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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 LPCAT1 |
 Gene summary |
| Gene information | Gene symbol | LPCAT1 | Gene ID | 79888 |
| Gene name | lysophosphatidylcholine acyltransferase 1 | |
| Synonyms | AGPAT10|AGPAT9|AYTL2|LPCAT-1|PFAAP3|lpcat|lysoPAFAT | |
| Cytomap | 5p15.33 | |
| Type of gene | protein-coding | |
| Description | lysophosphatidylcholine acyltransferase 11-acylglycerophosphocholine O-acyltransferase1-alkylglycerophosphocholine O-acetyltransferaseLPC acyltransferase 1acetyl-CoA:lyso-PAF acetyltransferaseacetyl-CoA:lyso-platelet-activating factor acetyltransfera | |
| Modification date | 20180519 | |
| UniProtAcc | Q8NF37 | |
| Context | PubMed: LPCAT1 [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 |
| LPCAT1 | GO:0036151 | phosphatidylcholine acyl-chain remodeling | 21498505 |
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Exon skipping events across known transcript of Ensembl for LPCAT1 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 LPCAT1 |
| 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 LPCAT1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_440920 | 5 | 1461954:1463950:1466863:1467005:1470940:1471039 | 1466863:1467005 | ENSG00000153395.5 | ENST00000475622.1,ENST00000283415.3 |
| exon_skip_440944 | 5 | 1466863:1467005:1470940:1471039:1474071:1474225 | 1470940:1471039 | ENSG00000153395.5 | ENST00000475622.1,ENST00000283415.3 |
| exon_skip_440957 | 5 | 1470940:1471039:1474071:1474225:1474674:1474800 | 1474071:1474225 | ENSG00000153395.5 | ENST00000475622.1,ENST00000283415.3 |
| exon_skip_440961 | 5 | 1474071:1474225:1474674:1474800:1477518:1477601 | 1474674:1474800 | ENSG00000153395.5 | ENST00000475622.1,ENST00000283415.3 |
| exon_skip_440969 | 5 | 1477518:1477601:1479735:1479790:1481056:1481091 | 1479735:1479790 | ENSG00000153395.5 | ENST00000475622.1,ENST00000283415.3 |
| exon_skip_440970 | 5 | 1481056:1481091:1483542:1483601:1488505:1488566 | 1483542:1483601 | ENSG00000153395.5 | ENST00000475622.1,ENST00000513757.1,ENST00000283415.3 |
| exon_skip_440974 | 5 | 1489860:1489973:1494814:1495029:1501575:1501718 | 1494814:1495029 | ENSG00000153395.5 | ENST00000475622.1,ENST00000283415.3,ENST00000514484.2 |
| exon_skip_440982 | 5 | 1501575:1501718:1521461:1521595:1523824:1523855 | 1521461:1521595 | ENSG00000153395.5 | ENST00000514484.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for LPCAT1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_440920 | 5 | 1461954:1463950:1466863:1467005:1470940:1471039 | 1466863:1467005 | ENSG00000153395.5 | ENST00000475622.1,ENST00000283415.3 |
| exon_skip_440944 | 5 | 1466863:1467005:1470940:1471039:1474071:1474225 | 1470940:1471039 | ENSG00000153395.5 | ENST00000475622.1,ENST00000283415.3 |
| exon_skip_440957 | 5 | 1470940:1471039:1474071:1474225:1474674:1474800 | 1474071:1474225 | ENSG00000153395.5 | ENST00000475622.1,ENST00000283415.3 |
| exon_skip_440961 | 5 | 1474071:1474225:1474674:1474800:1477518:1477601 | 1474674:1474800 | ENSG00000153395.5 | ENST00000475622.1,ENST00000283415.3 |
| exon_skip_440969 | 5 | 1477518:1477601:1479735:1479790:1481056:1481091 | 1479735:1479790 | ENSG00000153395.5 | ENST00000475622.1,ENST00000283415.3 |
| exon_skip_440970 | 5 | 1481056:1481091:1483542:1483601:1488505:1488566 | 1483542:1483601 | ENSG00000153395.5 | ENST00000475622.1,ENST00000283415.3,ENST00000513757.1 |
| exon_skip_440974 | 5 | 1489860:1489973:1494814:1495029:1501575:1501718 | 1494814:1495029 | ENSG00000153395.5 | ENST00000475622.1,ENST00000283415.3,ENST00000514484.2 |
| exon_skip_440982 | 5 | 1501575:1501718:1521461:1521595:1523824:1523855 | 1521461:1521595 | ENSG00000153395.5 | ENST00000514484.2 |
| 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 LPCAT1 |
| 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 |
| 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 |
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Infer the effects of exon skipping event on protein functional features for LPCAT1 |
| 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 |
| 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 |
| 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 |
| 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 |
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SNVs in the skipped exons for LPCAT1 |
| - 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. |
LPCAT1_COAD_exon_skip_440961_psi_boxplot.png |
LPCAT1_LIHC_exon_skip_440961_psi_boxplot.png |
| - 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-A39Y-01 | exon_skip_440920 | 1466864 | 1467005 | 1466905 | 1466905 | Frame_Shift_Del | A | - | p.F460fs |
| STAD | TCGA-BR-A4CQ-01 | exon_skip_440944 | 1470941 | 1471039 | 1471036 | 1471052 | Frame_Shift_Del | CGCTCTGTGGGGAGAGA | - | p.394_395del |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_440961 | 1474675 | 1474800 | 1474785 | 1474785 | Frame_Shift_Del | G | - | p.S305fs |
| STAD | TCGA-BR-4292-01 | exon_skip_440920 | 1466864 | 1467005 | 1466903 | 1466903 | Nonsense_Mutation | G | A | p.R461* |
| STAD | TCGA-BR-4292-01 | exon_skip_440920 | 1466864 | 1467005 | 1466903 | 1466903 | Nonsense_Mutation | G | A | p.R461X |
| UCEC | TCGA-B5-A0JY-01 | exon_skip_440974 | 1494815 | 1495029 | 1494891 | 1494891 | Nonsense_Mutation | G | A | p.R135* |
| LIHC | TCGA-DD-A39X-01 | exon_skip_440920 | 1466864 | 1467005 | 1467007 | 1467007 | Splice_Site | T | C | . |
| COAD | TCGA-DM-A28K-01 | exon_skip_440961 | 1474675 | 1474800 | 1474674 | 1474674 | Splice_Site | C | T | . |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-DM-A28K-01 |
| Cancer type: COAD | |
| ESID: exon_skip_440961 | |
| Skipped exon start: 1474675 | |
| Skipped exon end: 1474800 | |
| Mutation start: 1474674 | |
| Mutation end: 1474674 | |
| Mutation type: Splice_Site | |
| Reference seq: C | |
| Mutation seq: T | |
| AAchange: . | |
exon_skip_440961_COAD_TCGA-DM-A28K-01.png | |
| - 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 |
| OC316_OVARY | 1466864 | 1467005 | 1466978 | 1466978 | Missense_Mutation | C | T | p.V436I |
| OC314_OVARY | 1466864 | 1467005 | 1466978 | 1466978 | Missense_Mutation | C | T | p.V436I |
| OE19_OESOPHAGUS | 1470941 | 1471039 | 1470961 | 1470961 | Missense_Mutation | T | C | p.T420A |
| HEC265_ENDOMETRIUM | 1470941 | 1471039 | 1470964 | 1470964 | Missense_Mutation | C | T | p.D419N |
| CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 1470941 | 1471039 | 1470973 | 1470973 | Missense_Mutation | G | C | p.R416G |
| KYSE180_OESOPHAGUS | 1474072 | 1474225 | 1474115 | 1474115 | Missense_Mutation | G | A | p.P379L |
| T47D_BREAST | 1474072 | 1474225 | 1474127 | 1474127 | Missense_Mutation | G | A | p.S375F |
| OCIMY7_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 1474072 | 1474225 | 1474161 | 1474161 | Missense_Mutation | C | T | p.G364R |
| RKO_LARGE_INTESTINE | 1474675 | 1474800 | 1474696 | 1474696 | Missense_Mutation | G | A | p.A335V |
| LS411N_LARGE_INTESTINE | 1494815 | 1495029 | 1494834 | 1494834 | Missense_Mutation | T | G | p.R158S |
| LN464_CENTRAL_NERVOUS_SYSTEM | 1494815 | 1495029 | 1494878 | 1494878 | Missense_Mutation | C | A | p.V144L |
| HCC2998_LARGE_INTESTINE | 1494815 | 1495029 | 1494890 | 1494890 | Missense_Mutation | C | T | p.D140N |
| PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 1494815 | 1495029 | 1494910 | 1494910 | Missense_Mutation | G | A | p.A133V |
| MCC13_SKIN | 1494815 | 1495029 | 1494925 | 1494925 | Missense_Mutation | G | A | p.A128V |
| OVISE_OVARY | 1494815 | 1495029 | 1494959 | 1494959 | Missense_Mutation | C | T | p.V117M |
| RERFLCFM_LUNG | 1494815 | 1495029 | 1494959 | 1494959 | Missense_Mutation | C | T | p.V117M |
| LS411N_LARGE_INTESTINE | 1494815 | 1495029 | 1494994 | 1494994 | Missense_Mutation | G | C | p.T105S |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LPCAT1 |
| 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_440920 | 5 | 1461954:1463950:1466863:1467005:1470940:1471039 | 1466863:1467005 | ENST00000475622.1,ENST00000283415.3 | OV | rs35452723 | chr5:1467004 | A/G | 3.52e-04 |
| exon_skip_440920 | 5 | 1461954:1463950:1466863:1467005:1470940:1471039 | 1466863:1467005 | ENST00000475622.1,ENST00000283415.3 | OV | rs35452723 | chr5:1467004 | A/G | 3.62e-04 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LPCAT1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LPCAT1 |
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RelatedDrugs for LPCAT1 |
| 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 LPCAT1 |
| 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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