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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 RPAP3 |
 Gene summary |
| Gene information | Gene symbol | RPAP3 | Gene ID | 79657 |
| Gene name | RNA polymerase II associated protein 3 | |
| Synonyms | hSpagh | |
| Cytomap | 12q13.11 | |
| Type of gene | protein-coding | |
| Description | RNA polymerase II-associated protein 3 | |
| Modification date | 20180522 | |
| UniProtAcc | Q9H6T3 | |
| Context | PubMed: RPAP3 [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 RPAP3 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 RPAP3 |
| 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 RPAP3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_91393 | 12 | 48063889:48064128:48073275:48073377:48073486:48073557 | 48073275:48073377 | ENSG00000005175.5 | ENST00000005386.3,ENST00000432584.3 |
| exon_skip_91396 | 12 | 48090058:48090186:48091379:48091502:48095246:48095387 | 48091379:48091502 | ENSG00000005175.5 | ENST00000005386.3,ENST00000432584.3,ENST00000380650.4 |
| exon_skip_91397 | 12 | 48091379:48091502:48095246:48095387:48099734:48099769 | 48095246:48095387 | ENSG00000005175.5 | ENST00000432584.3 |
| exon_skip_91398 | 12 | 48095246:48095387:48096470:48096629:48099734:48099769 | 48096470:48096629 | ENSG00000005175.5 | ENST00000380650.4,ENST00000551293.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for RPAP3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_91393 | 12 | 48063889:48064128:48073275:48073377:48073486:48073557 | 48073275:48073377 | ENSG00000005175.5 | ENST00000005386.3,ENST00000432584.3 |
| exon_skip_91396 | 12 | 48090058:48090186:48091379:48091502:48095246:48095387 | 48091379:48091502 | ENSG00000005175.5 | ENST00000005386.3,ENST00000432584.3,ENST00000380650.4 |
| exon_skip_91397 | 12 | 48091379:48091502:48095246:48095387:48099734:48099769 | 48095246:48095387 | ENSG00000005175.5 | ENST00000432584.3 |
| exon_skip_91398 | 12 | 48095246:48095387:48096470:48096629:48099734:48099769 | 48096470:48096629 | ENSG00000005175.5 | ENST00000380650.4,ENST00000551293.1 |
| 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 RPAP3 |
| 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 |
| ENST00000005386 | 48073275 | 48073377 | In-frame |
| ENST00000005386 | 48091379 | 48091502 | 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 |
| ENST00000005386 | 48073275 | 48073377 | In-frame |
| ENST00000005386 | 48091379 | 48091502 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RPAP3 |
| 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 |
| ENST00000005386 | 2349 | 665 | 48091379 | 48091502 | 411 | 533 | 98 | 139 |
| ENST00000005386 | 2349 | 665 | 48073275 | 48073377 | 1302 | 1403 | 395 | 429 |
| 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 |
| ENST00000005386 | 2349 | 665 | 48091379 | 48091502 | 411 | 533 | 98 | 139 |
| ENST00000005386 | 2349 | 665 | 48073275 | 48073377 | 1302 | 1403 | 395 | 429 |
| 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 |
| Q9H6T3 | 98 | 139 | 1 | 159 | Alternative sequence | ID=VSP_044882;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9H6T3 | 98 | 139 | 2 | 665 | Chain | ID=PRO_0000302794;Note=RNA polymerase II-associated protein 3 |
| Q9H6T3 | 98 | 139 | 130 | 145 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4CGV |
| Q9H6T3 | 98 | 139 | 116 | 116 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:21406692;Dbxref=PMID:18669648,PMID:21406692 |
| Q9H6T3 | 98 | 139 | 119 | 119 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:24275569;Dbxref=PMID:18669648,PMID:21406692,PMID:24275569 |
| Q9H6T3 | 98 | 139 | 121 | 121 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:21406692;Dbxref=PMID:18669648,PMID:21406692 |
| Q9H6T3 | 98 | 139 | 133 | 166 | Repeat | Note=TPR 2 |
| Q9H6T3 | 395 | 429 | 396 | 429 | Alternative sequence | ID=VSP_027957;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9H6T3 | 395 | 429 | 2 | 665 | Chain | ID=PRO_0000302794;Note=RNA polymerase II-associated protein 3 |
| 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 |
| Q9H6T3 | 98 | 139 | 1 | 159 | Alternative sequence | ID=VSP_044882;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9H6T3 | 98 | 139 | 2 | 665 | Chain | ID=PRO_0000302794;Note=RNA polymerase II-associated protein 3 |
| Q9H6T3 | 98 | 139 | 130 | 145 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4CGV |
| Q9H6T3 | 98 | 139 | 116 | 116 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:21406692;Dbxref=PMID:18669648,PMID:21406692 |
| Q9H6T3 | 98 | 139 | 119 | 119 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:24275569;Dbxref=PMID:18669648,PMID:21406692,PMID:24275569 |
| Q9H6T3 | 98 | 139 | 121 | 121 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:21406692;Dbxref=PMID:18669648,PMID:21406692 |
| Q9H6T3 | 98 | 139 | 133 | 166 | Repeat | Note=TPR 2 |
| Q9H6T3 | 395 | 429 | 396 | 429 | Alternative sequence | ID=VSP_027957;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9H6T3 | 395 | 429 | 2 | 665 | Chain | ID=PRO_0000302794;Note=RNA polymerase II-associated protein 3 |
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SNVs in the skipped exons for RPAP3 |
| - 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. |
| - 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_91393 | 48073276 | 48073377 | 48073319 | 48073319 | Frame_Shift_Del | T | - | p.N415fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_91393 | 48073276 | 48073377 | 48073326 | 48073326 | Frame_Shift_Del | T | - | p.R413fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_91397 | 48095247 | 48095387 | 48095283 | 48095283 | Frame_Shift_Del | T | - | p.K86fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_91397 | 48095247 | 48095387 | 48095283 | 48095283 | Frame_Shift_Del | T | - | p.K86fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_91397 | 48095247 | 48095387 | 48095293 | 48095293 | Frame_Shift_Del | T | - | p.N83fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_91397 | 48095247 | 48095387 | 48095293 | 48095293 | Frame_Shift_Del | T | - | p.N83fs |
| KICH | TCGA-KN-8437-01 | exon_skip_91397 | 48095247 | 48095387 | 48095315 | 48095315 | Frame_Shift_Del | T | - | p.T76fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_91397 | 48095247 | 48095387 | 48095315 | 48095315 | Frame_Shift_Del | T | - | p.T76fs |
| LIHC | TCGA-BC-A112-01 | exon_skip_91393 | 48073276 | 48073377 | 48073370 | 48073371 | Frame_Shift_Ins | - | T | p.*398fs |
| LGG | TCGA-DB-5277-01 | exon_skip_91398 | 48096471 | 48096629 | 48096531 | 48096531 | Nonsense_Mutation | C | T | p.W31* |
| LGG | TCGA-DB-5277-01 | exon_skip_91398 | 48096471 | 48096629 | 48096531 | 48096531 | Nonsense_Mutation | C | T | p.W31X |
| - 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 |
| EN_ENDOMETRIUM | 48095247 | 48095387 | 48095314 | 48095315 | Frame_Shift_Ins | - | T | p.T76fs |
| NCIH28_PLEURA | 48091380 | 48091502 | 48091430 | 48091430 | Missense_Mutation | C | G | p.E123Q |
| CHLA218_BONE | 48095247 | 48095387 | 48095384 | 48095384 | Missense_Mutation | A | T | p.L53I |
| HO1N1_UPPER_AERODIGESTIVE_TRACT | 48096471 | 48096629 | 48096497 | 48096497 | Missense_Mutation | T | C | p.R43G |
| H3118_UPPER_AERODIGESTIVE_TRACT | 48096471 | 48096629 | 48096599 | 48096599 | Missense_Mutation | C | T | p.E9K |
| NB17_AUTONOMIC_GANGLIA | 48096471 | 48096629 | 48096599 | 48096599 | Missense_Mutation | C | T | p.E9K |
| MM127_SKIN | 48095247 | 48095387 | 48095372 | 48095372 | Nonsense_Mutation | G | A | p.R57* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RPAP3 |
| 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 RPAP3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RPAP3 |
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RelatedDrugs for RPAP3 |
| 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 RPAP3 |
| 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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