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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for PLSCR4 |
 Gene summary |
| Gene information | Gene symbol | PLSCR4 | Gene ID | 57088 |
| Gene name | phospholipid scramblase 4 | |
| Synonyms | TRA1 | |
| Cytomap | 3q24 | |
| Type of gene | protein-coding | |
| Description | phospholipid scramblase 4Ca(2+)-dependent phospholipid scramblase 4PL scramblase 4cell growth inhibiting protein 43 | |
| Modification date | 20200329 | |
| 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 |
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Gene structures and expression levels for PLSCR4 |
| 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. |
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ENSG00000114698
| 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. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | UP | ENST00000475019.1 | PLSCR4-207:retained_intron:PLSCR4 | 2.398838e+00 | 9.108117e-01 | 2.596435e-04 | 1.660090e-03 |
| TC | UP | ENST00000446574.6 | PLSCR4-204:protein_coding:PLSCR4 | 4.105831e+01 | 9.938871e-01 | 5.103014e-09 | 5.157607e-07 |
| TC | UP | ENST00000383083.6 | PLSCR4-202:protein_coding:PLSCR4 | 2.258215e+02 | 1.263095e+00 | 1.689042e-07 | 9.387388e-06 |
| TC | UP | ENST00000460350.5 | PLSCR4-205:protein_coding:PLSCR4 | 2.843798e+01 | 8.870686e-01 | 1.106783e-05 | 2.802220e-04 |
| TC | UP | ENST00000493382.5 | PLSCR4-210:protein_coding:PLSCR4 | 1.254478e+01 | 9.044768e-01 | 1.642764e-03 | 1.443173e-02 |
| TC | UP | ENST00000476202.5 | PLSCR4-208:protein_coding:PLSCR4 | 5.683782e+00 | 8.273080e-01 | 2.897345e-03 | 2.220319e-02 |
| 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 PLSCR4 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_101674 | chr3 | 146223733:146223777:146250557:146250637:146250960:146251079 | 146250557:146250637 |
| exon_skip_104506 | chr3 | 146196706:146196793:146201035:146201077:146206526:146206557 | 146201035:146201077 |
| exon_skip_192502 | chr3 | 146196405:146196793:146199813:146200039:146201035:146201077 | 146199813:146200039 |
| exon_skip_211847 | chr3 | 146196706:146196793:146206526:146206761:146220815:146220925 | 146206526:146206761 |
| exon_skip_213967 | chr3 | 146220815:146220925:146222065:146222092:146250960:146251079 | 146222065:146222092 |
| exon_skip_215816 | chr3 | 146196405:146196793:146201035:146201077:146206526:146206761 | 146201035:146201077 |
| exon_skip_238312 | chr3 | 146222065:146222092:146250557:146250637:146250960:146251079 | 146250557:146250637 |
| exon_skip_250545 | chr3 | 146200009:146200039:146201035:146201077:146206526:146206761 | 146201035:146201077 |
| exon_skip_257476 | chr3 | 146196706:146196793:146201035:146201077:146206526:146206761 | 146201035:146201077 |
| exon_skip_265949 | chr3 | 146222065:146222092:146223733:146223777:146250557:146250637 | 146223733:146223777 |
| exon_skip_39005 | chr3 | 146206587:146206761:146220815:146220925:146222065:146222092 | 146220815:146220925 |
| exon_skip_40297 | chr3 | 146220815:146220925:146222065:146222092:146250557:146250637 | 146222065:146222092 |
| exon_skip_65093 | chr3 | 146206587:146206761:146220815:146220925:146250960:146251079 | 146220815:146220925 |
| exon_skip_71841 | chr3 | 146196706:146196793:146199813:146200039:146201035:146201077 | 146199813:146200039 |
| exon_skip_75469 | chr3 | 146222065:146222092:146223733:146223777:146250960:146251079 | 146223733:146223777 |
| exon_skip_96906 | chr3 | 146196706:146196793:146201035:146201077:146206526:146206554 | 146201035:146201077 |
| 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 PLSCR4 |
| 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 |
| ENST00000446574 | 146222065 | 146222092 | 3UTR-3CDS |
| ENST00000493382 | 146223733 | 146223777 | 3UTR-3UTR |
| ENST00000493382 | 146250557 | 146250637 | 3UTR-3UTR |
| ENST00000354952 | 146199813 | 146200039 | Frame-shift |
| ENST00000446574 | 146199813 | 146200039 | Frame-shift |
| ENST00000493382 | 146199813 | 146200039 | Frame-shift |
| ENST00000354952 | 146201035 | 146201077 | Frame-shift |
| ENST00000446574 | 146201035 | 146201077 | Frame-shift |
| ENST00000493382 | 146201035 | 146201077 | 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 |
| ENST00000446574 | 146222065 | 146222092 | 3UTR-3CDS |
| ENST00000493382 | 146223733 | 146223777 | 3UTR-3UTR |
| ENST00000493382 | 146250557 | 146250637 | 3UTR-3UTR |
| ENST00000354952 | 146199813 | 146200039 | Frame-shift |
| ENST00000446574 | 146199813 | 146200039 | Frame-shift |
| ENST00000493382 | 146199813 | 146200039 | Frame-shift |
| ENST00000354952 | 146220815 | 146220925 | In-frame |
| ENST00000446574 | 146220815 | 146220925 | In-frame |
| ENST00000493382 | 146220815 | 146220925 | 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 |
| ENST00000446574 | 146222065 | 146222092 | 3UTR-3CDS |
| ENST00000493382 | 146223733 | 146223777 | 3UTR-3UTR |
| ENST00000493382 | 146250557 | 146250637 | 3UTR-3UTR |
| ENST00000354952 | 146199813 | 146200039 | Frame-shift |
| ENST00000446574 | 146199813 | 146200039 | Frame-shift |
| ENST00000493382 | 146199813 | 146200039 | Frame-shift |
| ENST00000354952 | 146201035 | 146201077 | Frame-shift |
| ENST00000446574 | 146201035 | 146201077 | Frame-shift |
| ENST00000493382 | 146201035 | 146201077 | Frame-shift |
| ENST00000354952 | 146220815 | 146220925 | In-frame |
| ENST00000446574 | 146220815 | 146220925 | In-frame |
| ENST00000493382 | 146220815 | 146220925 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PLSCR4 |
p-ENSG00000114698_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 |
| ENST00000354952 | 3320 | 329 | 146220815 | 146220925 | 249 | 358 | 2 | 39 |
| ENST00000446574 | 1459 | 329 | 146220815 | 146220925 | 340 | 449 | 2 | 39 |
| ENST00000493382 | 1392 | 329 | 146220815 | 146220925 | 339 | 448 | 2 | 39 |
| 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 |
| ENST00000354952 | 3320 | 329 | 146220815 | 146220925 | 249 | 358 | 2 | 39 |
| ENST00000446574 | 1459 | 329 | 146220815 | 146220925 | 340 | 449 | 2 | 39 |
| ENST00000493382 | 1392 | 329 | 146220815 | 146220925 | 339 | 448 | 2 | 39 |
| 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 |
| Q9NRQ2 | 2 | 39 | 1 | 15 | Alternative sequence | ID=VSP_042931;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9NRQ2 | 2 | 39 | 1 | 15 | Alternative sequence | ID=VSP_042931;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9NRQ2 | 2 | 39 | 1 | 15 | Alternative sequence | ID=VSP_042931;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9NRQ2 | 2 | 39 | 1 | 329 | Chain | ID=PRO_0000100792;Note=Phospholipid scramblase 4 |
| Q9NRQ2 | 2 | 39 | 1 | 329 | Chain | ID=PRO_0000100792;Note=Phospholipid scramblase 4 |
| Q9NRQ2 | 2 | 39 | 1 | 329 | Chain | ID=PRO_0000100792;Note=Phospholipid scramblase 4 |
| Q9NRQ2 | 2 | 39 | 18 | 25 | Motif | Note=SH3-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NRQ2 | 2 | 39 | 18 | 25 | Motif | Note=SH3-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NRQ2 | 2 | 39 | 18 | 25 | Motif | Note=SH3-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NRQ2 | 2 | 39 | 30 | 33 | Motif | Note=PPxY motif;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NRQ2 | 2 | 39 | 30 | 33 | Motif | Note=PPxY motif;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NRQ2 | 2 | 39 | 30 | 33 | Motif | Note=PPxY motif;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NRQ2 | 2 | 39 | 34 | 34 | Natural variant | ID=VAR_011315;Note=N->S;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10930526,ECO:0000269|Ref.2;Dbxref=dbSNP:rs3762685,PMID:10930526 |
| Q9NRQ2 | 2 | 39 | 34 | 34 | Natural variant | ID=VAR_011315;Note=N->S;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10930526,ECO:0000269|Ref.2;Dbxref=dbSNP:rs3762685,PMID:10930526 |
| Q9NRQ2 | 2 | 39 | 34 | 34 | Natural variant | ID=VAR_011315;Note=N->S;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10930526,ECO:0000269|Ref.2;Dbxref=dbSNP:rs3762685,PMID:10930526 |
| Q9NRQ2 | 2 | 39 | 1 | 98 | Region | Note=Proline-rich domain (PRD);Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9NRQ2 | 2 | 39 | 1 | 98 | Region | Note=Proline-rich domain (PRD);Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9NRQ2 | 2 | 39 | 1 | 98 | Region | Note=Proline-rich domain (PRD);Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9NRQ2 | 2 | 39 | 1 | 303 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9NRQ2 | 2 | 39 | 1 | 303 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9NRQ2 | 2 | 39 | 1 | 303 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| 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 |
| Q9NRQ2 | 2 | 39 | 1 | 15 | Alternative sequence | ID=VSP_042931;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9NRQ2 | 2 | 39 | 1 | 15 | Alternative sequence | ID=VSP_042931;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9NRQ2 | 2 | 39 | 1 | 15 | Alternative sequence | ID=VSP_042931;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9NRQ2 | 2 | 39 | 1 | 329 | Chain | ID=PRO_0000100792;Note=Phospholipid scramblase 4 |
| Q9NRQ2 | 2 | 39 | 1 | 329 | Chain | ID=PRO_0000100792;Note=Phospholipid scramblase 4 |
| Q9NRQ2 | 2 | 39 | 1 | 329 | Chain | ID=PRO_0000100792;Note=Phospholipid scramblase 4 |
| Q9NRQ2 | 2 | 39 | 18 | 25 | Motif | Note=SH3-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NRQ2 | 2 | 39 | 18 | 25 | Motif | Note=SH3-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NRQ2 | 2 | 39 | 18 | 25 | Motif | Note=SH3-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NRQ2 | 2 | 39 | 30 | 33 | Motif | Note=PPxY motif;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NRQ2 | 2 | 39 | 30 | 33 | Motif | Note=PPxY motif;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NRQ2 | 2 | 39 | 30 | 33 | Motif | Note=PPxY motif;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NRQ2 | 2 | 39 | 34 | 34 | Natural variant | ID=VAR_011315;Note=N->S;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10930526,ECO:0000269|Ref.2;Dbxref=dbSNP:rs3762685,PMID:10930526 |
| Q9NRQ2 | 2 | 39 | 34 | 34 | Natural variant | ID=VAR_011315;Note=N->S;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10930526,ECO:0000269|Ref.2;Dbxref=dbSNP:rs3762685,PMID:10930526 |
| Q9NRQ2 | 2 | 39 | 34 | 34 | Natural variant | ID=VAR_011315;Note=N->S;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10930526,ECO:0000269|Ref.2;Dbxref=dbSNP:rs3762685,PMID:10930526 |
| Q9NRQ2 | 2 | 39 | 1 | 98 | Region | Note=Proline-rich domain (PRD);Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9NRQ2 | 2 | 39 | 1 | 98 | Region | Note=Proline-rich domain (PRD);Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9NRQ2 | 2 | 39 | 1 | 98 | Region | Note=Proline-rich domain (PRD);Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9NRQ2 | 2 | 39 | 1 | 303 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9NRQ2 | 2 | 39 | 1 | 303 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9NRQ2 | 2 | 39 | 1 | 303 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
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3'-UTR located exon skipping events that lost miRNA binding sites in PLSCR4 |
| 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 |
| Mayo | ENST00000493382 | 146223733 | 146223777 | hsa-miR-3529-3p | chr3:146223748-146223755 | 8mer-1a | chr3:146223736-146223759 | 155.00 | -21.96 |
| Mayo | ENST00000493382 | 146250557 | 146250637 | hsa-miR-6839-3p | chr3:146250619-146250626 | 8mer-1a | chr3:146250606-146250626 | 149.00 | -15.10 |
| MSBB | ENST00000493382 | 146223733 | 146223777 | hsa-miR-3529-3p | chr3:146223748-146223755 | 8mer-1a | chr3:146223736-146223759 | 155.00 | -21.96 |
| MSBB | ENST00000493382 | 146250557 | 146250637 | hsa-miR-6839-3p | chr3:146250619-146250626 | 8mer-1a | chr3:146250606-146250626 | 149.00 | -15.10 |
| ROSMAP | ENST00000493382 | 146223733 | 146223777 | hsa-miR-3529-3p | chr3:146223748-146223755 | 8mer-1a | chr3:146223736-146223759 | 155.00 | -21.96 |
| ROSMAP | ENST00000493382 | 146250557 | 146250637 | hsa-miR-6839-3p | chr3:146250619-146250626 | 8mer-1a | chr3:146250606-146250626 | 149.00 | -15.10 |
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SNVs in the skipped exons for PLSCR4 |
| - 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 PLSCR4 |
| 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 PLSCR4 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| TC | exon_skip_265949 | rs12497460 | chr3:146296617 | 4.575120e-06 | 1.292789e-03 |
| PCC | exon_skip_265949 | rs3762687 | chr3:146220694 | 1.034370e-05 | 2.619996e-03 |
| PCC | exon_skip_265949 | rs9809574 | chr3:146223233 | 1.034370e-05 | 2.619996e-03 |
| PCC | exon_skip_265949 | rs7611459 | chr3:146224104 | 1.170971e-05 | 2.920500e-03 |
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Correlation with RNA binding proteins (RBPs) for PLSCR4 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for PLSCR4 |
| 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 PLSCR4 |
| 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)
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