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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 LIMS2 |
 Gene summary |
| Gene information | Gene symbol | LIMS2 | Gene ID | 55679 |
| Gene name | LIM zinc finger domain containing 2 | |
| Synonyms | LGMD2W|PINCH-2|PINCH2 | |
| Cytomap | 2q14.3 | |
| Type of gene | protein-coding | |
| Description | LIM and senescent cell antigen-like-containing domain protein 2ILK-binding proteinLIM and senescent cell antigen-like domains 2LIM-type zinc finger domains 2particularly interesting new Cys-His protein 2 | |
| Modification date | 20180519 | |
| UniProtAcc | Q7Z4I7 | |
| Context | PubMed: LIMS2 [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 LIMS2 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 LIMS2 |
| 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 LIMS2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_343222 | 2 | 128396771:128397003:128397644:128397720:128397844:128397893 | 128397644:128397720 | ENSG00000072163.14 | ENST00000426981.1,ENST00000409455.1,ENST00000409808.2,ENST00000484252.1,ENST00000355119.4,ENST00000413578.1,ENST00000476932.1,ENST00000324938.5,ENST00000409754.1,ENST00000545738.2,ENST00000410011.1,ENST00000409286.1,ENST00000410038.1,ENST00000409254.1,ENS |
| exon_skip_343225 | 2 | 128396771:128397003:128397644:128397893:128398470:128398563 | 128397644:128397893 | ENSG00000072163.14 | ENST00000469300.2 |
| exon_skip_343235 | 2 | 128397644:128397720:128397844:128397893:128398470:128398563 | 128397844:128397893 | ENSG00000072163.14 | ENST00000426981.1,ENST00000409455.1,ENST00000409808.2,ENST00000355119.4,ENST00000413578.1,ENST00000476932.1,ENST00000324938.5,ENST00000409754.1,ENST00000545738.2,ENST00000410011.1,ENST00000409286.1,ENST00000410038.1,ENST00000409254.1 |
| exon_skip_343254 | 2 | 128398470:128398563:128399623:128399774:128400497:128400647 | 128399623:128399774 | ENSG00000072163.14 | ENST00000409455.1,ENST00000409808.2,ENST00000355119.4,ENST00000476932.1,ENST00000324938.5,ENST00000409754.1,ENST00000545738.2,ENST00000410011.1,ENST00000409286.1,ENST00000410038.1,ENST00000409254.1,ENST00000466410.1 |
| exon_skip_343266 | 2 | 128400497:128400647:128401069:128401125:128401643:128401685 | 128401069:128401125 | ENSG00000072163.14 | ENST00000409754.1 |
| exon_skip_343271 | 2 | 128400497:128400647:128411997:128412470:128414976:128415136 | 128411997:128412470 | ENSG00000072163.14 | ENST00000476932.1 |
| exon_skip_343289 | 2 | 128412403:128412470:128414976:128415136:128431251:128431317 | 128414976:128415136 | ENSG00000072163.14 | ENST00000409455.1,ENST00000409808.2,ENST00000545738.2 |
| exon_skip_343291 | 2 | 128412403:128412470:128414976:128415136:128432587:128432676 | 128414976:128415136 | ENSG00000072163.14 | ENST00000355119.4 |
| exon_skip_343292 | 2 | 128412403:128412470:128414976:128415136:128438893:128439360 | 128414976:128415136 | ENSG00000072163.14 | ENST00000410011.1 |
| exon_skip_343306 | 2 | 128414976:128415136:128431251:128431317:128432587:128432676 | 128431251:128431317 | ENSG00000072163.14 | ENST00000545738.2 |
| exon_skip_343309 | 2 | 128431251:128431317:128431887:128431995:128432587:128432676 | 128431887:128431995 | ENSG00000072163.14 | ENST00000409808.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for LIMS2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_343222 | 2 | 128396771:128397003:128397644:128397720:128397844:128397893 | 128397644:128397720 | ENSG00000072163.14 | ENST00000426981.1,ENST00000409286.1,ENST00000409754.1,ENST00000476932.1,ENST00000324938.5,ENST00000484252.1,ENST00000466410.1,ENST00000409455.1,ENST00000355119.4,ENST00000409808.2,ENST00000410011.1,ENST00000410038.1,ENST00000545738.2,ENST00000413578.1,ENS |
| exon_skip_343225 | 2 | 128396771:128397003:128397644:128397893:128398470:128398563 | 128397644:128397893 | ENSG00000072163.14 | ENST00000469300.2 |
| exon_skip_343235 | 2 | 128397644:128397720:128397844:128397893:128398470:128398563 | 128397844:128397893 | ENSG00000072163.14 | ENST00000426981.1,ENST00000409286.1,ENST00000409754.1,ENST00000476932.1,ENST00000324938.5,ENST00000409455.1,ENST00000355119.4,ENST00000409808.2,ENST00000410011.1,ENST00000410038.1,ENST00000545738.2,ENST00000413578.1,ENST00000409254.1 |
| exon_skip_343254 | 2 | 128398470:128398563:128399623:128399774:128400497:128400647 | 128399623:128399774 | ENSG00000072163.14 | ENST00000409286.1,ENST00000409754.1,ENST00000476932.1,ENST00000324938.5,ENST00000466410.1,ENST00000409455.1,ENST00000355119.4,ENST00000409808.2,ENST00000410011.1,ENST00000410038.1,ENST00000545738.2,ENST00000409254.1 |
| exon_skip_343266 | 2 | 128400497:128400647:128401069:128401125:128401643:128401685 | 128401069:128401125 | ENSG00000072163.14 | ENST00000409754.1 |
| exon_skip_343271 | 2 | 128400497:128400647:128411997:128412470:128414976:128415136 | 128411997:128412470 | ENSG00000072163.14 | ENST00000476932.1 |
| exon_skip_343289 | 2 | 128412403:128412470:128414976:128415136:128431251:128431317 | 128414976:128415136 | ENSG00000072163.14 | ENST00000409455.1,ENST00000409808.2,ENST00000545738.2 |
| exon_skip_343291 | 2 | 128412403:128412470:128414976:128415136:128432587:128432676 | 128414976:128415136 | ENSG00000072163.14 | ENST00000355119.4 |
| exon_skip_343292 | 2 | 128412403:128412470:128414976:128415136:128438893:128439360 | 128414976:128415136 | ENSG00000072163.14 | ENST00000410011.1 |
| exon_skip_343306 | 2 | 128414976:128415136:128431251:128431317:128432587:128432676 | 128431251:128431317 | ENSG00000072163.14 | ENST00000545738.2 |
| exon_skip_343309 | 2 | 128431251:128431317:128431887:128431995:128432587:128432676 | 128431887:128431995 | ENSG00000072163.14 | ENST00000409808.2 |
| 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 LIMS2 |
| 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 |
| ENST00000355119 | 128397644 | 128397720 | Frame-shift |
| ENST00000355119 | 128397844 | 128397893 | Frame-shift |
| ENST00000355119 | 128399623 | 128399774 | Frame-shift |
| ENST00000355119 | 128414976 | 128415136 | Frame-shift |
| 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 |
| ENST00000355119 | 128397644 | 128397720 | Frame-shift |
| ENST00000355119 | 128397844 | 128397893 | Frame-shift |
| ENST00000355119 | 128399623 | 128399774 | Frame-shift |
| ENST00000355119 | 128414976 | 128415136 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for LIMS2 |
| 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 LIMS2 |
| - 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 |
| HNSC | TCGA-TN-A7HL-01 | exon_skip_343289 exon_skip_343291 exon_skip_343292 | 128414977 | 128415136 | 128414994 | 128414994 | Nonsense_Mutation | C | A | p.E47* |
| PAAD | TCGA-XN-A8T3-01 | exon_skip_343289 exon_skip_343291 exon_skip_343292 | 128414977 | 128415136 | 128415072 | 128415072 | Nonsense_Mutation | C | A | p.E50X |
| - 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 |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 128397645 | 128397720 | 128397666 | 128397666 | Missense_Mutation | C | T | p.C286Y |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 128397645 | 128397893 | 128397666 | 128397666 | Missense_Mutation | C | T | p.C286Y |
| HEC6_ENDOMETRIUM | 128397645 | 128397720 | 128397711 | 128397711 | Missense_Mutation | G | A | p.A271V |
| HEC6_ENDOMETRIUM | 128397645 | 128397893 | 128397711 | 128397711 | Missense_Mutation | G | A | p.A271V |
| ECGI10_OESOPHAGUS | 128397845 | 128397893 | 128397869 | 128397869 | Missense_Mutation | A | T | p.C260S |
| ECGI10_OESOPHAGUS | 128397645 | 128397893 | 128397869 | 128397869 | Missense_Mutation | A | T | p.C260S |
| EBC1_LUNG | 128397845 | 128397893 | 128397881 | 128397881 | Missense_Mutation | C | T | p.V256I |
| EBC1_LUNG | 128397645 | 128397893 | 128397881 | 128397881 | Missense_Mutation | C | T | p.V256I |
| KYSE510_OESOPHAGUS | 128397845 | 128397893 | 128397887 | 128397887 | Missense_Mutation | C | G | p.G254R |
| KYSE510_OESOPHAGUS | 128397645 | 128397893 | 128397887 | 128397887 | Missense_Mutation | C | G | p.G254R |
| TGBC11TKB_STOMACH | 128399624 | 128399774 | 128399635 | 128399635 | Missense_Mutation | A | G | p.W217R |
| CHLA266_SOFT_TISSUE | 128399624 | 128399774 | 128399661 | 128399661 | Missense_Mutation | C | T | p.R208Q |
| NCIH1435_LUNG | 128399624 | 128399774 | 128399676 | 128399676 | Missense_Mutation | C | A | p.R203L |
| HUCCT1_BILIARY_TRACT | 128399624 | 128399774 | 128399701 | 128399701 | Missense_Mutation | C | T | p.V195I |
| C84_LARGE_INTESTINE | 128399624 | 128399774 | 128399718 | 128399718 | Missense_Mutation | C | T | p.C189Y |
| SNU1040_LARGE_INTESTINE | 128411998 | 128412470 | 128412013 | 128412013 | Missense_Mutation | A | G | p.V115A |
| NCIH1373_LUNG | 128411998 | 128412470 | 128412014 | 128412014 | Missense_Mutation | C | T | p.V115M |
| HEC1A_ENDOMETRIUM | 128411998 | 128412470 | 128412101 | 128412101 | Missense_Mutation | G | A | p.R86C |
| MCC26_SKIN | 128411998 | 128412470 | 128412409 | 128412409 | Missense_Mutation | G | A | p.S78F |
| OVK18_OVARY | 128411998 | 128412470 | 128412431 | 128412431 | Missense_Mutation | G | T | p.L71M |
| NCIH838_LUNG | 128411998 | 128412470 | 128412460 | 128412460 | Missense_Mutation | C | A | p.R61L |
| SW756_CERVIX | 128414977 | 128415136 | 128414979 | 128414979 | Missense_Mutation | C | G | p.E57Q |
| JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 128414977 | 128415136 | 128415068 | 128415068 | Missense_Mutation | C | T | p.R27H |
| AN3CA_ENDOMETRIUM | 128399624 | 128399774 | 128399662 | 128399662 | Nonsense_Mutation | G | A | p.R208* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LIMS2 |
| 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 LIMS2 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LIMS2 |
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RelatedDrugs for LIMS2 |
| 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 LIMS2 |
| 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)
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