|
||||||
|
 | |
| |
| |
| |
| 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 LOXL3 |
 Gene summary |
| Gene information | Gene symbol | LOXL3 | Gene ID | 84695 |
| Gene name | lysyl oxidase like 3 | |
| Synonyms | LOXL | |
| Cytomap | 2p13.1 | |
| Type of gene | protein-coding | |
| Description | lysyl oxidase homolog 3lysyl oxidase-like protein 3 | |
| Modification date | 20180526 | |
| UniProtAcc | P58215 | |
| Context | PubMed: LOXL3 [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 |
| LOXL3 | GO:0001837 | epithelial to mesenchymal transition | 16096638 |
| LOXL3 | GO:0018057 | peptidyl-lysine oxidation | 28065600 |
| LOXL3 | GO:0045892 | negative regulation of transcription, DNA-templated | 16096638 |
Top |
Exon skipping events across known transcript of Ensembl for LOXL3 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 LOXL3 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for LOXL3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_340446 | 2 | 74760379:74760806:74761008:74761120:74761226:74761363 | 74761008:74761120 | ENSG00000115318.7 | ENST00000264094.3,ENST00000470907.2,ENST00000409549.1,ENST00000409249.1,ENST00000393937.2 |
| exon_skip_340448 | 2 | 74761226:74761363:74761442:74761558:74761657:74761901 | 74761442:74761558 | ENSG00000115318.7 | ENST00000264094.3,ENST00000470907.2,ENST00000409549.1,ENST00000393937.2,ENST00000409986.1 |
| exon_skip_340454 | 2 | 74762418:74762581:74762714:74762882:74763122:74763277 | 74762714:74762882 | ENSG00000115318.7 | ENST00000264094.3,ENST00000470907.2,ENST00000393937.2,ENST00000409986.1 |
| exon_skip_340455 | 2 | 74763417:74763598:74763835:74764055:74776495:74776586 | 74763835:74764055 | ENSG00000115318.7 | ENST00000264094.3,ENST00000409549.1,ENST00000409249.1 |
| exon_skip_340459 | 2 | 74763417:74763598:74777311:74777475:74779448:74779773 | 74777311:74777475 | ENSG00000115318.7 | ENST00000393937.2,ENST00000409986.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for LOXL3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_340446 | 2 | 74760379:74760806:74761008:74761120:74761226:74761363 | 74761008:74761120 | ENSG00000115318.7 | ENST00000470907.2,ENST00000264094.3,ENST00000409249.1,ENST00000393937.2,ENST00000409549.1 |
| exon_skip_340448 | 2 | 74761226:74761363:74761442:74761558:74761657:74761901 | 74761442:74761558 | ENSG00000115318.7 | ENST00000470907.2,ENST00000264094.3,ENST00000393937.2,ENST00000409549.1,ENST00000409986.1 |
| exon_skip_340454 | 2 | 74762418:74762581:74762714:74762882:74763122:74763277 | 74762714:74762882 | ENSG00000115318.7 | ENST00000470907.2,ENST00000264094.3,ENST00000393937.2,ENST00000409986.1 |
| exon_skip_340455 | 2 | 74763417:74763598:74763835:74764055:74776495:74776586 | 74763835:74764055 | ENSG00000115318.7 | ENST00000264094.3,ENST00000409249.1,ENST00000409549.1 |
| exon_skip_340459 | 2 | 74763417:74763598:74777311:74777475:74779448:74779773 | 74777311:74777475 | ENSG00000115318.7 | ENST00000393937.2,ENST00000409986.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for LOXL3 |
| 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 |
| ENST00000264094 | 74761008 | 74761120 | Frame-shift |
| ENST00000264094 | 74761442 | 74761558 | Frame-shift |
| ENST00000264094 | 74763835 | 74764055 | Frame-shift |
| ENST00000264094 | 74762714 | 74762882 | 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 |
| ENST00000264094 | 74761008 | 74761120 | Frame-shift |
| ENST00000264094 | 74761442 | 74761558 | Frame-shift |
| ENST00000264094 | 74763835 | 74764055 | Frame-shift |
| ENST00000264094 | 74762714 | 74762882 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for LOXL3 |
| 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 |
| ENST00000264094 | 3519 | 753 | 74762714 | 74762882 | 1321 | 1488 | 416 | 472 |
| 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 |
| ENST00000264094 | 3519 | 753 | 74762714 | 74762882 | 1321 | 1488 | 416 | 472 |
| 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 |
| P58215 | 416 | 472 | 26 | 753 | Chain | ID=PRO_0000018533;Note=Lysyl oxidase homolog 3 |
| P58215 | 416 | 472 | 446 | 511 | Disulfide bond | Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00196 |
| P58215 | 416 | 472 | 459 | 524 | Disulfide bond | Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00196 |
| P58215 | 416 | 472 | 417 | 525 | Domain | Note=SRCR 4;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00196 |
| P58215 | 416 | 472 | 446 | 446 | Mutagenesis | Note=Impaired ability to mediate deacetylation of STAT3%3B when associated with A-376 and A-492. C->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:28065600;Dbxref=PMID:28065600 |
| P58215 | 416 | 472 | 459 | 459 | Mutagenesis | Note=Impaired ability to mediate deacetylation of STAT3%3B when associated with A-83%3B A-214 and A-345. C->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:28065600;Dbxref=PMID:28065600 |
| 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 |
| P58215 | 416 | 472 | 26 | 753 | Chain | ID=PRO_0000018533;Note=Lysyl oxidase homolog 3 |
| P58215 | 416 | 472 | 446 | 511 | Disulfide bond | Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00196 |
| P58215 | 416 | 472 | 459 | 524 | Disulfide bond | Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00196 |
| P58215 | 416 | 472 | 417 | 525 | Domain | Note=SRCR 4;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00196 |
| P58215 | 416 | 472 | 446 | 446 | Mutagenesis | Note=Impaired ability to mediate deacetylation of STAT3%3B when associated with A-376 and A-492. C->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:28065600;Dbxref=PMID:28065600 |
| P58215 | 416 | 472 | 459 | 459 | Mutagenesis | Note=Impaired ability to mediate deacetylation of STAT3%3B when associated with A-83%3B A-214 and A-345. C->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:28065600;Dbxref=PMID:28065600 |
Top |
SNVs in the skipped exons for LOXL3 |
| - 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 |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_340448 | 74761443 | 74761558 | 74761511 | 74761511 | Frame_Shift_Del | G | - | p.P624fs |
| UCEC | TCGA-AX-A063-01 | exon_skip_340448 | 74761443 | 74761558 | 74761527 | 74761530 | Frame_Shift_Del | AGTG | - | p.H618fs |
| BLCA | TCGA-E7-A6MD-01 | exon_skip_340448 | 74761443 | 74761558 | 74761548 | 74761555 | Frame_Shift_Del | TGTGGTAA | - | p.HYHS609fs |
| UCEC | TCGA-B5-A0JR-01 | exon_skip_340455 | 74763836 | 74764055 | 74763921 | 74763921 | Frame_Shift_Del | G | - | p.P276fs |
| ACC | TCGA-PK-A5HB-01 | exon_skip_340455 | 74763836 | 74764055 | 74763924 | 74763924 | Frame_Shift_Del | C | - | p.G275fs |
| COAD | TCGA-D5-6930-01 | exon_skip_340455 | 74763836 | 74764055 | 74763924 | 74763924 | Frame_Shift_Del | C | - | p.G275fs |
| LUAD | TCGA-97-7553-01 | exon_skip_340455 | 74763836 | 74764055 | 74763924 | 74763924 | Frame_Shift_Del | C | - | p.G275fs |
| READ | TCGA-EI-6882-01 | exon_skip_340455 | 74763836 | 74764055 | 74763924 | 74763924 | Frame_Shift_Del | C | - | p.G275fs |
| UCEC | TCGA-D1-A101-01 | exon_skip_340455 | 74763836 | 74764055 | 74763924 | 74763924 | Frame_Shift_Del | C | - | p.G275fs |
| COAD | TCGA-CM-4743-01 | exon_skip_340455 | 74763836 | 74764055 | 74763923 | 74763924 | Frame_Shift_Ins | - | C | p.G275fs |
| COAD | TCGA-CM-6166-01 | exon_skip_340455 | 74763836 | 74764055 | 74763923 | 74763924 | Frame_Shift_Ins | - | C | p.G275fs |
| LUAD | TCGA-44-2659-01 | exon_skip_340455 | 74763836 | 74764055 | 74763923 | 74763924 | Frame_Shift_Ins | - | C | p.A275fs |
| MESO | TCGA-UD-AAC5-01 | exon_skip_340455 | 74763836 | 74764055 | 74763923 | 74763924 | Frame_Shift_Ins | - | C | p.A275fs |
| READ | TCGA-AG-3600-01 | exon_skip_340455 | 74763836 | 74764055 | 74763923 | 74763924 | Frame_Shift_Ins | - | C | p.G275fs |
| THCA | TCGA-DJ-A3V9-01 | exon_skip_340455 | 74763836 | 74764055 | 74763923 | 74763924 | Frame_Shift_Ins | - | C | p.A275fs |
| UCEC | TCGA-BG-A0M3-01 | exon_skip_340455 | 74763836 | 74764055 | 74763923 | 74763924 | Frame_Shift_Ins | - | C | p.G275fs |
| STAD | TCGA-HU-A4GN-01 | exon_skip_340455 | 74763836 | 74764055 | 74763924 | 74763925 | Frame_Shift_Ins | - | C | p.G275fs |
| LUAD | TCGA-95-7567-01 | exon_skip_340455 | 74763836 | 74764055 | 74763974 | 74763974 | Nonsense_Mutation | A | T | p.C258* |
| - 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 |
| HEC6_ENDOMETRIUM | 74763836 | 74764055 | 74763921 | 74763921 | Frame_Shift_Del | G | - | p.P276fs |
| IM95_STOMACH | 74763836 | 74764055 | 74763924 | 74763924 | Frame_Shift_Del | C | - | p.G275fs |
| RKO_LARGE_INTESTINE | 74763836 | 74764055 | 74763924 | 74763924 | Frame_Shift_Del | C | - | p.G275fs |
| CCK81_LARGE_INTESTINE | 74763836 | 74764055 | 74763924 | 74763924 | Frame_Shift_Del | C | - | p.G275fs |
| KM12_LARGE_INTESTINE | 74763836 | 74764055 | 74763924 | 74763924 | Frame_Shift_Del | C | - | p.G275fs |
| CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 74763836 | 74764055 | 74763924 | 74763924 | Frame_Shift_Del | C | - | p.G275fs |
| CW2_LARGE_INTESTINE | 74763836 | 74764055 | 74763924 | 74763924 | Frame_Shift_Del | C | - | p.G275fs |
| EN_ENDOMETRIUM | 74763836 | 74764055 | 74763924 | 74763924 | Frame_Shift_Del | C | - | p.G275fs |
| HCC1569_BREAST | 74763836 | 74764055 | 74763924 | 74763924 | Frame_Shift_Del | C | - | p.G275fs |
| SNU1040_LARGE_INTESTINE | 74763836 | 74764055 | 74763924 | 74763924 | Frame_Shift_Del | C | - | p.G275fs |
| HEC265_ENDOMETRIUM | 74777312 | 74777475 | 74777410 | 74777410 | Frame_Shift_Del | G | - | p.R127fs |
| HEC151_ENDOMETRIUM | 74762715 | 74762882 | 74762777 | 74762778 | Frame_Shift_Ins | - | C | p.T452fs |
| HOP62_LUNG | 74761009 | 74761120 | 74761083 | 74761083 | Missense_Mutation | T | G | p.D705A |
| NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 74761009 | 74761120 | 74761103 | 74761103 | Missense_Mutation | G | T | p.N698K |
| PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 74761443 | 74761558 | 74761454 | 74761454 | Missense_Mutation | T | C | p.E643G |
| PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 74761443 | 74761558 | 74761458 | 74761458 | Missense_Mutation | T | C | p.T642A |
| SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 74762715 | 74762882 | 74762722 | 74762722 | Missense_Mutation | C | T | p.G470D |
| TCYIK_CERVIX | 74762715 | 74762882 | 74762786 | 74762786 | Missense_Mutation | C | G | p.D449H |
| HCT15_LARGE_INTESTINE | 74762715 | 74762882 | 74762864 | 74762864 | Missense_Mutation | G | A | p.R423C |
| LNCAPCLONEFGC_PROSTATE | 74762715 | 74762882 | 74762872 | 74762872 | Missense_Mutation | C | T | p.S420N |
| MSTO211H_PLEURA | 74763836 | 74764055 | 74763880 | 74763880 | Missense_Mutation | A | T | p.S290T |
| MN60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 74763836 | 74764055 | 74763901 | 74763901 | Missense_Mutation | G | A | p.P283S |
| HCC2450_LUNG | 74763836 | 74764055 | 74763928 | 74763928 | Missense_Mutation | C | A | p.G274W |
| NCIH1573_LUNG | 74763836 | 74764055 | 74764036 | 74764036 | Missense_Mutation | G | C | p.Q238E |
| NCIH2342_LUNG | 74777312 | 74777475 | 74777422 | 74777422 | Missense_Mutation | C | T | p.E123K |
| TE9_OESOPHAGUS | 74761009 | 74761120 | 74761029 | 74761029 | Nonsense_Mutation | C | T | p.W723* |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 74761009 | 74761120 | 74761010 | 74761010 | Splice_Site | A | G | p.I729I |
| EPLC272H_LUNG | 74762715 | 74762882 | 74762882 | 74762882 | Splice_Site | T | A | p.I417F |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LOXL3 |
| 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 LOXL3 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LOXL3 |
Top |
RelatedDrugs for LOXL3 |
| 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 LOXL3 |
| 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)
|