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Fusion Protein:SS18L1-GID8 |
Fusion Gene and Fusion Protein Summary |
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Fusion partner gene information | Fusion gene name: SS18L1-GID8 | FusionPDB ID: 86667 | FusionGDB2.0 ID: 86667 | Hgene | Tgene | Gene symbol | SS18L1 | GID8 | Gene ID | 26039 | 54994 |
Gene name | SS18L1 subunit of BAF chromatin remodeling complex | GID complex subunit 8 homolog | |
Synonyms | CREST|LP2261 | C20orf11|TWA1 | |
Cytomap | 20q13.33 | 20q13.33 | |
Type of gene | protein-coding | protein-coding | |
Description | calcium-responsive transactivatorSS18-like protein 1SS18L1, nBAF chromatin remodeling complex subunitSYT homolog 1synovial sarcoma translocation gene on chromosome 18-like 1 | glucose-induced degradation protein 8 homologprotein C20orf11two hybrid associated protein No. 1 with RanBPMtwo hybrid-associated protein 1 with RanBPM | |
Modification date | 20200313 | 20200329 | |
UniProtAcc | O75177 Main function of 5'-partner protein: FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}. | Q9NWU2 Main function of 5'-partner protein: FUNCTION: Core component of the CTLH E3 ubiquitin-protein ligase complex that selectively accepts ubiquitin from UBE2H and mediates ubiquitination and subsequent proteasomal degradation of the transcription factor HBP1 (PubMed:29911972). Acts as a positive regulator of Wnt signaling pathway by promoting beta-catenin (CTNNB1) nuclear accumulation (PubMed:28829046). {ECO:0000269|PubMed:28829046, ECO:0000269|PubMed:29911972}. | |
Ensembl transtripts involved in fusion gene | ENST ids | ENST00000331758, ENST00000370848, ENST00000421564, ENST00000491916, | ENST00000497101, ENST00000266069, |
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 11 X 8 X 7=616 | 3 X 3 X 3=27 |
# samples | 12 | 3 | |
** MAII score | log2(12/616*10)=-2.35989594508638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(3/27*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
Fusion gene context | PubMed: SS18L1 [Title/Abstract] AND GID8 [Title/Abstract] AND fusion [Title/Abstract] | ||
Fusion neoantigen context | PubMed: SS18L1 [Title/Abstract] AND GID8 [Title/Abstract] AND neoantigen [Title/Abstract] | ||
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | SS18L1(60735017)-GID8(61574847), # samples:2 | ||
Anticipated loss of major functional domain due to fusion event. | SS18L1-GID8 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. SS18L1-GID8 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. SS18L1-GID8 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. SS18L1-GID8 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. |
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
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Partner | Gene | GO ID | GO term | PubMed ID |
![]() Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr20:60735017/chr20:61574847) - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. - How to search 1. Put your fusion gene symbol. 2. Press the tab key until there will be shown the breakpoint information filled. 4. Go down and press 'Search' tab twice. 4. Go down to have the hyperlink of the search result. 5. Click the hyperlink. 6. See the FGviewer result for your fusion gene. |
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![]() * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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![]() * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Fusion Amino Acid Sequences |
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Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
ENST00000421564 | SS18L1 | chr20 | 60735017 | + | ENST00000266069 | GID8 | chr20 | 61574847 | + | 1390 | 286 | 55 | 657 | 200 |
ENST00000331758 | SS18L1 | chr20 | 60735017 | + | ENST00000266069 | GID8 | chr20 | 61574847 | + | 1361 | 257 | 26 | 628 | 200 |
ENST00000370848 | SS18L1 | chr20 | 60735017 | + | ENST00000266069 | GID8 | chr20 | 61574847 | + | 1344 | 240 | 0 | 611 | 203 |
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Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
ENST00000421564 | ENST00000266069 | SS18L1 | chr20 | 60735017 | + | GID8 | chr20 | 61574847 | + | 0.004130719 | 0.9958692 |
ENST00000331758 | ENST00000266069 | SS18L1 | chr20 | 60735017 | + | GID8 | chr20 | 61574847 | + | 0.003507568 | 0.99649245 |
ENST00000370848 | ENST00000266069 | SS18L1 | chr20 | 60735017 | + | GID8 | chr20 | 61574847 | + | 0.013353219 | 0.9866468 |
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Get the fusion protein sequences from here. |
Fusion protein sequence information is available in the fasta format. >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP |
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Fusion Protein Breakpoint Sequences for SS18L1-GID8 |
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Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
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Potential FusionNeoAntigen Information of SS18L1-GID8 in HLA I |
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![]() * We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5) |
Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA I | FusionNeoAntigen peptide | Binding score | Immunogenic score | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
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Potential FusionNeoAntigen Information of SS18L1-GID8 in HLA II |
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![]() * We used NetMHCIIpan v4.1 (%rank<0.5). |
Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA II | FusionNeoAntigen peptide | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
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Fusion breakpoint peptide structures of SS18L1-GID8 |
![]() * The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA. |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SS18L1-GID8 |
![]() * We used Glide to predict the interaction between HLAs and neoantigens. |
HLA allele | PDB ID | File name | BPseq | Docking score | Glide score |
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Vaccine Design for the FusionNeoAntigens of SS18L1-GID8 |
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Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
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Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide | FusionNEoAntigen RNA sequence |
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Information of the samples that have these potential fusion neoantigens of SS18L1-GID8 |
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Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
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Potential target of CAR-T therapy development for SS18L1-GID8 |
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![]() * Minus value of BPloci means that the break point is located before the CDS. |
- In-frame and retained 'Transmembrane'. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
![]() * We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image. |
Hgene | Hchr | Hbp | Henst | Tgene | Tchr | Tbp | Tenst | DeepLoc result |
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Related Drugs to SS18L1-GID8 |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to SS18L1-GID8 |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Disease | Source | PMID |
![]() (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Hgene | SS18L1 | C1862939 | AMYOTROPHIC LATERAL SCLEROSIS 1 | 1 | GENOMICS_ENGLAND |