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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 SMARCB1 |
 Gene summary |
| Gene information | Gene symbol | SMARCB1 | Gene ID | 6598 |
| Gene name | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 | |
| Synonyms | BAF47|CSS3|INI1|MRD15|PPP1R144|RDT|RTPS1|SNF5|SNF5L1|SWNTS1|Sfh1p|Snr1|hSNFS | |
| Cytomap | 22q11.23|22q11 | |
| Type of gene | protein-coding | |
| Description | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1BRG1-associated factor 47SNF5 homologSWI/SNF-related matrix-associated proteinhSNF5integrase interactor 1 proteinmalignant rhabdoid tumor suppressorprotein | |
| Modification date | 20180523 | |
| UniProtAcc | Q12824 | |
| Context | PubMed: SMARCB1 [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 |
| SMARCB1 | GO:0006337 | nucleosome disassembly | 8895581 |
| SMARCB1 | GO:0006338 | chromatin remodeling | 11726552 |
| SMARCB1 | GO:0039692 | single stranded viral RNA replication via double stranded DNA intermediate | 14963118 |
| SMARCB1 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 11950834 |
| SMARCB1 | GO:0051091 | positive regulation of DNA binding transcription factor activity | 11950834 |
| SMARCB1 | GO:1902661 | positive regulation of glucose mediated signaling pathway | 22368283 |
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Exon skipping events across known transcript of Ensembl for SMARCB1 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 SMARCB1 |
| 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 SMARCB1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_363725 | 22 | 24129197:24129449:24133942:24134054:24135745:24135875 | 24133942:24134054 | ENSG00000099956.13 | ENST00000407422.3,ENST00000344921.6 |
| exon_skip_363727 | 22 | 24129197:24129449:24133942:24134081:24135745:24135875 | 24133942:24134081 | ENSG00000099956.13 | ENST00000407082.3,ENST00000263121.7 |
| exon_skip_363735 | 22 | 24135787:24135875:24143130:24143268:24145481:24145609 | 24143130:24143268 | ENSG00000099956.13 | ENST00000407422.3,ENST00000263121.7 |
| exon_skip_363737 | 22 | 24135787:24135875:24143130:24143322:24145481:24145609 | 24143130:24143322 | ENSG00000099956.13 | ENST00000344921.6,ENST00000417137.1 |
| exon_skip_363742 | 22 | 24158956:24159123:24167411:24167602:24175758:24175890 | 24167411:24167602 | ENSG00000099956.13 | ENST00000407082.3,ENST00000407422.3,ENST00000344921.6,ENST00000263121.7 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SMARCB1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_363725 | 22 | 24129197:24129449:24133942:24134054:24135745:24135875 | 24133942:24134054 | ENSG00000099956.13 | ENST00000344921.6,ENST00000407422.3 |
| exon_skip_363727 | 22 | 24129197:24129449:24133942:24134081:24135745:24135875 | 24133942:24134081 | ENSG00000099956.13 | ENST00000263121.7,ENST00000407082.3 |
| exon_skip_363735 | 22 | 24135787:24135875:24143130:24143268:24145481:24145609 | 24143130:24143268 | ENSG00000099956.13 | ENST00000263121.7,ENST00000407422.3 |
| exon_skip_363737 | 22 | 24135787:24135875:24143130:24143322:24145481:24145609 | 24143130:24143322 | ENSG00000099956.13 | ENST00000417137.1,ENST00000344921.6 |
| exon_skip_363742 | 22 | 24158956:24159123:24167411:24167602:24175758:24175890 | 24167411:24167602 | ENSG00000099956.13 | ENST00000344921.6,ENST00000263121.7,ENST00000407422.3,ENST00000407082.3 |
| 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 SMARCB1 |
| 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 |
| 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 |
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Infer the effects of exon skipping event on protein functional features for SMARCB1 |
| 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 SMARCB1 |
| - 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 |
| STAD | TCGA-BR-4201-01 | exon_skip_363727 | 24133943 | 24134081 | 24134057 | 24134057 | Frame_Shift_Del | A | - | p.G69fs |
| STAD | TCGA-HU-A4H8-01 | exon_skip_363727 | 24133943 | 24134081 | 24134057 | 24134057 | Frame_Shift_Del | A | - | p.G69fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_363737 | 24143131 | 24143322 | 24143292 | 24143292 | Frame_Shift_Del | C | - | p.T166fs |
| KIRP | TCGA-BQ-5876-01 | exon_skip_363742 | 24167412 | 24167602 | 24167461 | 24167461 | Frame_Shift_Del | A | - | p.D282fs |
| KIRP | TCGA-BQ-5876-01 | exon_skip_363742 | 24167412 | 24167602 | 24167461 | 24167461 | Frame_Shift_Del | A | - | p.D291fs |
| KIRP | TCGA-5P-A9KC-01 | exon_skip_363742 | 24167412 | 24167602 | 24167567 | 24167568 | Frame_Shift_Del | AC | - | p.317_317del |
| UCEC | TCGA-D1-A17H-01 | exon_skip_363727 | 24133943 | 24134081 | 24134056 | 24134057 | Frame_Shift_Ins | - | A | p.D69_splice |
| UCEC | TCGA-AP-A051-01 | exon_skip_363725 | 24133943 | 24134054 | 24134006 | 24134006 | Nonsense_Mutation | C | T | p.R53* |
| UCEC | TCGA-AP-A051-01 | exon_skip_363727 | 24133943 | 24134081 | 24134006 | 24134006 | Nonsense_Mutation | C | T | p.R53* |
| - 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 |
| BT12_SOFT_TISSUE | 24133943 | 24134081 | 24134023 | 24134024 | Frame_Shift_Del | AG | - | p.EE58fs |
| BT12_SOFT_TISSUE | 24133943 | 24134054 | 24134023 | 24134024 | Frame_Shift_Del | AG | - | p.EE58fs |
| SNUC2A_LARGE_INTESTINE | 24133943 | 24134081 | 24134057 | 24134057 | Frame_Shift_Del | A | - | p.K71fs |
| SNUC2A_LARGE_INTESTINE | 24133943 | 24134054 | 24134057 | 24134057 | Frame_Shift_Del | A | - | p.K71fs |
| SNUC2B_LARGE_INTESTINE | 24133943 | 24134081 | 24134057 | 24134057 | Frame_Shift_Del | A | - | p.K71fs |
| SNUC2B_LARGE_INTESTINE | 24133943 | 24134054 | 24134057 | 24134057 | Frame_Shift_Del | A | - | p.K71fs |
| MFE319_ENDOMETRIUM | 24133943 | 24134081 | 24134056 | 24134057 | Frame_Shift_Ins | - | A | p.K70fs |
| MFE319_ENDOMETRIUM | 24133943 | 24134054 | 24134056 | 24134057 | Frame_Shift_Ins | - | A | p.K70fs |
| HCC56_LARGE_INTESTINE | 24133943 | 24134081 | 24134068 | 24134069 | Frame_Shift_Ins | - | C | p.P74fs |
| IPC298_SKIN | 24133943 | 24134081 | 24134068 | 24134069 | Frame_Shift_Ins | - | C | p.P74fs |
| NCIH69_LUNG | 24133943 | 24134081 | 24134068 | 24134069 | Frame_Shift_Ins | - | C | p.P74fs |
| SNU175_LARGE_INTESTINE | 24133943 | 24134081 | 24134007 | 24134007 | Missense_Mutation | G | A | p.R53Q |
| SNU175_LARGE_INTESTINE | 24133943 | 24134054 | 24134007 | 24134007 | Missense_Mutation | G | A | p.R53Q |
| KMRC1_KIDNEY | 24143131 | 24143268 | 24143261 | 24143261 | Missense_Mutation | C | T | p.P165S |
| KMRC1_KIDNEY | 24143131 | 24143322 | 24143261 | 24143261 | Missense_Mutation | C | T | p.P165S |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 24167412 | 24167602 | 24167480 | 24167480 | Missense_Mutation | C | A | p.N288K |
| TTC642_SOFT_TISSUE | 24133943 | 24134081 | 24133967 | 24133967 | Nonsense_Mutation | C | T | p.R40* |
| TTC642_SOFT_TISSUE | 24133943 | 24134054 | 24133967 | 24133967 | Nonsense_Mutation | C | T | p.R40* |
| KPMRTRY_SOFT_TISSUE | 24133943 | 24134081 | 24134006 | 24134006 | Nonsense_Mutation | C | T | p.R53* |
| KPMRTRY_SOFT_TISSUE | 24133943 | 24134054 | 24134006 | 24134006 | Nonsense_Mutation | C | T | p.R53* |
| HEMCSS_BONE | 24143131 | 24143268 | 24143240 | 24143240 | Nonsense_Mutation | C | T | p.R158* |
| HEMCSS_BONE | 24143131 | 24143322 | 24143240 | 24143240 | Nonsense_Mutation | C | T | p.R158* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SMARCB1 |
| 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 SMARCB1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SMARCB1 |
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RelatedDrugs for SMARCB1 |
| 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 SMARCB1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SMARCB1 | C0206743 | Rhabdoid Tumor | 2 | CTD_human |
| SMARCB1 | C3553248 | MENTAL RETARDATION, AUTOSOMAL DOMINANT 15 | 2 | UNIPROT |
| SMARCB1 | C0265338 | Coffin-Siris syndrome | 1 | CTD_human;ORPHANET |
| SMARCB1 | C1335929 | Schwannomatosis | 1 | CTD_human;ORPHANET |
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