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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for SMARCE1 |
 Gene summary |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| SMARCE1 | GO:0006337 | nucleosome disassembly | 8895581 |
| SMARCE1 | GO:0006338 | chromatin remodeling | 11726552 |
| SMARCE1 | GO:0045892 | negative regulation of transcription, DNA-templated | 12192000 |
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Gene structures and expression levels for SMARCE1 |
| 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. |
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ENSG00000073584
| 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. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | UP | ENST00000644257.1 | SMARCE1-229:retained_intron:SMARCE1 | 1.184509e+01 | 1.648598e+00 | 1.169367e-03 | 5.893746e-03 |
| CB | UP | ENST00000644909.1 | SMARCE1-234:nonsense_mediated_decay:SMARCE1 | 6.617274e+01 | 1.272208e+00 | 2.326345e-03 | 1.044757e-02 |
| TC | UP | ENST00000647294.1 | SMARCE1-248:nonsense_mediated_decay:SMARCE1 | 1.151385e+02 | 8.409888e-01 | 2.620077e-03 | 2.059471e-02 |
| TC | UP | ENST00000646482.1 | SMARCE1-245:protein_coding:SMARCE1 | 2.164032e+00 | 1.921127e+00 | 6.447648e-03 | 4.045950e-02 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SMARCE1 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_105063 | chr17 | 40631592:40631693:40632195:40632367:40635931:40636102 | 40632195:40632367 |
| exon_skip_148021 | chr17 | 40645576:40645619:40645796:40645847:40647773:40647833 | 40645796:40645847 |
| exon_skip_164438 | chr17 | 40642455:40642559:40645796:40645847:40647773:40647839 | 40645796:40645847 |
| exon_skip_1728 | chr17 | 40637492:40637572:40639981:40640078:40642455:40642559 | 40639981:40640078 |
| exon_skip_203802 | chr17 | 40637492:40637572:40645576:40645619:40645796:40645847 | 40645576:40645619 |
| exon_skip_215931 | chr17 | 40642455:40642559:40645576:40645619:40645796:40645847 | 40645576:40645619 |
| exon_skip_228420 | chr17 | 40637492:40637572:40642455:40642559:40645576:40645619 | 40642455:40642559 |
| exon_skip_279414 | chr17 | 40627762:40628993:40630208:40630286:40630714:40630924 | 40630208:40630286 |
| exon_skip_40081 | chr17 | 40637492:40637572:40642455:40642559:40645796:40645847 | 40642455:40642559 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_203802 | Mayo_CB | 3.057317e-01 | 4.068116e-01 | -1.010799e-01 | 2.730762e-07 |
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Open reading frame (ORF) annotation in the exon skipping event for SMARCE1 |
| 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 |
| ENST00000348513 | 40632195 | 40632367 | Frame-shift |
| ENST00000643683 | 40632195 | 40632367 | Frame-shift |
| ENST00000348513 | 40645576 | 40645619 | Frame-shift |
| ENST00000643683 | 40645576 | 40645619 | Frame-shift |
| ENST00000348513 | 40642455 | 40642559 | In-frame |
| ENST00000643683 | 40642455 | 40642559 | In-frame |
| 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 |
| ENST00000348513 | 40645576 | 40645619 | Frame-shift |
| ENST00000643683 | 40645576 | 40645619 | Frame-shift |
| ENST00000348513 | 40642455 | 40642559 | In-frame |
| ENST00000643683 | 40642455 | 40642559 | In-frame |
| 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 |
| ENST00000348513 | 40632195 | 40632367 | Frame-shift |
| ENST00000643683 | 40632195 | 40632367 | Frame-shift |
| ENST00000348513 | 40645576 | 40645619 | Frame-shift |
| ENST00000643683 | 40645576 | 40645619 | Frame-shift |
| ENST00000348513 | 40642455 | 40642559 | In-frame |
| ENST00000643683 | 40642455 | 40642559 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SMARCE1 |
p-ENSG00000073584_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 |
| ENST00000348513 | 6213 | 411 | 40642455 | 40642559 | 1189 | 1292 | 17 | 51 |
| ENST00000643683 | 2509 | 411 | 40642455 | 40642559 | 286 | 389 | 17 | 51 |
| 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 |
| ENST00000348513 | 6213 | 411 | 40642455 | 40642559 | 1189 | 1292 | 17 | 51 |
| ENST00000643683 | 2509 | 411 | 40642455 | 40642559 | 286 | 389 | 17 | 51 |
| 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 |
| ENST00000348513 | 6213 | 411 | 40642455 | 40642559 | 1189 | 1292 | 17 | 51 |
| ENST00000643683 | 2509 | 411 | 40642455 | 40642559 | 286 | 389 | 17 | 51 |
| 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 |
| Q969G3 | 17 | 51 | 1 | 70 | Alternative sequence | ID=VSP_047604;Note=In isoform 3 and isoform 6. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|Ref.2;Dbxref=PMID:14702039 |
| Q969G3 | 17 | 51 | 1 | 70 | Alternative sequence | ID=VSP_047604;Note=In isoform 3 and isoform 6. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|Ref.2;Dbxref=PMID:14702039 |
| Q969G3 | 17 | 51 | 17 | 51 | Alternative sequence | ID=VSP_047825;Note=In isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| Q969G3 | 17 | 51 | 17 | 51 | Alternative sequence | ID=VSP_047825;Note=In isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| Q969G3 | 17 | 51 | 1 | 411 | Chain | ID=PRO_0000048577;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 |
| Q969G3 | 17 | 51 | 1 | 411 | Chain | ID=PRO_0000048577;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 |
| Q969G3 | 17 | 51 | 5 | 65 | Compositional bias | Note=Pro-rich |
| Q969G3 | 17 | 51 | 5 | 65 | Compositional bias | Note=Pro-rich |
| Q969G3 | 17 | 51 | 40 | 40 | Modified residue | Note=Omega-N-methylarginine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315 |
| Q969G3 | 17 | 51 | 40 | 40 | Modified residue | Note=Omega-N-methylarginine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315 |
| Q969G3 | 17 | 51 | 46 | 46 | Sequence conflict | Note=G->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q969G3 | 17 | 51 | 46 | 46 | Sequence conflict | Note=G->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q969G3 | 17 | 51 | 46 | 46 | Sequence conflict | Note=G->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q969G3 | 17 | 51 | 46 | 46 | Sequence conflict | Note=G->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q969G3 | 17 | 51 | 46 | 46 | Sequence conflict | Note=G->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q969G3 | 17 | 51 | 46 | 46 | Sequence conflict | Note=G->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| 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 |
| Q969G3 | 17 | 51 | 1 | 70 | Alternative sequence | ID=VSP_047604;Note=In isoform 3 and isoform 6. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|Ref.2;Dbxref=PMID:14702039 |
| Q969G3 | 17 | 51 | 1 | 70 | Alternative sequence | ID=VSP_047604;Note=In isoform 3 and isoform 6. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|Ref.2;Dbxref=PMID:14702039 |
| Q969G3 | 17 | 51 | 17 | 51 | Alternative sequence | ID=VSP_047825;Note=In isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| Q969G3 | 17 | 51 | 17 | 51 | Alternative sequence | ID=VSP_047825;Note=In isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| Q969G3 | 17 | 51 | 1 | 411 | Chain | ID=PRO_0000048577;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 |
| Q969G3 | 17 | 51 | 1 | 411 | Chain | ID=PRO_0000048577;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 |
| Q969G3 | 17 | 51 | 5 | 65 | Compositional bias | Note=Pro-rich |
| Q969G3 | 17 | 51 | 5 | 65 | Compositional bias | Note=Pro-rich |
| Q969G3 | 17 | 51 | 40 | 40 | Modified residue | Note=Omega-N-methylarginine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315 |
| Q969G3 | 17 | 51 | 40 | 40 | Modified residue | Note=Omega-N-methylarginine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315 |
| Q969G3 | 17 | 51 | 46 | 46 | Sequence conflict | Note=G->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q969G3 | 17 | 51 | 46 | 46 | Sequence conflict | Note=G->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q969G3 | 17 | 51 | 46 | 46 | Sequence conflict | Note=G->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q969G3 | 17 | 51 | 46 | 46 | Sequence conflict | Note=G->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q969G3 | 17 | 51 | 46 | 46 | Sequence conflict | Note=G->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q969G3 | 17 | 51 | 46 | 46 | Sequence conflict | Note=G->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| 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 |
| Q969G3 | 17 | 51 | 1 | 70 | Alternative sequence | ID=VSP_047604;Note=In isoform 3 and isoform 6. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|Ref.2;Dbxref=PMID:14702039 |
| Q969G3 | 17 | 51 | 1 | 70 | Alternative sequence | ID=VSP_047604;Note=In isoform 3 and isoform 6. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|Ref.2;Dbxref=PMID:14702039 |
| Q969G3 | 17 | 51 | 17 | 51 | Alternative sequence | ID=VSP_047825;Note=In isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| Q969G3 | 17 | 51 | 17 | 51 | Alternative sequence | ID=VSP_047825;Note=In isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| Q969G3 | 17 | 51 | 1 | 411 | Chain | ID=PRO_0000048577;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 |
| Q969G3 | 17 | 51 | 1 | 411 | Chain | ID=PRO_0000048577;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 |
| Q969G3 | 17 | 51 | 5 | 65 | Compositional bias | Note=Pro-rich |
| Q969G3 | 17 | 51 | 5 | 65 | Compositional bias | Note=Pro-rich |
| Q969G3 | 17 | 51 | 40 | 40 | Modified residue | Note=Omega-N-methylarginine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315 |
| Q969G3 | 17 | 51 | 40 | 40 | Modified residue | Note=Omega-N-methylarginine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315 |
| Q969G3 | 17 | 51 | 46 | 46 | Sequence conflict | Note=G->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q969G3 | 17 | 51 | 46 | 46 | Sequence conflict | Note=G->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q969G3 | 17 | 51 | 46 | 46 | Sequence conflict | Note=G->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q969G3 | 17 | 51 | 46 | 46 | Sequence conflict | Note=G->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q969G3 | 17 | 51 | 46 | 46 | Sequence conflict | Note=G->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q969G3 | 17 | 51 | 46 | 46 | Sequence conflict | Note=G->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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3'-UTR located exon skipping events that lost miRNA binding sites in SMARCE1 |
| 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 |
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SNVs in the skipped exons for SMARCE1 |
| - 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 |
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AD stage-associated exon skippint events for SMARCE1 |
| 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 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SMARCE1 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for SMARCE1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | RBM6 | exon_skip_203802 | -5.212445e-01 | 6.799589e-12 |
| CB | CNOT4 | exon_skip_203802 | -5.355842e-01 | 1.383140e-12 |
| CB | PCBP1 | exon_skip_203802 | -4.361482e-01 | 2.170847e-08 |
| CB | NUP42 | exon_skip_203802 | 4.570984e-01 | 3.638887e-09 |
| CB | EIF4G2 | exon_skip_203802 | -4.114712e-01 | 1.532543e-07 |
| CB | RBM23 | exon_skip_203802 | -4.014435e-01 | 3.245923e-07 |
| CB | CNOT4 | exon_skip_215931 | -4.799498e-01 | 6.727421e-10 |
| CB | PCBP1 | exon_skip_215931 | -4.630512e-01 | 3.106514e-09 |
| CB | EIF4G2 | exon_skip_215931 | -4.521881e-01 | 7.956306e-09 |
| CB | RBM23 | exon_skip_215931 | -4.345177e-01 | 3.430193e-08 |
| HCC | RBMS3 | exon_skip_228420 | 4.625063e-01 | 9.051222e-16 |
| HCC | RBM25 | exon_skip_228420 | 4.362221e-01 | 5.137088e-14 |
| HCC | CNOT4 | exon_skip_228420 | 4.142907e-01 | 1.155138e-12 |
| HCC | RBM5 | exon_skip_228420 | 6.095392e-01 | 5.854794e-29 |
| HCC | PCBP1 | exon_skip_228420 | 4.422730e-01 | 2.090298e-14 |
| HCC | HNRNPA2B1 | exon_skip_228420 | 4.855802e-01 | 1.939113e-17 |
| HCC | EIF4G2 | exon_skip_228420 | 5.788962e-01 | 1.201804e-25 |
| HCC | SRSF1 | exon_skip_228420 | 4.407516e-01 | 2.625009e-14 |
| HCC | HNRNPF | exon_skip_228420 | 6.570879e-01 | 7.096076e-35 |
| HCC | RBM5 | exon_skip_40081 | 4.080546e-01 | 2.817362e-10 |
| PCC | PUM1 | exon_skip_228420 | -5.426458e-01 | 1.245963e-17 |
| PCC | HNRNPF | exon_skip_228420 | 5.540102e-01 | 1.879581e-18 |
| TC | ILF2 | exon_skip_228420 | -4.532820e-01 | 1.756183e-09 |
| TC | PUM1 | exon_skip_228420 | -5.961297e-01 | 9.063378e-17 |
| TC | CELF1 | exon_skip_228420 | -5.421822e-01 | 1.314997e-13 |
| TC | HNRNPH2 | exon_skip_228420 | -6.551147e-01 | 5.569138e-21 |
| TC | YBX2 | exon_skip_228420 | -4.705416e-01 | 3.417212e-10 |
| TC | ESRP1 | exon_skip_228420 | -6.267154e-01 | 7.683040e-19 |
| TC | NOVA1 | exon_skip_228420 | -5.784413e-01 | 1.143559e-15 |
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RelatedDrugs for SMARCE1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for SMARCE1 |
| 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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