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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 LAMTOR4 |
 Gene summary |
| Gene information | Gene symbol | LAMTOR4 | Gene ID | 389541 |
| Gene name | late endosomal/lysosomal adaptor, MAPK and MTOR activator 4 | |
| Synonyms | C7orf59 | |
| Cytomap | 7q22.1 | |
| Type of gene | protein-coding | |
| Description | ragulator complex protein LAMTOR4UPF0539 protein C7orf59late endosomal/lysosomal adaptor and MAPK and MTOR activator 4 | |
| Modification date | 20180523 | |
| UniProtAcc | Q0VGL1 | |
| Context | PubMed: LAMTOR4 [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 LAMTOR4 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 LAMTOR4 |
| 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 LAMTOR4 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_468895 | 7 | 99746560:99746598:99747121:99747188:99751022:99751139 | 99747121:99747188 | ENSG00000188186.6 | ENST00000474831.1 |
| exon_skip_468897 | 7 | 99746560:99746598:99747121:99747202:99751022:99751139 | 99747121:99747202 | ENSG00000188186.6 | ENST00000460732.1,ENST00000441173.1 |
| exon_skip_468914 | 7 | 99747121:99747202:99750338:99750380:99751022:99751139 | 99750338:99750380 | ENSG00000188186.6 | ENST00000473459.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for LAMTOR4 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_468895 | 7 | 99746560:99746598:99747121:99747188:99751022:99751139 | 99747121:99747188 | ENSG00000188186.6 | ENST00000474831.1 |
| exon_skip_468897 | 7 | 99746560:99746598:99747121:99747202:99751022:99751139 | 99747121:99747202 | ENSG00000188186.6 | ENST00000460732.1,ENST00000441173.1 |
| exon_skip_468914 | 7 | 99747121:99747202:99750338:99750380:99751022:99751139 | 99750338:99750380 | ENSG00000188186.6 | ENST00000473459.1 |
| 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 LAMTOR4 |
| 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 LAMTOR4 |
| 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 LAMTOR4 |
| - 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. |
LAMTOR4_CESC_exon_skip_468895_psi_boxplot.png |
LAMTOR4_CESC_exon_skip_468897_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 |
| LUAD | TCGA-50-5055-01 | exon_skip_468895 | 99747122 | 99747188 | 99747177 | 99747180 | Frame_Shift_Del | TACT | - | p.VL20fs |
| LUAD | TCGA-50-5055-01 | exon_skip_468897 | 99747122 | 99747202 | 99747177 | 99747180 | Frame_Shift_Del | TACT | - | p.VL20fs |
| CESC | TCGA-IR-A3LI-01 | exon_skip_468895 | 99747122 | 99747188 | 99747121 | 99747121 | Splice_Site | G | A | e2-1 |
| CESC | TCGA-IR-A3LI-01 | exon_skip_468897 | 99747122 | 99747202 | 99747121 | 99747121 | Splice_Site | G | A | e2-1 |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-IR-A3LI-01 |
| Cancer type: CESC | |
| ESID: exon_skip_468895 | |
| Skipped exon start: 99747122 | |
| Skipped exon end: 99747188 | |
| Mutation start: 99747121 | |
| Mutation end: 99747121 | |
| Mutation type: Splice_Site | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: e2-1 | |
| Sample: TCGA-IR-A3LI-01 |
| Cancer type: CESC | |
| ESID: exon_skip_468897 | |
| Skipped exon start: 99747122 | |
| Skipped exon end: 99747202 | |
| Mutation start: 99747121 | |
| Mutation end: 99747121 | |
| Mutation type: Splice_Site | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: e2-1 | |
exon_skip_468895_CESC_TCGA-IR-A3LI-01.png | |
exon_skip_468897_CESC_TCGA-IR-A3LI-01.png | |
 | Sample: TCGA-IR-A3LI-01 |
| Cancer type: CESC | |
| ESID: exon_skip_468895 | |
| Skipped exon start: 99747122 | |
| Skipped exon end: 99747188 | |
| Mutation start: 99747121 | |
| Mutation end: 99747121 | |
| Mutation type: Splice_Site | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: e2-1 | |
| Sample: TCGA-IR-A3LI-01 |
| Cancer type: CESC | |
| ESID: exon_skip_468897 | |
| Skipped exon start: 99747122 | |
| Skipped exon end: 99747202 | |
| Mutation start: 99747121 | |
| Mutation end: 99747121 | |
| Mutation type: Splice_Site | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: e2-1 | |
| exon_skip_468895_CESC_TCGA-IR-A3LI-01.png | |
| exon_skip_468897_CESC_TCGA-IR-A3LI-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 |
| DMS153_LUNG | 99747122 | 99747188 | 99747140 | 99747140 | Missense_Mutation | G | T | p.G8W |
| DMS153_LUNG | 99747122 | 99747202 | 99747140 | 99747140 | Missense_Mutation | G | T | p.G8W |
| CAL27_UPPER_AERODIGESTIVE_TRACT | 99747122 | 99747188 | 99747158 | 99747158 | Missense_Mutation | G | A | p.D14N |
| CAL27_UPPER_AERODIGESTIVE_TRACT | 99747122 | 99747202 | 99747158 | 99747158 | Missense_Mutation | G | A | p.D14N |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LAMTOR4 |
| 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_468895 | 7 | 99746560:99746598:99747121:99747188:99751022:99751139 | 99747121:99747188 | ENST00000474831.1 | LGG | rs12878 | chr7:99747130 | A/G | 1.15e-04 |
| exon_skip_468897 | 7 | 99746560:99746598:99747121:99747202:99751022:99751139 | 99747121:99747202 | ENST00000460732.1,ENST00000441173.1 | LGG | rs12878 | chr7:99747130 | A/G | 1.15e-04 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LAMTOR4 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LAMTOR4 |
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RelatedDrugs for LAMTOR4 |
| 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 LAMTOR4 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
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