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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 AGXT |
 Gene summary |
| Gene information | Gene symbol | AGXT | Gene ID | 189 |
| Gene name | alanine--glyoxylate and serine--pyruvate aminotransferase | |
| Synonyms | AGT|AGT1|AGXT1|PH1|SPAT|SPT|TLH6 | |
| Cytomap | 2q37.3 | |
| Type of gene | protein-coding | |
| Description | serine--pyruvate aminotransferaseL-alanine: glyoxylate aminotransferase 1alanine-glyoxylate aminotransferasehepatic peroxisomal alanine:glyoxylate aminotransferase | |
| Modification date | 20180523 | |
| UniProtAcc | P21549 | |
| Context | PubMed: AGXT [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 |
| AGXT | GO:0009436 | glyoxylate catabolic process | 22198249 |
| AGXT | GO:0019265 | glycine biosynthetic process, by transamination of glyoxylate | 22198249 |
| AGXT | GO:0019448 | L-cysteine catabolic process | 18492492 |
| AGXT | GO:0042853 | L-alanine catabolic process | 17696873|18492492|22198249 |
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Exon skipping events across known transcript of Ensembl for AGXT 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 AGXT |
| 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 AGXT |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_335649 | 2 | 241810060:241810125:241810765:241810866:241812395:241812466 | 241810765:241810866 | ENSG00000172482.4 | ENST00000472436.1,ENST00000307503.3 |
| exon_skip_335653 | 2 | 241810765:241810866:241812395:241812466:241813394:241813479 | 241812395:241812466 | ENSG00000172482.4 | ENST00000307503.3 |
| exon_skip_335655 | 2 | 241810765:241810866:241812395:241812466:241814525:241814621 | 241812395:241812466 | ENSG00000172482.4 | ENST00000476698.1 |
| exon_skip_335667 | 2 | 241812395:241812466:241813394:241813479:241814525:241814621 | 241813394:241813479 | ENSG00000172482.4 | ENST00000307503.3 |
| exon_skip_335691 | 2 | 241814529:241814621:241815351:241815421:241816953:241817049 | 241815351:241815421 | ENSG00000172482.4 | ENST00000307503.3 |
| exon_skip_335712 | 2 | 241816953:241817049:241817438:241817567:241818130:241818537 | 241817438:241817567 | ENSG00000172482.4 | ENST00000307503.3,ENST00000470255.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for AGXT |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_335649 | 2 | 241810060:241810125:241810765:241810866:241812395:241812466 | 241810765:241810866 | ENSG00000172482.4 | ENST00000307503.3,ENST00000472436.1 |
| exon_skip_335653 | 2 | 241810765:241810866:241812395:241812466:241813394:241813479 | 241812395:241812466 | ENSG00000172482.4 | ENST00000307503.3 |
| exon_skip_335655 | 2 | 241810765:241810866:241812395:241812466:241814525:241814621 | 241812395:241812466 | ENSG00000172482.4 | ENST00000476698.1 |
| exon_skip_335667 | 2 | 241812395:241812466:241813394:241813479:241814525:241814621 | 241813394:241813479 | ENSG00000172482.4 | ENST00000307503.3 |
| exon_skip_335691 | 2 | 241814529:241814621:241815351:241815421:241816953:241817049 | 241815351:241815421 | ENSG00000172482.4 | ENST00000307503.3 |
| exon_skip_335712 | 2 | 241816953:241817049:241817438:241817567:241818130:241818537 | 241817438:241817567 | ENSG00000172482.4 | ENST00000307503.3,ENST00000470255.1 |
| 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 AGXT |
| 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 |
| ENST00000307503 | 241810765 | 241810866 | Frame-shift |
| ENST00000307503 | 241812395 | 241812466 | Frame-shift |
| ENST00000307503 | 241813394 | 241813479 | Frame-shift |
| ENST00000307503 | 241815351 | 241815421 | Frame-shift |
| ENST00000307503 | 241817438 | 241817567 | 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 |
| ENST00000307503 | 241810765 | 241810866 | Frame-shift |
| ENST00000307503 | 241812395 | 241812466 | Frame-shift |
| ENST00000307503 | 241813394 | 241813479 | Frame-shift |
| ENST00000307503 | 241815351 | 241815421 | Frame-shift |
| ENST00000307503 | 241817438 | 241817567 | In-frame |
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Infer the effects of exon skipping event on protein functional features for AGXT |
| 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 |
| ENST00000307503 | 1882 | 392 | 241817438 | 241817567 | 1330 | 1458 | 314 | 357 |
| 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 |
| ENST00000307503 | 1882 | 392 | 241817438 | 241817567 | 1330 | 1458 | 314 | 357 |
| 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 |
| P21549 | 314 | 357 | 321 | 325 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5F9S |
| P21549 | 314 | 357 | 344 | 346 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KYO |
| P21549 | 314 | 357 | 1 | 392 | Chain | ID=PRO_0000150237;Note=Serine--pyruvate aminotransferase |
| P21549 | 314 | 357 | 314 | 316 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5F9S |
| P21549 | 314 | 357 | 332 | 343 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5F9S |
| P21549 | 314 | 357 | 352 | 354 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5F9S |
| P21549 | 314 | 357 | 326 | 326 | Natural variant | ID=VAR_060570;Note=V->I;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12559847;Dbxref=dbSNP:rs115057148,PMID:12559847 |
| P21549 | 314 | 357 | 336 | 336 | Natural variant | ID=VAR_060571;Note=In HP1. V->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15253729;Dbxref=dbSNP:rs180177155,PMID:15253729 |
| P21549 | 314 | 357 | 340 | 340 | Natural variant | ID=VAR_000593;Note=Common polymorphism%3B associated with hyperoxaluria. I->M;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:1703535;Dbxref=dbSNP:rs4426527,PMID:1703535 |
| P21549 | 314 | 357 | 350 | 350 | Natural variant | ID=VAR_060572;Note=In HP1. G->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9604803;Dbxref=dbSNP:rs180177156,PMID:9604803 |
| P21549 | 314 | 357 | 355 | 357 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5F9S |
| 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 |
| P21549 | 314 | 357 | 321 | 325 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5F9S |
| P21549 | 314 | 357 | 344 | 346 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KYO |
| P21549 | 314 | 357 | 1 | 392 | Chain | ID=PRO_0000150237;Note=Serine--pyruvate aminotransferase |
| P21549 | 314 | 357 | 314 | 316 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5F9S |
| P21549 | 314 | 357 | 332 | 343 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5F9S |
| P21549 | 314 | 357 | 352 | 354 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5F9S |
| P21549 | 314 | 357 | 326 | 326 | Natural variant | ID=VAR_060570;Note=V->I;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12559847;Dbxref=dbSNP:rs115057148,PMID:12559847 |
| P21549 | 314 | 357 | 336 | 336 | Natural variant | ID=VAR_060571;Note=In HP1. V->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15253729;Dbxref=dbSNP:rs180177155,PMID:15253729 |
| P21549 | 314 | 357 | 340 | 340 | Natural variant | ID=VAR_000593;Note=Common polymorphism%3B associated with hyperoxaluria. I->M;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:1703535;Dbxref=dbSNP:rs4426527,PMID:1703535 |
| P21549 | 314 | 357 | 350 | 350 | Natural variant | ID=VAR_060572;Note=In HP1. G->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9604803;Dbxref=dbSNP:rs180177156,PMID:9604803 |
| P21549 | 314 | 357 | 355 | 357 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5F9S |
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SNVs in the skipped exons for AGXT |
| - 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 |
| LUSC | TCGA-22-5492-01 | exon_skip_335712 | 241817439 | 241817567 | 241817438 | 241817438 | Splice_Site | G | T | p.A315_splice |
| - 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 |
| SKOV3_OVARY | 241812396 | 241812466 | 241812422 | 241812422 | Missense_Mutation | C | T | p.S184L |
| NCIH596_LUNG | 241813395 | 241813479 | 241813400 | 241813400 | Missense_Mutation | G | A | p.D201N |
| GSU_STOMACH | 241815352 | 241815421 | 241815371 | 241815371 | Missense_Mutation | G | A | p.V266I |
| FTC133_THYROID | 241815352 | 241815421 | 241815377 | 241815377 | Missense_Mutation | A | G | p.S268G |
| NB5_AUTONOMIC_GANGLIA | 241817439 | 241817567 | 241817478 | 241817478 | Missense_Mutation | G | A | p.A328T |
| SNU1040_LARGE_INTESTINE | 241817439 | 241817567 | 241817479 | 241817479 | Missense_Mutation | C | T | p.A328V |
| L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 241817439 | 241817567 | 241817521 | 241817521 | Missense_Mutation | A | C | p.H342P |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for AGXT |
| 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 AGXT |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for AGXT |
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RelatedDrugs for AGXT |
| 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 |
| P21549 | DB00114 | Pyridoxal phosphate | Serine--pyruvate aminotransferase | small molecule | approved|investigational|nutraceutical | |
| P21549 | DB00145 | Glycine | Serine--pyruvate aminotransferase | small molecule | approved|nutraceutical|vet_approved |
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RelatedDiseases for AGXT |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| AGXT | C0268164 | Primary hyperoxaluria, type I | 10 | CTD_human;ORPHANET;UNIPROT |
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