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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 RPA3 |
 Gene summary |
| Gene information | Gene symbol | RPA3 | Gene ID | 6119 |
| Gene name | replication protein A3 | |
| Synonyms | REPA3|RP-A p14 | |
| Cytomap | 7p21.3 | |
| Type of gene | protein-coding | |
| Description | replication protein A 14 kDa subunitRF-A protein 3replication factor A protein 3replication protein A3, 14kDa | |
| Modification date | 20180523 | |
| UniProtAcc | P35244 | |
| Context | PubMed: RPA3 [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 |
| RPA3 | GO:0006284 | base-excision repair | 9765279 |
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Exon skipping events across known transcript of Ensembl for RPA3 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 RPA3 |
| 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 RPA3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_473730 | 7 | 7677494:7677603:7678700:7678775:7679950:7680208 | 7678700:7678775 | ENSG00000106399.7 | ENST00000396682.2,ENST00000223129.4 |
| exon_skip_473733 | 7 | 7678700:7678775:7679950:7680212:7680353:7680447 | 7679950:7680212 | ENSG00000106399.7 | ENST00000396682.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for RPA3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_473730 | 7 | 7677494:7677603:7678700:7678775:7679950:7680208 | 7678700:7678775 | ENSG00000106399.7 | ENST00000223129.4,ENST00000396682.2 |
| exon_skip_473733 | 7 | 7678700:7678775:7679950:7680212:7680353:7680447 | 7679950:7680212 | ENSG00000106399.7 | ENST00000396682.2 |
| 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 RPA3 |
| 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 |
| ENST00000396682 | 7679950 | 7680212 | 3UTR-3CDS |
| ENST00000223129 | 7678700 | 7678775 | In-frame |
| ENST00000396682 | 7678700 | 7678775 | 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 |
| ENST00000396682 | 7679950 | 7680212 | 3UTR-3CDS |
| ENST00000223129 | 7678700 | 7678775 | In-frame |
| ENST00000396682 | 7678700 | 7678775 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RPA3 |
| 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 |
| ENST00000223129 | 2037 | 121 | 7678700 | 7678775 | 1272 | 1346 | 33 | 58 |
| ENST00000396682 | 864 | 121 | 7678700 | 7678775 | 513 | 587 | 33 | 58 |
| 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 |
| ENST00000223129 | 2037 | 121 | 7678700 | 7678775 | 1272 | 1346 | 33 | 58 |
| ENST00000396682 | 864 | 121 | 7678700 | 7678775 | 513 | 587 | 33 | 58 |
| 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 |
| P35244 | 33 | 58 | 24 | 34 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3KDF |
| P35244 | 33 | 58 | 24 | 34 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3KDF |
| P35244 | 33 | 58 | 38 | 44 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3KDF |
| P35244 | 33 | 58 | 38 | 44 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3KDF |
| P35244 | 33 | 58 | 50 | 54 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3KDF |
| P35244 | 33 | 58 | 50 | 54 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3KDF |
| P35244 | 33 | 58 | 2 | 121 | Chain | ID=PRO_0000097276;Note=Replication protein A 14 kDa subunit |
| P35244 | 33 | 58 | 2 | 121 | Chain | ID=PRO_0000097276;Note=Replication protein A 14 kDa subunit |
| P35244 | 33 | 58 | 39 | 39 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin);Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26474068;Dbxref=PMID:26474068 |
| P35244 | 33 | 58 | 39 | 39 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin);Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26474068;Dbxref=PMID:26474068 |
| 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 |
| P35244 | 33 | 58 | 24 | 34 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3KDF |
| P35244 | 33 | 58 | 24 | 34 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3KDF |
| P35244 | 33 | 58 | 38 | 44 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3KDF |
| P35244 | 33 | 58 | 38 | 44 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3KDF |
| P35244 | 33 | 58 | 50 | 54 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3KDF |
| P35244 | 33 | 58 | 50 | 54 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3KDF |
| P35244 | 33 | 58 | 2 | 121 | Chain | ID=PRO_0000097276;Note=Replication protein A 14 kDa subunit |
| P35244 | 33 | 58 | 2 | 121 | Chain | ID=PRO_0000097276;Note=Replication protein A 14 kDa subunit |
| P35244 | 33 | 58 | 39 | 39 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin);Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26474068;Dbxref=PMID:26474068 |
| P35244 | 33 | 58 | 39 | 39 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin);Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26474068;Dbxref=PMID:26474068 |
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SNVs in the skipped exons for RPA3 |
| - 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-DD-A1EG-01 | exon_skip_473730 | 7678701 | 7678775 | 7678726 | 7678726 | Frame_Shift_Del | T | - | p.N50fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_473730 | 7678701 | 7678775 | 7678726 | 7678726 | Frame_Shift_Del | T | - | p.N50fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_473730 | 7678701 | 7678775 | 7678726 | 7678726 | Frame_Shift_Del | T | - | p.N50fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_473730 | 7678701 | 7678775 | 7678732 | 7678732 | Frame_Shift_Del | C | - | p.G48fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_473730 | 7678701 | 7678775 | 7678757 | 7678757 | Frame_Shift_Del | T | - | p.M40fs |
| UCEC | TCGA-AP-A0LM-01 | exon_skip_473730 | 7678701 | 7678775 | 7678706 | 7678706 | Nonsense_Mutation | C | A | p.E57* |
| BLCA | TCGA-G2-A2EF-01 | exon_skip_473730 | 7678701 | 7678775 | 7678739 | 7678739 | Nonsense_Mutation | C | A | p.G46* |
| - 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 |
| RKO_LARGE_INTESTINE | 7678701 | 7678775 | 7678726 | 7678726 | Frame_Shift_Del | T | - | p.N50fs |
| CHL1_SKIN | 7678701 | 7678775 | 7678703 | 7678703 | Missense_Mutation | G | A | p.P58S |
| HMCB_SKIN | 7678701 | 7678775 | 7678703 | 7678703 | Missense_Mutation | G | A | p.P58S |
| COLO792_SKIN | 7678701 | 7678775 | 7678736 | 7678736 | Missense_Mutation | C | T | p.E47K |
| DANG_PANCREAS | 7678701 | 7678775 | 7678742 | 7678742 | Missense_Mutation | C | G | p.D45H |
| FUOV1_OVARY | 7678701 | 7678775 | 7678765 | 7678765 | Missense_Mutation | G | A | p.T37I |
| DU145_PROSTATE | 7678701 | 7678775 | 7678768 | 7678768 | Missense_Mutation | G | A | p.P36L |
| SW982_SOFT_TISSUE | 7678701 | 7678775 | 7678701 | 7678701 | Splice_Site | G | T | p.P58P |
| HT1197_URINARY_TRACT | 7678701 | 7678775 | 7678701 | 7678701 | Splice_Site | G | T | p.P58P |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RPA3 |
| 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 RPA3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RPA3 |
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RelatedDrugs for RPA3 |
| 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 RPA3 |
| 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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