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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 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|CSS11|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 | 20200313 | |
| UniProtAcc | A0A024R102, | |
| Context |
| 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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Gene structures and expression levels for SMARCD1 |
| 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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ENSG00000066117
| 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 | ENST00000551966.5 | SMARCD1-212:protein_coding:SMARCD1 | 2.235432e+00 | 8.853736e-01 | 7.110833e-03 | 2.627961e-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 SMARCD1 |
| 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_138531 | chr12 | 50086756:50086878:50087363:50087485:50088521:50088535 | 50087363:50087485 |
| exon_skip_32117 | chr12 | 50088525:50088637:50089884:50089985:50090241:50090326 | 50089884:50089985 |
| exon_skip_41662 | chr12 | 50086834:50086878:50087363:50087485:50088521:50088637 | 50087363:50087485 |
| exon_skip_54533 | chr12 | 50086756:50086878:50088521:50088637:50089884:50089985 | 50088521:50088637 |
| exon_skip_59696 | chr12 | 50094506:50094572:50096850:50096972:50098714:50098815 | 50096850:50096972 |
| exon_skip_70441 | chr12 | 50086756:50086878:50087363:50087485:50088521:50088637 | 50087363:50087485 |
| exon_skip_94289 | chr12 | 50090493:50090590:50094437:50094572:50098714:50098815 | 50094437:50094572 |
| exon_skip_94560 | chr12 | 50086834:50086878:50088521:50088637:50089884:50089985 | 50088521:50088637 |
| 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 |
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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 ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000394963 | 50087363 | 50087485 | In-frame |
| ENST00000394963 | 50096850 | 50096972 | 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 |
| ENST00000394963 | 50087363 | 50087485 | In-frame |
| ENST00000394963 | 50096850 | 50096972 | 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 |
| ENST00000394963 | 50087363 | 50087485 | In-frame |
| ENST00000394963 | 50089884 | 50089985 | In-frame |
| ENST00000394963 | 50096850 | 50096972 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SMARCD1 |
p-ENSG00000066117_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 |
| ENST00000394963 | 3675 | 515 | 50087363 | 50087485 | 931 | 1052 | 177 | 218 |
| ENST00000394963 | 3675 | 515 | 50096850 | 50096972 | 1669 | 1790 | 423 | 464 |
| 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 |
| ENST00000394963 | 3675 | 515 | 50087363 | 50087485 | 931 | 1052 | 177 | 218 |
| ENST00000394963 | 3675 | 515 | 50096850 | 50096972 | 1669 | 1790 | 423 | 464 |
| 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 |
| ENST00000394963 | 3675 | 515 | 50087363 | 50087485 | 931 | 1052 | 177 | 218 |
| ENST00000394963 | 3675 | 515 | 50089884 | 50089985 | 1171 | 1271 | 257 | 291 |
| ENST00000394963 | 3675 | 515 | 50096850 | 50096972 | 1669 | 1790 | 423 | 464 |
| 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 |
| 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 | 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 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 |
| 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 | 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 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 |
| 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 | 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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3'-UTR located exon skipping events that lost miRNA binding sites in SMARCD1 |
| 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 SMARCD1 |
| - 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 SMARCD1 |
| 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 SMARCD1 |
| 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 SMARCD1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | NUP42 | exon_skip_94289 | 4.452792e-01 | 4.363772e-07 |
| CB | RBM6 | exon_skip_59696 | -5.221506e-01 | 1.681758e-12 |
| CB | RBM3 | exon_skip_59696 | 4.209762e-01 | 3.287743e-08 |
| CB | NUP42 | exon_skip_59696 | 4.560135e-01 | 1.536810e-09 |
| CB | RBM4B | exon_skip_59696 | -4.014223e-01 | 1.570750e-07 |
| IFG | RBM3 | exon_skip_59696 | 4.821802e-01 | 1.261195e-02 |
| PCC | RBM3 | exon_skip_59696 | 4.138685e-01 | 4.697410e-10 |
| TC | RBM3 | exon_skip_59696 | 4.083383e-01 | 9.137311e-08 |
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RelatedDrugs for SMARCD1 |
| 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 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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