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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 RFC1 |
 Gene summary |
| Gene information | Gene symbol | RFC1 | Gene ID | 5981 |
| Gene name | replication factor C subunit 1 | |
| Synonyms | A1|MHCBFB|PO-GA|RECC1|RFC|RFC140 | |
| Cytomap | 4p14 | |
| Type of gene | protein-coding | |
| Description | replication factor C subunit 1A1 140 kDa subunitDNA-binding protein PO-GAMHC binding factor, betaRF-C 140 kDa subunitactivator 1 140 kDa subunitactivator 1 large subunitactivator 1 subunit 1replication factor C (activator 1) 1, 145kDareplication | |
| Modification date | 20180523 | |
| UniProtAcc | P35251 | |
| Context | PubMed: RFC1 [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 RFC1 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 RFC1 |
| 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 RFC1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_429033 | 4 | 39304356:39304494:39304679:39304771:39306433:39306548 | 39304679:39304771 | ENSG00000035928.10 | ENST00000381897.1,ENST00000349703.2 |
| exon_skip_429036 | 4 | 39306433:39306548:39308211:39308321:39310255:39310652 | 39308211:39308321 | ENSG00000035928.10 | ENST00000349703.2 |
| exon_skip_429038 | 4 | 39306433:39306548:39308211:39308324:39310255:39310652 | 39308211:39308324 | ENSG00000035928.10 | ENST00000381897.1 |
| exon_skip_429044 | 4 | 39308211:39308321:39310255:39310652:39313064:39313169 | 39310255:39310652 | ENSG00000035928.10 | ENST00000349703.2 |
| exon_skip_429045 | 4 | 39308253:39308324:39308995:39309091:39310255:39310646 | 39308995:39309091 | ENSG00000035928.10 | ENST00000502706.1 |
| exon_skip_429047 | 4 | 39308253:39308324:39310255:39310652:39313064:39313169 | 39310255:39310652 | ENSG00000035928.10 | ENST00000381897.1 |
| exon_skip_429049 | 4 | 39322084:39322289:39322906:39322994:39324959:39325037 | 39322906:39322994 | ENSG00000035928.10 | ENST00000381897.1,ENST00000418436.1,ENST00000349703.2 |
| exon_skip_429055 | 4 | 39322906:39322994:39324959:39325037:39328182:39328260 | 39324959:39325037 | ENSG00000035928.10 | ENST00000381897.1,ENST00000418436.1,ENST00000349703.2 |
| exon_skip_429058 | 4 | 39324959:39325037:39328182:39328260:39329143:39329376 | 39328182:39328260 | ENSG00000035928.10 | ENST00000381897.1,ENST00000418436.1,ENST00000349703.2 |
| exon_skip_429059 | 4 | 39329227:39329376:39343106:39343285:39343964:39344087 | 39343106:39343285 | ENSG00000035928.10 | ENST00000512275.1 |
| exon_skip_429060 | 4 | 39343964:39344087:39347020:39347096:39352967:39353096 | 39347020:39347096 | ENSG00000035928.10 | ENST00000504849.1,ENST00000381897.1,ENST00000512275.1,ENST00000418436.1,ENST00000349703.2 |
| exon_skip_429061 | 4 | 39353051:39353096:39357496:39357617:39367858:39367955 | 39357496:39357617 | ENSG00000035928.10 | ENST00000418436.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for RFC1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_429033 | 4 | 39304356:39304494:39304679:39304771:39306433:39306548 | 39304679:39304771 | ENSG00000035928.10 | ENST00000349703.2,ENST00000381897.1 |
| exon_skip_429036 | 4 | 39306433:39306548:39308211:39308321:39310255:39310652 | 39308211:39308321 | ENSG00000035928.10 | ENST00000349703.2 |
| exon_skip_429038 | 4 | 39306433:39306548:39308211:39308324:39310255:39310652 | 39308211:39308324 | ENSG00000035928.10 | ENST00000381897.1 |
| exon_skip_429044 | 4 | 39308211:39308321:39310255:39310652:39313064:39313169 | 39310255:39310652 | ENSG00000035928.10 | ENST00000349703.2 |
| exon_skip_429045 | 4 | 39308253:39308324:39308995:39309091:39310255:39310646 | 39308995:39309091 | ENSG00000035928.10 | ENST00000502706.1 |
| exon_skip_429047 | 4 | 39308253:39308324:39310255:39310652:39313064:39313169 | 39310255:39310652 | ENSG00000035928.10 | ENST00000381897.1 |
| exon_skip_429049 | 4 | 39322084:39322289:39322906:39322994:39324959:39325037 | 39322906:39322994 | ENSG00000035928.10 | ENST00000349703.2,ENST00000381897.1,ENST00000418436.1 |
| exon_skip_429055 | 4 | 39322906:39322994:39324959:39325037:39328182:39328260 | 39324959:39325037 | ENSG00000035928.10 | ENST00000349703.2,ENST00000381897.1,ENST00000418436.1 |
| exon_skip_429058 | 4 | 39324959:39325037:39328182:39328260:39329143:39329376 | 39328182:39328260 | ENSG00000035928.10 | ENST00000349703.2,ENST00000381897.1,ENST00000418436.1 |
| exon_skip_429059 | 4 | 39329227:39329376:39343106:39343285:39343964:39344087 | 39343106:39343285 | ENSG00000035928.10 | ENST00000512275.1 |
| exon_skip_429060 | 4 | 39343964:39344087:39347020:39347096:39352967:39353096 | 39347020:39347096 | ENSG00000035928.10 | ENST00000349703.2,ENST00000381897.1,ENST00000418436.1,ENST00000504849.1,ENST00000512275.1 |
| exon_skip_429061 | 4 | 39353051:39353096:39357496:39357617:39367858:39367955 | 39357496:39357617 | ENSG00000035928.10 | ENST00000418436.1 |
| 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 RFC1 |
| 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 |
| ENST00000381897 | 39304679 | 39304771 | Frame-shift |
| ENST00000381897 | 39308211 | 39308324 | Frame-shift |
| ENST00000381897 | 39310255 | 39310652 | Frame-shift |
| ENST00000381897 | 39322906 | 39322994 | Frame-shift |
| ENST00000381897 | 39347020 | 39347096 | Frame-shift |
| ENST00000381897 | 39324959 | 39325037 | In-frame |
| ENST00000381897 | 39328182 | 39328260 | 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 |
| ENST00000381897 | 39304679 | 39304771 | Frame-shift |
| ENST00000381897 | 39308211 | 39308324 | Frame-shift |
| ENST00000381897 | 39310255 | 39310652 | Frame-shift |
| ENST00000381897 | 39322906 | 39322994 | Frame-shift |
| ENST00000381897 | 39347020 | 39347096 | Frame-shift |
| ENST00000381897 | 39324959 | 39325037 | In-frame |
| ENST00000381897 | 39328182 | 39328260 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RFC1 |
| 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 |
| ENST00000381897 | 4903 | 1148 | 39328182 | 39328260 | 699 | 776 | 188 | 214 |
| ENST00000381897 | 4903 | 1148 | 39324959 | 39325037 | 777 | 854 | 214 | 240 |
| 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 |
| ENST00000381897 | 4903 | 1148 | 39328182 | 39328260 | 699 | 776 | 188 | 214 |
| ENST00000381897 | 4903 | 1148 | 39324959 | 39325037 | 777 | 854 | 214 | 240 |
| 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 |
| P35251 | 188 | 214 | 1 | 1148 | Chain | ID=PRO_0000121772;Note=Replication factor C subunit 1 |
| P35251 | 188 | 214 | 190 | 190 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:17525332,ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:23186163;Dbxref=PMID:1 |
| P35251 | 214 | 240 | 1 | 1148 | Chain | ID=PRO_0000121772;Note=Replication factor C subunit 1 |
| 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 |
| P35251 | 188 | 214 | 1 | 1148 | Chain | ID=PRO_0000121772;Note=Replication factor C subunit 1 |
| P35251 | 188 | 214 | 190 | 190 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:17525332,ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:23186163;Dbxref=PMID:1 |
| P35251 | 214 | 240 | 1 | 1148 | Chain | ID=PRO_0000121772;Note=Replication factor C subunit 1 |
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SNVs in the skipped exons for RFC1 |
| - 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 |
| UCS | TCGA-N8-A56S-01 | exon_skip_429033 | 39304680 | 39304771 | 39304717 | 39304718 | Frame_Shift_Del | TC | - | p.723_723del |
| UCS | TCGA-N8-A56S-01 | exon_skip_429033 | 39304680 | 39304771 | 39304717 | 39304718 | Frame_Shift_Del | TC | - | p.D723fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_429044 exon_skip_429047 | 39310256 | 39310652 | 39310558 | 39310558 | Frame_Shift_Del | T | - | p.K528fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_429044 exon_skip_429047 | 39310256 | 39310652 | 39310598 | 39310598 | Frame_Shift_Del | T | - | p.R515fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_429044 exon_skip_429047 | 39310256 | 39310652 | 39310598 | 39310598 | Frame_Shift_Del | T | - | p.R515fs |
| ESCA | TCGA-ZR-A9CJ-01 | exon_skip_429044 exon_skip_429047 | 39310256 | 39310652 | 39310612 | 39310612 | Frame_Shift_Del | T | - | p.N510fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_429044 exon_skip_429047 | 39310256 | 39310652 | 39310612 | 39310612 | Frame_Shift_Del | T | - | p.N510fs |
| STAD | TCGA-CG-5733-01 | exon_skip_429044 exon_skip_429047 | 39310256 | 39310652 | 39310612 | 39310612 | Frame_Shift_Del | T | - | p.N510fs |
| STAD | TCGA-VQ-A8P2-01 | exon_skip_429044 exon_skip_429047 | 39310256 | 39310652 | 39310612 | 39310612 | Frame_Shift_Del | T | - | p.N510fs |
| STAD | TCGA-BR-7851-01 | exon_skip_429055 | 39324960 | 39325037 | 39324961 | 39324961 | Frame_Shift_Del | T | - | p.K240fs |
| LUAD | TCGA-53-7624-01 | exon_skip_429055 | 39324960 | 39325037 | 39325005 | 39325005 | Frame_Shift_Del | A | - | p.F225fs |
| KIRC | TCGA-B0-5094-01 | exon_skip_429058 | 39328183 | 39328260 | 39328257 | 39328258 | Frame_Shift_Del | AA | - | p.190_190del |
| KIRC | TCGA-B0-5094-01 | exon_skip_429058 | 39328183 | 39328260 | 39328257 | 39328258 | Frame_Shift_Del | AA | - | p.LS189fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_429060 | 39347021 | 39347096 | 39347041 | 39347041 | Frame_Shift_Del | T | - | p.K63fs |
| ACC | TCGA-OR-A5LL-01 | exon_skip_429044 exon_skip_429047 | 39310256 | 39310652 | 39310527 | 39310528 | Frame_Shift_Ins | - | A | p.C538fs |
| COAD | TCGA-AZ-6598-01 | exon_skip_429055 | 39324960 | 39325037 | 39324960 | 39324961 | Frame_Shift_Ins | - | T | p.K240fs |
| SKCM | TCGA-FS-A1ZK-06 | exon_skip_429033 | 39304680 | 39304771 | 39304682 | 39304682 | Nonsense_Mutation | G | A | p.Q735* |
| SKCM | TCGA-FS-A1ZK-06 | exon_skip_429033 | 39304680 | 39304771 | 39304682 | 39304682 | Nonsense_Mutation | G | A | p.Q735X |
| UCEC | TCGA-B5-A0JY-01 | exon_skip_429049 | 39322907 | 39322994 | 39322970 | 39322970 | Nonsense_Mutation | C | A | p.E249* |
| COAD | TCGA-AZ-6601-01 | exon_skip_429049 | 39322907 | 39322994 | 39322991 | 39322991 | Nonsense_Mutation | G | A | p.R242X |
| - 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 |
| HEC108_ENDOMETRIUM | 39310256 | 39310652 | 39310612 | 39310612 | Frame_Shift_Del | T | - | p.N510fs |
| SNGM_ENDOMETRIUM | 39310256 | 39310652 | 39310612 | 39310612 | Frame_Shift_Del | T | - | p.N510fs |
| SNU175_LARGE_INTESTINE | 39310256 | 39310652 | 39310612 | 39310612 | Frame_Shift_Del | T | - | p.N510fs |
| SNU1040_LARGE_INTESTINE | 39310256 | 39310652 | 39310612 | 39310612 | Frame_Shift_Del | T | - | p.N510fs |
| TGBC11TKB_STOMACH | 39310256 | 39310652 | 39310612 | 39310612 | Frame_Shift_Del | T | - | p.N510fs |
| MFE319_ENDOMETRIUM | 39310256 | 39310652 | 39310634 | 39310635 | Frame_Shift_Ins | - | T | p.L503fs |
| SNU1040_LARGE_INTESTINE | 39304680 | 39304771 | 39304750 | 39304750 | Missense_Mutation | C | G | p.S712T |
| BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 39308212 | 39308324 | 39308247 | 39308247 | Missense_Mutation | C | A | p.V655F |
| BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 39308212 | 39308321 | 39308247 | 39308247 | Missense_Mutation | C | A | p.V655F |
| HEC108_ENDOMETRIUM | 39308212 | 39308324 | 39308285 | 39308285 | Missense_Mutation | G | C | p.S642C |
| HEC108_ENDOMETRIUM | 39308212 | 39308321 | 39308285 | 39308285 | Missense_Mutation | G | C | p.S642C |
| BB30HNC_UPPER_AERODIGESTIVE_TRACT | 39308212 | 39308324 | 39308291 | 39308291 | Missense_Mutation | T | C | p.D640G |
| BB30HNC_UPPER_AERODIGESTIVE_TRACT | 39308212 | 39308321 | 39308291 | 39308291 | Missense_Mutation | T | C | p.D640G |
| BB30PBL_MATCHED_NORMAL_TISSUE | 39308212 | 39308324 | 39308291 | 39308291 | Missense_Mutation | T | C | p.D640G |
| BB30PBL_MATCHED_NORMAL_TISSUE | 39308212 | 39308321 | 39308291 | 39308291 | Missense_Mutation | T | C | p.D640G |
| LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 39310256 | 39310652 | 39310280 | 39310280 | Missense_Mutation | T | A | p.S621C |
| HT115_LARGE_INTESTINE | 39310256 | 39310652 | 39310294 | 39310294 | Missense_Mutation | C | T | p.R616Q |
| SNGM_ENDOMETRIUM | 39310256 | 39310652 | 39310303 | 39310303 | Missense_Mutation | C | T | p.R613H |
| INA6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 39310256 | 39310652 | 39310372 | 39310372 | Missense_Mutation | T | C | p.Y590C |
| SKUT1_SOFT_TISSUE | 39310256 | 39310652 | 39310441 | 39310441 | Missense_Mutation | C | T | p.S567N |
| RL952_ENDOMETRIUM | 39310256 | 39310652 | 39310562 | 39310562 | Missense_Mutation | T | C | p.K527E |
| SNUC2A_LARGE_INTESTINE | 39322907 | 39322994 | 39322916 | 39322916 | Missense_Mutation | G | T | p.P267T |
| SNUC2B_LARGE_INTESTINE | 39322907 | 39322994 | 39322916 | 39322916 | Missense_Mutation | G | T | p.P267T |
| CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 39328183 | 39328260 | 39328187 | 39328187 | Missense_Mutation | G | A | p.A213V |
| CAL12T_LUNG | 39347021 | 39347096 | 39347064 | 39347064 | Missense_Mutation | T | A | p.K55N |
| CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 39347021 | 39347096 | 39347083 | 39347083 | Missense_Mutation | C | T | p.R49H |
| HCC15_LUNG | 39347021 | 39347096 | 39347086 | 39347086 | Missense_Mutation | G | A | p.S48F |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RFC1 |
| 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 RFC1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RFC1 |
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RelatedDrugs for RFC1 |
| 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 RFC1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| RFC1 | C0001973 | Alcoholic Intoxication, Chronic | 1 | PSYGENET |
| RFC1 | C0009375 | Colonic Neoplasms | 1 | CTD_human |
| RFC1 | C0029463 | Osteosarcoma | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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