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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 SS18L1 |
Gene summary |
Gene information | Gene symbol | SS18L1 | Gene ID | 26039 |
Gene name | SS18L1 subunit of BAF chromatin remodeling complex | |
Synonyms | CREST|LP2261 | |
Cytomap | 20q13.33 | |
Type of gene | protein-coding | |
Description | calcium-responsive transactivatorSS18-like protein 1SS18L1, nBAF chromatin remodeling complex subunitSYT homolog 1synovial sarcoma translocation gene on chromosome 18-like 1 | |
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 SS18L1 |
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. |
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 | ENST00000450482.5 | SS18L1-203:protein_coding:SS18L1 | 1.807891e+01 | 8.356578e-01 | 1.273922e-10 | 7.740725e-09 |
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 SS18L1 |
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_10166 | chr20 | 62174517:62174644:62179182:62179356:62180169:62180280 | 62179182:62179356 |
exon_skip_162396 | chr20 | 62164145:62164246:62165422:62165514:62172682:62172801 | 62165422:62165514 |
exon_skip_217859 | chr20 | 62159877:62159961:62161436:62161580:62162752:62162931 | 62161436:62161580 |
exon_skip_234566 | chr20 | 62143795:62143889:62154281:62154465:62158672:62158748 | 62154281:62154465 |
exon_skip_51092 | chr20 | 62172682:62172801:62174517:62174644:62179182:62179356 | 62174517:62174644 |
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 |
exon_skip_217859 | Mayo_CB | 7.951852e-01 | 9.003175e-01 | -1.051323e-01 | 7.342124e-09 |
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Open reading frame (ORF) annotation in the exon skipping event for SS18L1 |
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 |
ENST00000331758 | 62161436 | 62161580 | Frame-shift |
ENST00000331758 | 62174517 | 62174644 | Frame-shift |
ENST00000331758 | 62165422 | 62165514 | 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 |
ENST00000331758 | 62161436 | 62161580 | Frame-shift |
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 |
ENST00000331758 | 62161436 | 62161580 | Frame-shift |
ENST00000331758 | 62174517 | 62174644 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for SS18L1 |
p-ENSG00000184402_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 |
ENST00000331758 | 4510 | 396 | 62165422 | 62165514 | 851 | 942 | 275 | 305 |
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 |
O75177 | 275 | 305 | 1 | 396 | Chain | ID=PRO_0000181825;Note=Calcium-responsive transactivator |
O75177 | 275 | 305 | 190 | 396 | Compositional bias | Note=Gln-rich |
O75177 | 275 | 305 | 246 | 317 | Region | Note=MFD domain;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
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 SS18L1 |
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 SS18L1 |
- 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 SS18L1 |
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 SS18L1 |
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 SS18L1 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | RBM3 | exon_skip_234566 | -4.053985e-01 | 1.264085e-07 |
CB | PCBP1 | exon_skip_234566 | 4.704621e-01 | 4.449745e-10 |
CB | PCBP4 | exon_skip_234566 | -5.007235e-01 | 2.085837e-11 |
CB | TRA2A | exon_skip_234566 | 5.569714e-01 | 2.968279e-14 |
CB | TARDBP | exon_skip_217859 | -4.361796e-01 | 4.636292e-08 |
CB | RBM6 | exon_skip_217859 | -4.656462e-01 | 4.079480e-09 |
CB | PCBP4 | exon_skip_217859 | 4.993460e-01 | 1.880117e-10 |
HCC | RBM3 | exon_skip_234566 | -5.469186e-01 | 4.635783e-21 |
IFG | MSI1 | exon_skip_234566 | 4.822331e-01 | 1.260082e-02 |
IFG | ELAVL1 | exon_skip_234566 | 6.135736e-01 | 8.575742e-04 |
IFG | RBM6 | exon_skip_234566 | 5.287787e-01 | 5.481746e-03 |
IFG | RBM3 | exon_skip_234566 | -5.618719e-01 | 2.816125e-03 |
IFG | TRA2A | exon_skip_234566 | 5.885599e-01 | 1.562452e-03 |
IFG | PCBP2 | exon_skip_234566 | 5.198827e-01 | 6.484586e-03 |
PCC | RBM3 | exon_skip_234566 | -5.033870e-01 | 1.337347e-13 |
TC | MSI1 | exon_skip_234566 | 4.030168e-01 | 4.573922e-07 |
TC | RBM3 | exon_skip_234566 | -5.540408e-01 | 4.041370e-13 |
TC | RALYL | exon_skip_234566 | -4.528329e-01 | 9.536137e-09 |
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RelatedDrugs for SS18L1 |
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 SS18L1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |