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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 SQSTM1 |
 Gene summary |
| Gene information | Gene symbol | SQSTM1 | Gene ID | 8878 |
| Gene name | sequestosome 1 | |
| Synonyms | A170|DMRV|FTDALS3|NADGP|OSIL|PDB3|ZIP3|p60|p62|p62B | |
| Cytomap | 5q35.3 | |
| Type of gene | protein-coding | |
| Description | sequestosome-1EBI3-associated protein of 60 kDaEBI3-associated protein p60EBIAPautophagy receptor p62oxidative stress induced likephosphotyrosine independent ligand for the Lck SH2 domain p62phosphotyrosine-independent ligand for the Lck SH2 domain | |
| Modification date | 20200327 | |
| UniProtAcc | ||
| Context | - 31951107(Novel Alzheimer risk genes determine the microglia response to amyloid-beta but not to TAU pathology) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| SQSTM1 | GO:0006914 | autophagy | 20452972 |
| SQSTM1 | GO:0007032 | endosome organization | 27368102 |
| SQSTM1 | GO:0031397 | negative regulation of protein ubiquitination | 20452972 |
| SQSTM1 | GO:0061635 | regulation of protein complex stability | 25127057 |
| SQSTM1 | GO:1905719 | protein localization to perinuclear region of cytoplasm | 27368102 |
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Gene structures and expression levels for SQSTM1 |
| 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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ENSG00000161011
| 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 | ENST00000504627.1 | SQSTM1-209:protein_coding:SQSTM1 | 1.333268e+00 | 1.024782e+00 | 7.845208e-04 | 4.213181e-03 |
| 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 SQSTM1 |
| 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_13178 | chr5 | 179806408:179806591:179811574:179811682:179822958:179823053 | 179811574:179811682 |
| exon_skip_132757 | chr5 | 179824182:179824323:179825146:179825226:179833032:179833227 | 179825146:179825226 |
| exon_skip_134380 | chr5 | 179820921:179821141:179821551:179821707:179822958:179823053 | 179821551:179821707 |
| exon_skip_141593 | chr5 | 179818967:179819037:179820104:179820387:179822958:179823053 | 179820104:179820387 |
| exon_skip_150398 | chr5 | 179823026:179823053:179823858:179824087:179824182:179824237 | 179823858:179824087 |
| exon_skip_225809 | chr5 | 179824291:179824323:179825146:179825226:179833032:179833227 | 179825146:179825226 |
| exon_skip_231481 | chr5 | 179811615:179811682:179822958:179823053:179823858:179823939 | 179822958:179823053 |
| exon_skip_2488 | chr5 | 179825146:179825226:179833032:179833246:179833587:179833782 | 179833032:179833246 |
| exon_skip_257933 | chr5 | 179820905:179821141:179821551:179821707:179822958:179823053 | 179821551:179821707 |
| 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 SQSTM1 |
| 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 |
| ENST00000389805 | 179825146 | 179825226 | 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 |
| 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 |
| ENST00000389805 | 179823858 | 179824087 | Frame-shift |
| ENST00000389805 | 179833032 | 179833246 | Frame-shift |
| ENST00000389805 | 179825146 | 179825226 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SQSTM1 |
p-ENSG00000161011_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 |
| ENST00000389805 | 3003 | 440 | 179825146 | 179825226 | 853 | 932 | 225 | 251 |
| 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 |
| ENST00000389805 | 3003 | 440 | 179825146 | 179825226 | 853 | 932 | 225 | 251 |
| 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 |
| Q13501 | 225 | 251 | 2 | 440 | Chain | ID=PRO_0000072176;Note=Sequestosome-1 |
| Q13501 | 225 | 251 | 233 | 233 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569 |
| Q13501 | 225 | 251 | 249 | 249 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:20068231;Dbxref=PMID:20068231 |
| Q13501 | 225 | 251 | 228 | 233 | Motif | Note=TRAF6-binding |
| Q13501 | 225 | 251 | 226 | 226 | Natural variant | ID=VAR_073919;Note=In FTDALS3. S->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24899140;Dbxref=dbSNP:rs765200636,PMID:24899140 |
| Q13501 | 225 | 251 | 228 | 228 | Natural variant | ID=VAR_073920;Note=In FTDALS3. P->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:22084127,ECO:0000269|PubMed:24899140;Dbxref=dbSNP:rs151191977,PMID:22084127,PMID:24899140 |
| Q13501 | 225 | 251 | 232 | 232 | Natural variant | ID=VAR_073921;Note=In FTDALS3. P->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24899140;Dbxref=PMID:24899140 |
| Q13501 | 225 | 251 | 238 | 238 | Natural variant | ID=VAR_068915;Note=Polymorphism%3B confirmed at protein level. K->E;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:17488105,ECO:0000269|PubMed:24899140;Dbxref=dbSNP:rs11548633,PMID:17488105,PMID:24899140 |
| Q13501 | 225 | 251 | 238 | 238 | Natural variant | ID=VAR_073922;Note=In FTDALS3. Missing;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:22084127,ECO:0000269|PubMed:24899140,ECO:0000269|PubMed:25114083;Dbxref=PMID:22084127,PMID:24899140,PMID:25114083 |
| 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 |
| Q13501 | 225 | 251 | 2 | 440 | Chain | ID=PRO_0000072176;Note=Sequestosome-1 |
| Q13501 | 225 | 251 | 233 | 233 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569 |
| Q13501 | 225 | 251 | 249 | 249 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:20068231;Dbxref=PMID:20068231 |
| Q13501 | 225 | 251 | 228 | 233 | Motif | Note=TRAF6-binding |
| Q13501 | 225 | 251 | 226 | 226 | Natural variant | ID=VAR_073919;Note=In FTDALS3. S->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24899140;Dbxref=dbSNP:rs765200636,PMID:24899140 |
| Q13501 | 225 | 251 | 228 | 228 | Natural variant | ID=VAR_073920;Note=In FTDALS3. P->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:22084127,ECO:0000269|PubMed:24899140;Dbxref=dbSNP:rs151191977,PMID:22084127,PMID:24899140 |
| Q13501 | 225 | 251 | 232 | 232 | Natural variant | ID=VAR_073921;Note=In FTDALS3. P->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24899140;Dbxref=PMID:24899140 |
| Q13501 | 225 | 251 | 238 | 238 | Natural variant | ID=VAR_068915;Note=Polymorphism%3B confirmed at protein level. K->E;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:17488105,ECO:0000269|PubMed:24899140;Dbxref=dbSNP:rs11548633,PMID:17488105,PMID:24899140 |
| Q13501 | 225 | 251 | 238 | 238 | Natural variant | ID=VAR_073922;Note=In FTDALS3. Missing;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:22084127,ECO:0000269|PubMed:24899140,ECO:0000269|PubMed:25114083;Dbxref=PMID:22084127,PMID:24899140,PMID:25114083 |
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3'-UTR located exon skipping events that lost miRNA binding sites in SQSTM1 |
| 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 SQSTM1 |
| - 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 SQSTM1 |
| 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 SQSTM1 |
| 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 SQSTM1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SQSTM1 |
| 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 SQSTM1 |
| 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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