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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 PRPF40B |
 Gene summary |
| Gene information | Gene symbol | PRPF40B | Gene ID | 25766 |
| Gene name | pre-mRNA processing factor 40 homolog B | |
| Synonyms | HYPC | |
| Cytomap | 12q13.12 | |
| Type of gene | protein-coding | |
| Description | pre-mRNA-processing factor 40 homolog BHuntingtin interacting protein CPRP40 pre-mRNA processing factor 40 homolog Bhuntingtin yeast partner C | |
| Modification date | 20200319 | |
| 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 PRPF40B |
| 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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ENSG00000110844
| 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. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PRPF40B |
| 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_112811 | chr12 | 49633886:49634092:49634332:49634455:49634538:49634602 | 49634332:49634455 |
| exon_skip_127204 | chr12 | 49631860:49631925:49632596:49632623:49632855:49632880 | 49632596:49632623 |
| exon_skip_132140 | chr12 | 49632855:49632880:49633014:49633124:49633427:49633547 | 49633014:49633124 |
| exon_skip_132511 | chr12 | 49634568:49634602:49635099:49635263:49635365:49635473 | 49635099:49635263 |
| exon_skip_144936 | chr12 | 49642235:49642372:49642580:49642675:49642930:49642978 | 49642580:49642675 |
| exon_skip_153284 | chr12 | 49633886:49634092:49634332:49634455:49634538:49634551 | 49634332:49634455 |
| exon_skip_162103 | chr12 | 49636716:49636849:49637470:49637584:49637733:49637824 | 49637470:49637584 |
| exon_skip_167217 | chr12 | 49634037:49634092:49634332:49634455:49634538:49634602 | 49634332:49634455 |
| exon_skip_20841 | chr12 | 49632855:49632880:49633014:49633547:49633637:49633661 | 49633014:49633547 |
| exon_skip_232017 | chr12 | 49623570:49623593:49630545:49630625:49631401:49631544 | 49630545:49630625 |
| exon_skip_89030 | chr12 | 49634538:49634602:49635099:49635263:49635365:49635473 | 49635099:49635263 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_127204 | Mayo_CB | 4.745570e-01 | 6.778571e-01 | -2.033002e-01 | 3.869671e-08 |
| exon_skip_132140 | Mayo_CB | 5.601235e-01 | 6.922368e-01 | -1.321134e-01 | 3.842978e-06 |
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Open reading frame (ORF) annotation in the exon skipping event for PRPF40B |
| 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 |
| ENST00000380281 | 49632596 | 49632623 | Frame-shift |
| ENST00000380281 | 49634332 | 49634455 | Frame-shift |
| ENST00000380281 | 49633014 | 49633124 | In-frame |
| ENST00000380281 | 49635099 | 49635263 | 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 |
| ENST00000380281 | 49632596 | 49632623 | Frame-shift |
| ENST00000380281 | 49634332 | 49634455 | Frame-shift |
| ENST00000380281 | 49633014 | 49633124 | In-frame |
| ENST00000380281 | 49635099 | 49635263 | 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 |
| ENST00000380281 | 49632596 | 49632623 | Frame-shift |
| ENST00000380281 | 49634332 | 49634455 | Frame-shift |
| ENST00000380281 | 49637470 | 49637584 | Frame-shift |
| ENST00000380281 | 49633014 | 49633124 | In-frame |
| ENST00000380281 | 49635099 | 49635263 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PRPF40B |
p-ENSG00000110844_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 |
| ENST00000380281 | 3171 | 871 | 49633014 | 49633124 | 348 | 457 | 94 | 131 |
| ENST00000380281 | 3171 | 871 | 49635099 | 49635263 | 1001 | 1164 | 312 | 366 |
| 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 |
| ENST00000380281 | 3171 | 871 | 49633014 | 49633124 | 348 | 457 | 94 | 131 |
| ENST00000380281 | 3171 | 871 | 49635099 | 49635263 | 1001 | 1164 | 312 | 366 |
| 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 |
| ENST00000380281 | 3171 | 871 | 49633014 | 49633124 | 348 | 457 | 94 | 131 |
| ENST00000380281 | 3171 | 871 | 49635099 | 49635263 | 1001 | 1164 | 312 | 366 |
| 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 |
| Q6NWY9 | 94 | 131 | 77 | 200 | Alternative sequence | ID=VSP_029120;Note=In isoform 4. TAPGADTASSAVAGTGPPRALWSEHVAPDGRIYYYNADDKQSVWEKPSVLKSKAELLLSQCPWKEYKSDTGKPYYYNNQSKESRWTRPKDLDDLEVLVKQEAAGKQQQQLPQTLQPQPPQPQPD->VSTRGQQVAGSALQSRESDLECRTMTSILSLFSSHPPRSPAALPTLKSFSPAMYSALLVSHSSPKAYTFSCYSRALSSSLKEHTYPHRATHCGHMN |
| Q6NWY9 | 94 | 131 | 1 | 871 | Chain | ID=PRO_0000309282;Note=Pre-mRNA-processing factor 40 homolog B |
| Q6NWY9 | 94 | 131 | 92 | 125 | Domain | Note=WW 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00224 |
| Q6NWY9 | 312 | 366 | 201 | 871 | Alternative sequence | ID=VSP_029121;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q6NWY9 | 312 | 366 | 1 | 871 | Chain | ID=PRO_0000309282;Note=Pre-mRNA-processing factor 40 homolog B |
| Q6NWY9 | 312 | 366 | 276 | 330 | Domain | Note=FF 1 |
| Q6NWY9 | 312 | 366 | 340 | 397 | Domain | Note=FF 2 |
| 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 |
| Q6NWY9 | 94 | 131 | 77 | 200 | Alternative sequence | ID=VSP_029120;Note=In isoform 4. TAPGADTASSAVAGTGPPRALWSEHVAPDGRIYYYNADDKQSVWEKPSVLKSKAELLLSQCPWKEYKSDTGKPYYYNNQSKESRWTRPKDLDDLEVLVKQEAAGKQQQQLPQTLQPQPPQPQPD->VSTRGQQVAGSALQSRESDLECRTMTSILSLFSSHPPRSPAALPTLKSFSPAMYSALLVSHSSPKAYTFSCYSRALSSSLKEHTYPHRATHCGHMN |
| Q6NWY9 | 94 | 131 | 1 | 871 | Chain | ID=PRO_0000309282;Note=Pre-mRNA-processing factor 40 homolog B |
| Q6NWY9 | 94 | 131 | 92 | 125 | Domain | Note=WW 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00224 |
| Q6NWY9 | 312 | 366 | 201 | 871 | Alternative sequence | ID=VSP_029121;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q6NWY9 | 312 | 366 | 1 | 871 | Chain | ID=PRO_0000309282;Note=Pre-mRNA-processing factor 40 homolog B |
| Q6NWY9 | 312 | 366 | 276 | 330 | Domain | Note=FF 1 |
| Q6NWY9 | 312 | 366 | 340 | 397 | Domain | Note=FF 2 |
| 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 |
| Q6NWY9 | 94 | 131 | 77 | 200 | Alternative sequence | ID=VSP_029120;Note=In isoform 4. TAPGADTASSAVAGTGPPRALWSEHVAPDGRIYYYNADDKQSVWEKPSVLKSKAELLLSQCPWKEYKSDTGKPYYYNNQSKESRWTRPKDLDDLEVLVKQEAAGKQQQQLPQTLQPQPPQPQPD->VSTRGQQVAGSALQSRESDLECRTMTSILSLFSSHPPRSPAALPTLKSFSPAMYSALLVSHSSPKAYTFSCYSRALSSSLKEHTYPHRATHCGHMN |
| Q6NWY9 | 94 | 131 | 1 | 871 | Chain | ID=PRO_0000309282;Note=Pre-mRNA-processing factor 40 homolog B |
| Q6NWY9 | 94 | 131 | 92 | 125 | Domain | Note=WW 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00224 |
| Q6NWY9 | 312 | 366 | 201 | 871 | Alternative sequence | ID=VSP_029121;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q6NWY9 | 312 | 366 | 1 | 871 | Chain | ID=PRO_0000309282;Note=Pre-mRNA-processing factor 40 homolog B |
| Q6NWY9 | 312 | 366 | 276 | 330 | Domain | Note=FF 1 |
| Q6NWY9 | 312 | 366 | 340 | 397 | Domain | Note=FF 2 |
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3'-UTR located exon skipping events that lost miRNA binding sites in PRPF40B |
| 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 PRPF40B |
| - 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 PRPF40B |
| 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 PRPF40B |
| 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 PRPF40B |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | RBM6 | exon_skip_127204 | -4.691855e-01 | 1.584329e-09 |
| CB | RBM45 | exon_skip_127204 | 6.212649e-01 | 2.829261e-17 |
| CB | RBM45 | exon_skip_132140 | 6.432065e-01 | 1.052792e-19 |
| CB | RBM4 | exon_skip_132140 | -7.351144e-01 | 5.920389e-28 |
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RelatedDrugs for PRPF40B |
| 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 PRPF40B |
| 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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