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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 LOXL2 |
 Gene summary |
| Gene information | Gene symbol | LOXL2 | Gene ID | 4017 |
| Gene name | lysyl oxidase like 2 | |
| Synonyms | LOR|LOR2|WS9-14 | |
| Cytomap | 8p21.3 | |
| Type of gene | protein-coding | |
| Description | lysyl oxidase homolog 2lysyl oxidase related 2lysyl oxidase-like 2 delta e13lysyl oxidase-like 2 proteinlysyl oxidase-like protein 2lysyl oxidase-related protein 2lysyl oxidase-related protein WS9-14 | |
| Modification date | 20180523 | |
| UniProtAcc | Q9Y4K0 | |
| Context | PubMed: LOXL2 [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 |
| LOXL2 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 25959397 |
| LOXL2 | GO:0001837 | epithelial to mesenchymal transition | 16096638 |
| LOXL2 | GO:0006464 | cellular protein modification process | 23319596 |
| LOXL2 | GO:0018057 | peptidyl-lysine oxidation | 25959397|27735137 |
| LOXL2 | GO:0045892 | negative regulation of transcription, DNA-templated | 16096638 |
| LOXL2 | GO:0046688 | response to copper ion | 23319596 |
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Exon skipping events across known transcript of Ensembl for LOXL2 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 LOXL2 |
| 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 LOXL2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_488788 | 8 | 23154701:23155635:23156348:23156460:23159539:23159676 | 23156348:23156460 | ENSG00000134013.11 | ENST00000389131.3 |
| exon_skip_488789 | 8 | 23160794:23160910:23167180:23167424:23174461:23174627 | 23167180:23167424 | ENSG00000134013.11 | ENST00000389131.3 |
| exon_skip_488791 | 8 | 23174461:23174627:23177397:23177565:23179642:23179794 | 23177397:23177565 | ENSG00000134013.11 | ENST00000389131.3 |
| exon_skip_488792 | 8 | 23177473:23177565:23179642:23179794:23185894:23186078 | 23179642:23179794 | ENSG00000134013.11 | ENST00000520349.1,ENST00000522446.1,ENST00000389131.3,ENST00000519809.1,ENST00000518878.1 |
| exon_skip_488793 | 8 | 23179642:23179794:23185894:23186078:23190913:23191008 | 23185894:23186078 | ENSG00000134013.11 | ENST00000389131.3,ENST00000520925.1 |
| exon_skip_488795 | 8 | 23179642:23179794:23185894:23186099:23190913:23191008 | 23185894:23186099 | ENSG00000134013.11 | ENST00000520349.1 |
| exon_skip_488796 | 8 | 23185894:23186078:23190913:23191136:23198504:23198689 | 23190913:23191136 | ENSG00000134013.11 | ENST00000389131.3 |
| exon_skip_488798 | 8 | 23198504:23198716:23217602:23217778:23225509:23225947 | 23217602:23217778 | ENSG00000134013.11 | ENST00000389131.3 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for LOXL2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_488788 | 8 | 23154701:23155635:23156348:23156460:23159539:23159676 | 23156348:23156460 | ENSG00000134013.11 | ENST00000389131.3 |
| exon_skip_488789 | 8 | 23160794:23160910:23167180:23167424:23174461:23174627 | 23167180:23167424 | ENSG00000134013.11 | ENST00000389131.3 |
| exon_skip_488791 | 8 | 23174461:23174627:23177397:23177565:23179642:23179794 | 23177397:23177565 | ENSG00000134013.11 | ENST00000389131.3 |
| exon_skip_488792 | 8 | 23177473:23177565:23179642:23179794:23185894:23186078 | 23179642:23179794 | ENSG00000134013.11 | ENST00000389131.3,ENST00000520349.1,ENST00000518878.1,ENST00000522446.1,ENST00000519809.1 |
| exon_skip_488793 | 8 | 23179642:23179794:23185894:23186078:23190913:23191008 | 23185894:23186078 | ENSG00000134013.11 | ENST00000389131.3,ENST00000520925.1 |
| exon_skip_488795 | 8 | 23179642:23179794:23185894:23186099:23190913:23191008 | 23185894:23186099 | ENSG00000134013.11 | ENST00000520349.1 |
| exon_skip_488796 | 8 | 23185894:23186078:23190913:23191136:23198504:23198689 | 23190913:23191136 | ENSG00000134013.11 | ENST00000389131.3 |
| exon_skip_488798 | 8 | 23198504:23198716:23217602:23217778:23225509:23225947 | 23217602:23217778 | ENSG00000134013.11 | ENST00000389131.3 |
| 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 LOXL2 |
| 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 |
| ENST00000389131 | 23156348 | 23156460 | Frame-shift |
| ENST00000389131 | 23167180 | 23167424 | Frame-shift |
| ENST00000389131 | 23179642 | 23179794 | Frame-shift |
| ENST00000389131 | 23185894 | 23186078 | Frame-shift |
| ENST00000389131 | 23190913 | 23191136 | Frame-shift |
| ENST00000389131 | 23217602 | 23217778 | Frame-shift |
| ENST00000389131 | 23177397 | 23177565 | 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 |
| ENST00000389131 | 23156348 | 23156460 | Frame-shift |
| ENST00000389131 | 23167180 | 23167424 | Frame-shift |
| ENST00000389131 | 23179642 | 23179794 | Frame-shift |
| ENST00000389131 | 23185894 | 23186078 | Frame-shift |
| ENST00000389131 | 23190913 | 23191136 | Frame-shift |
| ENST00000389131 | 23217602 | 23217778 | Frame-shift |
| ENST00000389131 | 23177397 | 23177565 | In-frame |
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Infer the effects of exon skipping event on protein functional features for LOXL2 |
| 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 |
| ENST00000389131 | 3566 | 774 | 23177397 | 23177565 | 1673 | 1840 | 434 | 490 |
| 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 |
| ENST00000389131 | 3566 | 774 | 23177397 | 23177565 | 1673 | 1840 | 434 | 490 |
| 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 |
| Q9Y4K0 | 434 | 490 | 434 | 441 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5ZE3 |
| Q9Y4K0 | 434 | 490 | 445 | 454 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5ZE3 |
| Q9Y4K0 | 434 | 490 | 457 | 463 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5ZE3 |
| Q9Y4K0 | 434 | 490 | 484 | 490 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5ZE3 |
| Q9Y4K0 | 434 | 490 | 26 | 774 | Chain | ID=PRO_0000018532;Note=Lysyl oxidase homolog 2 |
| Q9Y4K0 | 434 | 490 | 464 | 530 | Disulfide bond | Ontology_term=ECO:0000244,ECO:0000255,ECO:0000269;evidence=ECO:0000244|PDB:5ZE3,ECO:0000255|PROSITE-ProRule:PRU00196,ECO:0000269|PubMed:29581294;Dbxref=PMID:29581294 |
| Q9Y4K0 | 434 | 490 | 477 | 543 | Disulfide bond | Ontology_term=ECO:0000244,ECO:0000255,ECO:0000269;evidence=ECO:0000244|PDB:5ZE3,ECO:0000255|PROSITE-ProRule:PRU00196,ECO:0000269|PubMed:29581294;Dbxref=PMID:29581294 |
| Q9Y4K0 | 434 | 490 | 435 | 544 | Domain | Note=SRCR 4;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00196 |
| Q9Y4K0 | 434 | 490 | 455 | 455 | Glycosylation | Note=N-linked (GlcNAc...) (complex) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23319596;Dbxref=PMID:23319596 |
| Q9Y4K0 | 434 | 490 | 470 | 480 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5ZE3 |
| Q9Y4K0 | 434 | 490 | 455 | 455 | Mutagenesis | Note=Inhibits secretion. N->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23319596;Dbxref=PMID:23319596 |
| 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 |
| Q9Y4K0 | 434 | 490 | 434 | 441 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5ZE3 |
| Q9Y4K0 | 434 | 490 | 445 | 454 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5ZE3 |
| Q9Y4K0 | 434 | 490 | 457 | 463 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5ZE3 |
| Q9Y4K0 | 434 | 490 | 484 | 490 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5ZE3 |
| Q9Y4K0 | 434 | 490 | 26 | 774 | Chain | ID=PRO_0000018532;Note=Lysyl oxidase homolog 2 |
| Q9Y4K0 | 434 | 490 | 464 | 530 | Disulfide bond | Ontology_term=ECO:0000244,ECO:0000255,ECO:0000269;evidence=ECO:0000244|PDB:5ZE3,ECO:0000255|PROSITE-ProRule:PRU00196,ECO:0000269|PubMed:29581294;Dbxref=PMID:29581294 |
| Q9Y4K0 | 434 | 490 | 477 | 543 | Disulfide bond | Ontology_term=ECO:0000244,ECO:0000255,ECO:0000269;evidence=ECO:0000244|PDB:5ZE3,ECO:0000255|PROSITE-ProRule:PRU00196,ECO:0000269|PubMed:29581294;Dbxref=PMID:29581294 |
| Q9Y4K0 | 434 | 490 | 435 | 544 | Domain | Note=SRCR 4;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00196 |
| Q9Y4K0 | 434 | 490 | 455 | 455 | Glycosylation | Note=N-linked (GlcNAc...) (complex) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23319596;Dbxref=PMID:23319596 |
| Q9Y4K0 | 434 | 490 | 470 | 480 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5ZE3 |
| Q9Y4K0 | 434 | 490 | 455 | 455 | Mutagenesis | Note=Inhibits secretion. N->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23319596;Dbxref=PMID:23319596 |
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SNVs in the skipped exons for LOXL2 |
| - 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. |
| - 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 |
| PAAD | TCGA-3A-A9IO-01 | exon_skip_488789 | 23167181 | 23167424 | 23167294 | 23167294 | Frame_Shift_Del | G | - | p.P589fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_488789 | 23167181 | 23167424 | 23167360 | 23167360 | Frame_Shift_Del | G | - | p.P567fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_488791 | 23177398 | 23177565 | 23177485 | 23177485 | Frame_Shift_Del | C | - | p.G461fs |
| UCEC | TCGA-BS-A0TA-01 | exon_skip_488792 | 23179643 | 23179794 | 23179745 | 23179746 | Frame_Shift_Ins | - | T | p.K400fs |
| UCEC | TCGA-BS-A0TA-01 | exon_skip_488792 | 23179643 | 23179794 | 23179745 | 23179746 | Frame_Shift_Ins | - | T | p.S401fs |
| HNSC | TCGA-F7-A624-01 | exon_skip_488788 | 23156349 | 23156460 | 23156368 | 23156368 | Nonsense_Mutation | C | T | p.W742* |
| LGG | TCGA-DU-6392-01 | exon_skip_488791 | 23177398 | 23177565 | 23177529 | 23177529 | Nonsense_Mutation | G | A | p.R447* |
| BLCA | TCGA-E7-A4IJ-01 | exon_skip_488793 | 23185895 | 23186078 | 23185981 | 23185981 | Nonsense_Mutation | C | T | p.W355* |
| BLCA | TCGA-E7-A4IJ-01 | exon_skip_488795 | 23185895 | 23186099 | 23185981 | 23185981 | Nonsense_Mutation | C | T | p.W355* |
| ESCA | TCGA-L5-A4ON-01 | exon_skip_488793 | 23185895 | 23186078 | 23186066 | 23186066 | Nonsense_Mutation | G | A | p.R327* |
| ESCA | TCGA-L5-A4ON-01 | exon_skip_488793 | 23185895 | 23186078 | 23186066 | 23186066 | Nonsense_Mutation | G | A | p.R327X |
| ESCA | TCGA-L5-A4ON-01 | exon_skip_488795 | 23185895 | 23186099 | 23186066 | 23186066 | Nonsense_Mutation | G | A | p.R327* |
| ESCA | TCGA-L5-A4ON-01 | exon_skip_488795 | 23185895 | 23186099 | 23186066 | 23186066 | Nonsense_Mutation | G | A | p.R327X |
| COAD | TCGA-AA-3516-01 | exon_skip_488798 | 23217603 | 23217778 | 23217750 | 23217750 | Nonsense_Mutation | A | T | p.C128X |
| ACC | TCGA-OR-A5KB-01 | exon_skip_488792 | 23179643 | 23179794 | 23179795 | 23179795 | Splice_Site | C | T | . |
| - 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 |
| NCIH513_PLEURA | 23177398 | 23177565 | 23177475 | 23177476 | Frame_Shift_Del | CA | - | p.CG464fs |
| A172_CENTRAL_NERVOUS_SYSTEM | 23167181 | 23167424 | 23167257 | 23167257 | Missense_Mutation | G | T | p.Q602K |
| CCK81_LARGE_INTESTINE | 23167181 | 23167424 | 23167336 | 23167336 | Missense_Mutation | C | T | p.M575I |
| ISHIKAWAHERAKLIO02ER_ENDOMETRIUM | 23167181 | 23167424 | 23167400 | 23167400 | Missense_Mutation | G | A | p.A554V |
| HCC1954_BREAST | 23177398 | 23177565 | 23177446 | 23177446 | Missense_Mutation | C | T | p.M474I |
| HCC1954_MATCHED_NORMAL_TISSUE | 23177398 | 23177565 | 23177446 | 23177446 | Missense_Mutation | C | T | p.M474I |
| MCC13_SKIN | 23177398 | 23177565 | 23177472 | 23177472 | Missense_Mutation | G | T | p.Q466K |
| SKN3_UPPER_AERODIGESTIVE_TRACT | 23177398 | 23177565 | 23177507 | 23177507 | Missense_Mutation | C | G | p.R454T |
| HELA_CERVIX | 23179643 | 23179794 | 23179741 | 23179741 | Missense_Mutation | T | C | p.I402V |
| MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 23190914 | 23191136 | 23190934 | 23190934 | Missense_Mutation | G | A | p.R316W |
| NCIH196_LUNG | 23190914 | 23191136 | 23190988 | 23190988 | Missense_Mutation | C | T | p.V298M |
| SKMEL30_SKIN | 23190914 | 23191136 | 23191081 | 23191081 | Missense_Mutation | C | T | p.G267S |
| HS618T_FIBROBLAST | 23217603 | 23217778 | 23217622 | 23217622 | Missense_Mutation | G | A | p.S171L |
| LNCAPCLONEFGC_PROSTATE | 23217603 | 23217778 | 23217658 | 23217658 | Missense_Mutation | C | T | p.S159N |
| SW1573_LUNG | 23217603 | 23217778 | 23217736 | 23217736 | Missense_Mutation | G | A | p.A133V |
| NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 23177398 | 23177565 | 23177529 | 23177529 | Nonsense_Mutation | G | A | p.R447* |
| CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 23190914 | 23191136 | 23190967 | 23190967 | Nonsense_Mutation | G | A | p.Q305* |
| PACADD188_PANCREAS | 23167181 | 23167424 | 23167423 | 23167423 | Splice_Site | G | A | p.T546T |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LOXL2 |
| 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 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LOXL2 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LOXL2 |
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RelatedDrugs for LOXL2 |
| 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 LOXL2 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| LOXL2 | C1458155 | Mammary Neoplasms | 2 | CTD_human |
| LOXL2 | C0007621 | Neoplastic Cell Transformation | 1 | CTD_human |
| LOXL2 | C0019163 | Hepatitis B | 1 | CTD_human |
| LOXL2 | C0019196 | Hepatitis C | 1 | CTD_human |
| LOXL2 | C0019202 | Hepatolenticular Degeneration | 1 | CTD_human |
| LOXL2 | C0023892 | Biliary cirrhosis | 1 | CTD_human |
| LOXL2 | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
| LOXL2 | C0027626 | Neoplasm Invasiveness | 1 | CTD_human |
| LOXL2 | C0279626 | Squamous cell carcinoma of esophagus | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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