|
||||||
|
 | |
| |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
| |
|
Gene summary for AGPAT4 |
 Gene summary |
| Gene information | Gene symbol | AGPAT4 | Gene ID | 56895 |
| Gene name | 1-acylglycerol-3-phosphate O-acyltransferase 4 | |
| Synonyms | 1-AGPAT4|LPAAT-delta|dJ473J16.2 | |
| Cytomap | 6q26 | |
| Type of gene | protein-coding | |
| Description | 1-acyl-sn-glycerol-3-phosphate acyltransferase delta1-AGP acyltransferase 41-AGPAT 41-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)lysophosphatidic acid acyltransferase deltalysophosphatidic acid acyltran | |
| Modification date | 20180523 | |
| UniProtAcc | Q9NRZ5 | |
| Context | PubMed: AGPAT4 [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 |
Top |
Exon skipping events across known transcript of Ensembl for AGPAT4 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. |
 |
Top |
Gene isoform structures and expression levels for AGPAT4 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for AGPAT4 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_463231 | 6 | 161557286:161557666:161560453:161560652:161567555:161567631 | 161560453:161560652 | ENSG00000026652.9 | ENST00000457520.2,ENST00000366911.5,ENST00000320285.4 |
| exon_skip_463239 | 6 | 161574377:161574531:161575180:161575342:161586608:161586745 | 161575180:161575342 | ENSG00000026652.9 | ENST00000436279.1 |
| exon_skip_463240 | 6 | 161574377:161574531:161575180:161575342:161587279:161587449 | 161575180:161575342 | ENSG00000026652.9 | ENST00000320285.4 |
| exon_skip_463241 | 6 | 161574377:161574531:161575180:161575342:161653067:161653268 | 161575180:161575342 | ENSG00000026652.9 | ENST00000366911.5 |
| exon_skip_463244 | 6 | 161575180:161575342:161586608:161586745:161587279:161587449 | 161586608:161586745 | ENSG00000026652.9 | ENST00000436279.1,ENST00000366908.5 |
| exon_skip_463246 | 6 | 161575180:161575342:161587279:161587449:161653067:161653268 | 161587279:161587449 | ENSG00000026652.9 | ENST00000320285.4 |
| exon_skip_463247 | 6 | 161587279:161587449:161653067:161653334:161694969:161695082 | 161653067:161653334 | ENSG00000026652.9 | ENST00000366905.3,ENST00000320285.4,ENST00000366908.5 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for AGPAT4 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_463231 | 6 | 161557286:161557666:161560453:161560652:161567555:161567631 | 161560453:161560652 | ENSG00000026652.9 | ENST00000366911.5,ENST00000320285.4,ENST00000457520.2 |
| exon_skip_463239 | 6 | 161574377:161574531:161575180:161575342:161586608:161586745 | 161575180:161575342 | ENSG00000026652.9 | ENST00000436279.1 |
| exon_skip_463240 | 6 | 161574377:161574531:161575180:161575342:161587279:161587449 | 161575180:161575342 | ENSG00000026652.9 | ENST00000320285.4 |
| exon_skip_463241 | 6 | 161574377:161574531:161575180:161575342:161653067:161653268 | 161575180:161575342 | ENSG00000026652.9 | ENST00000366911.5 |
| exon_skip_463244 | 6 | 161575180:161575342:161586608:161586745:161587279:161587449 | 161586608:161586745 | ENSG00000026652.9 | ENST00000366908.5,ENST00000436279.1 |
| exon_skip_463246 | 6 | 161575180:161575342:161587279:161587449:161653067:161653268 | 161587279:161587449 | ENSG00000026652.9 | ENST00000320285.4 |
| exon_skip_463247 | 6 | 161587279:161587449:161653067:161653334:161694969:161695082 | 161653067:161653334 | ENSG00000026652.9 | ENST00000320285.4,ENST00000366908.5,ENST00000366905.3 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for AGPAT4 |
| 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 |
| ENST00000320285 | 161653067 | 161653334 | 3UTR-3CDS |
| ENST00000320285 | 161560453 | 161560652 | Frame-shift |
| ENST00000320285 | 161587279 | 161587449 | Frame-shift |
| ENST00000320285 | 161575180 | 161575342 | 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 |
| ENST00000320285 | 161653067 | 161653334 | 3UTR-3CDS |
| ENST00000320285 | 161560453 | 161560652 | Frame-shift |
| ENST00000320285 | 161587279 | 161587449 | Frame-shift |
| ENST00000320285 | 161575180 | 161575342 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for AGPAT4 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
 |
| 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 |
| ENST00000320285 | 7882 | 378 | 161575180 | 161575342 | 562 | 723 | 116 | 170 |
| 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 |
| ENST00000320285 | 7882 | 378 | 161575180 | 161575342 | 562 | 723 | 116 | 170 |
| 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 |
| Q9NRZ5 | 116 | 170 | 61 | 222 | Alternative sequence | ID=VSP_056929;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9NRZ5 | 116 | 170 | 1 | 378 | Chain | ID=PRO_0000208197;Note=1-acyl-sn-glycerol-3-phosphate acyltransferase delta |
| Q9NRZ5 | 116 | 170 | 125 | 145 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q9NRZ5 | 116 | 170 | 61 | 222 | Alternative sequence | ID=VSP_056929;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9NRZ5 | 116 | 170 | 1 | 378 | Chain | ID=PRO_0000208197;Note=1-acyl-sn-glycerol-3-phosphate acyltransferase delta |
| Q9NRZ5 | 116 | 170 | 125 | 145 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Top |
SNVs in the skipped exons for AGPAT4 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
 |
| - 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 |
| THYM | TCGA-ZB-A966-01 | exon_skip_463231 | 161560454 | 161560652 | 161560589 | 161560589 | Frame_Shift_Del | G | - | p.R303fs |
| THYM | TCGA-ZB-A966-01 | exon_skip_463231 | 161560454 | 161560652 | 161560589 | 161560589 | Frame_Shift_Del | G | - | p.R304fs |
| UCEC | TCGA-AX-A06H-01 | exon_skip_463231 | 161560454 | 161560652 | 161560589 | 161560589 | Frame_Shift_Del | G | - | p.R303fs |
| UCS | TCGA-N7-A4Y0-01 | exon_skip_463231 | 161560454 | 161560652 | 161560589 | 161560589 | Frame_Shift_Del | G | - | p.R304fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_463240 exon_skip_463241 exon_skip_463239 | 161575181 | 161575342 | 161575223 | 161575223 | Frame_Shift_Del | G | - | p.A156fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_463246 | 161587280 | 161587449 | 161587342 | 161587342 | Frame_Shift_Del | G | - | p.H96fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_463246 | 161587280 | 161587449 | 161587362 | 161587362 | Frame_Shift_Del | T | - | p.N89fs |
| KIRC | TCGA-A3-3380-01 | exon_skip_463231 | 161560454 | 161560652 | 161560588 | 161560589 | Frame_Shift_Ins | - | G | p.A303fs |
| LUAD | TCGA-67-3770-01 | exon_skip_463231 | 161560454 | 161560652 | 161560588 | 161560589 | Frame_Shift_Ins | - | G | p.A303fs |
| UCEC | TCGA-AP-A05H-01 | exon_skip_463231 | 161560454 | 161560652 | 161560588 | 161560589 | Frame_Shift_Ins | - | G | p.R303fs |
| BLCA | TCGA-E7-A4IJ-01 | exon_skip_463231 | 161560454 | 161560652 | 161560579 | 161560579 | Nonsense_Mutation | C | T | p.W306* |
| LUAD | TCGA-75-6211-01 | exon_skip_463240 exon_skip_463241 exon_skip_463239 | 161575181 | 161575342 | 161575192 | 161575192 | Nonsense_Mutation | C | A | p.E167* |
| SKCM | TCGA-EE-A2MR-06 | exon_skip_463246 | 161587280 | 161587449 | 161587427 | 161587427 | Nonsense_Mutation | C | T | p.W67* |
| SKCM | TCGA-EE-A2GO-06 | exon_skip_463247 | 161653068 | 161653334 | 161653068 | 161653068 | Nonsense_Mutation | G | A | p.Q60X |
| - 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 |
| HEC108_ENDOMETRIUM | 161560454 | 161560652 | 161560589 | 161560589 | Frame_Shift_Del | G | - | p.R304fs |
| SNU324_PANCREAS | 161560454 | 161560652 | 161560589 | 161560589 | Frame_Shift_Del | G | - | p.R304fs |
| SNU520_STOMACH | 161560454 | 161560652 | 161560589 | 161560589 | Frame_Shift_Del | G | - | p.R304fs |
| HS766T_PANCREAS | 161560454 | 161560652 | 161560465 | 161560465 | Missense_Mutation | A | G | p.V344A |
| 253J_URINARY_TRACT | 161560454 | 161560652 | 161560476 | 161560476 | Missense_Mutation | G | T | p.S340R |
| 253JBV_URINARY_TRACT | 161560454 | 161560652 | 161560476 | 161560476 | Missense_Mutation | G | T | p.S340R |
| MKN7_STOMACH | 161560454 | 161560652 | 161560490 | 161560490 | Missense_Mutation | G | T | p.L336M |
| HUCCT1_BILIARY_TRACT | 161560454 | 161560652 | 161560554 | 161560554 | Missense_Mutation | C | A | p.W314C |
| SKMEL28_SKIN | 161560454 | 161560652 | 161560608 | 161560608 | Missense_Mutation | C | A | p.E296D |
| CW2_LARGE_INTESTINE | 161560454 | 161560652 | 161560634 | 161560634 | Missense_Mutation | A | G | p.Y288H |
| TGW_AUTONOMIC_GANGLIA | 161575181 | 161575342 | 161575233 | 161575233 | Missense_Mutation | T | C | p.K153R |
| KNS81_CENTRAL_NERVOUS_SYSTEM | 161575181 | 161575342 | 161575300 | 161575300 | Missense_Mutation | T | C | p.I131V |
| KNS81FD_CENTRAL_NERVOUS_SYSTEM | 161575181 | 161575342 | 161575300 | 161575300 | Missense_Mutation | T | C | p.I131V |
| LS411N_LARGE_INTESTINE | 161587280 | 161587449 | 161587287 | 161587287 | Missense_Mutation | A | G | p.L114P |
| LS411N_LARGE_INTESTINE | 161587280 | 161587449 | 161587389 | 161587389 | Missense_Mutation | C | T | p.R80H |
| CW2_LARGE_INTESTINE | 161653068 | 161653334 | 161653137 | 161653137 | Missense_Mutation | G | T | p.L37I |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for AGPAT4 |
| 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 |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for AGPAT4 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for AGPAT4 |
Top |
RelatedDrugs for AGPAT4 |
| 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 |
Top |
RelatedDiseases for AGPAT4 |
| 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)
|