|
||||||
|
 | |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| 3'-UTR located exon skipping events lost miRNA binding sites |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| |
| |
|
Gene summary for SS18 |
 Gene summary |
| Gene information | Gene symbol | SS18 | Gene ID | 6760 |
| Gene name | SS18 subunit of BAF chromatin remodeling complex | |
| Synonyms | SSXT|SYT | |
| Cytomap | 18q11.2 | |
| Type of gene | protein-coding | |
| Description | protein SSXTSS18, nBAF chromatin remodeling complex subunitsynovial sarcoma translocated to X chromosome proteinsynovial sarcoma translocation, chromosome 18synovial sarcoma, translocated to X chromosome | |
| Modification date | 20200329 | |
| UniProtAcc | A0A024RC40, B4DLD3, F5GWN1, J3KRP6, J3KT22, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| SS18 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 15919756 |
Top |
Gene structures and expression levels for SS18 |
| 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. |
 |
ENSG00000141380
| 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. |
 |
| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | UP | ENST00000579640.5 | SS18-213:nonsense_mediated_decay:SS18 | 4.709587e+00 | 1.945206e+00 | 1.909500e-04 | 1.279715e-03 |
| CB | UP | ENST00000581021.5 | SS18-218:protein_coding:SS18 | 1.522658e+00 | 1.390990e+00 | 1.096941e-03 | 5.582159e-03 |
| CB | UP | ENST00000269138.9 | SS18-202:nonsense_mediated_decay:SS18 | 1.204687e+00 | 2.007326e+00 | 1.099377e-03 | 5.592230e-03 |
| TC | UP | ENST00000579640.5 | SS18-213:nonsense_mediated_decay:SS18 | 9.330550e+00 | 1.428890e+00 | 4.035411e-04 | 4.867973e-03 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SS18 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
 |
| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_116997 | chr18 | 26035091:26035127:26035831:26035923:26038555:26038659 | 26035831:26035923 |
| exon_skip_130248 | chr18 | 26078076:26078160:26087501:26087577:26090501:26090613 | 26087501:26087577 |
| exon_skip_142738 | chr18 | 26078103:26078160:26080305:26080423:26087501:26087577 | 26080305:26080423 |
| exon_skip_144400 | chr18 | 26078103:26078160:26079011:26079125:26087501:26087577 | 26079011:26079125 |
| exon_skip_163063 | chr18 | 26078103:26078160:26082363:26082528:26084052:26084175 | 26082363:26082528 |
| exon_skip_163754 | chr18 | 26078076:26078160:26082363:26082528:26084052:26084175 | 26082363:26082528 |
| exon_skip_164961 | chr18 | 26078076:26078160:26082363:26082528:26087501:26087577 | 26082363:26082528 |
| exon_skip_195433 | chr18 | 26078076:26078160:26080305:26080423:26082363:26082528 | 26080305:26080423 |
| exon_skip_197350 | chr18 | 26078103:26078160:26079011:26079146:26082363:26082528 | 26079011:26079146 |
| exon_skip_200181 | chr18 | 26082363:26082528:26084052:26084175:26087501:26087577 | 26084052:26084175 |
| exon_skip_213224 | chr18 | 26078103:26078160:26082363:26082528:26087501:26087577 | 26082363:26082528 |
| exon_skip_217555 | chr18 | 26078103:26078160:26084052:26084175:26087501:26087577 | 26084052:26084175 |
| exon_skip_24547 | chr18 | 26057589:26057742:26078076:26078160:26087501:26087577 | 26078076:26078160 |
| exon_skip_248702 | chr18 | 26078076:26078160:26084052:26084175:26087501:26087577 | 26084052:26084175 |
| exon_skip_261584 | chr18 | 26078103:26078160:26087501:26087577:26090501:26090597 | 26087501:26087577 |
| exon_skip_294291 | chr18 | 26082383:26082528:26084052:26084175:26087501:26087577 | 26084052:26084175 |
| exon_skip_4676 | chr18 | 26057699:26057742:26068494:26068557:26078076:26078160 | 26068494:26068557 |
| exon_skip_66520 | chr18 | 26057732:26057742:26068494:26068557:26078076:26078160 | 26068494:26068557 |
| exon_skip_75774 | chr18 | 26057732:26057742:26078076:26078160:26087501:26087577 | 26078076:26078160 |
| exon_skip_81505 | chr18 | 26080305:26080423:26082363:26082528:26087501:26087577 | 26082363:26082528 |
| exon_skip_86664 | chr18 | 26078103:26078160:26080305:26080423:26082363:26082528 | 26080305:26080423 |
| 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 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for SS18 |
| 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 |
| ENST00000415083 | 26078076 | 26078160 | Frame-shift |
| ENST00000415083 | 26035831 | 26035923 | 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 |
| ENST00000415083 | 26035831 | 26035923 | 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 |
| ENST00000415083 | 26078076 | 26078160 | Frame-shift |
| ENST00000415083 | 26035831 | 26035923 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for SS18 |
p-ENSG00000141380_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 |
| ENST00000415083 | 3431 | 418 | 26035831 | 26035923 | 937 | 1028 | 293 | 324 |
| 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 |
| ENST00000415083 | 3431 | 418 | 26035831 | 26035923 | 937 | 1028 | 293 | 324 |
| 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 |
| ENST00000415083 | 3431 | 418 | 26035831 | 26035923 | 937 | 1028 | 293 | 324 |
| 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 |
| Q15532 | 293 | 324 | 295 | 325 | Alternative sequence | ID=VSP_006258;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:7951320;Dbxref=PMID:7951320 |
| Q15532 | 293 | 324 | 2 | 418 | Chain | ID=PRO_0000181823;Note=Protein SSXT |
| Q15532 | 293 | 324 | 175 | 418 | Compositional bias | Note=Gln-rich |
| 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 |
| Q15532 | 293 | 324 | 295 | 325 | Alternative sequence | ID=VSP_006258;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:7951320;Dbxref=PMID:7951320 |
| Q15532 | 293 | 324 | 2 | 418 | Chain | ID=PRO_0000181823;Note=Protein SSXT |
| Q15532 | 293 | 324 | 175 | 418 | Compositional bias | Note=Gln-rich |
| 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 |
| Q15532 | 293 | 324 | 295 | 325 | Alternative sequence | ID=VSP_006258;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:7951320;Dbxref=PMID:7951320 |
| Q15532 | 293 | 324 | 2 | 418 | Chain | ID=PRO_0000181823;Note=Protein SSXT |
| Q15532 | 293 | 324 | 175 | 418 | Compositional bias | Note=Gln-rich |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in SS18 |
| 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 |
Top |
SNVs in the skipped exons for SS18 |
| - 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 |
Top |
AD stage-associated exon skippint events for SS18 |
| 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 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SS18 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
Top |
Correlation with RNA binding proteins (RBPs) for SS18 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| TC | NOVA1 | exon_skip_116997 | 5.297180e-01 | 8.269744e-13 |
Top |
RelatedDrugs for SS18 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for SS18 |
| 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)
|