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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 TYW1 |
 Gene summary |
| Gene information | Gene symbol | TYW1 | Gene ID | 55253 |
| Gene name | tRNA-yW synthesizing protein 1 homolog | |
| Synonyms | RSAFD1|TYW1A|YPL207W | |
| Cytomap | 7q11.21 | |
| Type of gene | protein-coding | |
| Description | S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthaseradical S-adenosyl methionine and flavodoxin domain-containing protein 1radical S-adenosyl methionine and flavodoxin domains 1tRNA wybutosine-synthesizing protein 1 homologtRNA-yW synthe | |
| Modification date | 20180519 | |
| UniProtAcc | Q9NV66 | |
| Context | PubMed: TYW1 [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 TYW1 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 TYW1 |
| 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 TYW1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_466652 | 7 | 66463803:66463941:66474569:66474671:66479353:66479548 | 66474569:66474671 | ENSG00000198874.8 | ENST00000359626.5,ENST00000361660.4 |
| exon_skip_466653 | 7 | 66474569:66474671:66479353:66479548:66482839:66482868 | 66479353:66479548 | ENSG00000198874.8 | ENST00000359626.5,ENST00000361660.4 |
| exon_skip_466655 | 7 | 66482839:66483130:66489886:66490009:66514935:66515053 | 66489886:66490009 | ENSG00000198874.8 | ENST00000359626.5,ENST00000361660.4 |
| exon_skip_466656 | 7 | 66489886:66490009:66514935:66515053:66532271:66532390 | 66514935:66515053 | ENSG00000198874.8 | ENST00000361660.4 |
| exon_skip_466657 | 7 | 66514935:66515053:66520821:66520874:66532271:66532390 | 66520821:66520874 | ENSG00000198874.8 | ENST00000359626.5 |
| exon_skip_466658 | 7 | 66514935:66515053:66532271:66532390:66548416:66548526 | 66532271:66532390 | ENSG00000198874.8 | ENST00000361660.4 |
| exon_skip_466662 | 7 | 66532271:66532390:66548416:66548526:66563527:66563705 | 66548416:66548526 | ENSG00000198874.8 | ENST00000359626.5,ENST00000495971.1,ENST00000361660.4 |
| exon_skip_466663 | 7 | 66548416:66548526:66563527:66563705:66582469:66582605 | 66563527:66563705 | ENSG00000198874.8 | ENST00000359626.5,ENST00000495971.1,ENST00000361660.4 |
| exon_skip_466665 | 7 | 66582469:66582605:66648112:66648223:66660156:66660324 | 66648112:66648223 | ENSG00000198874.8 | ENST00000359626.5,ENST00000495971.1,ENST00000361660.4 |
| exon_skip_466666 | 7 | 66648112:66648223:66660156:66660324:66703294:66703627 | 66660156:66660324 | ENSG00000198874.8 | ENST00000359626.5,ENST00000495971.1,ENST00000361660.4 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for TYW1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_466652 | 7 | 66463803:66463941:66474569:66474671:66479353:66479548 | 66474569:66474671 | ENSG00000198874.8 | ENST00000359626.5,ENST00000361660.4 |
| exon_skip_466653 | 7 | 66474569:66474671:66479353:66479548:66482839:66482868 | 66479353:66479548 | ENSG00000198874.8 | ENST00000359626.5,ENST00000361660.4 |
| exon_skip_466655 | 7 | 66482839:66483130:66489886:66490009:66514935:66515053 | 66489886:66490009 | ENSG00000198874.8 | ENST00000359626.5,ENST00000361660.4 |
| exon_skip_466656 | 7 | 66489886:66490009:66514935:66515053:66532271:66532390 | 66514935:66515053 | ENSG00000198874.8 | ENST00000361660.4 |
| exon_skip_466657 | 7 | 66514935:66515053:66520821:66520874:66532271:66532390 | 66520821:66520874 | ENSG00000198874.8 | ENST00000359626.5 |
| exon_skip_466658 | 7 | 66514935:66515053:66532271:66532390:66548416:66548526 | 66532271:66532390 | ENSG00000198874.8 | ENST00000361660.4 |
| exon_skip_466662 | 7 | 66532271:66532390:66548416:66548526:66563527:66563705 | 66548416:66548526 | ENSG00000198874.8 | ENST00000359626.5,ENST00000361660.4,ENST00000495971.1 |
| exon_skip_466663 | 7 | 66548416:66548526:66563527:66563705:66582469:66582605 | 66563527:66563705 | ENSG00000198874.8 | ENST00000359626.5,ENST00000361660.4,ENST00000495971.1 |
| exon_skip_466665 | 7 | 66582469:66582605:66648112:66648223:66660156:66660324 | 66648112:66648223 | ENSG00000198874.8 | ENST00000359626.5,ENST00000361660.4,ENST00000495971.1 |
| exon_skip_466666 | 7 | 66648112:66648223:66660156:66660324:66703294:66703627 | 66660156:66660324 | ENSG00000198874.8 | ENST00000359626.5,ENST00000361660.4,ENST00000495971.1 |
| 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 TYW1 |
| 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 |
| ENST00000359626 | 66520821 | 66520874 | Frame-shift |
| ENST00000359626 | 66548416 | 66548526 | Frame-shift |
| ENST00000359626 | 66563527 | 66563705 | Frame-shift |
| ENST00000359626 | 66474569 | 66474671 | In-frame |
| ENST00000359626 | 66479353 | 66479548 | In-frame |
| ENST00000359626 | 66489886 | 66490009 | In-frame |
| ENST00000359626 | 66648112 | 66648223 | In-frame |
| ENST00000359626 | 66660156 | 66660324 | 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 |
| ENST00000359626 | 66520821 | 66520874 | Frame-shift |
| ENST00000359626 | 66548416 | 66548526 | Frame-shift |
| ENST00000359626 | 66563527 | 66563705 | Frame-shift |
| ENST00000359626 | 66474569 | 66474671 | In-frame |
| ENST00000359626 | 66479353 | 66479548 | In-frame |
| ENST00000359626 | 66489886 | 66490009 | In-frame |
| ENST00000359626 | 66648112 | 66648223 | In-frame |
| ENST00000359626 | 66660156 | 66660324 | In-frame |
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Infer the effects of exon skipping event on protein functional features for TYW1 |
| 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 |
| ENST00000359626 | 3365 | 732 | 66474569 | 66474671 | 438 | 539 | 91 | 125 |
| ENST00000359626 | 3365 | 732 | 66479353 | 66479548 | 540 | 734 | 125 | 190 |
| ENST00000359626 | 3365 | 732 | 66489886 | 66490009 | 1026 | 1148 | 287 | 328 |
| ENST00000359626 | 3365 | 732 | 66648112 | 66648223 | 1863 | 1973 | 566 | 603 |
| ENST00000359626 | 3365 | 732 | 66660156 | 66660324 | 1974 | 2141 | 603 | 659 |
| 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 |
| ENST00000359626 | 3365 | 732 | 66474569 | 66474671 | 438 | 539 | 91 | 125 |
| ENST00000359626 | 3365 | 732 | 66479353 | 66479548 | 540 | 734 | 125 | 190 |
| ENST00000359626 | 3365 | 732 | 66489886 | 66490009 | 1026 | 1148 | 287 | 328 |
| ENST00000359626 | 3365 | 732 | 66648112 | 66648223 | 1863 | 1973 | 566 | 603 |
| ENST00000359626 | 3365 | 732 | 66660156 | 66660324 | 1974 | 2141 | 603 | 659 |
| 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 |
| Q9NV66 | 91 | 125 | 1 | 732 | Chain | ID=PRO_0000281826;Note=S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase |
| Q9NV66 | 91 | 125 | 79 | 237 | Domain | Note=Flavodoxin-like;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00088 |
| Q9NV66 | 125 | 190 | 1 | 732 | Chain | ID=PRO_0000281826;Note=S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase |
| Q9NV66 | 125 | 190 | 79 | 237 | Domain | Note=Flavodoxin-like;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00088 |
| Q9NV66 | 125 | 190 | 176 | 208 | Nucleotide binding | Note=FMN;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00088 |
| Q9NV66 | 287 | 328 | 1 | 732 | Chain | ID=PRO_0000281826;Note=S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase |
| Q9NV66 | 566 | 603 | 385 | 732 | Alternative sequence | ID=VSP_024067;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9NV66 | 566 | 603 | 1 | 732 | Chain | ID=PRO_0000281826;Note=S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase |
| Q9NV66 | 603 | 659 | 385 | 732 | Alternative sequence | ID=VSP_024067;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9NV66 | 603 | 659 | 1 | 732 | Chain | ID=PRO_0000281826;Note=S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase |
| Q9NV66 | 603 | 659 | 632 | 632 | Natural variant | ID=VAR_031289;Note=H->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14702039;Dbxref=dbSNP:rs2949097,PMID:14702039 |
| 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 |
| Q9NV66 | 91 | 125 | 1 | 732 | Chain | ID=PRO_0000281826;Note=S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase |
| Q9NV66 | 91 | 125 | 79 | 237 | Domain | Note=Flavodoxin-like;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00088 |
| Q9NV66 | 125 | 190 | 1 | 732 | Chain | ID=PRO_0000281826;Note=S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase |
| Q9NV66 | 125 | 190 | 79 | 237 | Domain | Note=Flavodoxin-like;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00088 |
| Q9NV66 | 125 | 190 | 176 | 208 | Nucleotide binding | Note=FMN;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00088 |
| Q9NV66 | 287 | 328 | 1 | 732 | Chain | ID=PRO_0000281826;Note=S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase |
| Q9NV66 | 566 | 603 | 385 | 732 | Alternative sequence | ID=VSP_024067;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9NV66 | 566 | 603 | 1 | 732 | Chain | ID=PRO_0000281826;Note=S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase |
| Q9NV66 | 603 | 659 | 385 | 732 | Alternative sequence | ID=VSP_024067;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9NV66 | 603 | 659 | 1 | 732 | Chain | ID=PRO_0000281826;Note=S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase |
| Q9NV66 | 603 | 659 | 632 | 632 | Natural variant | ID=VAR_031289;Note=H->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14702039;Dbxref=dbSNP:rs2949097,PMID:14702039 |
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SNVs in the skipped exons for TYW1 |
| - 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_466653 | 66479354 | 66479548 | 66479363 | 66479363 | Frame_Shift_Del | A | - | p.K129fs |
| HNSC | TCGA-BA-A6DA-01 | exon_skip_466653 | 66479354 | 66479548 | 66479503 | 66479503 | Frame_Shift_Del | G | - | p.A175fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_466658 | 66532272 | 66532390 | 66532284 | 66532284 | Frame_Shift_Del | G | - | p.G390fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_466666 | 66660157 | 66660324 | 66660261 | 66660261 | Frame_Shift_Del | C | - | p.I638fs |
| BLCA | TCGA-C4-A0EZ-01 | exon_skip_466653 | 66479354 | 66479548 | 66479465 | 66479465 | Nonsense_Mutation | C | T | p.R163* |
| LUSC | TCGA-22-4595-01 | exon_skip_466655 | 66489887 | 66490009 | 66490007 | 66490007 | Nonsense_Mutation | A | T | p.K328* |
| LGG | TCGA-DU-6392-01 | exon_skip_466662 | 66548417 | 66548526 | 66548517 | 66548517 | Nonsense_Mutation | C | T | p.Q459* |
| ESCA | TCGA-L5-A8NF-01 | exon_skip_466657 | 66520822 | 66520874 | 66520821 | 66520821 | 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 |
| SNGM_ENDOMETRIUM | 66474570 | 66474671 | 66474634 | 66474634 | Missense_Mutation | T | C | p.L113P |
| CAKI2_KIDNEY | 66479354 | 66479548 | 66479496 | 66479496 | Missense_Mutation | G | A | p.R173K |
| AN3CA_ENDOMETRIUM | 66489887 | 66490009 | 66489900 | 66489900 | Missense_Mutation | T | C | p.F292S |
| CHL1_SKIN | 66489887 | 66490009 | 66489920 | 66489920 | Missense_Mutation | G | A | p.E299K |
| HMCB_SKIN | 66489887 | 66490009 | 66489920 | 66489920 | Missense_Mutation | G | A | p.E299K |
| SNU719_STOMACH | 66489887 | 66490009 | 66489963 | 66489963 | Missense_Mutation | A | C | p.D313A |
| SNU449_LIVER | 66514936 | 66515053 | 66514976 | 66514976 | Missense_Mutation | G | A | p.R342K |
| HEC251_ENDOMETRIUM | 66514936 | 66515053 | 66514978 | 66514978 | Missense_Mutation | A | C | p.N343H |
| OC316_OVARY | 66514936 | 66515053 | 66515018 | 66515018 | Missense_Mutation | T | C | p.I356T |
| OC314_OVARY | 66514936 | 66515053 | 66515018 | 66515018 | Missense_Mutation | T | C | p.I356T |
| HS695T_SKIN | 66514936 | 66515053 | 66515024 | 66515024 | Missense_Mutation | C | T | p.P358L |
| NCIH596_LUNG | 66514936 | 66515053 | 66515026 | 66515026 | Missense_Mutation | G | T | p.A359S |
| RMUGS_OVARY | 66532272 | 66532390 | 66532282 | 66532282 | Missense_Mutation | G | A | p.R389Q |
| HCC2450_LUNG | 66532272 | 66532390 | 66532314 | 66532314 | Missense_Mutation | T | C | p.Y400H |
| PC9_LUNG | 66532272 | 66532390 | 66532333 | 66532333 | Missense_Mutation | G | A | p.R406H |
| CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 66532272 | 66532390 | 66532333 | 66532333 | Missense_Mutation | G | A | p.R406H |
| EN_ENDOMETRIUM | 66532272 | 66532390 | 66532360 | 66532360 | Missense_Mutation | C | T | p.A415V |
| COLO824_BREAST | 66548417 | 66548526 | 66548477 | 66548477 | Missense_Mutation | C | G | p.I445M |
| JHOS4_OVARY | 66548417 | 66548526 | 66548518 | 66548518 | Missense_Mutation | A | T | p.Q459L |
| SNU216_STOMACH | 66548417 | 66548526 | 66548518 | 66548518 | Missense_Mutation | A | T | p.Q459L |
| OVKATE_OVARY | 66548417 | 66548526 | 66548518 | 66548518 | Missense_Mutation | A | T | p.Q459L |
| JHH1_LIVER | 66563528 | 66563705 | 66563551 | 66563551 | Missense_Mutation | C | T | p.R470C |
| SKUT1_SOFT_TISSUE | 66563528 | 66563705 | 66563552 | 66563552 | Missense_Mutation | G | A | p.R470H |
| GP2D_LARGE_INTESTINE | 66563528 | 66563705 | 66563642 | 66563642 | Missense_Mutation | T | C | p.L500P |
| GP5D_LARGE_INTESTINE | 66563528 | 66563705 | 66563642 | 66563642 | Missense_Mutation | T | C | p.L500P |
| LS411N_LARGE_INTESTINE | 66563528 | 66563705 | 66563647 | 66563647 | Missense_Mutation | C | G | p.H502D |
| KYSE30_OESOPHAGUS | 66563528 | 66563705 | 66563663 | 66563663 | Missense_Mutation | C | T | p.S507F |
| ISHIKAWAHERAKLIO02ER_ENDOMETRIUM | 66648113 | 66648223 | 66648122 | 66648122 | Missense_Mutation | A | G | p.T570A |
| A2058_SKIN | 66648113 | 66648223 | 66648138 | 66648138 | Missense_Mutation | C | T | p.T575M |
| OC316_OVARY | 66648113 | 66648223 | 66648153 | 66648153 | Missense_Mutation | G | T | p.W580L |
| OC314_OVARY | 66648113 | 66648223 | 66648153 | 66648153 | Missense_Mutation | G | T | p.W580L |
| HEC59_ENDOMETRIUM | 66648113 | 66648223 | 66648158 | 66648158 | Missense_Mutation | G | A | p.V582M |
| SNU175_LARGE_INTESTINE | 66648113 | 66648223 | 66648215 | 66648215 | Missense_Mutation | G | A | p.E601K |
| KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 66660157 | 66660324 | 66660208 | 66660208 | Missense_Mutation | G | A | p.V621M |
| NCIH2110_LUNG | 66660157 | 66660324 | 66660220 | 66660220 | Missense_Mutation | G | C | p.E625Q |
| GP2D_LARGE_INTESTINE | 66660157 | 66660324 | 66660257 | 66660257 | Missense_Mutation | T | C | p.L637P |
| GP5D_LARGE_INTESTINE | 66660157 | 66660324 | 66660257 | 66660257 | Missense_Mutation | T | C | p.L637P |
| HT115_LARGE_INTESTINE | 66660157 | 66660324 | 66660289 | 66660289 | Missense_Mutation | G | A | p.E648K |
| SNU1040_LARGE_INTESTINE | 66660157 | 66660324 | 66660320 | 66660320 | Missense_Mutation | G | A | p.R658K |
| HCC44_LUNG | 66474570 | 66474671 | 66474570 | 66474570 | Splice_Site | G | T | p.G92* |
| SNU475_LIVER | 66489887 | 66490009 | 66489888 | 66489888 | Splice_Site | A | G | p.E288G |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TYW1 |
| 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 TYW1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TYW1 |
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RelatedDrugs for TYW1 |
| 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 TYW1 |
| 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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