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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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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 | 20180524 | |
| UniProtAcc | Q6NWY9 | |
| Context | PubMed: PRPF40B [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 |
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Exon skipping events across known transcript of Ensembl for PRPF40B 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. |
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Gene isoform structures and expression levels for PRPF40B |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for PRPF40B |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_81969 | 12 | 50017352:50017376:50024327:50024408:50025183:50025327 | 50024327:50024408 | ENSG00000110844.9 | ENST00000551418.1,ENST00000548825.2 |
| exon_skip_81974 | 12 | 50025642:50025708:50026378:50026406:50026637:50026663 | 50026378:50026406 | ENSG00000110844.9 | ENST00000548825.2,ENST00000261897.1,ENST00000551111.1,ENST00000380281.1 |
| exon_skip_81977 | 12 | 50026637:50026663:50026796:50026907:50027209:50027330 | 50026796:50026907 | ENSG00000110844.9 | ENST00000551320.1,ENST00000548825.2,ENST00000261897.1,ENST00000548436.1,ENST00000380281.1 |
| exon_skip_81980 | 12 | 50026637:50026663:50026796:50027330:50027419:50027444 | 50026796:50027330 | ENSG00000110844.9 | ENST00000551111.1 |
| exon_skip_81985 | 12 | 50027209:50027330:50027419:50027444:50027668:50027714 | 50027419:50027444 | ENSG00000110844.9 | ENST00000551320.1,ENST00000548825.2,ENST00000261897.1,ENST00000548436.1,ENST00000380281.1 |
| exon_skip_81986 | 12 | 50027668:50027875:50028114:50028238:50028320:50028385 | 50028114:50028238 | ENSG00000110844.9 | ENST00000548825.2,ENST00000261897.1,ENST00000548436.1,ENST00000380281.1 |
| exon_skip_81987 | 12 | 50028320:50028385:50028881:50029046:50029147:50029256 | 50028881:50029046 | ENSG00000110844.9 | ENST00000548825.2,ENST00000261897.1,ENST00000380281.1 |
| exon_skip_81991 | 12 | 50030498:50030632:50031252:50031367:50031515:50031607 | 50031252:50031367 | ENSG00000110844.9 | ENST00000548825.2,ENST00000261897.1,ENST00000380281.1 |
| exon_skip_82005 | 12 | 50036017:50036155:50036362:50036458:50036709:50036799 | 50036362:50036458 | ENSG00000110844.9 | ENST00000261897.1,ENST00000380281.1 |
| exon_skip_82006 | 12 | 50036017:50036155:50036362:50036458:50036712:50036761 | 50036362:50036458 | ENSG00000110844.9 | ENST00000548825.2,ENST00000549547.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PRPF40B |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_81969 | 12 | 50017352:50017376:50024327:50024408:50025183:50025327 | 50024327:50024408 | ENSG00000110844.9 | ENST00000551418.1,ENST00000548825.2 |
| exon_skip_81974 | 12 | 50025642:50025708:50026378:50026406:50026637:50026663 | 50026378:50026406 | ENSG00000110844.9 | ENST00000548825.2,ENST00000261897.1,ENST00000551111.1,ENST00000380281.1 |
| exon_skip_81977 | 12 | 50026637:50026663:50026796:50026907:50027209:50027330 | 50026796:50026907 | ENSG00000110844.9 | ENST00000548825.2,ENST00000548436.1,ENST00000261897.1,ENST00000380281.1,ENST00000551320.1 |
| exon_skip_81980 | 12 | 50026637:50026663:50026796:50027330:50027419:50027444 | 50026796:50027330 | ENSG00000110844.9 | ENST00000551111.1 |
| exon_skip_81985 | 12 | 50027209:50027330:50027419:50027444:50027668:50027714 | 50027419:50027444 | ENSG00000110844.9 | ENST00000548825.2,ENST00000548436.1,ENST00000261897.1,ENST00000380281.1,ENST00000551320.1 |
| exon_skip_81986 | 12 | 50027668:50027875:50028114:50028238:50028320:50028385 | 50028114:50028238 | ENSG00000110844.9 | ENST00000548825.2,ENST00000548436.1,ENST00000261897.1,ENST00000380281.1 |
| exon_skip_81987 | 12 | 50028320:50028385:50028881:50029046:50029147:50029256 | 50028881:50029046 | ENSG00000110844.9 | ENST00000548825.2,ENST00000261897.1,ENST00000380281.1 |
| exon_skip_81991 | 12 | 50030498:50030632:50031252:50031367:50031515:50031607 | 50031252:50031367 | ENSG00000110844.9 | ENST00000548825.2,ENST00000261897.1,ENST00000380281.1 |
| exon_skip_82005 | 12 | 50036017:50036155:50036362:50036458:50036709:50036799 | 50036362:50036458 | ENSG00000110844.9 | ENST00000261897.1,ENST00000380281.1 |
| exon_skip_82006 | 12 | 50036017:50036155:50036362:50036458:50036712:50036761 | 50036362:50036458 | ENSG00000110844.9 | ENST00000548825.2,ENST00000549547.1 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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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 TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000380281 | 50026378 | 50026406 | Frame-shift |
| ENST00000380281 | 50027419 | 50027444 | Frame-shift |
| ENST00000380281 | 50028114 | 50028238 | Frame-shift |
| ENST00000380281 | 50031252 | 50031367 | Frame-shift |
| ENST00000380281 | 50026796 | 50026907 | In-frame |
| ENST00000380281 | 50028881 | 50029046 | In-frame |
| ENST00000380281 | 50036362 | 50036458 | 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 |
| ENST00000380281 | 50026378 | 50026406 | Frame-shift |
| ENST00000380281 | 50027419 | 50027444 | Frame-shift |
| ENST00000380281 | 50028114 | 50028238 | Frame-shift |
| ENST00000380281 | 50031252 | 50031367 | Frame-shift |
| ENST00000380281 | 50026796 | 50026907 | In-frame |
| ENST00000380281 | 50028881 | 50029046 | In-frame |
| ENST00000380281 | 50036362 | 50036458 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PRPF40B |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| 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 |
| ENST00000380281 | 3171 | 871 | 50026796 | 50026907 | 347 | 457 | 94 | 131 |
| ENST00000380281 | 3171 | 871 | 50028881 | 50029046 | 1000 | 1164 | 312 | 366 |
| ENST00000380281 | 3171 | 871 | 50036362 | 50036458 | 2021 | 2116 | 652 | 684 |
| 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 |
| ENST00000380281 | 3171 | 871 | 50026796 | 50026907 | 347 | 457 | 94 | 131 |
| ENST00000380281 | 3171 | 871 | 50028881 | 50029046 | 1000 | 1164 | 312 | 366 |
| ENST00000380281 | 3171 | 871 | 50036362 | 50036458 | 2021 | 2116 | 652 | 684 |
| 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 |
| 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 |
| Q6NWY9 | 652 | 684 | 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 | 652 | 684 | 1 | 871 | Chain | ID=PRO_0000309282;Note=Pre-mRNA-processing factor 40 homolog B |
| Q6NWY9 | 652 | 684 | 625 | 682 | Domain | Note=FF 6 |
| 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 |
| 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 |
| Q6NWY9 | 652 | 684 | 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 | 652 | 684 | 1 | 871 | Chain | ID=PRO_0000309282;Note=Pre-mRNA-processing factor 40 homolog B |
| Q6NWY9 | 652 | 684 | 625 | 682 | Domain | Note=FF 6 |
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SNVs in the skipped exons for PRPF40B |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
PRPF40B_HNSC_exon_skip_81980_psi_boxplot.png |
| - 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_81977 | 50026797 | 50026907 | 50026873 | 50026873 | Frame_Shift_Del | G | - | p.W114fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_81980 | 50026797 | 50027330 | 50026873 | 50026873 | Frame_Shift_Del | G | - | p.W114fs |
| HNSC | TCGA-QK-A6VB-01 | exon_skip_81977 | 50026797 | 50026907 | 50026874 | 50026874 | Nonsense_Mutation | G | A | p.W114* |
| HNSC | TCGA-QK-A6VB-01 | exon_skip_81980 | 50026797 | 50027330 | 50026874 | 50026874 | Nonsense_Mutation | G | A | p.W114* |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-QK-A6VB-01 |
| Cancer type: HNSC | |
| ESID: exon_skip_81980 | |
| Skipped exon start: 50026797 | |
| Skipped exon end: 50027330 | |
| Mutation start: 50026874 | |
| Mutation end: 50026874 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: p.W114* | |
| Sample: TCGA-QK-A6VB-01 |
| Cancer type: HNSC | |
| ESID: exon_skip_81977 | |
| Skipped exon start: 50026797 | |
| Skipped exon end: 50026907 | |
| Mutation start: 50026874 | |
| Mutation end: 50026874 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: p.W114* | |
exon_skip_108215_HNSC_TCGA-QK-A6VB-01.png | |
exon_skip_135111_HNSC_TCGA-QK-A6VB-01.png | |
exon_skip_135112_HNSC_TCGA-QK-A6VB-01.png | |
exon_skip_135114_HNSC_TCGA-QK-A6VB-01.png | |
exon_skip_315273_HNSC_TCGA-QK-A6VB-01.png | |
exon_skip_457890_HNSC_TCGA-QK-A6VB-01.png | |
exon_skip_81980_HNSC_TCGA-QK-A6VB-01.png | |
| - 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 |
| LN18_CENTRAL_NERVOUS_SYSTEM | 50028882 | 50029046 | 50028904 | 50028904 | Frame_Shift_Del | A | - | p.K321fs |
| DU145_PROSTATE | 50026379 | 50026406 | 50026386 | 50026386 | Missense_Mutation | C | T | p.P79L |
| P32ISH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 50026797 | 50027330 | 50026836 | 50026836 | Missense_Mutation | A | G | p.I108V |
| P32ISH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 50026797 | 50026907 | 50026836 | 50026836 | Missense_Mutation | A | G | p.I108V |
| EWS502_BONE | 50026797 | 50027330 | 50026891 | 50026891 | Missense_Mutation | T | C | p.L126P |
| EWS502_BONE | 50026797 | 50026907 | 50026891 | 50026891 | Missense_Mutation | T | C | p.L126P |
| L542_MATCHED_NORMAL_TISSUE | 50026797 | 50027330 | 50026900 | 50026900 | Missense_Mutation | A | C | p.K129T |
| L542_MATCHED_NORMAL_TISSUE | 50026797 | 50026907 | 50026900 | 50026900 | Missense_Mutation | A | C | p.K129T |
| SNU175_LARGE_INTESTINE | 50028115 | 50028238 | 50028174 | 50028174 | Missense_Mutation | C | A | p.S269Y |
| KD_SOFT_TISSUE | 50028115 | 50028238 | 50028231 | 50028231 | Missense_Mutation | G | A | p.R288K |
| JHOS4_OVARY | 50031253 | 50031367 | 50031297 | 50031297 | Missense_Mutation | G | A | p.M513I |
| SISO_CERVIX | 50031253 | 50031367 | 50031328 | 50031328 | Missense_Mutation | A | G | p.S524G |
| GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 50031253 | 50031367 | 50031328 | 50031328 | Missense_Mutation | A | G | p.S524G |
| SNGM_ENDOMETRIUM | 50036363 | 50036458 | 50036373 | 50036373 | Missense_Mutation | G | A | p.R656H |
| NCIH2172_LUNG | 50031253 | 50031367 | 50031265 | 50031265 | Nonsense_Mutation | G | T | p.E503* |
| TC138_BONE | 50024328 | 50024408 | 50024408 | 50024408 | Splice_Site | C | T | p.F6F |
| SNU175_LARGE_INTESTINE | 50026379 | 50026406 | 50026380 | 50026380 | Splice_Site | C | T | p.T77M |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 50031253 | 50031367 | 50031254 | 50031254 | Splice_Site | C | G | p.T499S |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PRPF40B |
| 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 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PRPF40B |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PRPF40B |
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RelatedDrugs for PRPF40B |
| 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 |
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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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