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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 RRN3 |
 Gene summary |
| Gene information | Gene symbol | RRN3 | Gene ID | 54700 |
| Gene name | RRN3 homolog, RNA polymerase I transcription factor | |
| Synonyms | A-270G1.2|TIFIA | |
| Cytomap | 16p13.11 | |
| Type of gene | protein-coding | |
| Description | RNA polymerase I-specific transcription initiation factor RRN3RRN3 RNA polymerase I transcription factor homologTIF-IAtranscription initiation factor IAtranscription initiation factor TIF-IA | |
| Modification date | 20200313 | |
| 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 RRN3 |
| 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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ENSG00000085721
| 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 |
| PG | UP | ENST00000327307.11 | RRN3-202:protein_coding:RRN3 | 1.223609e+01 | 2.861954e+00 | 4.365036e-03 | 4.154867e-02 |
| CB | UP | ENST00000429751.6 | RRN3-203:protein_coding:RRN3 | 2.823118e+02 | 1.083177e+00 | 2.847915e-11 | 2.271897e-09 |
| 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 RRN3 |
| 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_45041 | chr16 | 15086129:15086258:15091315:15091371:15092509:15092614 | 15091315:15091371 |
| exon_skip_47528 | chr16 | 15091315:15091371:15092509:15092614:15094145:15094249 | 15092509:15092614 |
| exon_skip_5574 | chr16 | 15074723:15074861:15076558:15076650:15079998:15080096 | 15076558:15076650 |
| exon_skip_61436 | chr16 | 15071121:15071251:15072950:15073080:15074723:15074861 | 15072950:15073080 |
| exon_skip_70724 | chr16 | 15079998:15080096:15083513:15083582:15084642:15084705 | 15083513:15083582 |
| exon_skip_84240 | chr16 | 15086129:15086258:15086365:15086454:15091315:15091371 | 15086365:15086454 |
| 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_84240 | ROSMAP_PCC | 5.770339e-01 | 6.897561e-01 | -1.127222e-01 | 2.741848e-02 |
| exon_skip_84240 | ROSMAP_HCC | 5.495402e-01 | 6.787368e-01 | -1.291966e-01 | 1.968547e-04 |
| exon_skip_84240 | Mayo_CB | 4.224691e-01 | 6.564615e-01 | -2.339924e-01 | 3.771895e-08 |
| exon_skip_84240 | Mayo_TC | 5.341975e-01 | 6.663793e-01 | -1.321818e-01 | 1.318384e-06 |
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Open reading frame (ORF) annotation in the exon skipping event for RRN3 |
| 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 |
| ENST00000198767 | 15072950 | 15073080 | Frame-shift |
| ENST00000198767 | 15083513 | 15083582 | Frame-shift |
| ENST00000198767 | 15086365 | 15086454 | 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 |
| ENST00000198767 | 15083513 | 15083582 | Frame-shift |
| ENST00000198767 | 15086365 | 15086454 | 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 |
| ENST00000198767 | 15072950 | 15073080 | Frame-shift |
| ENST00000198767 | 15083513 | 15083582 | Frame-shift |
| ENST00000198767 | 15076558 | 15076650 | In-frame |
| ENST00000198767 | 15086365 | 15086454 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RRN3 |
p-ENSG00000085721_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 |
| ENST00000198767 | 3779 | 651 | 15086365 | 15086454 | 337 | 425 | 84 | 113 |
| 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 |
| ENST00000198767 | 3779 | 651 | 15086365 | 15086454 | 337 | 425 | 84 | 113 |
| 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 |
| ENST00000198767 | 3779 | 651 | 15086365 | 15086454 | 337 | 425 | 84 | 113 |
| ENST00000198767 | 3779 | 651 | 15076558 | 15076650 | 850 | 941 | 255 | 285 |
| 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 |
| Q9NYV6 | 84 | 113 | 1 | 149 | Alternative sequence | ID=VSP_056519;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9NYV6 | 84 | 113 | 1 | 651 | Chain | ID=PRO_0000211426;Note=RNA polymerase I-specific transcription initiation factor RRN3 |
| 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 |
| Q9NYV6 | 84 | 113 | 1 | 149 | Alternative sequence | ID=VSP_056519;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9NYV6 | 84 | 113 | 1 | 651 | Chain | ID=PRO_0000211426;Note=RNA polymerase I-specific transcription initiation factor RRN3 |
| 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 |
| Q9NYV6 | 84 | 113 | 1 | 149 | Alternative sequence | ID=VSP_056519;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9NYV6 | 84 | 113 | 1 | 651 | Chain | ID=PRO_0000211426;Note=RNA polymerase I-specific transcription initiation factor RRN3 |
| Q9NYV6 | 255 | 285 | 223 | 255 | Alternative sequence | ID=VSP_056521;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9NYV6 | 255 | 285 | 1 | 651 | Chain | ID=PRO_0000211426;Note=RNA polymerase I-specific transcription initiation factor RRN3 |
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3'-UTR located exon skipping events that lost miRNA binding sites in RRN3 |
| 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 RRN3 |
| - 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 RRN3 |
| 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 RRN3 |
| 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 RRN3 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | DAZAP1 | exon_skip_84240 | -4.422059e-01 | 2.296041e-08 |
| CB | ZNF638 | exon_skip_84240 | -6.532624e-01 | 4.015003e-19 |
| CB | FUBP1 | exon_skip_84240 | -4.957252e-01 | 1.992674e-10 |
| CB | HNRNPDL | exon_skip_84240 | 4.274156e-01 | 7.426801e-08 |
| CB | NUP42 | exon_skip_84240 | 6.072643e-01 | 4.438009e-16 |
| HCC | RBMS2 | exon_skip_84240 | -4.022379e-01 | 6.966824e-12 |
| HCC | MSI1 | exon_skip_84240 | -4.427691e-01 | 2.422085e-14 |
| IFG | DAZAP1 | exon_skip_84240 | -6.112189e-01 | 5.497261e-04 |
| IFG | RBMS3 | exon_skip_84240 | -5.090520e-01 | 5.666036e-03 |
| IFG | PABPN1L | exon_skip_84240 | -4.888297e-01 | 8.300232e-03 |
| IFG | ZNF326 | exon_skip_84240 | -4.297085e-01 | 2.248021e-02 |
| IFG | ZNF638 | exon_skip_84240 | -4.826556e-01 | 9.285242e-03 |
| IFG | TIA1 | exon_skip_84240 | -4.821071e-01 | 9.377297e-03 |
| IFG | FUBP1 | exon_skip_84240 | -5.492330e-01 | 2.469899e-03 |
| PCC | G3BP2 | exon_skip_84240 | 4.363970e-01 | 1.049343e-10 |
| TC | RBMS2 | exon_skip_84240 | -5.212814e-01 | 4.726750e-11 |
| TC | G3BP2 | exon_skip_84240 | 4.066844e-01 | 6.768896e-07 |
| TC | KHDRBS2 | exon_skip_84240 | 4.794219e-01 | 2.359101e-09 |
| TC | HNRNPDL | exon_skip_84240 | 5.072974e-01 | 1.851900e-10 |
| TC | HNRNPD | exon_skip_84240 | 5.230565e-01 | 3.956678e-11 |
| TC | NUP42 | exon_skip_84240 | 4.217339e-01 | 2.334199e-07 |
| TC | NOVA1 | exon_skip_84240 | 5.058242e-01 | 2.130809e-10 |
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RelatedDrugs for RRN3 |
| 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 RRN3 |
| 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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