|
Open reading frame (ORF) annotation in the exon skipping event | |
3'-UTR located exon skipping events lost miRNA binding sites | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Gene summary for PTPN21 |
Gene summary |
Gene information | Gene symbol | PTPN21 | Gene ID | 11099 |
Gene name | protein tyrosine phosphatase non-receptor type 21 | |
Synonyms | PTPD1|PTPRL10 | |
Cytomap | 14q31.3 | |
Type of gene | protein-coding | |
Description | tyrosine-protein phosphatase non-receptor type 21dJ1175B15.2 (protein tyrosine phosphatase, non-receptor type 21)protein-tyrosine phosphatase D1 | |
Modification date | 20200313 | |
UniProtAcc | ||
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
Top |
Gene structures and expression levels for PTPN21 |
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. |
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 |
PG | UP | ENST00000556564.6 | PTPN21-208:protein_coding:PTPN21 | 8.115887e+01 | 8.437658e-01 | 1.041543e-04 | 2.831984e-03 |
CB | UP | ENST00000555243.1 | PTPN21-207:protein_coding:PTPN21 | 1.033981e+00 | 9.454745e-01 | 4.529517e-03 | 1.814458e-02 |
TC | UP | ENST00000554178.1 | PTPN21-204:lncRNA:PTPN21 | 1.016533e+00 | 9.910655e-01 | 3.148461e-03 | 2.366610e-02 |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PTPN21 |
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_195578 | chr14 | 88496413:88496492:88497203:88497290:88500783:88500871 | 88497203:88497290 |
exon_skip_234163 | chr14 | 88505304:88505371:88507923:88508020:88517092:88517261 | 88507923:88508020 |
exon_skip_244555 | chr14 | 88497203:88497290:88500783:88500871:88501281:88501368 | 88500783:88500871 |
exon_skip_62205 | chr14 | 88469965:88470050:88472244:88472465:88473665:88473802 | 88472244:88472465 |
exon_skip_73460 | chr14 | 88517092:88517261:88547529:88547651:88550238:88550530 | 88547529:88547651 |
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 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for PTPN21 |
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 |
ENST00000328736 | 88507923 | 88508020 | Frame-shift |
ENST00000556564 | 88507923 | 88508020 | Frame-shift |
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 |
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 |
ENST00000328736 | 88497203 | 88497290 | Frame-shift |
ENST00000556564 | 88497203 | 88497290 | Frame-shift |
ENST00000328736 | 88500783 | 88500871 | Frame-shift |
ENST00000556564 | 88500783 | 88500871 | Frame-shift |
ENST00000328736 | 88507923 | 88508020 | Frame-shift |
ENST00000556564 | 88507923 | 88508020 | Frame-shift |
ENST00000328736 | 88472244 | 88472465 | In-frame |
ENST00000556564 | 88472244 | 88472465 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for PTPN21 |
p-ENSG00000070778_img4.png |
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 |
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 |
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 |
ENST00000328736 | 6106 | 1174 | 88472244 | 88472465 | 2855 | 3075 | 883 | 956 |
ENST00000556564 | 6183 | 1174 | 88472244 | 88472465 | 2935 | 3155 | 883 | 956 |
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 |
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 |
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 |
Q16825 | 883 | 956 | 1 | 1174 | Chain | ID=PRO_0000219439;Note=Tyrosine-protein phosphatase non-receptor type 21 |
Q16825 | 883 | 956 | 1 | 1174 | Chain | ID=PRO_0000219439;Note=Tyrosine-protein phosphatase non-receptor type 21 |
Q16825 | 883 | 956 | 896 | 1167 | Domain | Note=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00160 |
Q16825 | 883 | 956 | 896 | 1167 | Domain | Note=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00160 |
Q16825 | 883 | 956 | 906 | 906 | Natural variant | ID=VAR_055539;Note=K->N;Dbxref=dbSNP:rs12879993 |
Q16825 | 883 | 956 | 906 | 906 | Natural variant | ID=VAR_055539;Note=K->N;Dbxref=dbSNP:rs12879993 |
Q16825 | 883 | 956 | 936 | 936 | Natural variant | ID=VAR_060342;Note=V->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:7519780;Dbxref=dbSNP:rs2274736,PMID:7519780 |
Q16825 | 883 | 956 | 936 | 936 | Natural variant | ID=VAR_060342;Note=V->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:7519780;Dbxref=dbSNP:rs2274736,PMID:7519780 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in PTPN21 |
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 |
Top |
SNVs in the skipped exons for PTPN21 |
- 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 |
Top |
AD stage-associated exon skippint events for PTPN21 |
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 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PTPN21 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
Top |
Correlation with RNA binding proteins (RBPs) for PTPN21 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
Top |
RelatedDrugs for PTPN21 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for PTPN21 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |