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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 SMARCA1 |
 Gene summary |
| Gene information | Gene symbol | SMARCA1 | Gene ID | 6594 |
| Gene name | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 | |
| Synonyms | ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L | |
| Cytomap | Xq25-q26.1 | |
| Type of gene | protein-coding | |
| Description | probable global transcription activator SNF2L1ATP-dependent helicase SMARCA1SNF2-like 1global transcription activator homologous sequencenucleosome-remodeling factor subunit SNF2Lsucrose nonfermenting 2-like protein 1 | |
| Modification date | 20180519 | |
| UniProtAcc | P28370 | |
| Context | PubMed: SMARCA1 [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 |
| SMARCA1 | GO:0006338 | chromatin remodeling | 14609955 |
| SMARCA1 | GO:0043044 | ATP-dependent chromatin remodeling | 15640247 |
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Exon skipping events across known transcript of Ensembl for SMARCA1 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 SMARCA1 |
| 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 SMARCA1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_516635 | X | 128602749:128602882:128605180:128605303:128614677:128614791 | 128605180:128605303 | ENSG00000102038.11 | ENST00000371123.1,ENST00000371122.4,ENST00000371121.3 |
| exon_skip_516637 | X | 128605180:128605303:128614677:128614791:128615051:128615162 | 128614677:128614791 | ENSG00000102038.11 | ENST00000371123.1,ENST00000371122.4,ENST00000371121.3 |
| exon_skip_516639 | X | 128624036:128624169:128625917:128626070:128630726:128630848 | 128625917:128626070 | ENSG00000102038.11 | ENST00000371123.1,ENST00000371121.3 |
| exon_skip_516641 | X | 128625917:128626070:128627016:128627052:128630726:128630848 | 128627016:128627052 | ENSG00000102038.11 | ENST00000371122.4 |
| exon_skip_516643 | X | 128633708:128633818:128638710:128638779:128640056:128640188 | 128638710:128638779 | ENSG00000102038.11 | ENST00000371123.1,ENST00000371122.4,ENST00000371121.3 |
| exon_skip_516644 | X | 128638710:128638779:128640056:128640188:128641917:128642073 | 128640056:128640188 | ENSG00000102038.11 | ENST00000371123.1,ENST00000371122.4,ENST00000371121.3 |
| exon_skip_516645 | X | 128642031:128642073:128645780:128645960:128649663:128649764 | 128645780:128645960 | ENSG00000102038.11 | ENST00000478420.1,ENST00000371123.1,ENST00000371122.4,ENST00000371121.3 |
| exon_skip_516647 | X | 128649899:128649971:128650307:128650474:128652337:128652424 | 128650307:128650474 | ENSG00000102038.11 | ENST00000371123.1,ENST00000371122.4,ENST00000371121.3 |
| exon_skip_516648 | X | 128650307:128650474:128652337:128652424:128657173:128657223 | 128652337:128652424 | ENSG00000102038.11 | ENST00000371123.1,ENST00000371122.4 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SMARCA1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_516635 | X | 128602749:128602882:128605180:128605303:128614677:128614791 | 128605180:128605303 | ENSG00000102038.11 | ENST00000371121.3,ENST00000371123.1,ENST00000371122.4 |
| exon_skip_516637 | X | 128605180:128605303:128614677:128614791:128615051:128615162 | 128614677:128614791 | ENSG00000102038.11 | ENST00000371121.3,ENST00000371123.1,ENST00000371122.4 |
| exon_skip_516639 | X | 128624036:128624169:128625917:128626070:128630726:128630848 | 128625917:128626070 | ENSG00000102038.11 | ENST00000371121.3,ENST00000371123.1 |
| exon_skip_516641 | X | 128625917:128626070:128627016:128627052:128630726:128630848 | 128627016:128627052 | ENSG00000102038.11 | ENST00000371122.4 |
| exon_skip_516643 | X | 128633708:128633818:128638710:128638779:128640056:128640188 | 128638710:128638779 | ENSG00000102038.11 | ENST00000371121.3,ENST00000371123.1,ENST00000371122.4 |
| exon_skip_516644 | X | 128638710:128638779:128640056:128640188:128641917:128642073 | 128640056:128640188 | ENSG00000102038.11 | ENST00000371121.3,ENST00000371123.1,ENST00000371122.4 |
| exon_skip_516645 | X | 128642031:128642073:128645780:128645960:128649663:128649764 | 128645780:128645960 | ENSG00000102038.11 | ENST00000371121.3,ENST00000371123.1,ENST00000371122.4,ENST00000478420.1 |
| exon_skip_516647 | X | 128649899:128649971:128650307:128650474:128652337:128652424 | 128650307:128650474 | ENSG00000102038.11 | ENST00000371121.3,ENST00000371123.1,ENST00000371122.4 |
| exon_skip_516648 | X | 128650307:128650474:128652337:128652424:128657173:128657223 | 128652337:128652424 | ENSG00000102038.11 | ENST00000371123.1,ENST00000371122.4 |
| 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 SMARCA1 |
| 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 |
| ENST00000371122 | 128650307 | 128650474 | Frame-shift |
| ENST00000371122 | 128605180 | 128605303 | In-frame |
| ENST00000371122 | 128614677 | 128614791 | In-frame |
| ENST00000371122 | 128627016 | 128627052 | In-frame |
| ENST00000371122 | 128638710 | 128638779 | In-frame |
| ENST00000371122 | 128640056 | 128640188 | In-frame |
| ENST00000371122 | 128645780 | 128645960 | In-frame |
| ENST00000371122 | 128652337 | 128652424 | 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 |
| ENST00000371122 | 128650307 | 128650474 | Frame-shift |
| ENST00000371122 | 128605180 | 128605303 | In-frame |
| ENST00000371122 | 128614677 | 128614791 | In-frame |
| ENST00000371122 | 128627016 | 128627052 | In-frame |
| ENST00000371122 | 128638710 | 128638779 | In-frame |
| ENST00000371122 | 128640056 | 128640188 | In-frame |
| ENST00000371122 | 128645780 | 128645960 | In-frame |
| ENST00000371122 | 128652337 | 128652424 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SMARCA1 |
| 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 |
| ENST00000371122 | 4116 | 1054 | 128652337 | 128652424 | 305 | 391 | 58 | 87 |
| ENST00000371122 | 4116 | 1054 | 128645780 | 128645960 | 761 | 940 | 210 | 270 |
| ENST00000371122 | 4116 | 1054 | 128640056 | 128640188 | 1097 | 1228 | 322 | 366 |
| ENST00000371122 | 4116 | 1054 | 128638710 | 128638779 | 1229 | 1297 | 366 | 389 |
| ENST00000371122 | 4116 | 1054 | 128627016 | 128627052 | 1757 | 1792 | 542 | 554 |
| ENST00000371122 | 4116 | 1054 | 128614677 | 128614791 | 2459 | 2572 | 776 | 814 |
| ENST00000371122 | 4116 | 1054 | 128605180 | 128605303 | 2573 | 2695 | 814 | 855 |
| 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 |
| ENST00000371122 | 4116 | 1054 | 128652337 | 128652424 | 305 | 391 | 58 | 87 |
| ENST00000371122 | 4116 | 1054 | 128645780 | 128645960 | 761 | 940 | 210 | 270 |
| ENST00000371122 | 4116 | 1054 | 128640056 | 128640188 | 1097 | 1228 | 322 | 366 |
| ENST00000371122 | 4116 | 1054 | 128638710 | 128638779 | 1229 | 1297 | 366 | 389 |
| ENST00000371122 | 4116 | 1054 | 128627016 | 128627052 | 1757 | 1792 | 542 | 554 |
| ENST00000371122 | 4116 | 1054 | 128614677 | 128614791 | 2459 | 2572 | 776 | 814 |
| ENST00000371122 | 4116 | 1054 | 128605180 | 128605303 | 2573 | 2695 | 814 | 855 |
| 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 |
| P28370 | 58 | 87 | 1 | 1054 | Chain | ID=PRO_0000074351;Note=Probable global transcription activator SNF2L1 |
| P28370 | 210 | 270 | 1 | 1054 | Chain | ID=PRO_0000074351;Note=Probable global transcription activator SNF2L1 |
| P28370 | 210 | 270 | 195 | 360 | Domain | Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 |
| P28370 | 210 | 270 | 214 | 214 | Mutagenesis | Note=No effect on neurite outgrowth. K->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14609955;Dbxref=PMID:14609955 |
| P28370 | 210 | 270 | 208 | 215 | Nucleotide binding | Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 |
| P28370 | 322 | 366 | 1 | 1054 | Chain | ID=PRO_0000074351;Note=Probable global transcription activator SNF2L1 |
| P28370 | 322 | 366 | 195 | 360 | Domain | Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 |
| P28370 | 366 | 389 | 1 | 1054 | Chain | ID=PRO_0000074351;Note=Probable global transcription activator SNF2L1 |
| P28370 | 542 | 554 | 543 | 554 | Alternative sequence | ID=VSP_020406;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15310751;Dbxref=PMID:15310751 |
| P28370 | 542 | 554 | 1 | 1054 | Chain | ID=PRO_0000074351;Note=Probable global transcription activator SNF2L1 |
| P28370 | 542 | 554 | 490 | 653 | Domain | Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00542 |
| P28370 | 776 | 814 | 1 | 1054 | Chain | ID=PRO_0000074351;Note=Probable global transcription activator SNF2L1 |
| P28370 | 814 | 855 | 1 | 1054 | Chain | ID=PRO_0000074351;Note=Probable global transcription activator SNF2L1 |
| P28370 | 814 | 855 | 855 | 907 | Domain | Note=SANT 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00624 |
| 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 |
| P28370 | 58 | 87 | 1 | 1054 | Chain | ID=PRO_0000074351;Note=Probable global transcription activator SNF2L1 |
| P28370 | 210 | 270 | 1 | 1054 | Chain | ID=PRO_0000074351;Note=Probable global transcription activator SNF2L1 |
| P28370 | 210 | 270 | 195 | 360 | Domain | Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 |
| P28370 | 210 | 270 | 214 | 214 | Mutagenesis | Note=No effect on neurite outgrowth. K->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14609955;Dbxref=PMID:14609955 |
| P28370 | 210 | 270 | 208 | 215 | Nucleotide binding | Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 |
| P28370 | 322 | 366 | 1 | 1054 | Chain | ID=PRO_0000074351;Note=Probable global transcription activator SNF2L1 |
| P28370 | 322 | 366 | 195 | 360 | Domain | Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 |
| P28370 | 366 | 389 | 1 | 1054 | Chain | ID=PRO_0000074351;Note=Probable global transcription activator SNF2L1 |
| P28370 | 542 | 554 | 543 | 554 | Alternative sequence | ID=VSP_020406;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15310751;Dbxref=PMID:15310751 |
| P28370 | 542 | 554 | 1 | 1054 | Chain | ID=PRO_0000074351;Note=Probable global transcription activator SNF2L1 |
| P28370 | 542 | 554 | 490 | 653 | Domain | Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00542 |
| P28370 | 776 | 814 | 1 | 1054 | Chain | ID=PRO_0000074351;Note=Probable global transcription activator SNF2L1 |
| P28370 | 814 | 855 | 1 | 1054 | Chain | ID=PRO_0000074351;Note=Probable global transcription activator SNF2L1 |
| P28370 | 814 | 855 | 855 | 907 | Domain | Note=SANT 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00624 |
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SNVs in the skipped exons for SMARCA1 |
| - 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. |
SMARCA1_KIRP_exon_skip_516648_psi_boxplot.png |
| - 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-6852-01 | exon_skip_516635 | 128605181 | 128605303 | 128605245 | 128605245 | Frame_Shift_Del | T | - | p.K834fs |
| BRCA | TCGA-A1-A0SM-01 | exon_skip_516637 | 128614678 | 128614791 | 128614761 | 128614761 | Frame_Shift_Del | G | - | p.Q787fs |
| LIHC | TCGA-DD-A3A1-01 | exon_skip_516639 | 128625918 | 128626070 | 128625945 | 128625945 | Frame_Shift_Del | C | - | p.W596fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_516643 | 128638711 | 128638779 | 128638732 | 128638732 | Frame_Shift_Del | T | - | p.K382fs |
| COAD | TCGA-G4-6320-01 | exon_skip_516643 | 128638711 | 128638779 | 128638751 | 128638751 | Frame_Shift_Del | T | - | p.N376fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_516643 | 128638711 | 128638779 | 128638751 | 128638751 | Frame_Shift_Del | T | - | p.N376fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_516643 | 128638711 | 128638779 | 128638751 | 128638751 | Frame_Shift_Del | T | - | p.N376fs |
| PRAD | TCGA-HC-8256-01 | exon_skip_516643 | 128638711 | 128638779 | 128638774 | 128638774 | Frame_Shift_Del | A | - | p.D369fs |
| PRAD | TCGA-HC-8256-01 | exon_skip_516643 | 128638711 | 128638779 | 128638774 | 128638774 | Frame_Shift_Del | A | - | p.F368fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_516644 | 128640057 | 128640188 | 128640085 | 128640085 | Frame_Shift_Del | A | - | p.L357fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_516645 | 128645781 | 128645960 | 128645824 | 128645824 | Frame_Shift_Del | G | - | p.P256fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_516647 | 128650308 | 128650474 | 128650351 | 128650351 | Frame_Shift_Del | G | - | p.R129fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_516647 | 128650308 | 128650474 | 128650351 | 128650351 | Frame_Shift_Del | G | - | p.R129fs |
| LIHC | TCGA-BC-A112-01 | exon_skip_516644 | 128640057 | 128640188 | 128640184 | 128640185 | Frame_Shift_Ins | - | A | p.R324fs |
| BLCA | TCGA-K4-A3WS-01 | exon_skip_516637 | 128614678 | 128614791 | 128614761 | 128614761 | Nonsense_Mutation | G | A | p.Q787* |
| UCEC | TCGA-BS-A0UF-01 | exon_skip_516641 | 128627017 | 128627052 | 128627040 | 128627040 | Nonsense_Mutation | C | A | p.E547* |
| OV | TCGA-24-1474-01 | exon_skip_516645 | 128645781 | 128645960 | 128645834 | 128645834 | Nonsense_Mutation | G | A | p.R253* |
| LUAD | TCGA-78-7156-01 | exon_skip_516647 | 128650308 | 128650474 | 128650465 | 128650465 | Nonsense_Mutation | G | A | p.R91* |
| KIRP | TCGA-G7-A8LD-01 | exon_skip_516648 | 128652338 | 128652424 | 128652406 | 128652406 | Nonsense_Mutation | G | A | p.Q65X |
| BLCA | TCGA-FT-A3EE-01 | exon_skip_516643 | 128638711 | 128638779 | 128638781 | 128638781 | Splice_Site | T | C | p.D367_splice |
| BRCA | TCGA-E2-A1IH-01 | exon_skip_516647 | 128650308 | 128650474 | 128650475 | 128650475 | Splice_Site | C | G | e3-1 |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-G7-A8LD-01 |
| Cancer type: KIRP | |
| ESID: exon_skip_516648 | |
| Skipped exon start: 128652338 | |
| Skipped exon end: 128652424 | |
| Mutation start: 128652406 | |
| Mutation end: 128652406 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: p.Q65X | |
exon_skip_384808_KIRP_TCGA-G7-A8LD-01.png | |
exon_skip_516648_KIRP_TCGA-G7-A8LD-01.png | |
| - 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 |
| NCIH2066_LUNG | 128645781 | 128645960 | 128645816 | 128645816 | Frame_Shift_Del | G | - | p.R259fs |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 128652338 | 128652424 | 128652417 | 128652418 | Frame_Shift_Del | AC | - | p.V61fs |
| NCIH2347_LUNG | 128605181 | 128605303 | 128605273 | 128605273 | Missense_Mutation | C | A | p.A825S |
| CCRFCEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 128614678 | 128614791 | 128614697 | 128614697 | Missense_Mutation | C | T | p.R808Q |
| RPMI8866_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 128614678 | 128614791 | 128614785 | 128614785 | Missense_Mutation | G | A | p.R779W |
| NUGC3_STOMACH | 128614678 | 128614791 | 128614787 | 128614787 | Missense_Mutation | G | T | p.P778Q |
| KYSE150_OESOPHAGUS | 128625918 | 128626070 | 128626000 | 128626000 | Missense_Mutation | C | T | p.G578D |
| CW2_LARGE_INTESTINE | 128625918 | 128626070 | 128626007 | 128626007 | Missense_Mutation | C | T | p.A576T |
| HCC2998_LARGE_INTESTINE | 128625918 | 128626070 | 128626043 | 128626043 | Missense_Mutation | T | C | p.N564D |
| MFE296_ENDOMETRIUM | 128625918 | 128626070 | 128626045 | 128626045 | Missense_Mutation | G | T | p.P563H |
| MZ7MEL_SKIN | 128638711 | 128638779 | 128638719 | 128638719 | Missense_Mutation | G | T | p.L387I |
| HEC265_ENDOMETRIUM | 128640057 | 128640188 | 128640094 | 128640094 | Missense_Mutation | A | G | p.L354P |
| SAOS2_BONE | 128640057 | 128640188 | 128640100 | 128640100 | Missense_Mutation | G | C | p.A352G |
| SNU1077_ENDOMETRIUM | 128640057 | 128640188 | 128640155 | 128640155 | Missense_Mutation | T | A | p.N334Y |
| SKNMC_BONE | 128645781 | 128645960 | 128645791 | 128645791 | Missense_Mutation | T | G | p.K267T |
| HEC6_ENDOMETRIUM | 128645781 | 128645960 | 128645833 | 128645833 | Missense_Mutation | C | T | p.R253Q |
| HUH28_BILIARY_TRACT | 128652338 | 128652424 | 128652375 | 128652375 | Missense_Mutation | G | C | p.S75C |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SMARCA1 |
| 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 SMARCA1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SMARCA1 |
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RelatedDrugs for SMARCA1 |
| 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 SMARCA1 |
| 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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