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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 YTHDC1 |
 Gene summary |
| Gene information | Gene symbol | YTHDC1 | Gene ID | 91746 |
| Gene name | YTH domain containing 1 | |
| Synonyms | YT521|YT521-B | |
| Cytomap | 4q13.2 | |
| Type of gene | protein-coding | |
| Description | YTH domain-containing protein 1putative splicing factor YT521splicing factor YT521splicing factor YT521-B | |
| Modification date | 20180519 | |
| UniProtAcc | Q96MU7 | |
| Context | PubMed: YTHDC1 [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 |
| YTHDC1 | GO:0006376 | mRNA splice site selection | 20167602 |
| YTHDC1 | GO:0048024 | regulation of mRNA splicing, via spliceosome | 26876937 |
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Exon skipping events across known transcript of Ensembl for YTHDC1 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 YTHDC1 |
| 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 YTHDC1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_429893 | 4 | 69182031:69182166:69184236:69184299:69184407:69184439 | 69184236:69184299 | ENSG00000083896.8 | ENST00000507529.1,ENST00000355665.3,ENST00000579690.1,ENST00000344157.4 |
| exon_skip_429900 | 4 | 69184543:69184580:69185840:69185923:69188466:69188633 | 69185840:69185923 | ENSG00000083896.8 | ENST00000355665.3,ENST00000579690.1,ENST00000344157.4 |
| exon_skip_429906 | 4 | 69195719:69195837:69195919:69196028:69197820:69197915 | 69195919:69196028 | ENSG00000083896.8 | ENST00000355665.3,ENST00000579690.1,ENST00000344157.4 |
| exon_skip_429907 | 4 | 69197820:69197915:69198511:69198565:69199025:69199115 | 69198511:69198565 | ENSG00000083896.8 | ENST00000579690.1,ENST00000344157.4 |
| exon_skip_429909 | 4 | 69204000:69204102:69209766:69209798:69215443:69215471 | 69209766:69209798 | ENSG00000083896.8 | ENST00000510746.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for YTHDC1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_429893 | 4 | 69182031:69182166:69184236:69184299:69184407:69184439 | 69184236:69184299 | ENSG00000083896.8 | ENST00000344157.4,ENST00000355665.3,ENST00000579690.1,ENST00000507529.1 |
| exon_skip_429900 | 4 | 69184543:69184580:69185840:69185923:69188466:69188633 | 69185840:69185923 | ENSG00000083896.8 | ENST00000344157.4,ENST00000355665.3,ENST00000579690.1 |
| exon_skip_429906 | 4 | 69195719:69195837:69195919:69196028:69197820:69197915 | 69195919:69196028 | ENSG00000083896.8 | ENST00000344157.4,ENST00000355665.3,ENST00000579690.1 |
| exon_skip_429907 | 4 | 69197820:69197915:69198511:69198565:69199025:69199115 | 69198511:69198565 | ENSG00000083896.8 | ENST00000344157.4,ENST00000579690.1 |
| exon_skip_429909 | 4 | 69204000:69204102:69209766:69209798:69215443:69215471 | 69209766:69209798 | ENSG00000083896.8 | ENST00000510746.1 |
| 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 YTHDC1 |
| 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 |
| ENST00000344157 | 69185840 | 69185923 | Frame-shift |
| ENST00000344157 | 69195919 | 69196028 | Frame-shift |
| ENST00000344157 | 69184236 | 69184299 | In-frame |
| ENST00000344157 | 69198511 | 69198565 | 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 |
| ENST00000344157 | 69185840 | 69185923 | Frame-shift |
| ENST00000344157 | 69195919 | 69196028 | Frame-shift |
| ENST00000344157 | 69184236 | 69184299 | In-frame |
| ENST00000344157 | 69198511 | 69198565 | In-frame |
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Infer the effects of exon skipping event on protein functional features for YTHDC1 |
| 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 |
| ENST00000344157 | 6249 | 727 | 69198511 | 69198565 | 1310 | 1363 | 324 | 342 |
| ENST00000344157 | 6249 | 727 | 69184236 | 69184299 | 2098 | 2160 | 587 | 608 |
| 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 |
| ENST00000344157 | 6249 | 727 | 69198511 | 69198565 | 1310 | 1363 | 324 | 342 |
| ENST00000344157 | 6249 | 727 | 69184236 | 69184299 | 2098 | 2160 | 587 | 608 |
| 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 |
| Q96MU7 | 324 | 342 | 325 | 342 | Alternative sequence | ID=VSP_006818;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334 |
| Q96MU7 | 324 | 342 | 1 | 727 | Chain | ID=PRO_0000223076;Note=YTH domain-containing protein 1 |
| Q96MU7 | 587 | 608 | 1 | 727 | Chain | ID=PRO_0000223076;Note=YTH domain-containing protein 1 |
| Q96MU7 | 587 | 608 | 601 | 643 | Compositional bias | Note=Pro-rich |
| 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 |
| Q96MU7 | 324 | 342 | 325 | 342 | Alternative sequence | ID=VSP_006818;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334 |
| Q96MU7 | 324 | 342 | 1 | 727 | Chain | ID=PRO_0000223076;Note=YTH domain-containing protein 1 |
| Q96MU7 | 587 | 608 | 1 | 727 | Chain | ID=PRO_0000223076;Note=YTH domain-containing protein 1 |
| Q96MU7 | 587 | 608 | 601 | 643 | Compositional bias | Note=Pro-rich |
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SNVs in the skipped exons for YTHDC1 |
| - 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-A39Y-01 | exon_skip_429906 | 69195920 | 69196028 | 69195927 | 69195927 | Frame_Shift_Del | T | - | p.K408fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_429906 | 69195920 | 69196028 | 69195927 | 69195927 | Frame_Shift_Del | T | - | p.F409fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_429906 | 69195920 | 69196028 | 69195927 | 69195927 | Frame_Shift_Del | T | - | p.K408fs |
| HNSC | TCGA-BB-4224-01 | exon_skip_429906 | 69195920 | 69196028 | 69195943 | 69195944 | Frame_Shift_Del | AC | - | p.V403fs |
| STAD | TCGA-BR-6452-01 | exon_skip_429900 | 69185841 | 69185923 | 69185860 | 69185861 | Frame_Shift_Ins | - | G | p.P555fs |
| STAD | TCGA-BR-6452-01 | exon_skip_429900 | 69185841 | 69185923 | 69185861 | 69185862 | Frame_Shift_Ins | - | G | p.P555fs |
| SKCM | TCGA-FR-A3YO-06 | exon_skip_429900 | 69185841 | 69185923 | 69185919 | 69185919 | Nonsense_Mutation | G | A | p.R536* |
| SKCM | TCGA-FR-A3YO-06 | exon_skip_429900 | 69185841 | 69185923 | 69185919 | 69185919 | Nonsense_Mutation | G | A | p.R536X |
| - 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 |
| CP66MEL_SKIN | 69185841 | 69185923 | 69185864 | 69185864 | Missense_Mutation | G | A | p.P554L |
| HEC251_ENDOMETRIUM | 69185841 | 69185923 | 69185884 | 69185884 | Missense_Mutation | C | A | p.K547N |
| JHUEM7_ENDOMETRIUM | 69195920 | 69196028 | 69195996 | 69195996 | Missense_Mutation | C | A | p.K385N |
| GIMEN_AUTONOMIC_GANGLIA | 69195920 | 69196028 | 69196018 | 69196018 | Missense_Mutation | G | A | p.S378F |
| MM127_SKIN | 69198512 | 69198565 | 69198531 | 69198532 | Missense_Mutation | GG | AA | p.S336F |
| COLO792_SKIN | 69198512 | 69198565 | 69198518 | 69198518 | Nonsense_Mutation | G | A | p.R341* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for YTHDC1 |
| 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 YTHDC1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for YTHDC1 |
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RelatedDrugs for YTHDC1 |
| 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 YTHDC1 |
| 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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