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 | Fusion Gene Summary |
| Fusion Gene ORF analysis |
| Fusion Genomic Features |
| Fusion Protein Features |
| Fusion Gene Sequence |
| Fusion Gene PPI analysis |
| Related Drugs |
| Related Diseases |
Fusion gene:CPSF6-PDGFRB (FusionGDB2 ID:HG11052TG5159) |
Fusion Gene Summary for CPSF6-PDGFRB |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CPSF6-PDGFRB | Fusion gene ID: hg11052tg5159 | Hgene | Tgene | Gene symbol | CPSF6 | PDGFRB | Gene ID | 11052 | 5159 |
| Gene name | cleavage and polyadenylation specific factor 6 | platelet derived growth factor receptor beta | |
| Synonyms | CFIM|CFIM68|CFIM72|HPBRII-4|HPBRII-7 | CD140B|IBGC4|IMF1|JTK12|KOGS|PDGFR|PDGFR-1|PDGFR1|PENTT | |
| Cytomap | ('CPSF6')('PDGFRB') 12q15 | 5q32 | |
| Type of gene | protein-coding | protein-coding | |
| Description | cleavage and polyadenylation specificity factor subunit 6CPSF 68 kDa subunitcleavage and polyadenylation specific factor 6, 68kDacleavage and polyadenylation specificity factor 68 kDa subunitcleavage factor Im complex 68 kDa subunitpre-mRNA cleavage | platelet-derived growth factor receptor betaActivated tyrosine kinase PDGFRBCD140 antigen-like family member BNDEL1-PDGFRBPDGF-R-betaPDGFR-betabeta-type platelet-derived growth factor receptorplatelet-derived growth factor receptor 1platelet-deriv | |
| Modification date | 20200313 | 20200329 | |
| UniProtAcc | . | P09619 | |
| Ensembl transtripts involved in fusion gene | ENST00000266679, ENST00000435070, ENST00000456847, ENST00000550987, ENST00000551516, | ||
| Fusion gene scores | * DoF score | 69 X 12 X 19=15732 | 28 X 26 X 6=4368 |
| # samples | 71 | 15 | |
| ** MAII score | log2(71/15732*10)=-4.46973925655087 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(15/4368*10)=-4.86393845042397 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: CPSF6 [Title/Abstract] AND PDGFRB [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | |||
| Anticipated loss of major functional domain due to fusion event. | |||
| * 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 | CPSF6 | GO:0006397 | mRNA processing | 14690600 |
| Hgene | CPSF6 | GO:0051262 | protein tetramerization | 20695905 |
| Hgene | CPSF6 | GO:0051290 | protein heterotetramerization | 23187700 |
| Hgene | CPSF6 | GO:1990120 | messenger ribonucleoprotein complex assembly | 29276085 |
| Tgene | PDGFRB | GO:0007165 | signal transduction | 10821867 |
| Tgene | PDGFRB | GO:0010863 | positive regulation of phospholipase C activity | 1653029 |
| Tgene | PDGFRB | GO:0018108 | peptidyl-tyrosine phosphorylation | 1653029|2536956|2850496 |
| Tgene | PDGFRB | GO:0030335 | positive regulation of cell migration | 17470632 |
| Tgene | PDGFRB | GO:0032516 | positive regulation of phosphoprotein phosphatase activity | 7691811 |
| Tgene | PDGFRB | GO:0038091 | positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway | 17470632 |
| Tgene | PDGFRB | GO:0043552 | positive regulation of phosphatidylinositol 3-kinase activity | 1314164 |
| Tgene | PDGFRB | GO:0046777 | protein autophosphorylation | 1314164|2536956|2850496 |
| Tgene | PDGFRB | GO:0048008 | platelet-derived growth factor receptor signaling pathway | 1314164|2536956 |
| Tgene | PDGFRB | GO:0060326 | cell chemotaxis | 2554309|17991872 |
| Fusion gene information * 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 |
| ChimerKB4 | . | . | CPSF6 | chr12 | 69651511 | + | PDGFRB | chr5 | 69651511 | - |
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Fusion Gene ORF analysis for CPSF6-PDGFRB |
| 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 |
| intron-intron | ENST00000266679 | ENST00000261799 | CPSF6 | chr12 | 69651511 | + | PDGFRB | chr5 | 69651511 | - |
| intron-intron | ENST00000266679 | ENST00000523456 | CPSF6 | chr12 | 69651511 | + | PDGFRB | chr5 | 69651511 | - |
| intron-intron | ENST00000435070 | ENST00000261799 | CPSF6 | chr12 | 69651511 | + | PDGFRB | chr5 | 69651511 | - |
| intron-intron | ENST00000435070 | ENST00000523456 | CPSF6 | chr12 | 69651511 | + | PDGFRB | chr5 | 69651511 | - |
| intron-intron | ENST00000456847 | ENST00000261799 | CPSF6 | chr12 | 69651511 | + | PDGFRB | chr5 | 69651511 | - |
| intron-intron | ENST00000456847 | ENST00000523456 | CPSF6 | chr12 | 69651511 | + | PDGFRB | chr5 | 69651511 | - |
| intron-intron | ENST00000550987 | ENST00000261799 | CPSF6 | chr12 | 69651511 | + | PDGFRB | chr5 | 69651511 | - |
| intron-intron | ENST00000550987 | ENST00000523456 | CPSF6 | chr12 | 69651511 | + | PDGFRB | chr5 | 69651511 | - |
| intron-intron | ENST00000551516 | ENST00000261799 | CPSF6 | chr12 | 69651511 | + | PDGFRB | chr5 | 69651511 | - |
| intron-intron | ENST00000551516 | ENST00000523456 | CPSF6 | chr12 | 69651511 | + | PDGFRB | chr5 | 69651511 | - |
| ORFfinder result based on the fusion transcript sequence of in-frame fusion genes. |
| 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) |
| 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 |
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Fusion Genomic Features for CPSF6-PDGFRB |
| FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints. |
| Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | 1-p | p (fusion gene breakpoint) |
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Fusion Protein Features for CPSF6-PDGFRB |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:/:) - 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 |
| . | PDGFRB |
| 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}. | FUNCTION: Tyrosine-protein kinase that acts as cell-surface receptor for homodimeric PDGFB and PDGFD and for heterodimers formed by PDGFA and PDGFB, and plays an essential role in the regulation of embryonic development, cell proliferation, survival, differentiation, chemotaxis and migration. Plays an essential role in blood vessel development by promoting proliferation, migration and recruitment of pericytes and smooth muscle cells to endothelial cells. Plays a role in the migration of vascular smooth muscle cells and the formation of neointima at vascular injury sites. Required for normal development of the cardiovascular system. Required for normal recruitment of pericytes (mesangial cells) in the kidney glomerulus, and for normal formation of a branched network of capillaries in kidney glomeruli. Promotes rearrangement of the actin cytoskeleton and the formation of membrane ruffles. Binding of its cognate ligands - homodimeric PDGFB, heterodimers formed by PDGFA and PDGFB or homodimeric PDGFD -leads to the activation of several signaling cascades; the response depends on the nature of the bound ligand and is modulated by the formation of heterodimers between PDGFRA and PDGFRB. Phosphorylates PLCG1, PIK3R1, PTPN11, RASA1/GAP, CBL, SHC1 and NCK1. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate, mobilization of cytosolic Ca(2+) and the activation of protein kinase C. Phosphorylation of PIK3R1, the regulatory subunit of phosphatidylinositol 3-kinase, leads to the activation of the AKT1 signaling pathway. Phosphorylation of SHC1, or of the C-terminus of PTPN11, creates a binding site for GRB2, resulting in the activation of HRAS, RAF1 and down-stream MAP kinases, including MAPK1/ERK2 and/or MAPK3/ERK1. Promotes phosphorylation and activation of SRC family kinases. Promotes phosphorylation of PDCD6IP/ALIX and STAM. Receptor signaling is down-regulated by protein phosphatases that dephosphorylate the receptor and its down-stream effectors, and by rapid internalization of the activated receptor. {ECO:0000269|PubMed:11297552, ECO:0000269|PubMed:11331881, ECO:0000269|PubMed:1314164, ECO:0000269|PubMed:1396585, ECO:0000269|PubMed:1653029, ECO:0000269|PubMed:1709159, ECO:0000269|PubMed:1846866, ECO:0000269|PubMed:20494825, ECO:0000269|PubMed:20529858, ECO:0000269|PubMed:21098708, ECO:0000269|PubMed:21679854, ECO:0000269|PubMed:21733313, ECO:0000269|PubMed:2554309, ECO:0000269|PubMed:26599395, ECO:0000269|PubMed:2835772, ECO:0000269|PubMed:2850496, ECO:0000269|PubMed:7685273, ECO:0000269|PubMed:7691811, ECO:0000269|PubMed:7692233, ECO:0000269|PubMed:8195171}. |
| 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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Fusion Gene Sequence for CPSF6-PDGFRB |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
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Fusion Gene PPI Analysis for CPSF6-PDGFRB |
| 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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Related Drugs for CPSF6-PDGFRB |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.8 2021-05-08) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Tgene | PDGFRB | P09619 | DB00619 | Imatinib | Antagonist | Small molecule | Approved |
| Tgene | PDGFRB | P09619 | DB00619 | Imatinib | Antagonist | Small molecule | Approved |
| Tgene | PDGFRB | P09619 | DB00619 | Imatinib | Antagonist | Small molecule | Approved |
| Tgene | PDGFRB | P09619 | DB06589 | Pazopanib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRB | P09619 | DB06589 | Pazopanib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRB | P09619 | DB06589 | Pazopanib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRB | P09619 | DB08896 | Regorafenib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRB | P09619 | DB08896 | Regorafenib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRB | P09619 | DB08896 | Regorafenib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRB | P09619 | DB09079 | Nintedanib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRB | P09619 | DB09079 | Nintedanib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRB | P09619 | DB09079 | Nintedanib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRB | P09619 | DB10770 | Foreskin fibroblast (neonatal) | Agonist | Biotech | Approved |
| Tgene | PDGFRB | P09619 | DB10770 | Foreskin fibroblast (neonatal) | Agonist | Biotech | Approved |
| Tgene | PDGFRB | P09619 | DB10770 | Foreskin fibroblast (neonatal) | Agonist | Biotech | Approved |
| Tgene | PDGFRB | P09619 | DB14840 | Ripretinib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRB | P09619 | DB14840 | Ripretinib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRB | P09619 | DB14840 | Ripretinib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRB | P09619 | DB00102 | Becaplermin | Biotech | Approved|Investigational | |
| Tgene | PDGFRB | P09619 | DB00102 | Becaplermin | Biotech | Approved|Investigational | |
| Tgene | PDGFRB | P09619 | DB00102 | Becaplermin | Biotech | Approved|Investigational | |
| Tgene | PDGFRB | P09619 | DB00398 | Sorafenib | Antagonist | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB00398 | Sorafenib | Antagonist | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB00398 | Sorafenib | Antagonist | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB01254 | Dasatinib | Antagonist | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB01254 | Dasatinib | Antagonist | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB01254 | Dasatinib | Antagonist | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB01268 | Sunitinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB01268 | Sunitinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB01268 | Sunitinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB06595 | Midostaurin | Antagonist|Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB06595 | Midostaurin | Antagonist|Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB06595 | Midostaurin | Antagonist|Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB12010 | Fostamatinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB12010 | Fostamatinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB12010 | Fostamatinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB12147 | Erdafitinib | Substrate | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB12147 | Erdafitinib | Substrate | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB12147 | Erdafitinib | Substrate | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB12978 | Pexidartinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB12978 | Pexidartinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB12978 | Pexidartinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB15822 | Pralsetinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB15822 | Pralsetinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRB | P09619 | DB15822 | Pralsetinib | Inhibitor | Small molecule | Approved|Investigational |
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Related Diseases for CPSF6-PDGFRB |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | C3554321 | BASAL GANGLIA CALCIFICATION, IDIOPATHIC, 4 | 6 | CTD_human;GENOMICS_ENGLAND;UNIPROT | |
| Tgene | C0393590 | Fahr's syndrome (disorder) | 3 | GENOMICS_ENGLAND;ORPHANET | |
| Tgene | C4225270 | Kosaki overgrowth syndrome | 3 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT | |
| Tgene | C4551572 | MYOFIBROMATOSIS, INFANTILE, 1 | 3 | GENOMICS_ENGLAND;UNIPROT | |
| Tgene | C0013421 | Dystonia | 2 | GENOMICS_ENGLAND | |
| Tgene | C0023480 | Leukemia, Myelomonocytic, Chronic | 2 | ORPHANET | |
| Tgene | C0023893 | Liver Cirrhosis, Experimental | 2 | CTD_human | |
| Tgene | C0036341 | Schizophrenia | 2 | PSYGENET | |
| Tgene | C0432284 | Infantile myofibromatosis | 2 | CTD_human;GENOMICS_ENGLAND;ORPHANET | |
| Tgene | C0004782 | Basal Ganglia Diseases | 1 | CTD_human | |
| Tgene | C0006663 | Calcinosis | 1 | CTD_human | |
| Tgene | C0015371 | Extrapyramidal Disorders | 1 | CTD_human | |
| Tgene | C0036337 | Schizoaffective Disorder | 1 | PSYGENET | |
| Tgene | C0206648 | Myofibromatosis | 1 | GENOMICS_ENGLAND | |
| Tgene | C0263628 | Tumoral calcinosis | 1 | CTD_human | |
| Tgene | C0521174 | Microcalcification | 1 | CTD_human | |
| Tgene | C0750951 | Lenticulostriate Disorders | 1 | CTD_human | |
| Tgene | C1333046 | Myeloproliferative Neoplasm, Unclassifiable | 1 | ORPHANET | |
| Tgene | C1866182 | Penttinen-Aula syndrome | 1 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT | |
| Tgene | C3472621 | Myeloid neoplasm with beta-type platelet-derived growth factor receptor gene rearrangement | 1 | ORPHANET | |
| Tgene | C3714756 | Intellectual Disability | 1 | GENOMICS_ENGLAND |
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