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Fusion Protein:IL6ST-SKIV2L2 |
Fusion Gene and Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: IL6ST-SKIV2L2 | FusionPDB ID: 39593 | FusionGDB2.0 ID: 39593 | Hgene | Tgene | Gene symbol | IL6ST | SKIV2L2 | Gene ID | 3572 | 23517 |
| Gene name | interleukin 6 signal transducer | Mtr4 exosome RNA helicase | |
| Synonyms | CD130|CDW130|GP130|HIES4|IL-6RB|sGP130 | Dob1|KIAA0052|Mtr4|SKIV2L2|fSAP118 | |
| Cytomap | 5q11.2 | 5q11.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | interleukin-6 receptor subunit betaCD130 antigenIL-6 receptor subunit betaIL-6R subunit betagp130 of the rheumatoid arthritis antigenic peptide-bearing soluble formgp130, oncostatin M receptorinterleukin receptor beta chainmembrane glycoprotein 130 | exosome RNA helicase MTR4ATP-dependent RNA helicase DOB1ATP-dependent RNA helicase SKIV2L2ATP-dependent helicase SKIV2L2Ski2 like RNA helicase 2TRAMP-like complex helicasefunctional spliceosome-associated protein 118superkiller viralicidic activity | |
| Modification date | 20200327 | 20200313 | |
| UniProtAcc | P40189 Main function of 5'-partner protein: FUNCTION: Signal-transducing molecule (PubMed:2261637). The receptor systems for IL6, LIF, OSM, CNTF, IL11, CTF1 and BSF3 can utilize IL6ST for initiating signal transmission. Binding of IL6 to IL6R induces IL6ST homodimerization and formation of a high-affinity receptor complex, which activate the intracellular JAK-MAPK and JAK-STAT3 signaling pathways (PubMed:2261637, PubMed:19915009, PubMed:23294003). That causes phosphorylation of IL6ST tyrosine residues which in turn activates STAT3 (PubMed:19915009, PubMed:23294003, PubMed:25731159). In parallel, the IL6 signaling pathway induces the expression of two cytokine receptor signaling inhibitors, SOCS1 and SOCS3, which inhibit JAK and terminate the activity of the IL6 signaling pathway as a negative feedback loop (By similarity). Also activates the yes-associated protein 1 (YAP) and NOTCH pathways to control inflammation-induced epithelial regeneration, independently of STAT3 (By similarity). Mediates signals which regulate immune response, hematopoiesis, pain control and bone metabolism (By similarity). Has a role in embryonic development (By similarity). Essential for survival of motor and sensory neurons and for differentiation of astrocytes (By similarity). Required for expression of TRPA1 in nociceptive neurons (By similarity). Required for the maintenance of PTH1R expression in the osteoblast lineage and for the stimulation of PTH-induced osteoblast differentiation (By similarity). Required for normal trabecular bone mass and cortical bone composition (By similarity). {ECO:0000250|UniProtKB:Q00560, ECO:0000269|PubMed:19915009, ECO:0000269|PubMed:2261637, ECO:0000269|PubMed:23294003, ECO:0000269|PubMed:25731159, ECO:0000269|PubMed:28747427, ECO:0000269|PubMed:30309848}.; FUNCTION: [Isoform 2]: Binds to the soluble IL6:sIL6R complex (hyper-IL6), thereby blocking IL6 trans-signaling. Inhibits sIL6R-dependent acute phase response (PubMed:11121117, PubMed:21990364, PubMed:30279168). Also blocks IL11 cluster signaling through IL11R (PubMed:30279168). {ECO:0000269|PubMed:11121117, ECO:0000269|PubMed:21990364, ECO:0000269|PubMed:30279168}. | . | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000381287, ENST00000522633, ENST00000536319, ENST00000336909, ENST00000381294, ENST00000381298, ENST00000502326, ENST00000381286, ENST00000381293, ENST00000396816, ENST00000577363, | ENST00000230640, ENST00000545714, ENST00000504388, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 16 X 11 X 5=880 | 9 X 8 X 7=504 |
| # samples | 19 | 9 | |
| ** MAII score | log2(19/880*10)=-2.21150410519371 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(9/504*10)=-2.48542682717024 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Fusion gene context | PubMed: IL6ST [Title/Abstract] AND SKIV2L2 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Fusion neoantigen context | PubMed: IL6ST [Title/Abstract] AND SKIV2L2 [Title/Abstract] AND neoantigen [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | IL6ST(55251853)-SKIV2L2(54639159), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | IL6ST-SKIV2L2 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. IL6ST-SKIV2L2 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. IL6ST-SKIV2L2 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. IL6ST-SKIV2L2 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. IL6ST-SKIV2L2 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF. IL6ST-SKIV2L2 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. IL6ST-SKIV2L2 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF. | ||
| * DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Hgene | IL6ST | GO:0008284 | positive regulation of cell proliferation | 2261637 |
| Hgene | IL6ST | GO:0019221 | cytokine-mediated signaling pathway | 2261637 |
| Hgene | IL6ST | GO:0034097 | response to cytokine | 2261637|8999038 |
| Hgene | IL6ST | GO:0048861 | leukemia inhibitory factor signaling pathway | 8999038|12643274 |
| Hgene | IL6ST | GO:0070120 | ciliary neurotrophic factor-mediated signaling pathway | 12643274 |
| Tgene | SKIV2L2 | GO:0006401 | RNA catabolic process | 29906447 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr5:55251853/chr5:54639159) - 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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| Retention analysis results of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features, are available here. |
| Fusion gene breakpoints across IL6ST (5'-gene) * 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 gene breakpoints across SKIV2L2 (3'-gene) * 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 |
| Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB. |
| 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) |
| ENST00000381298 | IL6ST | chr5 | 55251853 | - | ENST00000230640 | SKIV2L2 | chr5 | 54639159 | + | 4737 | 1580 | 313 | 3927 | 1204 |
| ENST00000381298 | IL6ST | chr5 | 55251853 | - | ENST00000545714 | SKIV2L2 | chr5 | 54639159 | + | 4262 | 1580 | 313 | 3927 | 1204 |
| ENST00000336909 | IL6ST | chr5 | 55251853 | - | ENST00000230640 | SKIV2L2 | chr5 | 54639159 | + | 4460 | 1303 | 6 | 3650 | 1214 |
| ENST00000336909 | IL6ST | chr5 | 55251853 | - | ENST00000545714 | SKIV2L2 | chr5 | 54639159 | + | 3985 | 1303 | 6 | 3650 | 1214 |
| ENST00000381294 | IL6ST | chr5 | 55251853 | - | ENST00000230640 | SKIV2L2 | chr5 | 54639159 | + | 4424 | 1267 | 0 | 3614 | 1204 |
| ENST00000381294 | IL6ST | chr5 | 55251853 | - | ENST00000545714 | SKIV2L2 | chr5 | 54639159 | + | 3949 | 1267 | 0 | 3614 | 1204 |
| DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
| ENST00000381298 | ENST00000230640 | IL6ST | chr5 | 55251853 | - | SKIV2L2 | chr5 | 54639159 | + | 0.000180576 | 0.99981946 |
| ENST00000381298 | ENST00000545714 | IL6ST | chr5 | 55251853 | - | SKIV2L2 | chr5 | 54639159 | + | 0.000209841 | 0.99979013 |
| ENST00000336909 | ENST00000230640 | IL6ST | chr5 | 55251853 | - | SKIV2L2 | chr5 | 54639159 | + | 0.000137086 | 0.9998629 |
| ENST00000336909 | ENST00000545714 | IL6ST | chr5 | 55251853 | - | SKIV2L2 | chr5 | 54639159 | + | 0.000161607 | 0.99983835 |
| ENST00000381294 | ENST00000230640 | IL6ST | chr5 | 55251853 | - | SKIV2L2 | chr5 | 54639159 | + | 0.000138184 | 0.99986184 |
| ENST00000381294 | ENST00000545714 | IL6ST | chr5 | 55251853 | - | SKIV2L2 | chr5 | 54639159 | + | 0.00016175 | 0.99983823 |
| Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones. |
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 IL6ST-SKIV2L2 |
| +/-13 AA sequence from the breakpoints of the fusion protein sequences. |
| Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
| IL6ST | chr5 | 55251853 | SKIV2L2 | chr5 | 54639159 | 1267 | 420 | KSDAAVLTIPACDFQERGVVWEETII |
| IL6ST | chr5 | 55251853 | SKIV2L2 | chr5 | 54639159 | 1303 | 430 | KSDAAVLTIPACDFQERGVVWEETII |
| IL6ST | chr5 | 55251853 | SKIV2L2 | chr5 | 54639159 | 1580 | 420 | KSDAAVLTIPACDFQERGVVWEETII |
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Potential FusionNeoAntigen Information of IL6ST-SKIV2L2 in HLA I |
| Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific. |
| IL6ST-SKIV2L2_55251853_54639159.msa |
| Potential FusionNeoAntigen Information * 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) |
| IL6ST-SKIV2L2 | chr5 | 55251853 | chr5 | 54639159 | 1303 | HLA-B15:13 | DFQERGVVW | 0.5256 | 0.9854 | 12 | 21 |
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Potential FusionNeoAntigen Information of IL6ST-SKIV2L2 in HLA II |
| Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific. |
| Potential FusionNeoAntigen Information * 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 IL6ST-SKIV2L2 |
| 3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens * 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. |
| File name | BPseq | Hgene | Tgene | Hchr | Hbp | Tchr | Tbp | AAlen |
| 5702 | LTIPACDFQERGVV | IL6ST | SKIV2L2 | chr5 | 55251853 | chr5 | 54639159 | 1303 |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of IL6ST-SKIV2L2 |
| Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens * We used Glide to predict the interaction between HLAs and neoantigens. |
| HLA allele | PDB ID | File name | BPseq | Docking score | Glide score |
| HLA-B14:02 | 3BVN | 5702 | LTIPACDFQERGVV | -7.15543 | -7.26883 |
| HLA-B14:02 | 3BVN | 5702 | LTIPACDFQERGVV | -4.77435 | -5.80965 |
| HLA-B52:01 | 3W39 | 5702 | LTIPACDFQERGVV | -6.80875 | -6.92215 |
| HLA-B52:01 | 3W39 | 5702 | LTIPACDFQERGVV | -4.20386 | -5.23916 |
| HLA-A11:01 | 4UQ2 | 5702 | LTIPACDFQERGVV | -7.5194 | -8.5547 |
| HLA-A11:01 | 4UQ2 | 5702 | LTIPACDFQERGVV | -6.9601 | -7.0735 |
| HLA-A24:02 | 5HGA | 5702 | LTIPACDFQERGVV | -7.52403 | -7.63743 |
| HLA-A24:02 | 5HGA | 5702 | LTIPACDFQERGVV | -5.82433 | -6.85963 |
| HLA-B27:05 | 6PYJ | 5702 | LTIPACDFQERGVV | -3.28285 | -4.31815 |
| HLA-B44:05 | 3DX8 | 5702 | LTIPACDFQERGVV | -5.91172 | -6.94702 |
| HLA-B44:05 | 3DX8 | 5702 | LTIPACDFQERGVV | -4.24346 | -4.35686 |
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Vaccine Design for the FusionNeoAntigens of IL6ST-SKIV2L2 |
| mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is. |
| Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
| IL6ST-SKIV2L2 | chr5 | 55251853 | chr5 | 54639159 | 12 | 21 | DFQERGVVW | AAGAACGTGGTGTAGTATGGGAAGAAA |
| mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs. |
| 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 IL6ST-SKIV2L2 |
| These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens. |
| Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
| BRCA | IL6ST-SKIV2L2 | chr5 | 55251853 | ENST00000336909 | chr5 | 54639159 | ENST00000230640 | TCGA-AR-A0TZ-01A |
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Potential target of CAR-T therapy development for IL6ST-SKIV2L2 |
| Predicted 3D structure. We used RoseTTAFold. |
| Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features * 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 |
| Hgene | IL6ST | chr5:55251853 | chr5:54639159 | ENST00000522633 | - | 8 | 13 | 620_641 | 394 | 299.3333333333333 | Transmembrane | Helical |
| Subcellular localization prediction of the transmembrane domain retained fusion proteins * 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 IL6ST-SKIV2L2 |
| Drugs used for this fusion-positive patient. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to IL6ST-SKIV2L2 |
| Diseases that have this fusion gene. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Disease | Source | PMID |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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