|
||||||
|
 | |
| |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
| |
|
Gene summary for PPP4R2 |
 Gene summary |
| Gene information | Gene symbol | PPP4R2 | Gene ID | 151987 |
| Gene name | protein phosphatase 4 regulatory subunit 2 | |
| Synonyms | PP4R2 | |
| Cytomap | 3p13 | |
| Type of gene | protein-coding | |
| Description | serine/threonine-protein phosphatase 4 regulatory subunit 2 | |
| Modification date | 20180523 | |
| UniProtAcc | Q9NY27 | |
| Context | PubMed: PPP4R2 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
Top |
Exon skipping events across known transcript of Ensembl for PPP4R2 from UCSC genome browser |
| Skipped exons in TCGA and GTEx 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. |
 |
Top |
Gene isoform structures and expression levels for PPP4R2 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for PPP4R2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_375852 | 3 | 73047227:73047309:73096336:73096507:73108187:73108281 | 73096336:73096507 | ENSG00000163605.10 | ENST00000295862.9,ENST00000488810.1,ENST00000470976.1,ENST00000356692.5,ENST00000476505.2 |
| exon_skip_375853 | 3 | 73096336:73096507:73108187:73108281:73110173:73110211 | 73108187:73108281 | ENSG00000163605.10 | ENST00000295862.9,ENST00000488810.1,ENST00000470976.1,ENST00000356692.5 |
| exon_skip_375854 | 3 | 73110173:73110211:73112823:73112898:73113153:73113297 | 73112823:73112898 | ENSG00000163605.10 | ENST00000295862.9,ENST00000394284.3,ENST00000356692.5 |
| exon_skip_375855 | 3 | 73112823:73112898:73113153:73113297:73114002:73114117 | 73113153:73113297 | ENSG00000163605.10 | ENST00000295862.9,ENST00000394284.3,ENST00000356692.5 |
| exon_skip_375857 | 3 | 73112823:73112898:73113215:73113297:73114002:73114117 | 73113215:73113297 | ENSG00000163605.10 | ENST00000482242.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for PPP4R2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_375852 | 3 | 73047227:73047309:73096336:73096507:73108187:73108281 | 73096336:73096507 | ENSG00000163605.10 | ENST00000356692.5,ENST00000470976.1,ENST00000488810.1,ENST00000295862.9,ENST00000476505.2 |
| exon_skip_375853 | 3 | 73096336:73096507:73108187:73108281:73110173:73110211 | 73108187:73108281 | ENSG00000163605.10 | ENST00000356692.5,ENST00000470976.1,ENST00000488810.1,ENST00000295862.9 |
| exon_skip_375854 | 3 | 73110173:73110211:73112823:73112898:73113153:73113297 | 73112823:73112898 | ENSG00000163605.10 | ENST00000356692.5,ENST00000394284.3,ENST00000295862.9 |
| exon_skip_375855 | 3 | 73112823:73112898:73113153:73113297:73114002:73114117 | 73113153:73113297 | ENSG00000163605.10 | ENST00000356692.5,ENST00000394284.3,ENST00000295862.9 |
| exon_skip_375857 | 3 | 73112823:73112898:73113215:73113297:73114002:73114117 | 73113215:73113297 | ENSG00000163605.10 | ENST00000482242.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for PPP4R2 |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000356692 | 73108187 | 73108281 | Frame-shift |
| ENST00000356692 | 73096336 | 73096507 | In-frame |
| ENST00000356692 | 73112823 | 73112898 | In-frame |
| ENST00000356692 | 73113153 | 73113297 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000356692 | 73108187 | 73108281 | Frame-shift |
| ENST00000356692 | 73096336 | 73096507 | In-frame |
| ENST00000356692 | 73112823 | 73112898 | In-frame |
| ENST00000356692 | 73113153 | 73113297 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for PPP4R2 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
 |
| Loci of skipped exons in TCGA 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 |
| ENST00000356692 | 5001 | 417 | 73096336 | 73096507 | 370 | 540 | 39 | 95 |
| ENST00000356692 | 5001 | 417 | 73112823 | 73112898 | 673 | 747 | 140 | 164 |
| ENST00000356692 | 5001 | 417 | 73113153 | 73113297 | 748 | 891 | 165 | 212 |
| Loci of skipped exons in GTEx 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 |
| ENST00000356692 | 5001 | 417 | 73096336 | 73096507 | 370 | 540 | 39 | 95 |
| ENST00000356692 | 5001 | 417 | 73112823 | 73112898 | 673 | 747 | 140 | 164 |
| ENST00000356692 | 5001 | 417 | 73113153 | 73113297 | 748 | 891 | 165 | 212 |
| Lost protein functional features of individual exon skipping events in TCGA. |
| 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 |
| Q9NY27 | 39 | 95 | 1 | 56 | Alternative sequence | ID=VSP_027612;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9NY27 | 39 | 95 | 39 | 96 | Alternative sequence | ID=VSP_027613;Note=In isoform 2. MIQWSQFKGYFIFKLEKVMDDFRTSAPEPRGPPNPNVEYIPFDEMKERILKIVTGFNG->I;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9NY27 | 39 | 95 | 1 | 417 | Chain | ID=PRO_0000299365;Note=Serine/threonine-protein phosphatase 4 regulatory subunit 2 |
| Q9NY27 | 140 | 164 | 1 | 417 | Chain | ID=PRO_0000299365;Note=Serine/threonine-protein phosphatase 4 regulatory subunit 2 |
| Q9NY27 | 140 | 164 | 159 | 159 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:23186163;Dbxref=PMID:1 |
| Q9NY27 | 165 | 212 | 1 | 417 | Chain | ID=PRO_0000299365;Note=Serine/threonine-protein phosphatase 4 regulatory subunit 2 |
| Q9NY27 | 165 | 212 | 174 | 174 | Natural variant | ID=VAR_051749;Note=P->L;Dbxref=dbSNP:rs2306983 |
| Lost protein functional features of individual exon skipping events in GTEx. |
| 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 |
| Q9NY27 | 39 | 95 | 1 | 56 | Alternative sequence | ID=VSP_027612;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9NY27 | 39 | 95 | 39 | 96 | Alternative sequence | ID=VSP_027613;Note=In isoform 2. MIQWSQFKGYFIFKLEKVMDDFRTSAPEPRGPPNPNVEYIPFDEMKERILKIVTGFNG->I;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9NY27 | 39 | 95 | 1 | 417 | Chain | ID=PRO_0000299365;Note=Serine/threonine-protein phosphatase 4 regulatory subunit 2 |
| Q9NY27 | 140 | 164 | 1 | 417 | Chain | ID=PRO_0000299365;Note=Serine/threonine-protein phosphatase 4 regulatory subunit 2 |
| Q9NY27 | 140 | 164 | 159 | 159 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:23186163;Dbxref=PMID:1 |
| Q9NY27 | 165 | 212 | 1 | 417 | Chain | ID=PRO_0000299365;Note=Serine/threonine-protein phosphatase 4 regulatory subunit 2 |
| Q9NY27 | 165 | 212 | 174 | 174 | Natural variant | ID=VAR_051749;Note=P->L;Dbxref=dbSNP:rs2306983 |
Top |
SNVs in the skipped exons for PPP4R2 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
 |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_375854 | 73112824 | 73112898 | 73112867 | 73112867 | Frame_Shift_Del | T | - | p.F155fs |
| LUSC | TCGA-39-5036-01 | exon_skip_375853 | 73108188 | 73108281 | 73108204 | 73108204 | Nonsense_Mutation | C | T | p.Q102* |
| UCEC | TCGA-B5-A0JY-01 | exon_skip_375854 | 73112824 | 73112898 | 73112849 | 73112849 | Nonsense_Mutation | C | T | p.R149* |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - 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 |
| JHUEM1_ENDOMETRIUM | 73113216 | 73113297 | 73113216 | 73113216 | Frame_Shift_Del | C | - | p.A186fs |
| JHUEM1_ENDOMETRIUM | 73113154 | 73113297 | 73113216 | 73113216 | Frame_Shift_Del | C | - | p.A186fs |
| EN_ENDOMETRIUM | 73113216 | 73113297 | 73113286 | 73113287 | Frame_Shift_Ins | - | A | p.K210fs |
| EN_ENDOMETRIUM | 73113154 | 73113297 | 73113286 | 73113287 | Frame_Shift_Ins | - | A | p.K210fs |
| BFTC909_KIDNEY | 73096337 | 73096507 | 73096378 | 73096378 | Missense_Mutation | T | G | p.L53R |
| SNU81_LARGE_INTESTINE | 73096337 | 73096507 | 73096382 | 73096382 | Missense_Mutation | G | T | p.E54D |
| SHP77_LUNG | 73096337 | 73096507 | 73096387 | 73096387 | Missense_Mutation | T | A | p.V56E |
| EN_ENDOMETRIUM | 73096337 | 73096507 | 73096389 | 73096389 | Missense_Mutation | A | G | p.M57V |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 73096337 | 73096507 | 73096474 | 73096474 | Missense_Mutation | A | G | p.E85G |
| NCIH2172_LUNG | 73108188 | 73108281 | 73108192 | 73108192 | Missense_Mutation | C | T | p.P98S |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 73112824 | 73112898 | 73112896 | 73112896 | Missense_Mutation | G | C | p.E164D |
| SW1783_CENTRAL_NERVOUS_SYSTEM | 73113216 | 73113297 | 73113225 | 73113225 | Missense_Mutation | C | G | p.T189R |
| SW1783_CENTRAL_NERVOUS_SYSTEM | 73113154 | 73113297 | 73113225 | 73113225 | Missense_Mutation | C | G | p.T189R |
| CROAP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 73096337 | 73096507 | 73096341 | 73096341 | Nonsense_Mutation | C | T | p.Q41* |
| HEY_OVARY | 73096337 | 73096507 | 73096337 | 73096337 | Splice_Site | G | A | p.M39I |
| HEYA8_OVARY | 73096337 | 73096507 | 73096337 | 73096337 | Splice_Site | G | A | p.M39I |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PPP4R2 |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PPP4R2 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PPP4R2 |
Top |
RelatedDrugs for PPP4R2 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for PPP4R2 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|