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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 POLR1C |
 Gene summary |
| Gene information | Gene symbol | POLR1C | Gene ID | 9533 |
| Gene name | RNA polymerase I and III subunit C | |
| Synonyms | AC40|HLD11|RPA39|RPA40|RPA5|RPAC1|RPC40|TCS3 | |
| Cytomap | 6p21.1 | |
| Type of gene | protein-coding | |
| Description | DNA-directed RNA polymerases I and III subunit RPAC1DNA-directed RNA polymerase I subunit CDNA-directed RNA polymerases I and III 40 kDa polypeptideRNA polymerase I subunit CRNA polymerases I and III subunit AC1polymerase (RNA) I polypeptide C, 30kDa | |
| Modification date | 20180525 | |
| UniProtAcc | O15160 | |
| Context | PubMed: POLR1C [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 POLR1C 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 POLR1C |
| 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 POLR1C |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_452162 | 6 | 43485043:43485115:43487070:43487178:43487443:43487576 | 43487070:43487178 | ENSG00000171453.13 | ENST00000481352.2,ENST00000488601.2,ENST00000428025.2,ENST00000423780.1,ENST00000372389.3,ENST00000455605.2,ENST00000304004.3,ENST00000372344.2 |
| exon_skip_452165 | 6 | 43487443:43487576:43487803:43487923:43488012:43488050 | 43487803:43487923 | ENSG00000171453.13 | ENST00000428025.2,ENST00000372389.3,ENST00000304004.3,ENST00000372344.2 |
| exon_skip_452171 | 6 | 43487806:43487923:43488012:43488165:43488362:43488441 | 43488012:43488165 | ENSG00000171453.13 | ENST00000488601.2,ENST00000372389.3,ENST00000304004.3 |
| exon_skip_452172 | 6 | 43487803:43487923:43488012:43488165:43488669:43488786 | 43488012:43488165 | ENSG00000171453.13 | ENST00000372344.2 |
| exon_skip_452180 | 6 | 43488069:43488165:43488362:43488512:43488669:43488786 | 43488362:43488512 | ENSG00000171453.13 | ENST00000481352.2,ENST00000372389.3,ENST00000304004.3 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for POLR1C |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_452162 | 6 | 43485043:43485115:43487070:43487178:43487443:43487576 | 43487070:43487178 | ENSG00000171453.13 | ENST00000428025.2,ENST00000372389.3,ENST00000481352.2,ENST00000372344.2,ENST00000304004.3,ENST00000488601.2,ENST00000423780.1,ENST00000455605.2 |
| exon_skip_452165 | 6 | 43487443:43487576:43487803:43487923:43488012:43488050 | 43487803:43487923 | ENSG00000171453.13 | ENST00000428025.2,ENST00000372389.3,ENST00000372344.2,ENST00000304004.3 |
| exon_skip_452171 | 6 | 43487806:43487923:43488012:43488165:43488362:43488441 | 43488012:43488165 | ENSG00000171453.13 | ENST00000372389.3,ENST00000304004.3,ENST00000488601.2 |
| exon_skip_452172 | 6 | 43487803:43487923:43488012:43488165:43488669:43488786 | 43488012:43488165 | ENSG00000171453.13 | ENST00000372344.2 |
| exon_skip_452180 | 6 | 43488069:43488165:43488362:43488512:43488669:43488786 | 43488362:43488512 | ENSG00000171453.13 | ENST00000372389.3,ENST00000481352.2,ENST00000304004.3 |
| 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 POLR1C |
| 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 |
| ENST00000372389 | 43487070 | 43487178 | In-frame |
| ENST00000372389 | 43487803 | 43487923 | In-frame |
| ENST00000372389 | 43488012 | 43488165 | In-frame |
| ENST00000372389 | 43488362 | 43488512 | 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 |
| ENST00000372389 | 43487070 | 43487178 | In-frame |
| ENST00000372389 | 43487803 | 43487923 | In-frame |
| ENST00000372389 | 43488012 | 43488165 | In-frame |
| ENST00000372389 | 43488362 | 43488512 | In-frame |
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Infer the effects of exon skipping event on protein functional features for POLR1C |
| 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 |
| ENST00000372389 | 1372 | 346 | 43487070 | 43487178 | 230 | 337 | 47 | 83 |
| ENST00000372389 | 1372 | 346 | 43487803 | 43487923 | 471 | 590 | 127 | 167 |
| ENST00000372389 | 1372 | 346 | 43488012 | 43488165 | 591 | 743 | 167 | 218 |
| ENST00000372389 | 1372 | 346 | 43488362 | 43488512 | 744 | 893 | 218 | 268 |
| 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 |
| ENST00000372389 | 1372 | 346 | 43487070 | 43487178 | 230 | 337 | 47 | 83 |
| ENST00000372389 | 1372 | 346 | 43487803 | 43487923 | 471 | 590 | 127 | 167 |
| ENST00000372389 | 1372 | 346 | 43488012 | 43488165 | 591 | 743 | 167 | 218 |
| ENST00000372389 | 1372 | 346 | 43488362 | 43488512 | 744 | 893 | 218 | 268 |
| 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 |
| O15160 | 47 | 83 | 2 | 346 | Chain | ID=PRO_0000132739;Note=DNA-directed RNA polymerases I and III subunit RPAC1 |
| O15160 | 47 | 83 | 65 | 65 | Natural variant | ID=VAR_074657;Note=In HLD11. M->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26151409;Dbxref=dbSNP:rs141471029,PMID:26151409 |
| O15160 | 47 | 83 | 74 | 74 | Natural variant | ID=VAR_074658;Note=In HLD11%3B decreased localization to the nucleus and retained in the cytoplasm%3B loss of association with RNA polymerase III-transcribed genes%3B decreased association with RNA polymerase III complex%3B probably prevents RNA polymeras |
| O15160 | 127 | 167 | 2 | 346 | Chain | ID=PRO_0000132739;Note=DNA-directed RNA polymerases I and III subunit RPAC1 |
| O15160 | 127 | 167 | 132 | 132 | Natural variant | ID=VAR_074661;Note=In HLD11. G->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26151409;Dbxref=dbSNP:rs201320592,PMID:26151409 |
| O15160 | 127 | 167 | 146 | 146 | Natural variant | ID=VAR_074662;Note=In HLD11. C->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26151409;Dbxref=dbSNP:rs796052125,PMID:26151409 |
| O15160 | 167 | 218 | 2 | 346 | Chain | ID=PRO_0000132739;Note=DNA-directed RNA polymerases I and III subunit RPAC1 |
| O15160 | 167 | 218 | 191 | 191 | Natural variant | ID=VAR_074663;Note=In HLD11. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26151409;Dbxref=dbSNP:rs373046018,PMID:26151409 |
| O15160 | 218 | 268 | 2 | 346 | Chain | ID=PRO_0000132739;Note=DNA-directed RNA polymerases I and III subunit RPAC1 |
| O15160 | 218 | 268 | 262 | 262 | Natural variant | ID=VAR_074664;Note=In HLD11. I->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26151409;Dbxref=dbSNP:rs751006626,PMID:26151409 |
| 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 |
| O15160 | 47 | 83 | 2 | 346 | Chain | ID=PRO_0000132739;Note=DNA-directed RNA polymerases I and III subunit RPAC1 |
| O15160 | 47 | 83 | 65 | 65 | Natural variant | ID=VAR_074657;Note=In HLD11. M->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26151409;Dbxref=dbSNP:rs141471029,PMID:26151409 |
| O15160 | 47 | 83 | 74 | 74 | Natural variant | ID=VAR_074658;Note=In HLD11%3B decreased localization to the nucleus and retained in the cytoplasm%3B loss of association with RNA polymerase III-transcribed genes%3B decreased association with RNA polymerase III complex%3B probably prevents RNA polymeras |
| O15160 | 127 | 167 | 2 | 346 | Chain | ID=PRO_0000132739;Note=DNA-directed RNA polymerases I and III subunit RPAC1 |
| O15160 | 127 | 167 | 132 | 132 | Natural variant | ID=VAR_074661;Note=In HLD11. G->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26151409;Dbxref=dbSNP:rs201320592,PMID:26151409 |
| O15160 | 127 | 167 | 146 | 146 | Natural variant | ID=VAR_074662;Note=In HLD11. C->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26151409;Dbxref=dbSNP:rs796052125,PMID:26151409 |
| O15160 | 167 | 218 | 2 | 346 | Chain | ID=PRO_0000132739;Note=DNA-directed RNA polymerases I and III subunit RPAC1 |
| O15160 | 167 | 218 | 191 | 191 | Natural variant | ID=VAR_074663;Note=In HLD11. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26151409;Dbxref=dbSNP:rs373046018,PMID:26151409 |
| O15160 | 218 | 268 | 2 | 346 | Chain | ID=PRO_0000132739;Note=DNA-directed RNA polymerases I and III subunit RPAC1 |
| O15160 | 218 | 268 | 262 | 262 | Natural variant | ID=VAR_074664;Note=In HLD11. I->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26151409;Dbxref=dbSNP:rs751006626,PMID:26151409 |
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SNVs in the skipped exons for POLR1C |
| - 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 |
| ESCA | TCGA-V5-AASV-01 | exon_skip_452165 | 43487804 | 43487923 | 43487822 | 43487825 | Frame_Shift_Del | AGAT | - | p.134_135del |
| ESCA | TCGA-V5-AASV-01 | exon_skip_452165 | 43487804 | 43487923 | 43487822 | 43487825 | Frame_Shift_Del | AGAT | - | p.D136fs |
| ESCA | TCGA-V5-AASV-01 | exon_skip_452165 | 43487804 | 43487923 | 43487822 | 43487825 | Frame_Shift_Del | AGAT | - | p.EI134fs |
| ESCA | TCGA-L5-A4OI-01 | exon_skip_452172 exon_skip_452171 | 43488013 | 43488165 | 43488038 | 43488038 | Frame_Shift_Del | C | - | p.I176fs |
| ESCA | TCGA-L5-A4OI-01 | exon_skip_452172 exon_skip_452171 | 43488013 | 43488165 | 43488038 | 43488038 | Frame_Shift_Del | C | - | p.L178fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_452180 | 43488363 | 43488512 | 43488489 | 43488489 | Frame_Shift_Del | T | - | p.V261fs |
| UCEC | TCGA-A5-A0G9-01 | exon_skip_452172 exon_skip_452171 | 43488013 | 43488165 | 43488037 | 43488038 | Frame_Shift_Ins | - | C | p.I176fs |
| BRCA | TCGA-BH-A0BW-01 | exon_skip_452162 | 43487071 | 43487178 | 43487161 | 43487161 | Nonsense_Mutation | C | T | p.R78* |
| STAD | TCGA-F1-6874-01 | exon_skip_452180 | 43488363 | 43488512 | 43488475 | 43488475 | Nonsense_Mutation | C | A | p.C256* |
| STAD | TCGA-F1-6874-01 | exon_skip_452180 | 43488363 | 43488512 | 43488475 | 43488475 | Nonsense_Mutation | C | A | p.C256X |
| LIHC | TCGA-DD-AAD5-01 | exon_skip_452162 | 43487071 | 43487178 | 43487179 | 43487179 | Splice_Site | G | T | . |
| - 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 |
| ISHIKAWAHERAKLIO02ER_ENDOMETRIUM | 43488363 | 43488512 | 43488442 | 43488446 | Frame_Shift_Del | GGAAG | - | p.EG246fs |
| TOV21G_OVARY | 43487071 | 43487178 | 43487078 | 43487078 | Missense_Mutation | G | A | p.R50H |
| NCIH28_PLEURA | 43487071 | 43487178 | 43487078 | 43487078 | Missense_Mutation | G | A | p.R50H |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43487071 | 43487178 | 43487087 | 43487087 | Missense_Mutation | T | C | p.V53A |
| SNU1040_LARGE_INTESTINE | 43487071 | 43487178 | 43487087 | 43487087 | Missense_Mutation | T | C | p.V53A |
| CP67MEL_SKIN | 43487071 | 43487178 | 43487150 | 43487150 | Missense_Mutation | A | G | p.N74S |
| NCIH3122_LUNG | 43487804 | 43487923 | 43487881 | 43487881 | Missense_Mutation | A | G | p.K154E |
| HCT15_LARGE_INTESTINE | 43488013 | 43488165 | 43488045 | 43488045 | Missense_Mutation | G | T | p.G179W |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43488013 | 43488165 | 43488137 | 43488137 | Missense_Mutation | C | A | p.D209E |
| NCIH524_LUNG | 43488363 | 43488512 | 43488449 | 43488449 | Missense_Mutation | G | A | p.E248K |
| CHLA99_BONE | 43488363 | 43488512 | 43488472 | 43488472 | Missense_Mutation | G | C | p.R255S |
| SKUT1_SOFT_TISSUE | 43488013 | 43488165 | 43488017 | 43488017 | Nonsense_Mutation | T | A | p.Y169* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for POLR1C |
| 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 POLR1C |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for POLR1C |
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RelatedDrugs for POLR1C |
| 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 POLR1C |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| POLR1C | C1855433 | Mandibulofacial dysostosis, Treacher Collins type, autosomal recessive | 2 | CTD_human;UNIPROT |
| POLR1C | C0242387 | Mandibulofacial Dysostosis | 1 | CTD_human;HPO;ORPHANET |
| POLR1C | C4225305 | LEUKODYSTROPHY, HYPOMYELINATING, 11 | 1 | UNIPROT |
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