|
||||||
|
 | |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| 3'-UTR located exon skipping events lost miRNA binding sites |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| |
| |
|
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 | 20200313 | |
| UniProtAcc | A0A0G2JRV3, A0A0G2JSE9, A0A0U1RQQ2, A0A0U1RRB8, | |
| Context |
| 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 |
Top |
Gene structures and expression levels for SMARCB1 |
| Skipped exons in the ROSMAP, MSBB, and Mayo 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. |
 |
ENSG00000099956
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
 |
| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| DLPFC | UP | ENST00000644462.1 | SMARCB1-214:nonsense_mediated_decay:SMARCB1 | 2.734475e+00 | 2.403000e+00 | 6.692317e-05 | 5.386712e-03 |
| CB | UP | ENST00000646723.1 | SMARCB1-219:retained_intron:SMARCB1 | 2.710395e+02 | 9.809252e-01 | 1.128223e-08 | 3.328553e-07 |
| CB | UP | ENST00000644462.1 | SMARCB1-214:nonsense_mediated_decay:SMARCB1 | 1.281786e+02 | 1.152548e+00 | 1.944558e-07 | 3.729244e-06 |
| CB | DOWN | ENST00000647057.1 | SMARCB1-221:nonsense_mediated_decay:SMARCB1 | 9.514956e+01 | -2.036046e+00 | 1.418608e-02 | 4.612001e-02 |
| TC | DOWN | ENST00000647057.1 | SMARCB1-221:nonsense_mediated_decay:SMARCB1 | 5.691067e+01 | -2.029052e+00 | 7.418214e-03 | 4.492273e-02 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SMARCB1 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
 |
| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_130122 | chr22 | 23793559:23793688:23800944:23801135:23803295:23803322 | 23800944:23801135 |
| exon_skip_14225 | chr22 | 23786983:23787262:23791756:23793688:23800944:23801081 | 23791756:23793688 |
| exon_skip_151007 | chr22 | 23793559:23793688:23800944:23800970:23803295:23803401 | 23800944:23800970 |
| exon_skip_152649 | chr22 | 23793559:23793688:23800944:23800970:23803295:23803322 | 23800944:23800970 |
| exon_skip_153837 | chr22 | 23787128:23787262:23791756:23793688:23800944:23801081 | 23791756:23793688 |
| exon_skip_209906 | chr22 | 23803295:23803422:23816625:23816936:23825225:23825415 | 23816625:23816936 |
| exon_skip_232765 | chr22 | 23793559:23793688:23800944:23801135:23803295:23803401 | 23800944:23801135 |
| exon_skip_248600 | chr22 | 23793559:23793688:23800944:23801081:23803295:23803401 | 23800944:23801081 |
| exon_skip_249222 | chr22 | 23793559:23793688:23800944:23801081:23803295:23803322 | 23800944:23801081 |
| exon_skip_281047 | chr22 | 23793559:23793688:23800944:23801964:23803295:23803322 | 23800944:23801964 |
| exon_skip_45464 | chr22 | 23816770:23816936:23825225:23825415:23833572:23833587 | 23825225:23825415 |
| exon_skip_53406 | chr22 | 23803295:23803422:23816770:23816936:23825225:23825415 | 23816770:23816936 |
| exon_skip_65359 | chr22 | 23793559:23793688:23800944:23801964:23803295:23803401 | 23800944:23801964 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
Top |
Open reading frame (ORF) annotation in the exon skipping event for SMARCB1 |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP 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 MSBB 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 Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
Top |
Infer the effects of exon skipping event on protein functional features for SMARCB1 |
p-ENSG00000099956_img4.png |
| Loci of skipped exons in ROSMAP 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 MSBB 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 Mayo 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 ROSMAP. |
| 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 MSBB. |
| 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 Mayo. |
| 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 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in SMARCB1 |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
Top |
SNVs in the skipped exons for SMARCB1 |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - 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 |
Top |
AD stage-associated exon skippint events for SMARCB1 |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SMARCB1 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
Top |
Correlation with RNA binding proteins (RBPs) for SMARCB1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
Top |
RelatedDrugs for SMARCB1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for SMARCB1 |
| 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)
|