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Kinase Fusion Gene:TOPBP1_NEK11 |
Kinase Fusion Protein Summary |
 Kinase Fusion gene summary |
| Kinase Fusion partner gene information | Kinase Fusion gene name: TOPBP1_NEK11 | KinaseFusionDB ID: KFG6686 | FusionGDB2.0 ID: KFG6686 | Hgene | Tgene | Gene symbol | TOPBP1 | NEK11 | Gene ID | 11073 | 79858 | |
| Gene name | DNA topoisomerase II binding protein 1 | NIMA related kinase 11 | ||||||||||
| Synonyms | Dpb11|TOP2BP1 | - | ||||||||||
| Cytomap | 3q22.1 | 3q22.1 | ||||||||||
| Type of gene | protein-coding | protein-coding | ||||||||||
| Description | DNA topoisomerase 2-binding protein 1DNA topoisomerase II-beta-binding protein 1topoisomerase (DNA) II binding protein 1 | serine/threonine-protein kinase Nek11NIMA (never in mitosis gene a)- related kinase 11 | ||||||||||
| Modification date | 20240411 | 20240403 | ||||||||||
| UniProtAcc | Q92547 | Q8NG66 | ||||||||||
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000260810, ENST00000511439, | ENST00000356918, ENST00000383366, ENST00000412440, ENST00000426022, ENST00000429253, ENST00000507910, ENST00000508196, ENST00000510688, ENST00000510769, ENST00000511262, | |||||||||
| Context (manual curation of fusion genes in KinaseFusionDB) | PubMed: TOPBP1 [Title/Abstract] AND NEK11 [Title/Abstract] AND fusion [Title/Abstract] | |||||||||||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | TOPBP1(133356720)-NEK11(131068401), # samples:3 | |||||||||||
| 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 | TOPBP1 | GO:0000076 | DNA replication checkpoint signaling | 21482717|21777809 |
| Hgene | TOPBP1 | GO:0000077 | DNA damage checkpoint signaling | 17575048|21777809|31135337 |
| Hgene | TOPBP1 | GO:0000724 | double-strand break repair via homologous recombination | 26811421|35597237 |
| Hgene | TOPBP1 | GO:0006974 | DNA damage response | 12773567|30898438|35842428|37165191|37316668 |
| Hgene | TOPBP1 | GO:0010212 | response to ionizing radiation | 12773567 |
| Hgene | TOPBP1 | GO:0051276 | chromosome organization | 35121901|35842428|37165191|37316668 |
| Hgene | TOPBP1 | GO:0097680 | double-strand break repair via classical nonhomologous end joining | 31135337 |
| Hgene | TOPBP1 | GO:0097681 | double-strand break repair via alternative nonhomologous end joining | 37674080 |
| Hgene | TOPBP1 | GO:0141112 | broken chromosome clustering | 37165191|37316668 |
| Hgene | TOPBP1 | GO:1990166 | protein localization to site of double-strand break | 26811421|37674080 |
| Tgene | NEK11 | GO:0006468 | protein phosphorylation | 15161910|19734889 |
| Tgene | NEK11 | GO:0031573 | mitotic intra-S DNA damage checkpoint signaling | 15161910 |
| Tgene | NEK11 | GO:0035556 | intracellular signal transduction | 15161910 |
| Kinase Fusion gene breakpoints across TOPBP1 (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Kinase Fusion gene breakpoints across NEK11 (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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Kinase Fusion Gene Sample Information |
| Kinase Fusion gene information. |
| Kinase Fusion gene information from four resources (ChiTars 5.0, ChimerDB 4.0, COSMIC, and CCLE) * 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. |
| Source | Sample | Hgene | Hchr | Hbp | Tgene | Tchr | Tbp |
| ChimerDB4 | TCGA-A8-A06U-01A | TOPBP1 | chr3 | 133356720 | NEK11 | chr3 | 131068401 |
| ChimerDB4 | TCGA-A8-A06U | TOPBP1 | chr3 | 133356719 | NEK11 | chr3 | 131068400 |
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Kinase Fusion ORF Analysis |
| Kinase Fusion information from ORFfinder translation from full-length transcript sequence from KinaseFusionDB. |
| Henst | Tenst | Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Seq length (transcript) | Seq length (amino acids) |
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Kinase Fusion Amino Acid Sequences |
| For individual full-length fusion transcript sequence from KinaseFusionDB, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
| >Henst_Tenst_Hgene_Hchr_Hbp_Tgene_Tchr_Tbp_length(fusion AA)_AAseq |
Multiple Sequence Alignment of All Fusion Protein Isoforms |
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Kinase Fusion Protein Functional Features |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:133356720/:131068401) - 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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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| TOPBP1 | NEK11 |
| FUNCTION: Scaffold protein that acts as a key protein-protein adapter in DNA replication and DNA repair (PubMed:10498869, PubMed:11395493, PubMed:11714696, PubMed:17575048, PubMed:20545769, PubMed:21777809, PubMed:26811421, PubMed:30898438, PubMed:33592542, PubMed:35597237, PubMed:37674080, PubMed:31135337). Composed of multiple BRCT domains, which specifically recognize and bind phosphorylated proteins, bringing proteins together into functional combinations (PubMed:17575048, PubMed:20545769, PubMed:21777809, PubMed:26811421, PubMed:30898438, PubMed:35597237, PubMed:37674080, PubMed:31135337). Required for DNA replication initiation but not for the formation of pre-replicative complexes or the elongation stages (By similarity). Necessary for the loading of replication factors onto chromatin, including GMNC, CDC45, DNA polymerases and components of the GINS complex (By similarity). Plays a central role in DNA repair by bridging proteins and promoting recruitment of proteins to DNA damage sites (PubMed:30898438, PubMed:35597237, PubMed:37674080). Involved in double-strand break (DSB) repair via homologous recombination in S-phase by promoting the exchange between the DNA replication factor A (RPA) complex and RAD51 (PubMed:26811421, PubMed:35597237). Mechanistically, TOPBP1 is recruited to DNA damage sites in S-phase via interaction with phosphorylated HTATSF1, and promotes the loading of RAD51, thereby facilitating RAD51 nucleofilaments formation and RPA displacement, followed by homologous recombination (PubMed:35597237). Involved in microhomology-mediated end-joining (MMEJ) DNA repair by promoting recruitment of polymerase theta (POLQ) to DNA damage sites during mitosis (PubMed:37674080). MMEJ is an alternative non-homologous end-joining (NHEJ) machinery that takes place during mitosis to repair DSBs in DNA that originate in S-phase (PubMed:37674080). Recognizes and binds POLQ phosphorylated by PLK1, enabling its recruitment to DSBs for subsequent repair (PubMed:37674080). Involved in G1 DNA damage checkpoint by acting as a molecular adapter that couples TP53BP1 and the 9-1-1 complex (PubMed:31135337). In response to DNA damage, triggers the recruitment of checkpoint signaling proteins on chromatin, which activate the CHEK1 signaling pathway and block S-phase progression (PubMed:16530042, PubMed:21777809). Acts as an activator of the kinase activity of ATR (PubMed:16530042, PubMed:21777809). Also required for chromosomal stability when DSBs occur during mitosis by forming filamentous assemblies that bridge MDC1 and tether broken chromosomes during mitosis (PubMed:30898438). Together with CIP2A, plays an essential role in the response to genome instability generated by the presence of acentric chromosome fragments derived from shattered chromosomes within micronuclei (PubMed:35121901, PubMed:35842428, PubMed:37165191, PubMed:37316668). Micronuclei, which are frequently found in cancer cells, consist of chromatin surrounded by their own nuclear membrane: following breakdown of the micronuclear envelope, a process associated with chromothripsis, the CIP2A-TOPBP1 complex tethers chromosome fragments during mitosis to ensure clustered segregation of the fragments to a single daughter cell nucleus, facilitating re-ligation with limited chromosome scattering and loss (PubMed:37165191, PubMed:37316668). Recruits the SWI/SNF chromatin remodeling complex to E2F1-responsive promoters, thereby down-regulating E2F1 activity and inhibiting E2F1-dependent apoptosis during G1/S transition and after DNA damage (PubMed:12697828, PubMed:15075294). {ECO:0000250|UniProtKB:Q800K6, ECO:0000269|PubMed:10498869, ECO:0000269|PubMed:11395493, ECO:0000269|PubMed:11714696, ECO:0000269|PubMed:12697828, ECO:0000269|PubMed:15075294, ECO:0000269|PubMed:16530042, ECO:0000269|PubMed:17575048, ECO:0000269|PubMed:20545769, ECO:0000269|PubMed:21777809, ECO:0000269|PubMed:26811421, ECO:0000269|PubMed:30898438, ECO:0000269|PubMed:31135337, ECO:0000269|PubMed:33592542, ECO:0000269|PubMed:35121901, ECO:0000269|PubMed:35597237, ECO:0000269|PubMed:35842428, ECO:0000269|PubMed:37165191, ECO:0000269|PubMed:37316668, ECO:0000269|PubMed:37674080}. | FUNCTION: Protein kinase which plays an important role in the G2/M checkpoint response to DNA damage. Controls degradation of CDC25A by directly phosphorylating it on residues whose phosphorylation is required for BTRC-mediated polyubiquitination and degradation. {ECO:0000269|PubMed:12154088, ECO:0000269|PubMed:19734889, ECO:0000269|PubMed:20090422}. |
| 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. |
| - Retained domain in the 5'-partner of fusion protein (protein functional feature from UniProt). |
| Partner | Hgeneene | Hbp | Tgeneene | Tbp | ENST | BPexon | TotalExon | Protein feature loci | BPloci | TotalLen | Feature | Note |
| - Retained domain in the 3'-partner of fusion protein (protein functional feature from UniProt). |
| Partner | Hgeneene | Hbp | Tgeneene | Tbp | ENST | BPexon | TotalExon | Protein feature loci | BPloci | TotalLen | Feature | Note |
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Kinase-Substrate Information of TOPBP1_NEK11 |
| Phosphorylation target of the kinase (phosphosite, 03-17-2024) |
| Kinase | Kinase UniProt Acc | Kinase species | Substrate | Substrate UniProt Acc | Substrate phosphorylated residues | Substrate phosphorylated sites (+/-7AA) | Domain |
| NEK11 | Q8NG66 | human | CDC25A | P30304 | S82 | GssEstDsGFCLDsP | |
| NEK11 | Q8NG66 | human | BLM | P54132 | S338 | kEDVLSTskDLLskP | BLM_N |
| NEK11 | Q8NG66 | human | CDC25A | P30304 | S88 | DsGFCLDsPGPLDSK | M-inducer_phosp |
| NEK11 | Q8NG66 | human | CDC25A | P30304 | S79 | QRMGssEstDsGFCL |
| Biological Network Integration of This Kinase and Substrates (GeneMANIA website) |
| Enriched GO biological processes of the phosphorylation target genes of the kinase |
| Kinase | GOID | GO term | P.adjust |
| NEK11 | ID | Description | 0.00e+00 |
| NEK11 | GO:0000079 | regulation of cyclin-dependent protein serine/threonine kinase activity | 8.62e-04 |
| NEK11 | GO:1904029 | regulation of cyclin-dependent protein kinase activity | 8.62e-04 |
| NEK11 | GO:0010389 | regulation of G2/M transition of mitotic cell cycle | 8.62e-04 |
| NEK11 | GO:1902749 | regulation of cell cycle G2/M phase transition | 8.62e-04 |
| NEK11 | GO:0000086 | G2/M transition of mitotic cell cycle | 1.01e-03 |
| NEK11 | GO:0044839 | cell cycle G2/M phase transition | 1.03e-03 |
| NEK11 | GO:0071478 | cellular response to radiation | 1.20e-03 |
| NEK11 | GO:0071900 | regulation of protein serine/threonine kinase activity | 2.61e-03 |
| NEK11 | GO:0071214 | cellular response to abiotic stimulus | 2.87e-03 |
| NEK11 | GO:0104004 | cellular response to environmental stimulus | 2.87e-03 |
| NEK11 | GO:1901990 | regulation of mitotic cell cycle phase transition | 2.95e-03 |
| NEK11 | GO:0009314 | response to radiation | 3.94e-03 |
| NEK11 | GO:1901987 | regulation of cell cycle phase transition | 4.07e-03 |
| NEK11 | GO:0044772 | mitotic cell cycle phase transition | 4.07e-03 |
| NEK11 | GO:1901993 | regulation of meiotic cell cycle phase transition | 6.31e-03 |
| NEK11 | GO:0072711 | cellular response to hydroxyurea | 6.31e-03 |
| NEK11 | GO:0090657 | telomeric loop disassembly | 6.31e-03 |
| NEK11 | GO:0072710 | response to hydroxyurea | 6.50e-03 |
| NEK11 | GO:0044771 | meiotic cell cycle phase transition | 6.65e-03 |
| NEK11 | GO:0001325 | formation of extrachromosomal circular DNA | 6.65e-03 |
| NEK11 | GO:0090656 | t-circle formation | 6.65e-03 |
| NEK11 | GO:0090737 | telomere maintenance via telomere trimming | 6.65e-03 |
| NEK11 | GO:0051782 | negative regulation of cell division | 7.20e-03 |
| NEK11 | GO:0000729 | DNA double-strand break processing | 8.19e-03 |
| NEK11 | GO:0006268 | DNA unwinding involved in DNA replication | 8.19e-03 |
| NEK11 | GO:0051446 | positive regulation of meiotic cell cycle | 1.01e-02 |
| NEK11 | GO:0010165 | response to X-ray | 1.01e-02 |
| NEK11 | GO:0010971 | positive regulation of G2/M transition of mitotic cell cycle | 1.01e-02 |
| NEK11 | GO:1902751 | positive regulation of cell cycle G2/M phase transition | 1.08e-02 |
| NEK11 | GO:0007095 | mitotic G2 DNA damage checkpoint signaling | 1.16e-02 |
| NEK11 | GO:0071312 | cellular response to alkaloid | 1.16e-02 |
| NEK11 | GO:0033260 | nuclear DNA replication | 1.22e-02 |
| NEK11 | GO:0044786 | cell cycle DNA replication | 1.30e-02 |
| NEK11 | GO:0090329 | regulation of DNA-templated DNA replication | 1.35e-02 |
| NEK11 | GO:0031297 | replication fork processing | 1.35e-02 |
| NEK11 | GO:0045910 | negative regulation of DNA recombination | 1.35e-02 |
| NEK11 | GO:0044818 | mitotic G2/M transition checkpoint | 1.39e-02 |
| NEK11 | GO:0045005 | DNA-templated DNA replication maintenance of fidelity | 1.43e-02 |
| NEK11 | GO:0051445 | regulation of meiotic cell cycle | 1.62e-02 |
| NEK11 | GO:0010972 | negative regulation of G2/M transition of mitotic cell cycle | 1.62e-02 |
| NEK11 | GO:0071479 | cellular response to ionizing radiation | 1.62e-02 |
| NEK11 | GO:1902750 | negative regulation of cell cycle G2/M phase transition | 1.62e-02 |
| NEK11 | GO:0032508 | DNA duplex unwinding | 1.79e-02 |
| NEK11 | GO:0044773 | mitotic DNA damage checkpoint signaling | 1.80e-02 |
| NEK11 | GO:0032392 | DNA geometric change | 1.80e-02 |
| NEK11 | GO:2000243 | positive regulation of reproductive process | 1.80e-02 |
| NEK11 | GO:0044774 | mitotic DNA integrity checkpoint signaling | 1.80e-02 |
| NEK11 | GO:0034644 | cellular response to UV | 1.81e-02 |
| NEK11 | GO:0071103 | DNA conformation change | 1.81e-02 |
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Related Drugs to TOPBP1_NEK11 |
| Drugs used for this fusion-positive patient. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Drug | Source | PMID |
| Distribution of the number of studies mentioning TOPBP1-NEK11 and kinase inhibitors the PubMed Abstract (04-01-2024) |
| Fusion gene - drug pair 1 | Fusion gene - drug pair 2 | PMID | Publication date | DOI | Study title |
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Related Diseases to TOPBP1_NEK11 |
| Diseases that have this fusion gene. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Disease | Source | PMID |
| Related diseases from the literature mentioned this fusion gene and drug. (PubMed, 04-01-2024) |
| MeSH ID | MeSH term |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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Clinical Trials of the Found Drugs/Small Molecules |
| Statistics of the Clinical Trials of the Found Kinase Inibitors from clinicaltrials.gov (06-17-2024) |
| Clinical Trials from clinicaltrials.gov (06-17-2024) |
| Fusion Gene | Kinase Inhibitor | NCT ID | Study Status | Phases | Disease | # Enrolment | Date |
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