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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 LMNB1 |
 Gene summary |
| Gene information | Gene symbol | LMNB1 | Gene ID | 4001 |
| Gene name | lamin B1 | |
| Synonyms | ADLD|LMN|LMN2|LMNB | |
| Cytomap | 5q23.2 | |
| Type of gene | protein-coding | |
| Description | lamin-B1 | |
| Modification date | 20180523 | |
| UniProtAcc | P20700 | |
| Context | PubMed: LMNB1 [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 LMNB1 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 LMNB1 |
| 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 LMNB1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_437060 | 5 | 126112852:126112944:126113052:126113559:126140467:126140606 | 126113052:126113559 | ENSG00000113368.7 | ENST00000492190.1 |
| exon_skip_437062 | 5 | 126147464:126147590:126150861:126150939:126154613:126154671 | 126150861:126150939 | ENSG00000113368.7 | ENST00000460265.1 |
| exon_skip_437063 | 5 | 126156601:126156827:126158472:126158577:126161679:126161799 | 126158472:126158577 | ENSG00000113368.7 | ENST00000504788.1,ENST00000512460.1,ENST00000261366.5,ENST00000460265.1 |
| exon_skip_437065 | 5 | 126158472:126158577:126161679:126161799:126168385:126168493 | 126161679:126161799 | ENSG00000113368.7 | ENST00000504788.1,ENST00000261366.5,ENST00000460265.1 |
| exon_skip_437066 | 5 | 126161679:126161799:126168385:126168493:126171914:126172263 | 126168385:126168493 | ENSG00000113368.7 | ENST00000504788.1,ENST00000261366.5,ENST00000460265.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for LMNB1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_437060 | 5 | 126112852:126112944:126113052:126113559:126140467:126140606 | 126113052:126113559 | ENSG00000113368.7 | ENST00000492190.1 |
| exon_skip_437062 | 5 | 126147464:126147590:126150861:126150939:126154613:126154671 | 126150861:126150939 | ENSG00000113368.7 | ENST00000460265.1 |
| exon_skip_437063 | 5 | 126156601:126156827:126158472:126158577:126161679:126161799 | 126158472:126158577 | ENSG00000113368.7 | ENST00000460265.1,ENST00000261366.5,ENST00000504788.1,ENST00000512460.1 |
| exon_skip_437065 | 5 | 126158472:126158577:126161679:126161799:126168385:126168493 | 126161679:126161799 | ENSG00000113368.7 | ENST00000460265.1,ENST00000261366.5,ENST00000504788.1 |
| exon_skip_437066 | 5 | 126161679:126161799:126168385:126168493:126171914:126172263 | 126168385:126168493 | ENSG00000113368.7 | ENST00000460265.1,ENST00000261366.5,ENST00000504788.1 |
| 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 LMNB1 |
| 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 |
| ENST00000261366 | 126158472 | 126158577 | In-frame |
| ENST00000261366 | 126161679 | 126161799 | In-frame |
| ENST00000261366 | 126168385 | 126168493 | 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 |
| ENST00000261366 | 126158472 | 126158577 | In-frame |
| ENST00000261366 | 126161679 | 126161799 | In-frame |
| ENST00000261366 | 126168385 | 126168493 | In-frame |
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Infer the effects of exon skipping event on protein functional features for LMNB1 |
| 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 |
| ENST00000261366 | 2895 | 586 | 126158472 | 126158577 | 1748 | 1852 | 462 | 497 |
| ENST00000261366 | 2895 | 586 | 126161679 | 126161799 | 1853 | 1972 | 497 | 537 |
| ENST00000261366 | 2895 | 586 | 126168385 | 126168493 | 1973 | 2080 | 537 | 573 |
| 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 |
| ENST00000261366 | 2895 | 586 | 126158472 | 126158577 | 1748 | 1852 | 462 | 497 |
| ENST00000261366 | 2895 | 586 | 126161679 | 126161799 | 1853 | 1972 | 497 | 537 |
| ENST00000261366 | 2895 | 586 | 126168385 | 126168493 | 1973 | 2080 | 537 | 573 |
| 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 |
| P20700 | 462 | 497 | 460 | 462 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 462 | 497 | 470 | 475 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 462 | 497 | 478 | 483 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 462 | 497 | 495 | 500 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 462 | 497 | 2 | 583 | Chain | ID=PRO_0000063816;Note=Lamin-B1 |
| P20700 | 462 | 497 | 430 | 546 | Domain | Note=LTD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01187 |
| P20700 | 462 | 497 | 483 | 483 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P20700 | 462 | 497 | 387 | 586 | Region | Note=Tail |
| P20700 | 497 | 537 | 495 | 500 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 497 | 537 | 512 | 515 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 497 | 537 | 523 | 525 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 497 | 537 | 527 | 532 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 497 | 537 | 2 | 583 | Chain | ID=PRO_0000063816;Note=Lamin-B1 |
| P20700 | 497 | 537 | 532 | 532 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 |
| P20700 | 497 | 537 | 430 | 546 | Domain | Note=LTD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01187 |
| P20700 | 497 | 537 | 534 | 534 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P20700 | 497 | 537 | 501 | 501 | Natural variant | ID=VAR_031646;Note=A->V;Dbxref=dbSNP:rs36105360 |
| P20700 | 497 | 537 | 387 | 586 | Region | Note=Tail |
| P20700 | 497 | 537 | 509 | 511 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 537 | 573 | 538 | 546 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 537 | 573 | 2 | 583 | Chain | ID=PRO_0000063816;Note=Lamin-B1 |
| P20700 | 537 | 573 | 552 | 559 | Compositional bias | Note=Glu-rich (highly acidic%3B could be involved in chromatin binding) |
| P20700 | 537 | 573 | 547 | 547 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 |
| P20700 | 537 | 573 | 430 | 546 | Domain | Note=LTD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01187 |
| P20700 | 537 | 573 | 387 | 586 | Region | Note=Tail |
| 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 |
| P20700 | 462 | 497 | 460 | 462 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 462 | 497 | 470 | 475 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 462 | 497 | 478 | 483 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 462 | 497 | 495 | 500 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 462 | 497 | 2 | 583 | Chain | ID=PRO_0000063816;Note=Lamin-B1 |
| P20700 | 462 | 497 | 430 | 546 | Domain | Note=LTD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01187 |
| P20700 | 462 | 497 | 483 | 483 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P20700 | 462 | 497 | 387 | 586 | Region | Note=Tail |
| P20700 | 497 | 537 | 495 | 500 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 497 | 537 | 512 | 515 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 497 | 537 | 523 | 525 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 497 | 537 | 527 | 532 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 497 | 537 | 2 | 583 | Chain | ID=PRO_0000063816;Note=Lamin-B1 |
| P20700 | 497 | 537 | 532 | 532 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 |
| P20700 | 497 | 537 | 430 | 546 | Domain | Note=LTD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01187 |
| P20700 | 497 | 537 | 534 | 534 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P20700 | 497 | 537 | 501 | 501 | Natural variant | ID=VAR_031646;Note=A->V;Dbxref=dbSNP:rs36105360 |
| P20700 | 497 | 537 | 387 | 586 | Region | Note=Tail |
| P20700 | 497 | 537 | 509 | 511 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 537 | 573 | 538 | 546 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3UMN |
| P20700 | 537 | 573 | 2 | 583 | Chain | ID=PRO_0000063816;Note=Lamin-B1 |
| P20700 | 537 | 573 | 552 | 559 | Compositional bias | Note=Glu-rich (highly acidic%3B could be involved in chromatin binding) |
| P20700 | 537 | 573 | 547 | 547 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 |
| P20700 | 537 | 573 | 430 | 546 | Domain | Note=LTD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01187 |
| P20700 | 537 | 573 | 387 | 586 | Region | Note=Tail |
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SNVs in the skipped exons for LMNB1 |
| - 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 |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_437063 | 126158473 | 126158577 | 126158505 | 126158505 | Frame_Shift_Del | A | - | p.R473fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_437065 | 126161680 | 126161799 | 126161712 | 126161712 | Frame_Shift_Del | C | - | p.S508fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_437065 | 126161680 | 126161799 | 126161712 | 126161712 | Frame_Shift_Del | C | - | p.S508fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_437065 | 126161680 | 126161799 | 126161712 | 126161712 | Frame_Shift_Del | C | - | p.S508fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_437065 | 126161680 | 126161799 | 126161782 | 126161782 | Frame_Shift_Del | A | - | p.K532fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_437066 | 126168386 | 126168493 | 126168447 | 126168447 | Frame_Shift_Del | A | - | p.E559fs |
| BLCA | TCGA-XF-AAN0-01 | exon_skip_437063 | 126158473 | 126158577 | 126158476 | 126158476 | Nonsense_Mutation | C | T | p.Q464* |
| LUAD | TCGA-17-Z045-01 | exon_skip_437065 | 126161680 | 126161799 | 126161782 | 126161782 | Nonsense_Mutation | A | T | p.K532* |
| LUAD | TCGA-50-5930-01 | exon_skip_437066 | 126168386 | 126168493 | 126168413 | 126168413 | Nonsense_Mutation | A | T | p.K547* |
| - 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 |
| RH41_SOFT_TISSUE | 126113053 | 126113559 | 126113285 | 126113285 | Missense_Mutation | C | T | p.R29W |
| RH4_SOFT_TISSUE | 126113053 | 126113559 | 126113285 | 126113285 | Missense_Mutation | C | T | p.R29W |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 126113053 | 126113559 | 126113334 | 126113334 | Missense_Mutation | T | G | p.V45G |
| HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 126113053 | 126113559 | 126113460 | 126113460 | Missense_Mutation | C | G | p.A87G |
| NB13_AUTONOMIC_GANGLIA | 126168386 | 126168493 | 126168388 | 126168388 | Missense_Mutation | G | T | p.E538D |
| OCILY12_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 126168386 | 126168493 | 126168399 | 126168399 | Missense_Mutation | G | A | p.R542K |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LMNB1 |
| 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 LMNB1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LMNB1 |
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RelatedDrugs for LMNB1 |
| 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 LMNB1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
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