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Fusion Protein:NIPBL-FGF10 |
Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: NIPBL-FGF10 | FusionPDB ID: 59197 | FusionGDB2.0 ID: 59197 | Hgene | Tgene | Gene symbol | NIPBL | FGF10 | Gene ID | 25836 | 2255 |
| Gene name | NIPBL cohesin loading factor | fibroblast growth factor 10 | |
| Synonyms | CDLS|CDLS1|IDN3|IDN3-B|Scc2 | - | |
| Cytomap | 5p13.2 | 5p12 | |
| Type of gene | protein-coding | protein-coding | |
| Description | nipped-B-like proteinNipped-B homologSCC2 homologdelanginsister chromatid cohesion 2 homolog | fibroblast growth factor 10FGF-10keratinocyte growth factor 2produced by fibroblasts of urinary bladder lamina propria | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | Q6KC79 | O15520 | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000504430, ENST00000282516, ENST00000448238, | ENST00000264664, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 26 X 13 X 16=5408 | 8 X 3 X 6=144 |
| # samples | 43 | 8 | |
| ** MAII score | log2(43/5408*10)=-3.65268658669272 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(8/144*10)=-0.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context (manual curation of fusion genes in FusionPDB) | PubMed: NIPBL [Title/Abstract] AND FGF10 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | NIPBL(36962376)-FGF10(44310632), # samples:4 | ||
| Anticipated loss of major functional domain due to fusion event. | NIPBL-FGF10 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. NIPBL-FGF10 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) |
| 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 | NIPBL | GO:0000122 | negative regulation of transcription by RNA polymerase II | 18854353 |
| Hgene | NIPBL | GO:0031065 | positive regulation of histone deacetylation | 18854353 |
| Hgene | NIPBL | GO:0045892 | negative regulation of transcription, DNA-templated | 18854353 |
| Hgene | NIPBL | GO:0071921 | cohesin loading | 22628566 |
| Tgene | FGF10 | GO:0000187 | activation of MAPK activity | 14975937 |
| Tgene | FGF10 | GO:0010634 | positive regulation of epithelial cell migration | 17500053 |
| Tgene | FGF10 | GO:0010838 | positive regulation of keratinocyte proliferation | 17449030 |
| Tgene | FGF10 | GO:0031532 | actin cytoskeleton reorganization | 17449030 |
| Tgene | FGF10 | GO:0032781 | positive regulation of ATPase activity | 12804770 |
| Tgene | FGF10 | GO:0034394 | protein localization to cell surface | 17449030 |
| Tgene | FGF10 | GO:0042060 | wound healing | 11896977|19152659 |
| Tgene | FGF10 | GO:0043410 | positive regulation of MAPK cascade | 12804770 |
| Tgene | FGF10 | GO:0045739 | positive regulation of DNA repair | 14975937 |
| Tgene | FGF10 | GO:0046579 | positive regulation of Ras protein signal transduction | 12804770 |
| Tgene | FGF10 | GO:0048538 | thymus development | 17969154 |
| Tgene | FGF10 | GO:0048754 | branching morphogenesis of an epithelial tube | 17959718 |
| Tgene | FGF10 | GO:0050671 | positive regulation of lymphocyte proliferation | 19152659 |
| Tgene | FGF10 | GO:0050673 | epithelial cell proliferation | 19224135 |
| Tgene | FGF10 | GO:0050674 | urothelial cell proliferation | 11923311 |
| Tgene | FGF10 | GO:0050677 | positive regulation of urothelial cell proliferation | 11923311 |
| Tgene | FGF10 | GO:0050679 | positive regulation of epithelial cell proliferation | 15690149 |
| Tgene | FGF10 | GO:0050731 | positive regulation of peptidyl-tyrosine phosphorylation | 17449030 |
| Tgene | FGF10 | GO:0050918 | positive chemotaxis | 9740653|17449030 |
| Tgene | FGF10 | GO:0051549 | positive regulation of keratinocyte migration | 17449030|19152659 |
| Tgene | FGF10 | GO:0060428 | lung epithelium development | 9740653 |
| Tgene | FGF10 | GO:0060447 | bud outgrowth involved in lung branching | 9740653 |
| Tgene | FGF10 | GO:0060595 | fibroblast growth factor receptor signaling pathway involved in mammary gland specification | 11923311 |
| Tgene | FGF10 | GO:0061033 | secretion by lung epithelial cell involved in lung growth | 10541313 |
| Tgene | FGF10 | GO:0070371 | ERK1 and ERK2 cascade | 17959718 |
| Tgene | FGF10 | GO:0070374 | positive regulation of ERK1 and ERK2 cascade | 14975937 |
| Tgene | FGF10 | GO:0071157 | negative regulation of cell cycle arrest | 17188682 |
| Tgene | FGF10 | GO:0071338 | positive regulation of hair follicle cell proliferation | 16086254 |
| Tgene | FGF10 | GO:1900087 | positive regulation of G1/S transition of mitotic cell cycle | 17188682 |
| Fusion gene breakpoints across NIPBL (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 FGF10 (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 Gene Sample Information |
| Fusion gene information from FusionGDB2.0. |
| Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0) * 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 | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChimerDB4 | LUSC | TCGA-22-4595-01A | NIPBL | chr5 | 36962376 | - | FGF10 | chr5 | 44310632 | - |
| ChimerDB4 | LUSC | TCGA-22-4595-01A | NIPBL | chr5 | 36962376 | + | FGF10 | chr5 | 44310632 | - |
| ChimerDB4 | LUSC | TCGA-22-4595 | NIPBL | chr5 | 36962376 | + | FGF10 | chr5 | 44310632 | - |
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Fusion ORF Analysis |
| 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) |
| ENST00000282516 | NIPBL | chr5 | 36962376 | + | ENST00000264664 | FGF10 | chr5 | 44310632 | - | 2862 | 1109 | 499 | 1410 | 303 |
| ENST00000448238 | NIPBL | chr5 | 36962376 | + | ENST00000264664 | FGF10 | chr5 | 44310632 | - | 2831 | 1078 | 468 | 1379 | 303 |
| 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 |
| ENST00000282516 | ENST00000264664 | NIPBL | chr5 | 36962376 | + | FGF10 | chr5 | 44310632 | - | 0.000523799 | 0.99947625 |
| ENST00000448238 | ENST00000264664 | NIPBL | chr5 | 36962376 | + | FGF10 | chr5 | 44310632 | - | 0.000533962 | 0.999466 |
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Fusion Amino Acid Sequences |
| For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
| >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP >59197_59197_1_NIPBL-FGF10_NIPBL_chr5_36962376_ENST00000282516_FGF10_chr5_44310632_ENST00000264664_length(amino acids)=303AA_BP=203 MNGDMPHVPITTLAGIASLTDLLNQLPLPSPLPATTTKSLLFNARIAEEVNCLLACRDDNLVSQLVHSLNQVSTDHIELKDNLGSDDPEG DIPVLLQAVLARSPNVFREKSMQNRYVQSGMMMSQYKLSQNSMHSSPASSNYQQTTISHSPSSRFVPPQTSSGNRFMPQQNSPVPSPYAP QSPAGYMPYSHPSSYTTHPQMQQGILEITSVEIGVVAVKAINSNYYLAMNKKGKLYGSKEFNNDCKLKERIEENGYNTYASFNWQHNGRQ -------------------------------------------------------------- >59197_59197_2_NIPBL-FGF10_NIPBL_chr5_36962376_ENST00000448238_FGF10_chr5_44310632_ENST00000264664_length(amino acids)=303AA_BP=203 MNGDMPHVPITTLAGIASLTDLLNQLPLPSPLPATTTKSLLFNARIAEEVNCLLACRDDNLVSQLVHSLNQVSTDHIELKDNLGSDDPEG DIPVLLQAVLARSPNVFREKSMQNRYVQSGMMMSQYKLSQNSMHSSPASSNYQQTTISHSPSSRFVPPQTSSGNRFMPQQNSPVPSPYAP QSPAGYMPYSHPSSYTTHPQMQQGILEITSVEIGVVAVKAINSNYYLAMNKKGKLYGSKEFNNDCKLKERIEENGYNTYASFNWQHNGRQ -------------------------------------------------------------- |
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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/chr5:36962376/chr5:44310632) - 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 |
| NIPBL | FGF10 |
| FUNCTION: Plays an important role in the loading of the cohesin complex on to DNA. Forms a heterodimeric complex (also known as cohesin loading complex) with MAU2/SCC4 which mediates the loading of the cohesin complex onto chromatin (PubMed:22628566, PubMed:28914604). Plays a role in cohesin loading at sites of DNA damage. Its recruitment to double-strand breaks (DSBs) sites occurs in a CBX3-, RNF8- and RNF168-dependent manner whereas its recruitment to UV irradiation-induced DNA damage sites occurs in a ATM-, ATR-, RNF8- and RNF168-dependent manner (PubMed:28167679). Along with ZNF609, promotes cortical neuron migration during brain development by regulating the transcription of crucial genes in this process. Preferentially binds promoters containing paused RNA polymerase II. Up-regulates the expression of SEMA3A, NRP1, PLXND1 and GABBR2 genes, among others (By similarity). {ECO:0000250|UniProtKB:Q6KCD5, ECO:0000269|PubMed:22628566, ECO:0000269|PubMed:28167679, ECO:0000269|PubMed:28914604}. | FUNCTION: Plays an important role in the regulation of embryonic development, cell proliferation and cell differentiation. Required for normal branching morphogenesis. May play a role in wound healing. {ECO:0000269|PubMed:16597617}. |
| 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 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 |
| - 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 |
| Hgene | NIPBL | chr5:36962376 | chr5:44310632 | ENST00000282516 | + | 6 | 47 | 418_462 | 203.33333333333334 | 2805.0 | Compositional bias | Note=Gln-rich |
| Hgene | NIPBL | chr5:36962376 | chr5:44310632 | ENST00000448238 | + | 6 | 46 | 418_462 | 203.33333333333334 | 2698.0 | Compositional bias | Note=Gln-rich |
| Hgene | NIPBL | chr5:36962376 | chr5:44310632 | ENST00000282516 | + | 6 | 47 | 996_1009 | 203.33333333333334 | 2805.0 | Motif | PxVxL motif |
| Hgene | NIPBL | chr5:36962376 | chr5:44310632 | ENST00000448238 | + | 6 | 46 | 996_1009 | 203.33333333333334 | 2698.0 | Motif | PxVxL motif |
| Hgene | NIPBL | chr5:36962376 | chr5:44310632 | ENST00000282516 | + | 6 | 47 | 1767_1805 | 203.33333333333334 | 2805.0 | Repeat | Note=HEAT 1 |
| Hgene | NIPBL | chr5:36962376 | chr5:44310632 | ENST00000282516 | + | 6 | 47 | 1843_1881 | 203.33333333333334 | 2805.0 | Repeat | Note=HEAT 2 |
| Hgene | NIPBL | chr5:36962376 | chr5:44310632 | ENST00000282516 | + | 6 | 47 | 1945_1984 | 203.33333333333334 | 2805.0 | Repeat | Note=HEAT 3 |
| Hgene | NIPBL | chr5:36962376 | chr5:44310632 | ENST00000282516 | + | 6 | 47 | 2227_2267 | 203.33333333333334 | 2805.0 | Repeat | Note=HEAT 4 |
| Hgene | NIPBL | chr5:36962376 | chr5:44310632 | ENST00000282516 | + | 6 | 47 | 2313_2351 | 203.33333333333334 | 2805.0 | Repeat | Note=HEAT 5 |
| Hgene | NIPBL | chr5:36962376 | chr5:44310632 | ENST00000448238 | + | 6 | 46 | 1767_1805 | 203.33333333333334 | 2698.0 | Repeat | Note=HEAT 1 |
| Hgene | NIPBL | chr5:36962376 | chr5:44310632 | ENST00000448238 | + | 6 | 46 | 1843_1881 | 203.33333333333334 | 2698.0 | Repeat | Note=HEAT 2 |
| Hgene | NIPBL | chr5:36962376 | chr5:44310632 | ENST00000448238 | + | 6 | 46 | 1945_1984 | 203.33333333333334 | 2698.0 | Repeat | Note=HEAT 3 |
| Hgene | NIPBL | chr5:36962376 | chr5:44310632 | ENST00000448238 | + | 6 | 46 | 2227_2267 | 203.33333333333334 | 2698.0 | Repeat | Note=HEAT 4 |
| Hgene | NIPBL | chr5:36962376 | chr5:44310632 | ENST00000448238 | + | 6 | 46 | 2313_2351 | 203.33333333333334 | 2698.0 | Repeat | Note=HEAT 5 |
| Tgene | FGF10 | chr5:36962376 | chr5:44310632 | ENST00000264664 | 0 | 3 | 52_62 | 108.33333333333333 | 209.0 | Compositional bias | Note=Poly-Ser |
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Fusion Protein Structures |
| PDB and CIF files of the predicted fusion proteins * Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| Fusion protein PDB link (fusion AA seq ID in FusionPDB) | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | AA seq | Len(AA seq) |
| PDB file >>>544_NIPBL_36962376_FGF10_44310632_ranked_0.pdb | NIPBL | 36962376 | 36962376 | ENST00000264664 | FGF10 | chr5 | 44310632 | - | MNGDMPHVPITTLAGIASLTDLLNQLPLPSPLPATTTKSLLFNARIAEEVNCLLACRDDNLVSQLVHSLNQVSTDHIELKDNLGSDDPEG DIPVLLQAVLARSPNVFREKSMQNRYVQSGMMMSQYKLSQNSMHSSPASSNYQQTTISHSPSSRFVPPQTSSGNRFMPQQNSPVPSPYAP QSPAGYMPYSHPSSYTTHPQMQQGILEITSVEIGVVAVKAINSNYYLAMNKKGKLYGSKEFNNDCKLKERIEENGYNTYASFNWQHNGRQ | 303 |
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pLDDT score distribution |
| pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
NIPBL_pLDDT.png  |
FGF10_pLDDT.png  |
| pLDDT score distribution of the predicted fusion protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
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Ramachandran Plot of Fusion Protein Structure |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide. |
| Fusion AA seq ID in FusionPDB and their Ramachandran plots |
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Fusion Protein-Protein Interaction |
| 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 from validated records (BIOGRID-3.4.160) |
| Gene | PPI interactors |
| Protein-protein interactors based on sequence similarity (STRING) |
| Gene | STRING network |
| NIPBL | |
| FGF10 |
| - Retained interactions in fusion protein (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost interactions due to fusion (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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Related Drugs to NIPBL-FGF10 |
| 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 NIPBL-FGF10 |
| 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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