|
||||||
|
 | |
| |
| |
| |
| 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 LCLAT1 |
 Gene summary |
| Gene information | Gene symbol | LCLAT1 | Gene ID | 253558 |
| Gene name | lysocardiolipin acyltransferase 1 | |
| Synonyms | 1AGPAT8|AGPAT8|ALCAT1|HSRG1849|LYCAT|UNQ1849 | |
| Cytomap | 2p23.1 | |
| Type of gene | protein-coding | |
| Description | lysocardiolipin acyltransferase 11-AGP acyltransferase 81-AGPAT 81-acylglycerol-3-phosphate O-acyltransferase 8acyl-CoA:lysocardiolipin acyltransferase 1 | |
| Modification date | 20180527 | |
| UniProtAcc | Q6UWP7 | |
| Context | PubMed: LCLAT1 [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 LCLAT1 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 LCLAT1 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for LCLAT1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_324544 | 2 | 30670141:30670249:30682417:30682588:30748452:30748621 | 30682417:30682588 | ENSG00000172954.9 | ENST00000319406.4 |
| exon_skip_324547 | 2 | 30670141:30670249:30699442:30699501:30748452:30748621 | 30699442:30699501 | ENSG00000172954.9 | ENST00000465538.1 |
| exon_skip_324548 | 2 | 30670141:30670249:30712025:30712106:30748452:30748621 | 30712025:30712106 | ENSG00000172954.9 | ENST00000488144.1 |
| exon_skip_324549 | 2 | 30670141:30670249:30748452:30748621:30755981:30756132 | 30748452:30748621 | ENSG00000172954.9 | ENST00000379509.3,ENST00000476038.1 |
| exon_skip_324551 | 2 | 30670122:30670270:30682417:30682588:30748452:30748621 | 30682417:30682588 | ENSG00000172954.9 | ENST00000359433.1,ENST00000309052.4 |
| exon_skip_324554 | 2 | 30670111:30670270:30748452:30748621:30755981:30756180 | 30748452:30748621 | ENSG00000172954.9 | ENST00000465200.1 |
| exon_skip_324558 | 2 | 30682417:30682588:30699267:30699501:30748452:30748621 | 30699267:30699501 | ENSG00000172954.9 | ENST00000540623.1,ENST00000478015.1 |
| exon_skip_324563 | 2 | 30682417:30682588:30748452:30748621:30755981:30756132 | 30748452:30748621 | ENSG00000172954.9 | ENST00000497423.1,ENST00000319406.4,ENST00000359433.1,ENST00000309052.4 |
| exon_skip_324565 | 2 | 30755981:30756180:30775358:30775515:30785011:30785056 | 30775358:30775515 | ENSG00000172954.9 | ENST00000491680.2 |
| exon_skip_324566 | 2 | 30755981:30756180:30785011:30785158:30790925:30791033 | 30785011:30785158 | ENSG00000172954.9 | ENST00000540623.1,ENST00000379509.3,ENST00000319406.4,ENST00000359433.1,ENST00000309052.4,ENST00000478015.1 |
| exon_skip_324570 | 2 | 30785011:30785158:30790925:30791042:30862982:30863696 | 30790925:30791042 | ENSG00000172954.9 | ENST00000540623.1,ENST00000379509.3,ENST00000491680.2,ENST00000309052.4,ENST00000478015.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for LCLAT1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_324544 | 2 | 30670141:30670249:30682417:30682588:30748452:30748621 | 30682417:30682588 | ENSG00000172954.9 | ENST00000319406.4 |
| exon_skip_324547 | 2 | 30670141:30670249:30699442:30699501:30748452:30748621 | 30699442:30699501 | ENSG00000172954.9 | ENST00000465538.1 |
| exon_skip_324548 | 2 | 30670141:30670249:30712025:30712106:30748452:30748621 | 30712025:30712106 | ENSG00000172954.9 | ENST00000488144.1 |
| exon_skip_324549 | 2 | 30670141:30670249:30748452:30748621:30755981:30756132 | 30748452:30748621 | ENSG00000172954.9 | ENST00000379509.3,ENST00000476038.1 |
| exon_skip_324551 | 2 | 30670122:30670270:30682417:30682588:30748452:30748621 | 30682417:30682588 | ENSG00000172954.9 | ENST00000309052.4,ENST00000359433.1 |
| exon_skip_324554 | 2 | 30670111:30670270:30748452:30748621:30755981:30756180 | 30748452:30748621 | ENSG00000172954.9 | ENST00000465200.1 |
| exon_skip_324565 | 2 | 30755981:30756180:30775358:30775515:30785011:30785056 | 30775358:30775515 | ENSG00000172954.9 | ENST00000491680.2 |
| exon_skip_324566 | 2 | 30755981:30756180:30785011:30785158:30790925:30791033 | 30785011:30785158 | ENSG00000172954.9 | ENST00000379509.3,ENST00000319406.4,ENST00000309052.4,ENST00000359433.1,ENST00000478015.1,ENST00000540623.1 |
| exon_skip_324570 | 2 | 30785011:30785158:30790925:30791042:30862982:30863696 | 30790925:30791042 | ENSG00000172954.9 | ENST00000379509.3,ENST00000491680.2,ENST00000309052.4,ENST00000478015.1,ENST00000540623.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for LCLAT1 |
| 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 |
| ENST00000309052 | 30682417 | 30682588 | 5CDS-5UTR |
| ENST00000309052 | 30748452 | 30748621 | Frame-shift |
| ENST00000309052 | 30785011 | 30785158 | In-frame |
| ENST00000309052 | 30790925 | 30791042 | 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 |
| ENST00000309052 | 30682417 | 30682588 | 5CDS-5UTR |
| ENST00000309052 | 30785011 | 30785158 | In-frame |
| ENST00000309052 | 30790925 | 30791042 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for LCLAT1 |
| 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 |
| ENST00000309052 | 5077 | 414 | 30785011 | 30785158 | 688 | 834 | 159 | 208 |
| ENST00000309052 | 5077 | 414 | 30790925 | 30791042 | 835 | 951 | 208 | 247 |
| 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 |
| ENST00000309052 | 5077 | 414 | 30785011 | 30785158 | 688 | 834 | 159 | 208 |
| ENST00000309052 | 5077 | 414 | 30790925 | 30791042 | 835 | 951 | 208 | 247 |
| 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 |
| Q6UWP7 | 159 | 208 | 1 | 414 | Chain | ID=PRO_0000291577;Note=Lysocardiolipin acyltransferase 1 |
| Q6UWP7 | 159 | 208 | 206 | 206 | Mutagenesis | Note=Abolishes LPIAT and LPGAT activities. D->C;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:16620771,ECO:0000269|PubMed:19075029;Dbxref=PMID:16620771,PMID:19075029 |
| Q6UWP7 | 159 | 208 | 206 | 206 | Mutagenesis | Note=Does not increase enzyme activity. D->R;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:16620771,ECO:0000269|PubMed:19075029;Dbxref=PMID:16620771,PMID:19075029 |
| Q6UWP7 | 159 | 208 | 207 | 207 | Mutagenesis | Note=Abolishes LPIAT activity. No effect on LPGAT activity. L->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19075029;Dbxref=PMID:19075029 |
| Q6UWP7 | 208 | 247 | 1 | 414 | Chain | ID=PRO_0000291577;Note=Lysocardiolipin acyltransferase 1 |
| Q6UWP7 | 208 | 247 | 221 | 221 | 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 |
| Q6UWP7 | 159 | 208 | 1 | 414 | Chain | ID=PRO_0000291577;Note=Lysocardiolipin acyltransferase 1 |
| Q6UWP7 | 159 | 208 | 206 | 206 | Mutagenesis | Note=Abolishes LPIAT and LPGAT activities. D->C;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:16620771,ECO:0000269|PubMed:19075029;Dbxref=PMID:16620771,PMID:19075029 |
| Q6UWP7 | 159 | 208 | 206 | 206 | Mutagenesis | Note=Does not increase enzyme activity. D->R;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:16620771,ECO:0000269|PubMed:19075029;Dbxref=PMID:16620771,PMID:19075029 |
| Q6UWP7 | 159 | 208 | 207 | 207 | Mutagenesis | Note=Abolishes LPIAT activity. No effect on LPGAT activity. L->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19075029;Dbxref=PMID:19075029 |
| Q6UWP7 | 208 | 247 | 1 | 414 | Chain | ID=PRO_0000291577;Note=Lysocardiolipin acyltransferase 1 |
| Q6UWP7 | 208 | 247 | 221 | 221 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
Top |
SNVs in the skipped exons for LCLAT1 |
| - 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 |
| COAD | TCGA-D5-6540-01 | exon_skip_324570 | 30790926 | 30791042 | 30790959 | 30790959 | Frame_Shift_Del | A | - | p.E182fs |
| BLCA | TCGA-ZF-A9R7-01 | exon_skip_324570 | 30790926 | 30791042 | 30790973 | 30790973 | Nonsense_Mutation | C | T | p.Q225* |
| STAD | TCGA-BR-4361-01 | exon_skip_324563 exon_skip_324549 exon_skip_324554 | 30748453 | 30748621 | 30748623 | 30748623 | Splice_Site | T | C | . |
| STAD | TCGA-BR-4361-01 | exon_skip_324563 exon_skip_324549 exon_skip_324554 | 30748453 | 30748621 | 30748623 | 30748623 | Splice_Site | T | C | p.V93_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 |
| CCK81_LARGE_INTESTINE | 30790926 | 30791042 | 30790959 | 30790959 | Frame_Shift_Del | A | - | p.E220fs |
| SNU175_LARGE_INTESTINE | 30748453 | 30748621 | 30748466 | 30748466 | Missense_Mutation | T | C | p.W42R |
| HEC59_ENDOMETRIUM | 30748453 | 30748621 | 30748532 | 30748532 | Missense_Mutation | A | C | p.S64R |
| KMS12BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 30748453 | 30748621 | 30748548 | 30748548 | Missense_Mutation | T | C | p.L69S |
| SNGM_ENDOMETRIUM | 30748453 | 30748621 | 30748574 | 30748574 | Missense_Mutation | C | T | p.R78C |
| DMS53_LUNG | 30785012 | 30785158 | 30785030 | 30785030 | Missense_Mutation | C | G | p.A166G |
| SW1463_LARGE_INTESTINE | 30785012 | 30785158 | 30785030 | 30785030 | Missense_Mutation | C | G | p.A166G |
| HEC251_ENDOMETRIUM | 30785012 | 30785158 | 30785072 | 30785072 | Missense_Mutation | G | T | p.S180I |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LCLAT1 |
| 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_324544 | 2 | 30670141:30670249:30682417:30682588:30748452:30748621 | 30682417:30682588 | ENST00000319406.4 | ESCA | rs55723517 | chr2:30682470 | A/T | 3.37e-05 |
| exon_skip_324544 | 2 | 30670141:30670249:30682417:30682588:30748452:30748621 | 30682417:30682588 | ENST00000319406.4 | PRAD | rs55723517 | chr2:30682470 | A/T | 3.77e-05 |
| exon_skip_324551 | 2 | 30670122:30670270:30682417:30682588:30748452:30748621 | 30682417:30682588 | ENST00000359433.1,ENST00000309052.4 | ESCA | rs55723517 | chr2:30682470 | A/T | 3.37e-05 |
| exon_skip_324551 | 2 | 30670122:30670270:30682417:30682588:30748452:30748621 | 30682417:30682588 | ENST00000359433.1,ENST00000309052.4 | PRAD | rs55723517 | chr2:30682470 | A/T | 3.77e-05 |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LCLAT1 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LCLAT1 |
Top |
RelatedDrugs for LCLAT1 |
| 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 LCLAT1 |
| 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)
|