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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 LCN2 |
 Gene summary |
| Gene information | Gene symbol | LCN2 | Gene ID | 3934 |
| Gene name | lipocalin 2 | |
| Synonyms | 24p3|MSFI|NGAL|p25 | |
| Cytomap | 9q34.11 | |
| Type of gene | protein-coding | |
| Description | neutrophil gelatinase-associated lipocalin25 kDa alpha-2-microglobulin-related subunit of MMP-9migration-stimulating factor inhibitoroncogene 24p3siderocalin LCN2 | |
| Modification date | 20180527 | |
| UniProtAcc | P80188 | |
| Context | PubMed: LCN2 [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 LCN2 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 LCN2 |
| 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 LCN2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_499425 | 9 | 130911929:130911942:130912516:130912653:130913916:130913996 | 130912516:130912653 | ENSG00000148346.7 | ENST00000540948.1,ENST00000373017.1,ENST00000277480.2 |
| exon_skip_499431 | 9 | 130911929:130911942:130912653:130912835:130913916:130913996 | 130912653:130912835 | ENSG00000148346.7 | ENST00000470902.1 |
| exon_skip_499456 | 9 | 130912522:130912653:130912829:130912835:130913916:130913957 | 130912829:130912835 | ENSG00000148346.7 | ENST00000373013.2 |
| exon_skip_499469 | 9 | 130912522:130912653:130913727:130913740:130913923:130913996 | 130913727:130913740 | ENSG00000148346.7 | ENST00000372998.1 |
| exon_skip_499471 | 9 | 130912522:130912653:130913916:130913996:130914184:130914304 | 130913916:130913996 | ENSG00000148346.7 | ENST00000540948.1,ENST00000373017.1,ENST00000277480.2 |
| exon_skip_499474 | 9 | 130913947:130913996:130914184:130914304:130914461:130914563 | 130914184:130914304 | ENSG00000148346.7 | ENST00000372998.1,ENST00000470902.1,ENST00000488391.1,ENST00000540948.1,ENST00000373013.2,ENST00000494317.1,ENST00000373017.1,ENST00000277480.2 |
| exon_skip_499488 | 9 | 130914184:130914304:130914461:130914563:130915378:130915405 | 130914461:130914563 | ENSG00000148346.7 | ENST00000372998.1,ENST00000470902.1,ENST00000488391.1,ENST00000373013.2,ENST00000494317.1,ENST00000373017.1,ENST00000277480.2 |
| exon_skip_499499 | 9 | 130914461:130914563:130915378:130915405:130915589:130915607 | 130915378:130915405 | ENSG00000148346.7 | ENST00000470902.1,ENST00000488391.1,ENST00000373013.2,ENST00000277480.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for LCN2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_499425 | 9 | 130911929:130911942:130912516:130912653:130913916:130913996 | 130912516:130912653 | ENSG00000148346.7 | ENST00000373017.1,ENST00000277480.2,ENST00000540948.1 |
| exon_skip_499431 | 9 | 130911929:130911942:130912653:130912835:130913916:130913996 | 130912653:130912835 | ENSG00000148346.7 | ENST00000470902.1 |
| exon_skip_499456 | 9 | 130912522:130912653:130912829:130912835:130913916:130913957 | 130912829:130912835 | ENSG00000148346.7 | ENST00000373013.2 |
| exon_skip_499469 | 9 | 130912522:130912653:130913727:130913740:130913923:130913996 | 130913727:130913740 | ENSG00000148346.7 | ENST00000372998.1 |
| exon_skip_499471 | 9 | 130912522:130912653:130913916:130913996:130914184:130914304 | 130913916:130913996 | ENSG00000148346.7 | ENST00000373017.1,ENST00000277480.2,ENST00000540948.1 |
| exon_skip_499474 | 9 | 130913947:130913996:130914184:130914304:130914461:130914563 | 130914184:130914304 | ENSG00000148346.7 | ENST00000373017.1,ENST00000470902.1,ENST00000277480.2,ENST00000373013.2,ENST00000540948.1,ENST00000372998.1,ENST00000488391.1,ENST00000494317.1 |
| exon_skip_499488 | 9 | 130914184:130914304:130914461:130914563:130915378:130915405 | 130914461:130914563 | ENSG00000148346.7 | ENST00000373017.1,ENST00000470902.1,ENST00000277480.2,ENST00000373013.2,ENST00000372998.1,ENST00000488391.1,ENST00000494317.1 |
| exon_skip_499499 | 9 | 130914461:130914563:130915378:130915405:130915589:130915607 | 130915378:130915405 | ENSG00000148346.7 | ENST00000470902.1,ENST00000277480.2,ENST00000373013.2,ENST00000488391.1 |
| 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 LCN2 |
| 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 |
| ENST00000277480 | 130915378 | 130915405 | 3UTR-3CDS |
| ENST00000277480 | 130912516 | 130912653 | Frame-shift |
| ENST00000373017 | 130912516 | 130912653 | Frame-shift |
| ENST00000277480 | 130913916 | 130913996 | Frame-shift |
| ENST00000373017 | 130913916 | 130913996 | Frame-shift |
| ENST00000277480 | 130914184 | 130914304 | In-frame |
| ENST00000373017 | 130914184 | 130914304 | In-frame |
| ENST00000277480 | 130914461 | 130914563 | In-frame |
| ENST00000373017 | 130914461 | 130914563 | 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 |
| ENST00000277480 | 130915378 | 130915405 | 3UTR-3CDS |
| ENST00000277480 | 130912516 | 130912653 | Frame-shift |
| ENST00000373017 | 130912516 | 130912653 | Frame-shift |
| ENST00000277480 | 130913916 | 130913996 | Frame-shift |
| ENST00000373017 | 130913916 | 130913996 | Frame-shift |
| ENST00000277480 | 130914184 | 130914304 | In-frame |
| ENST00000373017 | 130914184 | 130914304 | In-frame |
| ENST00000277480 | 130914461 | 130914563 | In-frame |
| ENST00000373017 | 130914461 | 130914563 | In-frame |
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Infer the effects of exon skipping event on protein functional features for LCN2 |
| 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 |
| ENST00000277480 | 839 | 198 | 130914184 | 130914304 | 429 | 548 | 118 | 158 |
| ENST00000373017 | 865 | 198 | 130914184 | 130914304 | 593 | 712 | 118 | 158 |
| ENST00000277480 | 839 | 198 | 130914461 | 130914563 | 549 | 650 | 158 | 192 |
| ENST00000373017 | 865 | 198 | 130914461 | 130914563 | 713 | 814 | 158 | 192 |
| 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 |
| ENST00000277480 | 839 | 198 | 130914184 | 130914304 | 429 | 548 | 118 | 158 |
| ENST00000373017 | 865 | 198 | 130914184 | 130914304 | 593 | 712 | 118 | 158 |
| ENST00000277480 | 839 | 198 | 130914461 | 130914563 | 549 | 650 | 158 | 192 |
| ENST00000373017 | 865 | 198 | 130914461 | 130914563 | 713 | 814 | 158 | 192 |
| 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 LCN2 |
| - 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 |
| ESCA | TCGA-L5-A4OI-01 | exon_skip_499474 | 130914185 | 130914304 | 130914272 | 130914272 | Frame_Shift_Del | A | - | p.N151fs |
| ESCA | TCGA-L5-A4OI-01 | exon_skip_499474 | 130914185 | 130914304 | 130914272 | 130914272 | Frame_Shift_Del | A | - | p.Q148fs |
| LUAD | TCGA-38-7271-01 | exon_skip_499425 | 130912517 | 130912653 | 130912526 | 130912526 | Nonsense_Mutation | A | T | p.K50* |
| - 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 |
| EW1_BONE | 130912517 | 130912653 | 130912547 | 130912547 | Missense_Mutation | G | C | p.A57P |
| DMS53_LUNG | 130912517 | 130912653 | 130912553 | 130912553 | Missense_Mutation | A | G | p.N59D |
| NCIH1092_LUNG | 130912517 | 130912653 | 130912591 | 130912591 | Missense_Mutation | G | T | p.M71I |
| SNUC5_LARGE_INTESTINE | 130912517 | 130912653 | 130912593 | 130912593 | Missense_Mutation | A | G | p.Y72C |
| JHUEM7_ENDOMETRIUM | 130913917 | 130913996 | 130913923 | 130913923 | Missense_Mutation | G | T | p.K94N |
| IHH4_THYROID | 130913917 | 130913996 | 130913945 | 130913945 | Missense_Mutation | A | T | p.T102S |
| PANC1_PANCREAS | 130914185 | 130914304 | 130914248 | 130914248 | Missense_Mutation | T | C | p.M140T |
| KP1N_PANCREAS | 130914185 | 130914304 | 130914248 | 130914248 | Missense_Mutation | T | C | p.M140T |
| NCIH1105_LUNG | 130914462 | 130914563 | 130914470 | 130914470 | Missense_Mutation | A | G | p.K162E |
| NCIH1155_LUNG | 130914462 | 130914563 | 130914507 | 130914507 | Missense_Mutation | G | A | p.R174H |
| COV318_OVARY | 130915379 | 130915405 | 130915381 | 130915381 | Missense_Mutation | C | G | p.Q194E |
| ESO51_OESOPHAGUS | 130914462 | 130914563 | 130914562 | 130914562 | Splice_Site | C | T | p.I192I |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LCN2 |
| 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 LCN2 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LCN2 |
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RelatedDrugs for LCN2 |
| 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 LCN2 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| LCN2 | C0022658 | Kidney Diseases | 4 | CTD_human |
| LCN2 | C2609414 | Acute kidney injury | 3 | CTD_human |
| LCN2 | C0023893 | Liver Cirrhosis, Experimental | 2 | CTD_human |
| LCN2 | C4277682 | Chemical and Drug Induced Liver Injury | 2 | CTD_human |
| LCN2 | C0003873 | Rheumatoid Arthritis | 1 | CTD_human |
| LCN2 | C0005283 | beta Thalassemia | 1 | CTD_human |
| LCN2 | C0006663 | Calcinosis | 1 | CTD_human |
| LCN2 | C0011616 | Contact Dermatitis | 1 | CTD_human |
| LCN2 | C0018824 | Heart valve disease | 1 | CTD_human |
| LCN2 | C0019188 | Hepatitis, Animal | 1 | CTD_human |
| LCN2 | C0021368 | Inflammation | 1 | CTD_human |
| LCN2 | C0027627 | Neoplasm Metastasis | 1 | CTD_human |
| LCN2 | C0035222 | Respiratory Distress Syndrome, Adult | 1 | CTD_human |
| LCN2 | C0036341 | Schizophrenia | 1 | PSYGENET |
| LCN2 | C0403447 | Chronic Kidney Insufficiency | 1 | CTD_human |
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