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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 SMARCD1 |
 Gene summary |
| Gene information | Gene symbol | SMARCD1 | Gene ID | 6602 |
| Gene name | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 | |
| Synonyms | BAF60A|CRACD1|Rsc6p | |
| Cytomap | 12q13.12 | |
| Type of gene | protein-coding | |
| Description | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 160 kDa BRG-1/Brm-associated factor subunit ABRG1-associated factor 60ASWI/SNF complex 60 kDa subunit ASwp73-like proteinchromatin remodeling complex BAF60A s | |
| Modification date | 20180522 | |
| UniProtAcc | Q96GM5 | |
| Context | PubMed: SMARCD1 [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 |
| SMARCD1 | GO:0006337 | nucleosome disassembly | 8895581 |
| SMARCD1 | GO:0006338 | chromatin remodeling | 11726552 |
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Exon skipping events across known transcript of Ensembl for SMARCD1 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 SMARCD1 |
| 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 SMARCD1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_82144 | 12 | 50480538:50480661:50481145:50481268:50482303:50482420 | 50481145:50481268 | ENSG00000066117.10 | ENST00000381513.4,ENST00000394963.4,ENST00000547247.1 |
| exon_skip_82150 | 12 | 50480538:50480661:50482303:50482420:50483666:50483768 | 50482303:50482420 | ENSG00000066117.10 | ENST00000551966.1 |
| exon_skip_82155 | 12 | 50481145:50481268:50482303:50482420:50483666:50483768 | 50482303:50482420 | ENSG00000066117.10 | ENST00000381513.4,ENST00000394963.4 |
| exon_skip_82158 | 12 | 50482307:50482420:50483666:50483768:50484023:50484109 | 50483666:50483768 | ENSG00000066117.10 | ENST00000548573.1,ENST00000381513.4,ENST00000394963.4,ENST00000551966.1 |
| exon_skip_82162 | 12 | 50484275:50484373:50488219:50488355:50492496:50492598 | 50488219:50488355 | ENSG00000066117.10 | ENST00000381513.4 |
| exon_skip_82163 | 12 | 50488288:50488355:50490632:50490755:50492496:50492598 | 50490632:50490755 | ENSG00000066117.10 | ENST00000548573.1,ENST00000394963.4,ENST00000549274.1 |
| exon_skip_82166 | 12 | 50492496:50492598:50492729:50492924:50493269:50493348 | 50492729:50492924 | ENSG00000066117.10 | ENST00000549274.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SMARCD1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_82144 | 12 | 50480538:50480661:50481145:50481268:50482303:50482420 | 50481145:50481268 | ENSG00000066117.10 | ENST00000394963.4,ENST00000381513.4,ENST00000547247.1 |
| exon_skip_82150 | 12 | 50480538:50480661:50482303:50482420:50483666:50483768 | 50482303:50482420 | ENSG00000066117.10 | ENST00000551966.1 |
| exon_skip_82155 | 12 | 50481145:50481268:50482303:50482420:50483666:50483768 | 50482303:50482420 | ENSG00000066117.10 | ENST00000394963.4,ENST00000381513.4 |
| exon_skip_82158 | 12 | 50482307:50482420:50483666:50483768:50484023:50484109 | 50483666:50483768 | ENSG00000066117.10 | ENST00000394963.4,ENST00000381513.4,ENST00000551966.1,ENST00000548573.1 |
| exon_skip_82162 | 12 | 50484275:50484373:50488219:50488355:50492496:50492598 | 50488219:50488355 | ENSG00000066117.10 | ENST00000381513.4 |
| exon_skip_82163 | 12 | 50488288:50488355:50490632:50490755:50492496:50492598 | 50490632:50490755 | ENSG00000066117.10 | ENST00000394963.4,ENST00000548573.1,ENST00000549274.1 |
| exon_skip_82166 | 12 | 50492496:50492598:50492729:50492924:50493269:50493348 | 50492729:50492924 | ENSG00000066117.10 | ENST00000549274.1 |
| 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 SMARCD1 |
| 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 |
| ENST00000394963 | 50481145 | 50481268 | In-frame |
| ENST00000394963 | 50482303 | 50482420 | In-frame |
| ENST00000394963 | 50483666 | 50483768 | In-frame |
| ENST00000394963 | 50490632 | 50490755 | 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 |
| ENST00000394963 | 50481145 | 50481268 | In-frame |
| ENST00000394963 | 50482303 | 50482420 | In-frame |
| ENST00000394963 | 50483666 | 50483768 | In-frame |
| ENST00000394963 | 50490632 | 50490755 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SMARCD1 |
| 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 |
| ENST00000394963 | 3675 | 515 | 50481145 | 50481268 | 930 | 1052 | 177 | 218 |
| ENST00000394963 | 3675 | 515 | 50482303 | 50482420 | 1053 | 1169 | 218 | 257 |
| ENST00000394963 | 3675 | 515 | 50483666 | 50483768 | 1170 | 1271 | 257 | 291 |
| ENST00000394963 | 3675 | 515 | 50490632 | 50490755 | 1668 | 1790 | 423 | 464 |
| 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 |
| ENST00000394963 | 3675 | 515 | 50481145 | 50481268 | 930 | 1052 | 177 | 218 |
| ENST00000394963 | 3675 | 515 | 50482303 | 50482420 | 1053 | 1169 | 218 | 257 |
| ENST00000394963 | 3675 | 515 | 50483666 | 50483768 | 1170 | 1271 | 257 | 291 |
| ENST00000394963 | 3675 | 515 | 50490632 | 50490755 | 1668 | 1790 | 423 | 464 |
| 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 |
| Q96GM5 | 177 | 218 | 1 | 515 | Chain | ID=PRO_0000071983;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 |
| Q96GM5 | 177 | 218 | 203 | 203 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q92925 |
| Q96GM5 | 177 | 218 | 168 | 474 | Region | Note=Interaction with SMARCC1 and SMARCC2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12917342;Dbxref=PMID:12917342 |
| Q96GM5 | 177 | 218 | 180 | 515 | Region | Note=Necessary for GR/NR3C1-mediated remodeling and transcription from chromatin%3B required for GR/NR3C1 interaction with the BRG1/SMARCA4 complex in vivo |
| Q96GM5 | 218 | 257 | 1 | 515 | Chain | ID=PRO_0000071983;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 |
| Q96GM5 | 218 | 257 | 223 | 223 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q61466 |
| Q96GM5 | 218 | 257 | 168 | 474 | Region | Note=Interaction with SMARCC1 and SMARCC2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12917342;Dbxref=PMID:12917342 |
| Q96GM5 | 218 | 257 | 180 | 515 | Region | Note=Necessary for GR/NR3C1-mediated remodeling and transcription from chromatin%3B required for GR/NR3C1 interaction with the BRG1/SMARCA4 complex in vivo |
| Q96GM5 | 257 | 291 | 1 | 515 | Chain | ID=PRO_0000071983;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 |
| Q96GM5 | 257 | 291 | 291 | 390 | Domain | Note=SWIB |
| Q96GM5 | 257 | 291 | 168 | 474 | Region | Note=Interaction with SMARCC1 and SMARCC2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12917342;Dbxref=PMID:12917342 |
| Q96GM5 | 257 | 291 | 180 | 515 | Region | Note=Necessary for GR/NR3C1-mediated remodeling and transcription from chromatin%3B required for GR/NR3C1 interaction with the BRG1/SMARCA4 complex in vivo |
| Q96GM5 | 423 | 464 | 423 | 463 | Alternative sequence | ID=VSP_004179;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8804307;Dbxref=PMID:8804307 |
| Q96GM5 | 423 | 464 | 1 | 515 | Chain | ID=PRO_0000071983;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 |
| Q96GM5 | 423 | 464 | 412 | 440 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96GM5 | 423 | 464 | 168 | 474 | Region | Note=Interaction with SMARCC1 and SMARCC2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12917342;Dbxref=PMID:12917342 |
| Q96GM5 | 423 | 464 | 180 | 515 | Region | Note=Necessary for GR/NR3C1-mediated remodeling and transcription from chromatin%3B required for GR/NR3C1 interaction with the BRG1/SMARCA4 complex in vivo |
| 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 |
| Q96GM5 | 177 | 218 | 1 | 515 | Chain | ID=PRO_0000071983;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 |
| Q96GM5 | 177 | 218 | 203 | 203 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q92925 |
| Q96GM5 | 177 | 218 | 168 | 474 | Region | Note=Interaction with SMARCC1 and SMARCC2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12917342;Dbxref=PMID:12917342 |
| Q96GM5 | 177 | 218 | 180 | 515 | Region | Note=Necessary for GR/NR3C1-mediated remodeling and transcription from chromatin%3B required for GR/NR3C1 interaction with the BRG1/SMARCA4 complex in vivo |
| Q96GM5 | 218 | 257 | 1 | 515 | Chain | ID=PRO_0000071983;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 |
| Q96GM5 | 218 | 257 | 223 | 223 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q61466 |
| Q96GM5 | 218 | 257 | 168 | 474 | Region | Note=Interaction with SMARCC1 and SMARCC2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12917342;Dbxref=PMID:12917342 |
| Q96GM5 | 218 | 257 | 180 | 515 | Region | Note=Necessary for GR/NR3C1-mediated remodeling and transcription from chromatin%3B required for GR/NR3C1 interaction with the BRG1/SMARCA4 complex in vivo |
| Q96GM5 | 257 | 291 | 1 | 515 | Chain | ID=PRO_0000071983;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 |
| Q96GM5 | 257 | 291 | 291 | 390 | Domain | Note=SWIB |
| Q96GM5 | 257 | 291 | 168 | 474 | Region | Note=Interaction with SMARCC1 and SMARCC2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12917342;Dbxref=PMID:12917342 |
| Q96GM5 | 257 | 291 | 180 | 515 | Region | Note=Necessary for GR/NR3C1-mediated remodeling and transcription from chromatin%3B required for GR/NR3C1 interaction with the BRG1/SMARCA4 complex in vivo |
| Q96GM5 | 423 | 464 | 423 | 463 | Alternative sequence | ID=VSP_004179;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8804307;Dbxref=PMID:8804307 |
| Q96GM5 | 423 | 464 | 1 | 515 | Chain | ID=PRO_0000071983;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 |
| Q96GM5 | 423 | 464 | 412 | 440 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96GM5 | 423 | 464 | 168 | 474 | Region | Note=Interaction with SMARCC1 and SMARCC2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12917342;Dbxref=PMID:12917342 |
| Q96GM5 | 423 | 464 | 180 | 515 | Region | Note=Necessary for GR/NR3C1-mediated remodeling and transcription from chromatin%3B required for GR/NR3C1 interaction with the BRG1/SMARCA4 complex in vivo |
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SNVs in the skipped exons for SMARCD1 |
| - 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 |
| CHOL | TCGA-ZH-A8Y2-01 | exon_skip_82155 exon_skip_82150 | 50482304 | 50482420 | 50482343 | 50482359 | Frame_Shift_Del | AAGTTCTCTTCCTTTTT | - | p.231_237del |
| CHOL | TCGA-ZH-A8Y2-01 | exon_skip_82155 exon_skip_82150 | 50482304 | 50482420 | 50482343 | 50482359 | Frame_Shift_Del | AAGTTCTCTTCCTTTTT | - | p.KFSSFF232fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_82162 | 50488220 | 50488355 | 50488239 | 50488239 | Frame_Shift_Del | A | - | p.K386fs |
| CHOL | TCGA-ZH-A8Y2-01 | exon_skip_82155 exon_skip_82150 | 50482304 | 50482420 | 50482343 | 50482343 | Nonsense_Mutation | A | T | p.K232X |
| HNSC | TCGA-D6-6516-01 | exon_skip_82158 | 50483667 | 50483768 | 50483706 | 50483706 | Nonsense_Mutation | C | T | p.Q271* |
| UCEC | TCGA-BS-A0UF-01 | exon_skip_82166 | 50492730 | 50492924 | 50492748 | 50492748 | Nonsense_Mutation | G | T | p.E505* |
| PAAD | TCGA-IB-7651-01 | exon_skip_82158 | 50483667 | 50483768 | 50483666 | 50483666 | Splice_Site | G | T | . |
| - 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 |
| SNU81_LARGE_INTESTINE | 50481146 | 50481268 | 50481162 | 50481162 | Missense_Mutation | G | A | p.R183Q |
| DOV13_OVARY | 50481146 | 50481268 | 50481180 | 50481180 | Missense_Mutation | C | G | p.T189S |
| JHUEM7_ENDOMETRIUM | 50482304 | 50482420 | 50482331 | 50482331 | Missense_Mutation | A | C | p.K228Q |
| NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 50482304 | 50482420 | 50482338 | 50482338 | Missense_Mutation | A | C | p.K230T |
| HEC59_ENDOMETRIUM | 50483667 | 50483768 | 50483746 | 50483746 | Missense_Mutation | T | C | p.V284A |
| LNCAPCLONEFGC_PROSTATE | 50483667 | 50483768 | 50483761 | 50483761 | Missense_Mutation | A | G | p.D289G |
| SNU1040_LARGE_INTESTINE | 50490633 | 50490755 | 50490755 | 50490755 | Splice_Site | G | T | p.K464N |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SMARCD1 |
| 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 SMARCD1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SMARCD1 |
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RelatedDrugs for SMARCD1 |
| 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 SMARCD1 |
| 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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