|
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 PLPPR4 |
Gene summary |
Gene information | Gene symbol | PLPPR4 | Gene ID | 9890 |
Gene name | phospholipid phosphatase related 4 | |
Synonyms | LPPR4|LPR4|PHP1|PRG-1|PRG1 | |
Cytomap | 1p21.3-p21.2 | |
Type of gene | protein-coding | |
Description | phospholipid phosphatase-related protein type 4brain-specific phosphatidic acid phosphatase-like protein 1lipid phosphate phosphatase-related protein type 4plasticity related gene 1plasticity-related gene 1 protein | |
Modification date | 20200313 | |
UniProtAcc | Q7Z2D5, W4VSQ3, | |
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 PLPPR4 |
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 |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PLPPR4 |
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_152056 | chr1 | 99264292:99264671:99287965:99288150:99296738:99296867 | 99287965:99288150 |
exon_skip_220827 | chr1 | 99300909:99300966:99301724:99301897:99305685:99309580 | 99301724:99301897 |
exon_skip_91107 | chr1 | 99300909:99300966:99301724:99301897:99305685:99306443 | 99301724:99301897 |
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 PLPPR4 |
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 |
ENST00000370185 | 99301724 | 99301897 | 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 |
ENST00000370185 | 99301724 | 99301897 | 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 |
ENST00000370185 | 99301724 | 99301897 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for PLPPR4 |
p-ENSG00000117600_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 |
ENST00000370185 | 5386 | 763 | 99301724 | 99301897 | 1291 | 1463 | 264 | 322 |
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 |
ENST00000370185 | 5386 | 763 | 99301724 | 99301897 | 1291 | 1463 | 264 | 322 |
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 |
ENST00000370185 | 5386 | 763 | 99301724 | 99301897 | 1291 | 1463 | 264 | 322 |
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 |
Q7Z2D5 | 264 | 322 | 265 | 322 | Alternative sequence | ID=VSP_046784;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q7Z2D5 | 264 | 322 | 1 | 763 | Chain | ID=PRO_0000317436;Note=Phospholipid phosphatase-related protein type 4 |
Q7Z2D5 | 264 | 322 | 268 | 268 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q7Z2D5 | 264 | 322 | 247 | 267 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q7Z2D5 | 264 | 322 | 276 | 296 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q7Z2D5 | 264 | 322 | 308 | 328 | Transmembrane | Note=Helical;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 |
Q7Z2D5 | 264 | 322 | 265 | 322 | Alternative sequence | ID=VSP_046784;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q7Z2D5 | 264 | 322 | 1 | 763 | Chain | ID=PRO_0000317436;Note=Phospholipid phosphatase-related protein type 4 |
Q7Z2D5 | 264 | 322 | 268 | 268 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q7Z2D5 | 264 | 322 | 247 | 267 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q7Z2D5 | 264 | 322 | 276 | 296 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q7Z2D5 | 264 | 322 | 308 | 328 | Transmembrane | Note=Helical;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 |
Q7Z2D5 | 264 | 322 | 265 | 322 | Alternative sequence | ID=VSP_046784;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q7Z2D5 | 264 | 322 | 1 | 763 | Chain | ID=PRO_0000317436;Note=Phospholipid phosphatase-related protein type 4 |
Q7Z2D5 | 264 | 322 | 268 | 268 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q7Z2D5 | 264 | 322 | 247 | 267 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q7Z2D5 | 264 | 322 | 276 | 296 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q7Z2D5 | 264 | 322 | 308 | 328 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in PLPPR4 |
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 PLPPR4 |
- 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 PLPPR4 |
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 PLPPR4 |
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 PLPPR4 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
PCC | MSI1 | exon_skip_220827 | -4.066956e-01 | 6.978934e-09 |
TC | MSI1 | exon_skip_91107 | -5.070724e-01 | 1.009952e-09 |
TC | ILF2 | exon_skip_91107 | 5.305273e-01 | 1.186732e-10 |
TC | KHDRBS2 | exon_skip_91107 | 7.345765e-01 | 5.746100e-23 |
TC | KHDRBS3 | exon_skip_91107 | 6.587274e-01 | 2.877963e-17 |
TC | RBM24 | exon_skip_91107 | 6.536335e-01 | 6.075113e-17 |
TC | PTBP3 | exon_skip_91107 | 4.004171e-01 | 2.823839e-06 |
TC | CPEB1 | exon_skip_91107 | 5.862016e-01 | 3.604645e-13 |
TC | SRSF9 | exon_skip_91107 | 4.706693e-01 | 2.066429e-08 |
TC | ESRP1 | exon_skip_91107 | 4.082376e-01 | 1.722923e-06 |
Top |
RelatedDrugs for PLPPR4 |
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 PLPPR4 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |