	46	110	87	90	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3TKZ
Q06124	46	110	91	93	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NWG
Q06124	46	110	2	597	Chain	ID=PRO_0000094767;Note=Tyrosine-protein phosphatase non-receptor type 11
Q06124	46	110	6	102	Domain	Note=SH2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00191
Q06124	46	110	74	82	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	46	110	107	109	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4DGX
Q06124	46	110	62	62	Modified residue	Note=Phosphotyrosine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19690332;Dbxref=PMID:19690332
Q06124	46	110	66	66	Modified residue	Note=Phosphotyrosine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P35235
Q06124	46	110	58	58	Natural variant	ID=VAR_027184;Note=In NS1. N->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12634870;Dbxref=dbSNP:rs397507506,PMID:12634870
Q06124	46	110	59	59	Natural variant	ID=VAR_066060;Note=In NS1. T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:19020799;Dbxref=dbSNP:rs886043790,PMID:19020799
Q06124	46	110	60	60	Natural variant	ID=VAR_015602;Note=In NS1. G->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11992261;Dbxref=dbSNP:rs397507509,PMID:11992261
Q06124	46	110	60	60	Natural variant	ID=VAR_015990;Note=In myelodysplastic syndrome. G->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs397507509,PMID:12717436
Q06124	46	110	61	61	Natural variant	ID=VAR_015603;Note=In NS1. D->G;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11704759,ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12161469,ECO:0000269\|PubMed:12634870;Dbxref=dbSNP:rs121918461,PMID:11704759,P
Q06124	46	110	61	61	Natural variant	ID=VAR_015604;Note=In NS1. D->N;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12634870;Dbxref=dbSNP:rs397507510,PMID:11992261,PMID:12634870
Q06124	46	110	61	61	Natural variant	ID=VAR_015991;Note=In JMML%3B also in myelodysplastic syndrome. D->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs121918461,PMID:12717436
Q06124	46	110	61	61	Natural variant	ID=VAR_015992;Note=In JMML. D->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs397507510,PMID:12717436
Q06124	46	110	62	62	Natural variant	ID=VAR_015605;Note=In NS1%3B also in Noonan patients manifesting juvenile myelomonocytic leukemia. Y->D;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12325025,ECO:0000269\|PubMed:12717
Q06124	46	110	63	63	Natural variant	ID=VAR_015606;Note=In NS1. Y->C;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11704759,ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12161469,ECO:0000269\|PubMed:12325025,ECO:0000269\|PubM
Q06124	46	110	69	69	Natural variant	ID=VAR_015993;Note=In JMML%3B also in myelodysplastic syndrome. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs397507511,PMID:12717436
Q06124	46	110	69	69	Natural variant	ID=VAR_027185;Note=In NS1. E->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12634870;Dbxref=dbSNP:rs397507511,PMID:12634870
Q06124	46	110	71	71	Natural variant	ID=VAR_015994;Note=In acute myeloid leukemia%3B requires 2 nucleotide substitutions. F->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=PMID:12717436
Q06124	46	110	71	71	Natural variant	ID=VAR_015995;Note=In myelodysplastic syndrome. F->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12634870,ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs397507512,PMID:12634870,PMID:12717436
Q06124	46	110	72	72	Natural variant	ID=VAR_015607;Note=In NS1. A->G;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11704759,ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12960218;Dbxref=dbSNP:rs121918454,PMID:11704759,PMID:11992261,PMID:12960218
Q06124	46	110	72	72	Natural variant	ID=VAR_015608;Note=In NS1. A->S;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11704759,ECO:0000269\|PubMed:12161469,ECO:0000269\|PubMed:12634870;Dbxref=dbSNP:rs121918453,PMID:11704759,PMID:12161469,PMID:12634870
Q06124	46	110	72	72	Natural variant	ID=VAR_015996;Note=In JMML. A->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs121918453,PMID:12717436
Q06124	46	110	72	72	Natural variant	ID=VAR_015997;Note=In JMML. A->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs121918454,PMID:12717436
Q06124	46	110	73	73	Natural variant	ID=VAR_015609;Note=In NS1%3B also in Noonan patients manifesting juvenile myelomonocytic leukemia. T->I;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12161469,ECO:0000269\|PubMed:12634
Q06124	46	110	76	76	Natural variant	ID=VAR_015998;Note=In JMML%3B also in myelodysplastic syndrome. E->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs121918465,PMID:12717436
Q06124	46	110	76	76	Natural variant	ID=VAR_015610;Note=In NS1. E->D;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11704759,ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12634870;Dbxref=dbSNP:rs397507514,PMID:11704759,PMID:11992261,PMID:12634870
Q06124	46	110	76	76	Natural variant	ID=VAR_015999;Note=In JMML. E->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs121918465,PMID:12717436
Q06124	46	110	76	76	Natural variant	ID=VAR_016000;Note=In JMML%3B increases protein tyrosine phosphatase activity against CDC73. E->K;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12717436,ECO:0000269\|PubMed:26742426;Dbxref=dbSNP:rs121918464,PMID:12717436,PMID:26742426
Q06124	46	110	76	76	Natural variant	ID=VAR_016001;Note=In JMML. E->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs121918465,PMID:12717436
Q06124	46	110	79	79	Natural variant	ID=VAR_027186;Note=In NS1. Q->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12960218;Dbxref=PMID:12960218
Q06124	46	110	79	79	Natural variant	ID=VAR_015611;Note=In NS1. Q->R;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11704759,ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12529711,ECO:0000269\|PubMed:12634870;Dbxref=dbSNP:rs121918466,PMID:11704759,P
Q06124	46	110	106	106	Natural variant	ID=VAR_015612;Note=In NS1. D->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12960218;Dbxref=dbSNP:rs397507517,PMID:11992261,PMID:12960218
Q06124	214	252	218	222	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4OHD
Q06124	214	252	2	597	Chain	ID=PRO_0000094767;Note=Tyrosine-protein phosphatase non-receptor type 11
Q06124	214	252	112	216	Domain	Note=SH2 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00191
Q06124	214	252	247	521	Domain	Note=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00160
Q06124	214	252	223	225	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	214	252	226	234	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	214	252	251	253	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3ZM1

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
Q06124	46	110	41	47	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	46	110	50	57	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	46	110	59	61	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	46	110	63	65	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	46	110	70	73	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	46	110	83	85	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4OHD
Q06124	46	110	87	90	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3TKZ
Q06124	46	110	91	93	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NWG
Q06124	46	110	2	597	Chain	ID=PRO_0000094767;Note=Tyrosine-protein phosphatase non-receptor type 11
Q06124	46	110	6	102	Domain	Note=SH2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00191
Q06124	46	110	74	82	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	46	110	107	109	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4DGX
Q06124	46	110	62	62	Modified residue	Note=Phosphotyrosine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19690332;Dbxref=PMID:19690332
Q06124	46	110	66	66	Modified residue	Note=Phosphotyrosine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P35235
Q06124	46	110	58	58	Natural variant	ID=VAR_027184;Note=In NS1. N->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12634870;Dbxref=dbSNP:rs397507506,PMID:12634870
Q06124	46	110	59	59	Natural variant	ID=VAR_066060;Note=In NS1. T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:19020799;Dbxref=dbSNP:rs886043790,PMID:19020799
Q06124	46	110	60	60	Natural variant	ID=VAR_015602;Note=In NS1. G->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11992261;Dbxref=dbSNP:rs397507509,PMID:11992261
Q06124	46	110	60	60	Natural variant	ID=VAR_015990;Note=In myelodysplastic syndrome. G->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs397507509,PMID:12717436
Q06124	46	110	61	61	Natural variant	ID=VAR_015603;Note=In NS1. D->G;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11704759,ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12161469,ECO:0000269\|PubMed:12634870;Dbxref=dbSNP:rs121918461,PMID:11704759,P
Q06124	46	110	61	61	Natural variant	ID=VAR_015604;Note=In NS1. D->N;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12634870;Dbxref=dbSNP:rs397507510,PMID:11992261,PMID:12634870
Q06124	46	110	61	61	Natural variant	ID=VAR_015991;Note=In JMML%3B also in myelodysplastic syndrome. D->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs121918461,PMID:12717436
Q06124	46	110	61	61	Natural variant	ID=VAR_015992;Note=In JMML. D->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs397507510,PMID:12717436
Q06124	46	110	62	62	Natural variant	ID=VAR_015605;Note=In NS1%3B also in Noonan patients manifesting juvenile myelomonocytic leukemia. Y->D;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12325025,ECO:0000269\|PubMed:12717
Q06124	46	110	63	63	Natural variant	ID=VAR_015606;Note=In NS1. Y->C;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11704759,ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12161469,ECO:0000269\|PubMed:12325025,ECO:0000269\|PubM
Q06124	46	110	69	69	Natural variant	ID=VAR_015993;Note=In JMML%3B also in myelodysplastic syndrome. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs397507511,PMID:12717436
Q06124	46	110	69	69	Natural variant	ID=VAR_027185;Note=In NS1. E->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12634870;Dbxref=dbSNP:rs397507511,PMID:12634870
Q06124	46	110	71	71	Natural variant	ID=VAR_015994;Note=In acute myeloid leukemia%3B requires 2 nucleotide substitutions. F->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=PMID:12717436
Q06124	46	110	71	71	Natural variant	ID=VAR_015995;Note=In myelodysplastic syndrome. F->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12634870,ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs397507512,PMID:12634870,PMID:12717436
Q06124	46	110	72	72	Natural variant	ID=VAR_015607;Note=In NS1. A->G;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11704759,ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12960218;Dbxref=dbSNP:rs121918454,PMID:11704759,PMID:11992261,PMID:12960218
Q06124	46	110	72	72	Natural variant	ID=VAR_015608;Note=In NS1. A->S;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11704759,ECO:0000269\|PubMed:12161469,ECO:0000269\|PubMed:12634870;Dbxref=dbSNP:rs121918453,PMID:11704759,PMID:12161469,PMID:12634870
Q06124	46	110	72	72	Natural variant	ID=VAR_015996;Note=In JMML. A->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs121918453,PMID:12717436
Q06124	46	110	72	72	Natural variant	ID=VAR_015997;Note=In JMML. A->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs121918454,PMID:12717436
Q06124	46	110	73	73	Natural variant	ID=VAR_015609;Note=In NS1%3B also in Noonan patients manifesting juvenile myelomonocytic leukemia. T->I;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12161469,ECO:0000269\|PubMed:12634
Q06124	46	110	76	76	Natural variant	ID=VAR_015998;Note=In JMML%3B also in myelodysplastic syndrome. E->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs121918465,PMID:12717436
Q06124	46	110	76	76	Natural variant	ID=VAR_015610;Note=In NS1. E->D;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11704759,ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12634870;Dbxref=dbSNP:rs397507514,PMID:11704759,PMID:11992261,PMID:12634870
Q06124	46	110	76	76	Natural variant	ID=VAR_015999;Note=In JMML. E->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs121918465,PMID:12717436
Q06124	46	110	76	76	Natural variant	ID=VAR_016000;Note=In JMML%3B increases protein tyrosine phosphatase activity against CDC73. E->K;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12717436,ECO:0000269\|PubMed:26742426;Dbxref=dbSNP:rs121918464,PMID:12717436,PMID:26742426
Q06124	46	110	76	76	Natural variant	ID=VAR_016001;Note=In JMML. E->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12717436;Dbxref=dbSNP:rs121918465,PMID:12717436
Q06124	46	110	79	79	Natural variant	ID=VAR_027186;Note=In NS1. Q->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12960218;Dbxref=PMID:12960218
Q06124	46	110	79	79	Natural variant	ID=VAR_015611;Note=In NS1. Q->R;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11704759,ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12529711,ECO:0000269\|PubMed:12634870;Dbxref=dbSNP:rs121918466,PMID:11704759,P
Q06124	46	110	106	106	Natural variant	ID=VAR_015612;Note=In NS1. D->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12960218;Dbxref=dbSNP:rs397507517,PMID:11992261,PMID:12960218
Q06124	214	252	218	222	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4OHD
Q06124	214	252	2	597	Chain	ID=PRO_0000094767;Note=Tyrosine-protein phosphatase non-receptor type 11
Q06124	214	252	112	216	Domain	Note=SH2 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00191
Q06124	214	252	247	521	Domain	Note=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00160
Q06124	214	252	223	225	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	214	252	226	234	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	214	252	251	253	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3ZM1

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
Q06124	5	45	28	33	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	5	45	35	37	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	5	45	41	47	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	5	45	2	597	Chain	ID=PRO_0000094767;Note=Tyrosine-protein phosphatase non-receptor type 11
Q06124	5	45	6	102	Domain	Note=SH2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00191
Q06124	5	45	13	23	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	5	45	42	42	Natural variant	ID=VAR_015601;Note=In NS1. T->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11992261,ECO:0000269\|PubMed:12960218;Dbxref=dbSNP:rs397507501,PMID:11992261,PMID:12960218
Q06124	5	45	4	6	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5X7B
Q06124	214	252	218	222	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4OHD
Q06124	214	252	2	597	Chain	ID=PRO_0000094767;Note=Tyrosine-protein phosphatase non-receptor type 11
Q06124	214	252	112	216	Domain	Note=SH2 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00191
Q06124	214	252	247	521	Domain	Note=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00160
Q06124	214	252	223	225	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	214	252	226	234	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EHR
Q06124	214	252	251	253	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3ZM1

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3'-UTR located exon skipping events that lost miRNA binding sites in PTPN11

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 PTPN11

- 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 PTPN11

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 PTPN11

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

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Correlation with RNA binding proteins (RBPs) for PTPN11

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	SAMD4A	exon_skip_191182	-4.924376e-01	9.834339e-10
CB	PCBP1	exon_skip_191182	-4.237234e-01	2.478868e-07
CB	HNRNPA2B1	exon_skip_191182	-4.280730e-01	1.809051e-07
CB	SRSF1	exon_skip_191182	-4.300667e-01	1.563506e-07
CB	HNRNPF	exon_skip_191182	-4.096230e-01	6.679636e-07
CB	RBM4	exon_skip_191182	-4.039100e-01	9.854932e-07

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RelatedDrugs for PTPN11

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 PTPN11

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 PTPN11

Gene structures and expression levels for PTPN11

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PTPN11

Open reading frame (ORF) annotation in the exon skipping event for PTPN11

Infer the effects of exon skipping event on protein functional features for PTPN11

3'-UTR located exon skipping events that lost miRNA binding sites in PTPN11

SNVs in the skipped exons for PTPN11

AD stage-associated exon skippint events for PTPN11

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PTPN11

Correlation with RNA binding proteins (RBPs) for PTPN11

RelatedDrugs for PTPN11

RelatedDiseases for PTPN11