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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 PSAT1 |
 Gene summary |
| Gene information | Gene symbol | PSAT1 | Gene ID | 29968 |
| Gene name | phosphoserine aminotransferase 1 | |
| Synonyms | EPIP|NLS2|PSA|PSAT|PSATD | |
| Cytomap | 9q21.2 | |
| Type of gene | protein-coding | |
| Description | phosphoserine aminotransferaseendometrial progesterone-induced proteinphosphohydroxythreonine aminotransferase | |
| Modification date | 20180523 | |
| UniProtAcc | Q9Y617 | |
| Context | PubMed: PSAT1 [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 PSAT1 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 PSAT1 |
| 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 PSAT1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_496654 | 9 | 80912058:80912186:80915517:80915578:80916869:80916939 | 80915517:80915578 | ENSG00000135069.9 | ENST00000376588.3 |
| exon_skip_496655 | 9 | 80915517:80915578:80916869:80916939:80919650:80919856 | 80916869:80916939 | ENSG00000135069.9 | ENST00000376588.3,ENST00000347159.2 |
| exon_skip_496656 | 9 | 80916869:80916939:80919650:80919856:80921229:80921402 | 80919650:80919856 | ENSG00000135069.9 | ENST00000376588.3,ENST00000347159.2 |
| exon_skip_496658 | 9 | 80919650:80919856:80921229:80921402:80923329:80923499 | 80921229:80921402 | ENSG00000135069.9 | ENST00000376588.3,ENST00000347159.2 |
| exon_skip_496660 | 9 | 80921229:80921402:80923329:80923499:80932591:80932720 | 80923329:80923499 | ENSG00000135069.9 | ENST00000376588.3,ENST00000347159.2 |
| exon_skip_496661 | 9 | 80923329:80923499:80932591:80932720:80942966:80943104 | 80932591:80932720 | ENSG00000135069.9 | ENST00000376588.3 |
| exon_skip_496665 | 9 | 80932591:80932720:80942966:80943104:80943896:80944370 | 80942966:80943104 | ENSG00000135069.9 | ENST00000376588.3 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PSAT1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_496654 | 9 | 80912058:80912186:80915517:80915578:80916869:80916939 | 80915517:80915578 | ENSG00000135069.9 | ENST00000376588.3 |
| exon_skip_496655 | 9 | 80915517:80915578:80916869:80916939:80919650:80919856 | 80916869:80916939 | ENSG00000135069.9 | ENST00000347159.2,ENST00000376588.3 |
| exon_skip_496656 | 9 | 80916869:80916939:80919650:80919856:80921229:80921402 | 80919650:80919856 | ENSG00000135069.9 | ENST00000347159.2,ENST00000376588.3 |
| exon_skip_496658 | 9 | 80919650:80919856:80921229:80921402:80923329:80923499 | 80921229:80921402 | ENSG00000135069.9 | ENST00000347159.2,ENST00000376588.3 |
| exon_skip_496660 | 9 | 80921229:80921402:80923329:80923499:80932591:80932720 | 80923329:80923499 | ENSG00000135069.9 | ENST00000347159.2,ENST00000376588.3 |
| exon_skip_496661 | 9 | 80923329:80923499:80932591:80932720:80942966:80943104 | 80932591:80932720 | ENSG00000135069.9 | ENST00000376588.3 |
| exon_skip_496665 | 9 | 80932591:80932720:80942966:80943104:80943896:80944370 | 80942966:80943104 | ENSG00000135069.9 | ENST00000376588.3 |
| 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 PSAT1 |
| 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 |
| ENST00000376588 | 80915517 | 80915578 | Frame-shift |
| ENST00000376588 | 80916869 | 80916939 | Frame-shift |
| ENST00000376588 | 80919650 | 80919856 | Frame-shift |
| ENST00000376588 | 80921229 | 80921402 | Frame-shift |
| ENST00000376588 | 80923329 | 80923499 | Frame-shift |
| ENST00000376588 | 80932591 | 80932720 | In-frame |
| ENST00000376588 | 80942966 | 80943104 | 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 |
| ENST00000376588 | 80915517 | 80915578 | Frame-shift |
| ENST00000376588 | 80916869 | 80916939 | Frame-shift |
| ENST00000376588 | 80919650 | 80919856 | Frame-shift |
| ENST00000376588 | 80921229 | 80921402 | Frame-shift |
| ENST00000376588 | 80923329 | 80923499 | Frame-shift |
| ENST00000376588 | 80932591 | 80932720 | In-frame |
| ENST00000376588 | 80942966 | 80943104 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PSAT1 |
| 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 |
| ENST00000376588 | 2205 | 370 | 80932591 | 80932720 | 809 | 937 | 247 | 289 |
| ENST00000376588 | 2205 | 370 | 80942966 | 80943104 | 938 | 1075 | 290 | 335 |
| 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 |
| ENST00000376588 | 2205 | 370 | 80932591 | 80932720 | 809 | 937 | 247 | 289 |
| ENST00000376588 | 2205 | 370 | 80942966 | 80943104 | 938 | 1075 | 290 | 335 |
| 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 |
| Q9Y617 | 247 | 289 | 288 | 290 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3E77 |
| Q9Y617 | 247 | 289 | 1 | 370 | Chain | ID=PRO_0000150135;Note=Phosphoserine aminotransferase |
| Q9Y617 | 247 | 289 | 245 | 260 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3E77 |
| Q9Y617 | 247 | 289 | 263 | 283 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3E77 |
| Q9Y617 | 247 | 289 | 269 | 269 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| Q9Y617 | 290 | 335 | 291 | 336 | Alternative sequence | ID=VSP_000237;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12633500,ECO:0000303|PubMed:15489334;Dbxref=PMID:12633500,PMID:15489334 |
| Q9Y617 | 290 | 335 | 288 | 290 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3E77 |
| Q9Y617 | 290 | 335 | 300 | 309 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3E77 |
| Q9Y617 | 290 | 335 | 329 | 331 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3E77 |
| Q9Y617 | 290 | 335 | 1 | 370 | Chain | ID=PRO_0000150135;Note=Phosphoserine aminotransferase |
| Q9Y617 | 290 | 335 | 295 | 297 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3E77 |
| Q9Y617 | 290 | 335 | 314 | 326 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3E77 |
| Q9Y617 | 290 | 335 | 318 | 318 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| Q9Y617 | 290 | 335 | 323 | 323 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| Q9Y617 | 290 | 335 | 331 | 331 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q9Y617 | 290 | 335 | 333 | 333 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| 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 |
| Q9Y617 | 247 | 289 | 288 | 290 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3E77 |
| Q9Y617 | 247 | 289 | 1 | 370 | Chain | ID=PRO_0000150135;Note=Phosphoserine aminotransferase |
| Q9Y617 | 247 | 289 | 245 | 260 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3E77 |
| Q9Y617 | 247 | 289 | 263 | 283 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3E77 |
| Q9Y617 | 247 | 289 | 269 | 269 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| Q9Y617 | 290 | 335 | 291 | 336 | Alternative sequence | ID=VSP_000237;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12633500,ECO:0000303|PubMed:15489334;Dbxref=PMID:12633500,PMID:15489334 |
| Q9Y617 | 290 | 335 | 288 | 290 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3E77 |
| Q9Y617 | 290 | 335 | 300 | 309 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3E77 |
| Q9Y617 | 290 | 335 | 329 | 331 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3E77 |
| Q9Y617 | 290 | 335 | 1 | 370 | Chain | ID=PRO_0000150135;Note=Phosphoserine aminotransferase |
| Q9Y617 | 290 | 335 | 295 | 297 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3E77 |
| Q9Y617 | 290 | 335 | 314 | 326 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3E77 |
| Q9Y617 | 290 | 335 | 318 | 318 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| Q9Y617 | 290 | 335 | 323 | 323 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| Q9Y617 | 290 | 335 | 331 | 331 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q9Y617 | 290 | 335 | 333 | 333 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
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SNVs in the skipped exons for PSAT1 |
| - 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_496656 | 80919651 | 80919856 | 80919844 | 80919844 | Frame_Shift_Del | G | - | p.G129fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_496658 | 80921230 | 80921402 | 80921395 | 80921395 | Frame_Shift_Del | T | - | p.V188fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_496665 | 80942967 | 80943104 | 80942980 | 80942980 | Frame_Shift_Del | C | - | p.P295fs |
| OV | TCGA-23-1031-01 | exon_skip_496665 | 80942967 | 80943104 | 80943096 | 80943102 | Frame_Shift_Del | AGGGCAT | - | p.K333fs |
| COAD | TCGA-AD-6895-01 | exon_skip_496656 | 80919651 | 80919856 | 80919676 | 80919677 | Frame_Shift_Ins | - | T | p.I73fs |
| KIRP | TCGA-AL-3472-01 | exon_skip_496665 | 80942967 | 80943104 | 80942983 | 80942984 | Frame_Shift_Ins | - | A | p.K296fs |
| KIRP | TCGA-AL-3472-01 | exon_skip_496665 | 80942967 | 80943104 | 80942983 | 80942984 | Frame_Shift_Ins | - | A | p.Q296fs |
| KIRC | TCGA-B8-4148-01 | exon_skip_496654 | 80915518 | 80915578 | 80915578 | 80915578 | Nonsense_Mutation | G | T | p.E41X |
| LUSC | TCGA-85-6561-01 | exon_skip_496658 | 80921230 | 80921402 | 80921340 | 80921340 | Nonsense_Mutation | G | T | p.G170* |
| STAD | TCGA-VQ-A8P2-01 | exon_skip_496656 | 80919651 | 80919856 | 80919650 | 80919650 | 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 |
| JHUEM7_ENDOMETRIUM | 80915518 | 80915578 | 80915552 | 80915552 | Missense_Mutation | A | G | p.Y32C |
| RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 80915518 | 80915578 | 80915575 | 80915575 | Missense_Mutation | C | G | p.L40V |
| HCC2814_LUNG | 80919651 | 80919856 | 80919757 | 80919757 | Missense_Mutation | G | C | p.D100H |
| HEC265_ENDOMETRIUM | 80919651 | 80919856 | 80919764 | 80919764 | Missense_Mutation | T | C | p.V102A |
| FUOV1_OVARY | 80921230 | 80921402 | 80921257 | 80921257 | Missense_Mutation | T | C | p.L142P |
| DU145_PROSTATE | 80921230 | 80921402 | 80921287 | 80921287 | Missense_Mutation | G | A | p.C152Y |
| NB10_AUTONOMIC_GANGLIA | 80921230 | 80921402 | 80921289 | 80921289 | Missense_Mutation | G | T | p.A153S |
| HCC2108_LUNG | 80921230 | 80921402 | 80921327 | 80921327 | Missense_Mutation | A | G | p.I165M |
| MFE319_ENDOMETRIUM | 80921230 | 80921402 | 80921362 | 80921362 | Missense_Mutation | T | C | p.M177T |
| OCUBM_BREAST | 80923330 | 80923499 | 80923396 | 80923396 | Missense_Mutation | C | T | p.R213C |
| SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 80932592 | 80932720 | 80932599 | 80932599 | Missense_Mutation | G | A | p.V250I |
| SHP77_LUNG | 80932592 | 80932720 | 80932604 | 80932604 | Missense_Mutation | G | C | p.M251I |
| DU145_PROSTATE | 80932592 | 80932720 | 80932605 | 80932605 | Missense_Mutation | G | T | p.G252C |
| HEC108_ENDOMETRIUM | 80932592 | 80932720 | 80932648 | 80932648 | Missense_Mutation | C | T | p.A266V |
| HEC251_ENDOMETRIUM | 80932592 | 80932720 | 80932692 | 80932692 | Missense_Mutation | A | G | p.I281V |
| LOVO_LARGE_INTESTINE | 80942967 | 80943104 | 80942974 | 80942974 | Missense_Mutation | G | A | p.V293M |
| KMRC2_KIDNEY | 80942967 | 80943104 | 80943037 | 80943037 | Missense_Mutation | G | T | p.D314Y |
| PCI4B_UPPER_AERODIGESTIVE_TRACT | 80919651 | 80919856 | 80919780 | 80919780 | Nonsense_Mutation | G | A | p.W107* |
| MFE319_ENDOMETRIUM | 80921230 | 80921402 | 80921402 | 80921402 | Splice_Site | G | A | p.K190K |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PSAT1 |
| 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 PSAT1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PSAT1 |
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RelatedDrugs for PSAT1 |
| 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 |
| Q9Y617 | DB00114 | Pyridoxal phosphate | Phosphoserine aminotransferase | small molecule | approved|investigational|nutraceutical | |
| Q9Y617 | DB00142 | Glutamic Acid | Phosphoserine aminotransferase | small molecule | approved|nutraceutical |
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RelatedDiseases for PSAT1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| PSAT1 | C0007131 | Non-Small Cell Lung Carcinoma | 1 | CTD_human |
| PSAT1 | C0036341 | Schizophrenia | 1 | PSYGENET |
| PSAT1 | C1970253 | Phosphoserine Aminotransferase Deficiency | 1 | CTD_human;ORPHANET;UNIPROT |
| PSAT1 | C4015019 | NEU-LAXOVA SYNDROME 2 | 1 | UNIPROT |
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