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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 SMARCA5 |
 Gene summary |
| Gene information | Gene symbol | SMARCA5 | Gene ID | 8467 |
| Gene name | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 | |
| Synonyms | ISWI|SNF2H|WCRF135|hISWI|hSNF2H | |
| Cytomap | 4q31.21 | |
| Type of gene | protein-coding | |
| Description | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5SWI/SNF-related matrix-associated actin-dependent regulator of chromatin A5sucrose nonfermenting protein 2 homologsucrose nonfermenting-like 5 | |
| Modification date | 20180519 | |
| UniProtAcc | O60264 | |
| Context | PubMed: SMARCA5 [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 |
| SMARCA5 | GO:0006334 | nucleosome assembly | 12972596 |
| SMARCA5 | GO:0006338 | chromatin remodeling | 9836642 |
| SMARCA5 | GO:0006352 | DNA-templated transcription, initiation | 9836642 |
| SMARCA5 | GO:0016584 | nucleosome positioning | 9836642 |
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Exon skipping events across known transcript of Ensembl for SMARCA5 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 SMARCA5 |
| 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 SMARCA5 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_426342 | 4 | 144446603:144446704:144447433:144447613:144449020:144449176 | 144447433:144447613 | ENSG00000153147.5 | ENST00000283131.3 |
| exon_skip_426343 | 4 | 144447433:144447613:144449020:144449176:144449735:144449867 | 144449020:144449176 | ENSG00000153147.5 | ENST00000283131.3 |
| exon_skip_426347 | 4 | 144459938:144460091:144461515:144461648:144464661:144464810 | 144461515:144461648 | ENSG00000153147.5 | ENST00000283131.3 |
| exon_skip_426349 | 4 | 144466622:144466736:144467077:144467200:144467928:144468061 | 144467077:144467200 | ENSG00000153147.5 | ENST00000283131.3 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SMARCA5 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_426342 | 4 | 144446603:144446704:144447433:144447613:144449020:144449176 | 144447433:144447613 | ENSG00000153147.5 | ENST00000283131.3 |
| exon_skip_426343 | 4 | 144447433:144447613:144449020:144449176:144449735:144449867 | 144449020:144449176 | ENSG00000153147.5 | ENST00000283131.3 |
| exon_skip_426347 | 4 | 144459938:144460091:144461515:144461648:144464661:144464810 | 144461515:144461648 | ENSG00000153147.5 | ENST00000283131.3 |
| exon_skip_426349 | 4 | 144466622:144466736:144467077:144467200:144467928:144468061 | 144467077:144467200 | ENSG00000153147.5 | ENST00000283131.3 |
| 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 SMARCA5 |
| 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 |
| ENST00000283131 | 144461515 | 144461648 | Frame-shift |
| ENST00000283131 | 144447433 | 144447613 | In-frame |
| ENST00000283131 | 144449020 | 144449176 | In-frame |
| ENST00000283131 | 144467077 | 144467200 | 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 |
| ENST00000283131 | 144461515 | 144461648 | Frame-shift |
| ENST00000283131 | 144447433 | 144447613 | In-frame |
| ENST00000283131 | 144449020 | 144449176 | In-frame |
| ENST00000283131 | 144467077 | 144467200 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SMARCA5 |
| 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 |
| ENST00000283131 | 7940 | 1052 | 144447433 | 144447613 | 1084 | 1263 | 207 | 267 |
| ENST00000283131 | 7940 | 1052 | 144449020 | 144449176 | 1264 | 1419 | 267 | 319 |
| ENST00000283131 | 7940 | 1052 | 144467077 | 144467200 | 2860 | 2982 | 799 | 840 |
| 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 |
| ENST00000283131 | 7940 | 1052 | 144447433 | 144447613 | 1084 | 1263 | 207 | 267 |
| ENST00000283131 | 7940 | 1052 | 144449020 | 144449176 | 1264 | 1419 | 267 | 319 |
| ENST00000283131 | 7940 | 1052 | 144467077 | 144467200 | 2860 | 2982 | 799 | 840 |
| 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 |
| O60264 | 207 | 267 | 2 | 1052 | Chain | ID=PRO_0000074354;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 |
| O60264 | 207 | 267 | 192 | 357 | Domain | Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 |
| O60264 | 207 | 267 | 211 | 211 | Mutagenesis | Note=Loss of ATP hydrolysis and no association of the SMARCA5/cohesin/NuRD complex with chromatin. K->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12198550;Dbxref=PMID:12198550 |
| O60264 | 207 | 267 | 205 | 212 | Nucleotide binding | Note=ATP;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| O60264 | 267 | 319 | 2 | 1052 | Chain | ID=PRO_0000074354;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 |
| O60264 | 267 | 319 | 192 | 357 | Domain | Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 |
| O60264 | 267 | 319 | 308 | 311 | Motif | Note=DEAH box |
| O60264 | 799 | 840 | 2 | 1052 | Chain | ID=PRO_0000074354;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 |
| O60264 | 799 | 840 | 840 | 892 | Domain | Note=SANT 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00624 |
| O60264 | 799 | 840 | 825 | 825 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:21406692;Dbxref=PMID:20068231,PMID:21406692 |
| 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 |
| O60264 | 207 | 267 | 2 | 1052 | Chain | ID=PRO_0000074354;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 |
| O60264 | 207 | 267 | 192 | 357 | Domain | Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 |
| O60264 | 207 | 267 | 211 | 211 | Mutagenesis | Note=Loss of ATP hydrolysis and no association of the SMARCA5/cohesin/NuRD complex with chromatin. K->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12198550;Dbxref=PMID:12198550 |
| O60264 | 207 | 267 | 205 | 212 | Nucleotide binding | Note=ATP;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| O60264 | 267 | 319 | 2 | 1052 | Chain | ID=PRO_0000074354;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 |
| O60264 | 267 | 319 | 192 | 357 | Domain | Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 |
| O60264 | 267 | 319 | 308 | 311 | Motif | Note=DEAH box |
| O60264 | 799 | 840 | 2 | 1052 | Chain | ID=PRO_0000074354;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 |
| O60264 | 799 | 840 | 840 | 892 | Domain | Note=SANT 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00624 |
| O60264 | 799 | 840 | 825 | 825 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:21406692;Dbxref=PMID:20068231,PMID:21406692 |
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SNVs in the skipped exons for SMARCA5 |
| - 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-CG-4442-01 | exon_skip_426349 | 144467078 | 144467200 | 144467118 | 144467118 | Frame_Shift_Del | A | - | p.Q813fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_426349 | 144467078 | 144467200 | 144467135 | 144467135 | Frame_Shift_Del | A | - | p.K819fs |
| UCEC | TCGA-BS-A0UF-01 | exon_skip_426349 | 144467078 | 144467200 | 144467183 | 144467183 | Nonsense_Mutation | G | T | p.E835* |
| - 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 |
| T3M10_LUNG | 144447434 | 144447613 | 144447513 | 144447514 | Frame_Shift_Del | TT | - | p.V234fs |
| SNUC2B_LARGE_INTESTINE | 144447434 | 144447613 | 144447507 | 144447507 | Missense_Mutation | A | G | p.H232R |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 144447434 | 144447613 | 144447566 | 144447566 | Missense_Mutation | G | A | p.V252I |
| HCC2998_LARGE_INTESTINE | 144449021 | 144449176 | 144449112 | 144449112 | Missense_Mutation | A | C | p.K298T |
| TE5_OESOPHAGUS | 144461516 | 144461648 | 144461595 | 144461595 | Missense_Mutation | T | C | p.I617T |
| HUCCT1_BILIARY_TRACT | 144467078 | 144467200 | 144467105 | 144467105 | Missense_Mutation | G | T | p.A809S |
| MDST8_LARGE_INTESTINE | 144467078 | 144467200 | 144467156 | 144467156 | Missense_Mutation | C | T | p.L826F |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SMARCA5 |
| 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 SMARCA5 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SMARCA5 |
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RelatedDrugs for SMARCA5 |
| 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 SMARCA5 |
| 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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