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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 CMSS1 |
 Gene summary |
| Gene information | Gene symbol | CMSS1 | Gene ID | 84319 |
| Gene name | cms1 ribosomal small subunit homolog (yeast) | |
| Synonyms | C3orf26 | |
| Cytomap | 3q12.1 | |
| Type of gene | protein-coding | |
| Description | protein CMSS1 | |
| Modification date | 20180519 | |
| UniProtAcc | Q9BQ75 | |
| Context | PubMed: CMSS1 [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 CMSS1 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 CMSS1 |
| 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 CMSS1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_376098 | 3 | 99536755:99536887:99770075:99770150:99865816:99865905 | 99770075:99770150 | ENSG00000184220.6 | ENST00000463526.1 |
| exon_skip_376104 | 3 | 99536755:99536887:99860373:99860489:99865816:99865905 | 99860373:99860489 | ENSG00000184220.6 | ENST00000491299.1 |
| exon_skip_376115 | 3 | 99865816:99865905:99879273:99879345:99881146:99881276 | 99879273:99879345 | ENSG00000184220.6 | ENST00000421999.2,ENST00000489081.1,ENST00000491299.1 |
| exon_skip_376119 | 3 | 99879273:99879345:99881146:99881276:99885178:99885238 | 99881146:99881276 | ENSG00000184220.6 | ENST00000478909.1,ENST00000421999.2,ENST00000489081.1,ENST00000491299.1 |
| exon_skip_376121 | 3 | 99881196:99881276:99885178:99885238:99886581:99886684 | 99885178:99885238 | ENSG00000184220.6 | ENST00000478909.1,ENST00000421999.2,ENST00000497345.1,ENST00000489081.1,ENST00000491299.1 |
| exon_skip_376123 | 3 | 99891159:99891247:99895170:99895259:99897148:99897199 | 99895170:99895259 | ENSG00000184220.6 | ENST00000478909.1,ENST00000421999.2,ENST00000489081.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for CMSS1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_376098 | 3 | 99536755:99536887:99770075:99770150:99865816:99865905 | 99770075:99770150 | ENSG00000184220.6 | ENST00000463526.1 |
| exon_skip_376104 | 3 | 99536755:99536887:99860373:99860489:99865816:99865905 | 99860373:99860489 | ENSG00000184220.6 | ENST00000491299.1 |
| exon_skip_376115 | 3 | 99865816:99865905:99879273:99879345:99881146:99881276 | 99879273:99879345 | ENSG00000184220.6 | ENST00000421999.2,ENST00000491299.1,ENST00000489081.1 |
| exon_skip_376119 | 3 | 99879273:99879345:99881146:99881276:99885178:99885238 | 99881146:99881276 | ENSG00000184220.6 | ENST00000421999.2,ENST00000491299.1,ENST00000489081.1,ENST00000478909.1 |
| exon_skip_376121 | 3 | 99881196:99881276:99885178:99885238:99886581:99886684 | 99885178:99885238 | ENSG00000184220.6 | ENST00000421999.2,ENST00000491299.1,ENST00000489081.1,ENST00000478909.1,ENST00000497345.1 |
| exon_skip_376123 | 3 | 99891159:99891247:99895170:99895259:99897148:99897199 | 99895170:99895259 | ENSG00000184220.6 | ENST00000421999.2,ENST00000489081.1,ENST00000478909.1 |
| 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 CMSS1 |
| 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 |
| ENST00000421999 | 99881146 | 99881276 | Frame-shift |
| ENST00000421999 | 99895170 | 99895259 | Frame-shift |
| ENST00000421999 | 99879273 | 99879345 | In-frame |
| ENST00000421999 | 99885178 | 99885238 | 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 |
| ENST00000421999 | 99881146 | 99881276 | Frame-shift |
| ENST00000421999 | 99895170 | 99895259 | Frame-shift |
| ENST00000421999 | 99879273 | 99879345 | In-frame |
| ENST00000421999 | 99885178 | 99885238 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CMSS1 |
| 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 |
| ENST00000421999 | 1218 | 279 | 99879273 | 99879345 | 300 | 371 | 51 | 75 |
| ENST00000421999 | 1218 | 279 | 99885178 | 99885238 | 502 | 561 | 118 | 138 |
| 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 |
| ENST00000421999 | 1218 | 279 | 99879273 | 99879345 | 300 | 371 | 51 | 75 |
| ENST00000421999 | 1218 | 279 | 99885178 | 99885238 | 502 | 561 | 118 | 138 |
| 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 |
| Q9BQ75 | 51 | 75 | 1 | 279 | Chain | ID=PRO_0000239014;Note=Protein CMSS1 |
| Q9BQ75 | 51 | 75 | 75 | 75 | Sequence conflict | Note=K->E;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9BQ75 | 118 | 138 | 1 | 279 | Chain | ID=PRO_0000239014;Note=Protein CMSS1 |
| Q9BQ75 | 118 | 138 | 138 | 138 | Natural variant | ID=VAR_047645;Note=E->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15489334;Dbxref=dbSNP:rs11537817,PMID:15489334 |
| 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 |
| Q9BQ75 | 51 | 75 | 1 | 279 | Chain | ID=PRO_0000239014;Note=Protein CMSS1 |
| Q9BQ75 | 51 | 75 | 75 | 75 | Sequence conflict | Note=K->E;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9BQ75 | 118 | 138 | 1 | 279 | Chain | ID=PRO_0000239014;Note=Protein CMSS1 |
| Q9BQ75 | 118 | 138 | 138 | 138 | Natural variant | ID=VAR_047645;Note=E->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15489334;Dbxref=dbSNP:rs11537817,PMID:15489334 |
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SNVs in the skipped exons for CMSS1 |
| - 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 |
| SKCM | TCGA-D3-A8GM-06 | exon_skip_376115 | 99879274 | 99879345 | 99879285 | 99879285 | Frame_Shift_Del | T | - | p.C55fs |
| LUAD | TCGA-86-8359-01 | exon_skip_376119 | 99881147 | 99881276 | 99881242 | 99881243 | Frame_Shift_Ins | - | T | p.G108fs |
| BLCA | TCGA-CF-A47X-01 | exon_skip_376121 | 99885179 | 99885238 | 99885224 | 99885224 | Nonsense_Mutation | C | G | p.S134* |
| - 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 |
| HCT15_LARGE_INTESTINE | 99879274 | 99879345 | 99879296 | 99879296 | Missense_Mutation | A | G | p.Q59R |
| SNU1040_LARGE_INTESTINE | 99881147 | 99881276 | 99881232 | 99881232 | Missense_Mutation | G | A | p.S104N |
| CCK81_LARGE_INTESTINE | 99895171 | 99895259 | 99895230 | 99895230 | Missense_Mutation | A | G | p.K243E |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CMSS1 |
| 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 CMSS1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CMSS1 |
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RelatedDrugs for CMSS1 |
| 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 CMSS1 |
| 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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