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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 SIL1 |
 Gene summary |
| Gene information | Gene symbol | SIL1 | Gene ID | 64374 |
| Gene name | SIL1 nucleotide exchange factor | |
| Synonyms | BAP|MSS|ULG5 | |
| Cytomap | 5q31.2 | |
| Type of gene | protein-coding | |
| Description | nucleotide exchange factor SIL1BiP-associated proteinSIL1 homolog, endoplasmic reticulum chaperoneSIL1-like protein endoplasmic reticulum chaperone | |
| Modification date | 20200313 | |
| UniProtAcc | ||
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
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Gene structures and expression levels for SIL1 |
| 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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ENSG00000120725
| 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 | DOWN | ENST00000515008.1 | SIL1-215:lncRNA:SIL1 | 1.783657e+01 | -2.719014e+00 | 1.136853e-04 | 8.252818e-04 |
| TC | DOWN | ENST00000515008.1 | SIL1-215:lncRNA:SIL1 | 5.269314e+01 | -1.672077e+00 | 3.912826e-05 | 7.637756e-04 |
| 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 SIL1 |
| 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_121285 | chr5 | 139127739:139127853:139196441:139196528:139198269:139198297 | 139196441:139196528 |
| exon_skip_275581 | chr5 | 139127809:139127853:139196441:139196528:139198269:139198297 | 139196441:139196528 |
| exon_skip_290558 | chr5 | 138951820:138951884:139021171:139021292:139026801:139026992 | 139021171:139021292 |
| exon_skip_79191 | chr5 | 139042703:139042719:139050938:139051046:139121035:139121170 | 139050938:139051046 |
| 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 SIL1 |
| 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 |
| ENST00000265195 | 139196441 | 139196528 | 3UTR-3UTR |
| ENST00000265195 | 139021171 | 139021292 | Frame-shift |
| ENST00000394817 | 139021171 | 139021292 | Frame-shift |
| ENST00000265195 | 139050938 | 139051046 | Frame-shift |
| ENST00000394817 | 139050938 | 139051046 | Frame-shift |
| 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 |
| ENST00000265195 | 139196441 | 139196528 | 3UTR-3UTR |
| 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 |
| ENST00000265195 | 139196441 | 139196528 | 3UTR-3UTR |
| ENST00000265195 | 139021171 | 139021292 | Frame-shift |
| ENST00000394817 | 139021171 | 139021292 | Frame-shift |
| ENST00000265195 | 139050938 | 139051046 | Frame-shift |
| ENST00000394817 | 139050938 | 139051046 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for SIL1 |
p-ENSG00000120725_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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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3'-UTR located exon skipping events that lost miRNA binding sites in SIL1 |
| 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 |
| Mayo | ENST00000265195 | 139196441 | 139196528 | hsa-miR-4684-5p | chr5:139196509-139196516 | 8mer-1a | chr5:139196497-139196518 | 166.00 | -24.19 |
| Mayo | ENST00000265195 | 139196441 | 139196528 | hsa-miR-1233-3p | chr5:139196489-139196496 | 8mer-1a | chr5:139196484-139196508 | 140.00 | -30.14 |
| Mayo | ENST00000265195 | 139196441 | 139196528 | hsa-miR-3682-5p | chr5:139196513-139196520 | 8mer-1a | chr5:139196505-139196527 | 141.00 | -20.31 |
| Mayo | ENST00000265195 | 139196441 | 139196528 | hsa-miR-3650 | chr5:139196482-139196489 | 8mer-1a | chr5:139196471-139196491 | 157.00 | -19.40 |
| Mayo | ENST00000265195 | 139196441 | 139196528 | hsa-miR-7150 | chr5:139196470-139196477 | 8mer-1a | chr5:139196460-139196477 | 172.00 | -31.26 |
| MSBB | ENST00000265195 | 139196441 | 139196528 | hsa-miR-4684-5p | chr5:139196509-139196516 | 8mer-1a | chr5:139196497-139196518 | 166.00 | -24.19 |
| MSBB | ENST00000265195 | 139196441 | 139196528 | hsa-miR-1233-3p | chr5:139196489-139196496 | 8mer-1a | chr5:139196484-139196508 | 140.00 | -30.14 |
| MSBB | ENST00000265195 | 139196441 | 139196528 | hsa-miR-3682-5p | chr5:139196513-139196520 | 8mer-1a | chr5:139196505-139196527 | 141.00 | -20.31 |
| MSBB | ENST00000265195 | 139196441 | 139196528 | hsa-miR-3650 | chr5:139196482-139196489 | 8mer-1a | chr5:139196471-139196491 | 157.00 | -19.40 |
| MSBB | ENST00000265195 | 139196441 | 139196528 | hsa-miR-7150 | chr5:139196470-139196477 | 8mer-1a | chr5:139196460-139196477 | 172.00 | -31.26 |
| ROSMAP | ENST00000265195 | 139196441 | 139196528 | hsa-miR-4684-5p | chr5:139196509-139196516 | 8mer-1a | chr5:139196497-139196518 | 166.00 | -24.19 |
| ROSMAP | ENST00000265195 | 139196441 | 139196528 | hsa-miR-1233-3p | chr5:139196489-139196496 | 8mer-1a | chr5:139196484-139196508 | 140.00 | -30.14 |
| ROSMAP | ENST00000265195 | 139196441 | 139196528 | hsa-miR-3682-5p | chr5:139196513-139196520 | 8mer-1a | chr5:139196505-139196527 | 141.00 | -20.31 |
| ROSMAP | ENST00000265195 | 139196441 | 139196528 | hsa-miR-3650 | chr5:139196482-139196489 | 8mer-1a | chr5:139196471-139196491 | 157.00 | -19.40 |
| ROSMAP | ENST00000265195 | 139196441 | 139196528 | hsa-miR-7150 | chr5:139196470-139196477 | 8mer-1a | chr5:139196460-139196477 | 172.00 | -31.26 |
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SNVs in the skipped exons for SIL1 |
| - 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 SIL1 |
| 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 SIL1 |
| 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 SIL1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SIL1 |
| 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 SIL1 |
| 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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