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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 PPM1D |
Gene summary |
Gene information | Gene symbol | PPM1D | Gene ID | 8493 |
Gene name | protein phosphatase, Mg2+/Mn2+ dependent 1D | |
Synonyms | IDDGIP|JDVS|PP2C-DELTA|WIP1 | |
Cytomap | 17q23.2 | |
Type of gene | protein-coding | |
Description | protein phosphatase 1Dprotein phosphatase 1D magnesium-dependent, delta isoformprotein phosphatase 2C delta isoformprotein phosphatase Wip1wild-type p53-induced phosphatase 1 | |
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 |
PPM1D | GO:0035970 | peptidyl-threonine dephosphorylation | 20801214 |
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Gene structures and expression levels for PPM1D |
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 |
CB | UP | ENST00000392995.7 | PPM1D-202:nonsense_mediated_decay:PPM1D | 3.816537e+02 | 1.183168e+00 | 8.892354e-05 | 6.708618e-04 |
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 PPM1D |
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_177250 | chr17 | 60656599:60656841:60656932:60657042:60662995:60664473 | 60656932:60657042 |
exon_skip_214224 | chr17 | 60623521:60623749:60633853:60633977:60647892:60648082 | 60633853:60633977 |
exon_skip_221843 | chr17 | 60656599:60656841:60656932:60657042:60662995:60663015 | 60656932:60657042 |
exon_skip_24630 | chr17 | 60600269:60600886:60623521:60623749:60633853:60633957 | 60623521:60623749 |
exon_skip_258240 | chr17 | 60647892:60648082:60656599:60656841:60662995:60664473 | 60656599:60656841 |
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 PPM1D |
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 |
ENST00000305921 | 60623521 | 60623749 | Frame-shift |
ENST00000305921 | 60633853 | 60633977 | 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 |
ENST00000305921 | 60633853 | 60633977 | Frame-shift |
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 |
ENST00000305921 | 60623521 | 60623749 | Frame-shift |
ENST00000305921 | 60633853 | 60633977 | Frame-shift |
ENST00000305921 | 60656599 | 60656841 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PPM1D |
p-ENSG00000170836_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 |
ENST00000305921 | 4795 | 605 | 60656599 | 60656841 | 1251 | 1492 | 339 | 420 |
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 |
O15297 | 339 | 420 | 1 | 605 | Chain | ID=PRO_0000057752;Note=Protein phosphatase 1D |
O15297 | 339 | 420 | 8 | 375 | Domain | Note=PPM-type phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01082 |
O15297 | 339 | 420 | 366 | 366 | Metal binding | Note=Manganese 2;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
O15297 | 339 | 420 | 404 | 605 | Natural variant | ID=VAR_080081;Note=In IDDGIP. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:28343630;Dbxref=PMID:28343630 |
O15297 | 339 | 420 | 407 | 605 | Natural variant | ID=VAR_080082;Note=In IDDGIP. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:28343630;Dbxref=PMID:28343630 |
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3'-UTR located exon skipping events that lost miRNA binding sites in PPM1D |
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 PPM1D |
- 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 PPM1D |
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 PPM1D |
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 PPM1D |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for PPM1D |
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 PPM1D |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |