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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 CTPS1 |
 Gene summary |
| Gene information | Gene symbol | CTPS1 | Gene ID | 1503 |
| Gene name | CTP synthase 1 | |
| Synonyms | CTPS|GATD5|IMD24 | |
| Cytomap | 1p34.2 | |
| Type of gene | protein-coding | |
| Description | CTP synthase 1CTP synthetase 1UTP--ammonia ligase 1cytidine 5'-triphosphate synthetasecytidine 5-prime triphosphate synthetase | |
| Modification date | 20180522 | |
| UniProtAcc | P17812 | |
| Context | PubMed: CTPS1 [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 |
| CTPS1 | GO:0006241 | CTP biosynthetic process | 16179339 |
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Exon skipping events across known transcript of Ensembl for CTPS1 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 CTPS1 |
| 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 CTPS1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_4790 | 1 | 41456836:41456920:41457436:41457517:41461588:41461740 | 41457436:41457517 | ENSG00000171793.9 | ENST00000543104.1,ENST00000541520.1,ENST00000372621.4,ENST00000480420.1,ENST00000372616.1 |
| exon_skip_4795 | 1 | 41463065:41463198:41466700:41466789:41467831:41467908 | 41466700:41466789 | ENSG00000171793.9 | ENST00000463285.1,ENST00000541520.1,ENST00000486889.1,ENST00000372621.4,ENST00000372616.1 |
| exon_skip_4796 | 1 | 41471735:41471766:41473120:41473217:41474330:41474386 | 41473120:41473217 | ENSG00000171793.9 | ENST00000541520.1,ENST00000464283.1,ENST00000372621.4,ENST00000372616.1 |
| exon_skip_4797 | 1 | 41471735:41471766:41474330:41474562:41475116:41475261 | 41474330:41474562 | ENSG00000171793.9 | ENST00000498694.1 |
| exon_skip_4798 | 1 | 41474465:41474562:41475116:41475261:41475832:41475926 | 41475116:41475261 | ENSG00000171793.9 | ENST00000498694.1,ENST00000541520.1,ENST00000463423.1,ENST00000372621.4,ENST00000372616.1 |
| exon_skip_4799 | 1 | 41475116:41475261:41475832:41475926:41477329:41477426 | 41475832:41475926 | ENSG00000171793.9 | ENST00000498694.1,ENST00000541520.1,ENST00000372621.4,ENST00000372616.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for CTPS1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_4790 | 1 | 41456836:41456920:41457436:41457517:41461588:41461740 | 41457436:41457517 | ENSG00000171793.9 | ENST00000372621.4,ENST00000541520.1,ENST00000543104.1,ENST00000372616.1,ENST00000480420.1 |
| exon_skip_4791 | 1 | 41457436:41457517:41461588:41461740:41463065:41463198 | 41461588:41461740 | ENSG00000171793.9 | ENST00000372621.4,ENST00000541520.1,ENST00000372616.1,ENST00000480420.1 |
| exon_skip_4795 | 1 | 41463065:41463198:41466700:41466789:41467831:41467908 | 41466700:41466789 | ENSG00000171793.9 | ENST00000372621.4,ENST00000541520.1,ENST00000372616.1,ENST00000463285.1,ENST00000486889.1 |
| exon_skip_4796 | 1 | 41471735:41471766:41473120:41473217:41474330:41474386 | 41473120:41473217 | ENSG00000171793.9 | ENST00000372621.4,ENST00000541520.1,ENST00000372616.1,ENST00000464283.1 |
| exon_skip_4797 | 1 | 41471735:41471766:41474330:41474562:41475116:41475261 | 41474330:41474562 | ENSG00000171793.9 | ENST00000498694.1 |
| exon_skip_4798 | 1 | 41474465:41474562:41475116:41475261:41475832:41475926 | 41475116:41475261 | ENSG00000171793.9 | ENST00000372621.4,ENST00000541520.1,ENST00000372616.1,ENST00000463423.1,ENST00000498694.1 |
| exon_skip_4799 | 1 | 41475116:41475261:41475832:41475926:41477329:41477426 | 41475832:41475926 | ENSG00000171793.9 | ENST00000372621.4,ENST00000541520.1,ENST00000372616.1,ENST00000498694.1 |
| 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 CTPS1 |
| 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 |
| ENST00000372616 | 41475832 | 41475926 | 3UTR-3CDS |
| ENST00000372621 | 41475832 | 41475926 | 3UTR-3CDS |
| ENST00000372616 | 41466700 | 41466789 | Frame-shift |
| ENST00000372621 | 41466700 | 41466789 | Frame-shift |
| ENST00000372616 | 41473120 | 41473217 | Frame-shift |
| ENST00000372621 | 41473120 | 41473217 | Frame-shift |
| ENST00000372616 | 41475116 | 41475261 | Frame-shift |
| ENST00000372621 | 41475116 | 41475261 | Frame-shift |
| ENST00000372616 | 41457436 | 41457517 | In-frame |
| ENST00000372621 | 41457436 | 41457517 | 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 |
| ENST00000372616 | 41475832 | 41475926 | 3UTR-3CDS |
| ENST00000372621 | 41475832 | 41475926 | 3UTR-3CDS |
| ENST00000372616 | 41461588 | 41461740 | Frame-shift |
| ENST00000372621 | 41461588 | 41461740 | Frame-shift |
| ENST00000372616 | 41466700 | 41466789 | Frame-shift |
| ENST00000372621 | 41466700 | 41466789 | Frame-shift |
| ENST00000372616 | 41473120 | 41473217 | Frame-shift |
| ENST00000372621 | 41473120 | 41473217 | Frame-shift |
| ENST00000372616 | 41475116 | 41475261 | Frame-shift |
| ENST00000372621 | 41475116 | 41475261 | Frame-shift |
| ENST00000372616 | 41457436 | 41457517 | In-frame |
| ENST00000372621 | 41457436 | 41457517 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CTPS1 |
| 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 |
| ENST00000372616 | 2054 | 591 | 41457436 | 41457517 | 770 | 850 | 213 | 240 |
| ENST00000372621 | 3216 | 591 | 41457436 | 41457517 | 1148 | 1228 | 213 | 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 |
| ENST00000372616 | 2054 | 591 | 41457436 | 41457517 | 770 | 850 | 213 | 240 |
| ENST00000372621 | 3216 | 591 | 41457436 | 41457517 | 1148 | 1228 | 213 | 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 |
| P17812 | 213 | 240 | 1 | 231 | Alternative sequence | ID=VSP_055827;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P17812 | 213 | 240 | 1 | 231 | Alternative sequence | ID=VSP_055827;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P17812 | 213 | 240 | 212 | 217 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2VO1 |
| P17812 | 213 | 240 | 212 | 217 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2VO1 |
| P17812 | 213 | 240 | 1 | 591 | Chain | ID=PRO_0000138275;Note=CTP synthase 1 |
| P17812 | 213 | 240 | 1 | 591 | Chain | ID=PRO_0000138275;Note=CTP synthase 1 |
| P17812 | 213 | 240 | 224 | 233 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2VO1 |
| P17812 | 213 | 240 | 224 | 233 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2VO1 |
| P17812 | 213 | 240 | 238 | 240 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2VO1 |
| P17812 | 213 | 240 | 238 | 240 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2VO1 |
| 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 |
| P17812 | 213 | 240 | 1 | 231 | Alternative sequence | ID=VSP_055827;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P17812 | 213 | 240 | 1 | 231 | Alternative sequence | ID=VSP_055827;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P17812 | 213 | 240 | 212 | 217 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2VO1 |
| P17812 | 213 | 240 | 212 | 217 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2VO1 |
| P17812 | 213 | 240 | 1 | 591 | Chain | ID=PRO_0000138275;Note=CTP synthase 1 |
| P17812 | 213 | 240 | 1 | 591 | Chain | ID=PRO_0000138275;Note=CTP synthase 1 |
| P17812 | 213 | 240 | 224 | 233 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2VO1 |
| P17812 | 213 | 240 | 224 | 233 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2VO1 |
| P17812 | 213 | 240 | 238 | 240 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2VO1 |
| P17812 | 213 | 240 | 238 | 240 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2VO1 |
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SNVs in the skipped exons for CTPS1 |
| - 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-A3A0-01 | exon_skip_4790 | 41457437 | 41457517 | 41457462 | 41457462 | Frame_Shift_Del | T | - | p.L222fs |
| LUSC | TCGA-18-3409-01 | exon_skip_4795 | 41466701 | 41466789 | 41466737 | 41466737 | Frame_Shift_Del | C | - | p.Q348fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_4798 | 41475117 | 41475261 | 41475214 | 41475214 | Frame_Shift_Del | G | - | p.V548fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_4798 | 41475117 | 41475261 | 41475214 | 41475214 | Frame_Shift_Del | G | - | p.V548fs |
| - 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 |
| CHL1_SKIN | 41466701 | 41466789 | 41466747 | 41466747 | Missense_Mutation | C | T | p.P351L |
| HMCB_SKIN | 41466701 | 41466789 | 41466747 | 41466747 | Missense_Mutation | C | T | p.P351L |
| HEC251_ENDOMETRIUM | 41473121 | 41473217 | 41473204 | 41473204 | Missense_Mutation | G | T | p.K460N |
| MFE319_ENDOMETRIUM | 41473121 | 41473217 | 41473215 | 41473215 | Missense_Mutation | T | C | p.M464T |
| HCC1569_BREAST | 41474331 | 41474562 | 41474339 | 41474339 | Missense_Mutation | T | C | p.Y468H |
| CORL321_PLEURA | 41474331 | 41474562 | 41474384 | 41474384 | Missense_Mutation | G | A | p.E483K |
| RERFLCAD2_LUNG | 41474331 | 41474562 | 41474500 | 41474500 | Missense_Mutation | A | G | p.Q495R |
| LS411N_LARGE_INTESTINE | 41474331 | 41474562 | 41474518 | 41474518 | Missense_Mutation | G | A | p.G501D |
| ANGMCSS_CENTRAL_NERVOUS_SYSTEM | 41475117 | 41475261 | 41475131 | 41475131 | Missense_Mutation | G | T | p.V521F |
| BICR78_UPPER_AERODIGESTIVE_TRACT | 41475117 | 41475261 | 41475131 | 41475131 | Missense_Mutation | G | T | p.V521F |
| C10_LARGE_INTESTINE | 41475117 | 41475261 | 41475131 | 41475131 | Missense_Mutation | G | T | p.V521F |
| C125PM_LARGE_INTESTINE | 41475117 | 41475261 | 41475131 | 41475131 | Missense_Mutation | G | T | p.V521F |
| CME1_SOFT_TISSUE | 41475117 | 41475261 | 41475131 | 41475131 | Missense_Mutation | G | T | p.V521F |
| LN428_CENTRAL_NERVOUS_SYSTEM | 41475117 | 41475261 | 41475131 | 41475131 | Missense_Mutation | G | T | p.V521F |
| MM415_SKIN | 41475117 | 41475261 | 41475131 | 41475131 | Missense_Mutation | G | T | p.V521F |
| CCLFPEDS0008T_SOFT_TISSUE | 41475117 | 41475261 | 41475131 | 41475131 | Missense_Mutation | G | T | p.V521F |
| PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 41475117 | 41475261 | 41475131 | 41475131 | Missense_Mutation | G | T | p.V521F |
| ANGMCSS_CENTRAL_NERVOUS_SYSTEM | 41475117 | 41475261 | 41475134 | 41475134 | Missense_Mutation | G | T | p.G522W |
| BICR78_UPPER_AERODIGESTIVE_TRACT | 41475117 | 41475261 | 41475134 | 41475135 | Missense_Mutation | GG | TT | p.G522L |
| DIPG007_CENTRAL_NERVOUS_SYSTEM | 41475117 | 41475261 | 41475134 | 41475134 | Missense_Mutation | G | T | p.G522W |
| MM370_SKIN | 41475117 | 41475261 | 41475134 | 41475134 | Missense_Mutation | G | T | p.G522W |
| MM415_SKIN | 41475117 | 41475261 | 41475134 | 41475135 | Missense_Mutation | GG | TT | p.G522L |
| RH28_SOFT_TISSUE | 41475117 | 41475261 | 41475134 | 41475134 | Missense_Mutation | G | T | p.G522W |
| RH41_SOFT_TISSUE | 41475117 | 41475261 | 41475134 | 41475134 | Missense_Mutation | G | T | p.G522W |
| HMVII_SKIN | 41475833 | 41475926 | 41475833 | 41475833 | Splice_Site | G | A | p.R564R |
| KYAE1_OESOPHAGUS | 41475833 | 41475926 | 41475833 | 41475833 | Splice_Site | G | A | p.R564R |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CTPS1 |
| 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 |
| exon_skip_4797 | 1 | 41471735:41471766:41474330:41474562:41475116:41475261 | 41474330:41474562 | ENST00000498694.1 | BLCA | rs35044078 | chr1:41474400 | C/G | 1.41e-03 |
| exon_skip_4797 | 1 | 41471735:41471766:41474330:41474562:41475116:41475261 | 41474330:41474562 | ENST00000498694.1 | BLCA | rs35044078 | chr1:41474400 | C/G | 1.42e-03 |
| exon_skip_4797 | 1 | 41471735:41471766:41474330:41474562:41475116:41475261 | 41474330:41474562 | ENST00000498694.1 | LUAD | rs35044078 | chr1:41474400 | C/G | 2.78e-03 |
| exon_skip_4797 | 1 | 41471735:41471766:41474330:41474562:41475116:41475261 | 41474330:41474562 | ENST00000498694.1 | LUAD | rs35044078 | chr1:41474400 | C/G | 2.78e-03 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CTPS1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CTPS1 |
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RelatedDrugs for CTPS1 |
| 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 |
| P17812 | DB00130 | L-Glutamine | CTP synthase 1 {ECO:0000305} | small molecule | approved|investigational|nutraceutical |
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RelatedDiseases for CTPS1 |
| 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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