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Fusion gene ID: 36969 |
FusionGeneSummary for SYT11_HMGB1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: SYT11_HMGB1 | Fusion gene ID: 36969 | Hgene | Tgene | Gene symbol | SYT11 | HMGB1 | Gene ID | 91683 | 3146 |
| Gene name | synaptotagmin 12 | high mobility group box 1 | |
| Synonyms | SYT11|sytXII | HMG-1|HMG1|HMG3|SBP-1 | |
| Cytomap | 11q13.2 | 13q12.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | synaptotagmin-12synaptotagmin-XII | high mobility group protein B1AmphoterinSulfoglucuronyl carbohydrate binding proteinhigh-mobility group (nonhistone chromosomal) protein 1 | |
| Modification date | 20180523 | 20180529 | |
| UniProtAcc | Q9BT88 | P09429 | |
| Ensembl transtripts involved in fusion gene | ENST00000368324, ENST00000539162, | ENST00000405805, ENST00000339872, ENST00000341423, ENST00000399489, ENST00000399494, ENST00000326004, ENST00000468384, | |
| Fusion gene scores | * DoF score | 1 X 1 X 1=1 | 4 X 4 X 1=16 |
| # samples | 1 | 4 | |
| ** MAII score | log2(1/1*10)=3.32192809488736 | log2(4/16*10)=1.32192809488736 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: SYT11 [Title/Abstract] AND HMGB1 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | |||
| * 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 |
| Tgene | HMGB1 | GO:0002218 | activation of innate immune response | 24971542 |
| Tgene | HMGB1 | GO:0002643 | regulation of tolerance induction | 18631454 |
| Tgene | HMGB1 | GO:0006357 | regulation of transcription by RNA polymerase II | 11748232 |
| Tgene | HMGB1 | GO:0006954 | inflammatory response | 23146691 |
| Tgene | HMGB1 | GO:0007204 | positive regulation of cytosolic calcium ion concentration | 22370717 |
| Tgene | HMGB1 | GO:0017055 | negative regulation of RNA polymerase II transcriptional preinitiation complex assembly | 8006019 |
| Tgene | HMGB1 | GO:0032072 | regulation of restriction endodeoxyribonuclease activity | 17803946 |
| Tgene | HMGB1 | GO:0032425 | positive regulation of mismatch repair | 15014079 |
| Tgene | HMGB1 | GO:0032689 | negative regulation of interferon-gamma production | 22473704 |
| Tgene | HMGB1 | GO:0032733 | positive regulation of interleukin-10 production | 22473704 |
| Tgene | HMGB1 | GO:0033151 | V(D)J recombination | 9166431 |
| Tgene | HMGB1 | GO:0035711 | T-helper 1 cell activation | 22473704 |
| Tgene | HMGB1 | GO:0043065 | positive regulation of apoptotic process | 19800306 |
| Tgene | HMGB1 | GO:0043277 | apoptotic cell clearance | 18768881 |
| Tgene | HMGB1 | GO:0043280 | positive regulation of cysteine-type endopeptidase activity involved in apoptotic process | 19800306 |
| Tgene | HMGB1 | GO:0043371 | negative regulation of CD4-positive, alpha-beta T cell differentiation | 22473704 |
| Tgene | HMGB1 | GO:0043388 | positive regulation of DNA binding | 11748232|19223331 |
| Tgene | HMGB1 | GO:0043410 | positive regulation of MAPK cascade | 12765338 |
| Tgene | HMGB1 | GO:0043537 | negative regulation of blood vessel endothelial cell migration | 23148224 |
| Tgene | HMGB1 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 19223331 |
| Tgene | HMGB1 | GO:0046330 | positive regulation of JNK cascade | 12765338 |
| Tgene | HMGB1 | GO:0050716 | positive regulation of interleukin-1 secretion | 12765338 |
| Tgene | HMGB1 | GO:0070374 | positive regulation of ERK1 and ERK2 cascade | 22370717 |
| Tgene | HMGB1 | GO:0090026 | positive regulation of monocyte chemotaxis | 22370717 |
| Tgene | HMGB1 | GO:0097350 | neutrophil clearance | 18768881 |
| Tgene | HMGB1 | GO:1990774 | tumor necrosis factor secretion | 12765338 |
| Tgene | HMGB1 | GO:2000426 | negative regulation of apoptotic cell clearance | 20826760 |
| Tgene | HMGB1 | GO:2000778 | positive regulation of interleukin-6 secretion | 12765338 |
| Fusion gene information from three resources (ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018)) * All genome coordinats were lifted-over on hg19. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| Data type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChiTaRS3.1 | D38522 | SYT11 | chr1 | 155854061 | + | HMGB1 | chr13 | 31110473 | - |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| 3UTR-intron | ENST00000368324 | ENST00000405805 | SYT11 | chr1 | 155854061 | + | HMGB1 | chr13 | 31110473 | - |
| 3UTR-intron | ENST00000368324 | ENST00000339872 | SYT11 | chr1 | 155854061 | + | HMGB1 | chr13 | 31110473 | - |
| 3UTR-intron | ENST00000368324 | ENST00000341423 | SYT11 | chr1 | 155854061 | + | HMGB1 | chr13 | 31110473 | - |
| 3UTR-intron | ENST00000368324 | ENST00000399489 | SYT11 | chr1 | 155854061 | + | HMGB1 | chr13 | 31110473 | - |
| 3UTR-intron | ENST00000368324 | ENST00000399494 | SYT11 | chr1 | 155854061 | + | HMGB1 | chr13 | 31110473 | - |
| 3UTR-intron | ENST00000368324 | ENST00000326004 | SYT11 | chr1 | 155854061 | + | HMGB1 | chr13 | 31110473 | - |
| 3UTR-intron | ENST00000368324 | ENST00000468384 | SYT11 | chr1 | 155854061 | + | HMGB1 | chr13 | 31110473 | - |
| intron-intron | ENST00000539162 | ENST00000405805 | SYT11 | chr1 | 155854061 | + | HMGB1 | chr13 | 31110473 | - |
| intron-intron | ENST00000539162 | ENST00000339872 | SYT11 | chr1 | 155854061 | + | HMGB1 | chr13 | 31110473 | - |
| intron-intron | ENST00000539162 | ENST00000341423 | SYT11 | chr1 | 155854061 | + | HMGB1 | chr13 | 31110473 | - |
| intron-intron | ENST00000539162 | ENST00000399489 | SYT11 | chr1 | 155854061 | + | HMGB1 | chr13 | 31110473 | - |
| intron-intron | ENST00000539162 | ENST00000399494 | SYT11 | chr1 | 155854061 | + | HMGB1 | chr13 | 31110473 | - |
| intron-intron | ENST00000539162 | ENST00000326004 | SYT11 | chr1 | 155854061 | + | HMGB1 | chr13 | 31110473 | - |
| intron-intron | ENST00000539162 | ENST00000468384 | SYT11 | chr1 | 155854061 | + | HMGB1 | chr13 | 31110473 | - |
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FusionProtFeatures for SYT11_HMGB1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| SYT11 | HMGB1 |
| May be involved in Ca(2+)-dependent exocytosis ofsecretory vesicles through Ca(2+) and phospholipid binding to theC2 domain or may serve as Ca(2+) sensors in the process ofvesicular trafficking and exocytosis. {ECO:0000250}. | Multifunctional redox sensitive protein with variousroles in different cellular compartments. In the nucleus is one ofthe major chromatin-associated non-histone proteins and acts as aDNA chaperone involved in replication, transcription, chromatinremodeling, V(D)J recombination, DNA repair and genome stability.Proposed to be an universal biosensor for nucleic acids. Promoteshost inflammatory response to sterile and infectious signals andis involved in the coordination and integration of innate andadaptive immune responses. In the cytoplasm functions as sensorand/or chaperone for immunogenic nucleic acids implicating theactivation of TLR9-mediated immune responses, and mediatesautophagy. Acts as danger associated molecular pattern (DAMP)molecule that amplifies immune responses during tissue injury(PubMed:27362237). Released to the extracellular environment canbind DNA, nucleosomes, IL-1 beta, CXCL12, AGER isoform 2/sRAGE,lipopolysaccharide (LPS) and lipoteichoic acid (LTA), andactivates cells through engagement of multiple surface receptors.In the extracellular compartment fully reduced HMGB1 (released bynecrosis) acts as a chemokine, disulfide HMGB1 (actively secreted)as a cytokine, and sulfonyl HMGB1 (released from apoptotic cells)promotes immunological tolerance (PubMed:23519706,PubMed:23446148, PubMed:23994764, PubMed:25048472). Hasproangiogdenic activity (By similarity). May be involved inplatelet activation (By similarity). Binds to phosphatidylserineand phosphatidylethanolamide (By similarity). Bound to RAGEmediates signaling for neuronal outgrowth (By similarity). Mayplay a role in accumulation of expanded polyglutamine (polyQ)proteins such as huntingtin (HTT) or TBP (PubMed:23303669,PubMed:25549101). {ECO:0000250|UniProtKB:P10103,ECO:0000250|UniProtKB:P12682, ECO:0000250|UniProtKB:P63158,ECO:0000250|UniProtKB:P63159, ECO:0000269|PubMed:23303669,ECO:0000269|PubMed:25549101, ECO:0000269|PubMed:27362237,ECO:0000305|PubMed:23446148, ECO:0000305|PubMed:23519706,ECO:0000305|PubMed:23994764, ECO:0000305|PubMed:25048472}. Nuclear functions are attributed to fully reduced HGMB1.Associates with chromatin and binds DNA with a preference to non-canonical DNA structures such as single-stranded DNA, DNA-containing cruciforms or bent structures, supercoiled DNA andZDNA. Can bent DNA and enhance DNA flexibility by looping thusproviding a mechanism to promote activities on various genepromoters by enhancing transcription factor binding and/orbringing distant regulatory sequences into close proximity(PubMed:20123072). May have an enhancing role in nucleotideexcision repair (NER) (By similarity). However, effects in NERusing in vitro systems have been reported conflictingly(PubMed:19446504, PubMed:19360789). May be involved in mismatchrepair (MMR) and base excision repair (BER) pathways(PubMed:15014079, PubMed:16143102, PubMed:17803946). May beinvolved in double strand break repair such as non-homologous endjoining (NHEJ) (By similarity). Involved in V(D)J recombination byacting as a cofactor of the RAG complex: acts by stimulatingcleavage and RAG protein binding at the 23 bp spacer of conservedrecombination signal sequences (RSS) (By similarity). In vitro candisplace histone H1 from highly bent DNA (By similarity). Canrestructure the canonical nucleosome leading to relaxation ofstructural constraints for transcription factor-binding (Bysimilarity). Enhances binding of sterol regulatory element-bindingproteins (SREBPs) such as SREBF1 to their cognate DNA sequencesand increases their transcriptional activities (By similarity).Facilitates binding of TP53 to DNA (PubMed:23063560). Proposed tobe involved in mitochondrial quality control and autophagy in atranscription-dependent fashion implicating HSPB1; however, thisfunction has been questioned (By similarity). Can modulate theactivity of the telomerase complex and may be involved in telomeremaintenance (By similarity). {ECO:0000250|UniProtKB:P10103,ECO:0000250|UniProtKB:P63158, ECO:0000250|UniProtKB:P63159,ECO:0000269|PubMed:15014079, ECO:0000269|PubMed:16143102,ECO:0000269|PubMed:17803946, ECO:0000269|PubMed:19446504,ECO:0000269|PubMed:23063560, ECO:0000305|PubMed:19360789,ECO:0000305|PubMed:20123072}. In the cytoplasm proposed to dissociate the BECN1:BCL2complex via competitive interaction with BECN1 leading toautophagy activation (PubMed:20819940). Involved in oxidativestress-mediated autophagy (PubMed:21395369). Can protect BECN1 andATG5 from calpain-mediated cleavage and thus proposed to controltheir proautophagic and proapoptotic functions and to regulate theextent and severity of inflammation-associated cellular injury (Bysimilarity). In myeloid cells has a protective role againstendotoxemia and bacterial infection by promoting autophagy (Bysimilarity). Involved in endosomal translocation and activation ofTLR9 in response to CpG-DNA in macrophages (By similarity).{ECO:0000250|UniProtKB:P63158, ECO:0000269|PubMed:20819940,ECO:0000269|PubMed:21395369}. In the extracellular compartment (following eitheractive secretion or passive release) involved in regulation of theinflammatory response. Fully reduced HGMB1 (which subsequentlygets oxidized after release) in association with CXCL12 mediatesthe recruitment of inflammatory cells during the initial phase oftissue injury; the CXCL12:HMGB1 complex triggers CXCR4homodimerization (PubMed:22370717). Induces the migration ofmonocyte-derived immature dendritic cells and seems to regulateadhesive and migratory functions of neutrophils implicatingAGER/RAGE and ITGAM (By similarity). Can bind to various types ofDNA and RNA including microbial unmethylated CpG-DNA to enhancethe innate immune response to nucleic acids. Proposed to act inpromiscuous DNA/RNA sensing which cooperates with subsequentdiscriminative sensing by specific pattern recognition receptors(By similarity). Promotes extracellular DNA-induced AIM2inflammasome activation implicating AGER/RAGE (PubMed:24971542).Disulfide HMGB1 binds to transmembrane receptors, such asAGER/RAGE, TLR2, TLR4 and probably TREM1, thus activating theirsignal transduction pathways. Mediates the release ofcytokines/chemokines such as TNF, IL-1, IL-6, IL-8, CCL2, CCL3,CCL4 and CXCL10 (PubMed:12765338, PubMed:18354232,PubMed:19264983, PubMed:20547845, PubMed:24474694). Promotessecretion of interferon-gamma by macrophage-stimulated naturalkiller (NK) cells in concert with other cytokines like IL-2 or IL-12 (PubMed:15607795). TLR4 is proposed to be the primary receptorpromoting macrophage activation and signaling through TLR4 seemsto implicate LY96/MD-2 (PubMed:20547845). In bacterial LPS- orLTA-mediated inflammatory responses binds to the endotoxins andtransfers them to CD14 for signaling to the respective TLR4:LY96and TLR2 complexes (PubMed:18354232, PubMed:21660935,PubMed:25660311). Contributes to tumor proliferation byassociation with ACER/RAGE (By similarity). Can bind to IL1-betaand signals through the IL1R1:IL1RAP receptor complex(PubMed:18250463). Binding to class A CpG activates cytokineproduction in plasmacytoid dendritic cells implicating TLR9, MYD88and AGER/RAGE and can activate autoreactive B cells. Via HMGB1-containing chromatin immune complexes may also promote B cellresponses to endogenous TLR9 ligands through a B-cell receptor(BCR)-dependent and ACER/RAGE-independent mechanism (Bysimilarity). Inhibits phagocytosis of apoptotic cells bymacrophages; the function is dependent on poly-ADP-ribosylationand involves binding to phosphatidylserine on the cell surface ofapoptotic cells (By similarity). In adaptive immunity may beinvolved in enhancing immunity through activation of effector Tcells and suppression of regulatory T (TReg) cells(PubMed:15944249, PubMed:22473704). In contrast, withoutimplicating effector or regulatory T-cells, required for tumorinfiltration and activation of T-cells expressing the lymphotoxinLTA:LTB heterotrimer thus promoting tumor malignant progression(By similarity). Also reported to limit proliferation of T-cells(By similarity). Released HMGB1:nucleosome complexes formed duringapoptosis can signal through TLR2 to induce cytokine production(PubMed:19064698). Involved in induction of immunologicaltolerance by apoptotic cells; its pro-inflammatory activities whenreleased by apoptotic cells are neutralized by reactive oxygenspecies (ROS)-dependent oxidation specifically on Cys-106(PubMed:18631454). During macrophage activation by activatedlymphocyte-derived self apoptotic DNA (ALD-DNA) promotesrecruitment of ALD-DNA to endosomes (By similarity).{ECO:0000250|UniProtKB:P10103, ECO:0000250|UniProtKB:P63158,ECO:0000250|UniProtKB:P63159, ECO:0000269|PubMed:12765338,ECO:0000269|PubMed:15607795, ECO:0000269|PubMed:15944249,ECO:0000269|PubMed:18250463, ECO:0000269|PubMed:18354232,ECO:0000269|PubMed:18631454, ECO:0000269|PubMed:19064698,ECO:0000269|PubMed:19264983, ECO:0000269|PubMed:20547845,ECO:0000269|PubMed:21660935, ECO:0000269|PubMed:22370717,ECO:0000269|PubMed:22473704, ECO:0000269|PubMed:24474694,ECO:0000269|PubMed:24971542, ECO:0000269|PubMed:25660311,ECO:0000269|Ref.8}. |
| 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, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at . * Minus value of BPloci means that the break pointn is located before the CDS. |
| - In-frame and retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| - In-frame and not-retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
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FusionGeneSequence for SYT11_HMGB1 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. (nt: nucleotides, aa: amino acids) |
| * Fusion amino acid sequences. |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| * Fusion transcript sequences (Full-length transcript). |
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FusionGenePPI for SYT11_HMGB1 |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in . |
| Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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RelatedDrugs for SYT11_HMGB1 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for SYT11_HMGB1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | SYT11 | C0036341 | Schizophrenia | 1 | PSYGENET |
| Tgene | HMGB1 | C0021368 | Inflammation | 5 | CTD_human |
| Tgene | HMGB1 | C0027540 | Necrosis | 2 | CTD_human |
| Tgene | HMGB1 | C0243026 | Sepsis | 2 | CTD_human |
| Tgene | HMGB1 | C0001973 | Alcoholic Intoxication, Chronic | 1 | PSYGENET |
| Tgene | HMGB1 | C0015967 | Fever | 1 | CTD_human |
| Tgene | HMGB1 | C0020429 | Hyperalgesia | 1 | CTD_human |
| Tgene | HMGB1 | C0026766 | Multiple Organ Failure | 1 | CTD_human |
| Tgene | HMGB1 | C0027051 | Myocardial Infarction | 1 | CTD_human |
| Tgene | HMGB1 | C0027055 | Myocardial Reperfusion Injury | 1 | CTD_human |
| Tgene | HMGB1 | C0027796 | Neuralgia | 1 | CTD_human |
| Tgene | HMGB1 | C0034069 | Pulmonary Fibrosis | 1 | CTD_human |
| Tgene | HMGB1 | C0041755 | Adverse reaction to drug | 1 | CTD_human |
| Tgene | HMGB1 | C0151744 | Myocardial Ischemia | 1 | CTD_human |
| Tgene | HMGB1 | C0264939 | Systemic Vasculitis | 1 | CTD_human |
| Tgene | HMGB1 | C0279626 | Squamous cell carcinoma of esophagus | 1 | CTD_human |
| Tgene | HMGB1 | C1850383 | Neuropathy, Painful | 1 | CTD_human |
| Tgene | HMGB1 | C4277682 | Chemical and Drug Induced Liver Injury | 1 | CTD_human |
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