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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:PDGFRA-UBAP2L (FusionGDB2 ID:HG5156TG9898)

Fusion Gene Summary for PDGFRA-UBAP2L

check button Fusion gene summary
Fusion gene informationFusion gene name: PDGFRA-UBAP2L
Fusion gene ID: hg5156tg9898
HgeneTgene
Gene symbol

PDGFRA

UBAP2L

Gene ID

5156

9898

Gene nameplatelet derived growth factor receptor alphaubiquitin associated protein 2 like
SynonymsCD140A|PDGFR-2|PDGFR2NICE-4|NICE4
Cytomap('PDGFRA')('UBAP2L')

4q12

1q21.3

Type of geneprotein-codingprotein-coding
Descriptionplatelet-derived growth factor receptor alphaCD140 antigen-like family member ACD140a antigenPDGF-R-alphaalpha-type platelet-derived growth factor receptorplatelet-derived growth factor receptor 2platelet-derived growth factor receptor, alpha polypeubiquitin-associated protein 2-likeprotein NICE-4
Modification date2020032920200313
UniProtAcc

P16234

.
Ensembl transtripts involved in fusion geneENST00000257290, ENST00000508170, 
Fusion gene scores* DoF score10 X 7 X 6=42017 X 15 X 7=1785
# samples 1118
** MAII scorelog2(11/420*10)=-1.93288580414146
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(18/1785*10)=-3.30985526258679
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PDGFRA [Title/Abstract] AND UBAP2L [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPDGFRA(55095582)-UBAP2L(154238976), # samples:1
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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgenePDGFRA

GO:0008284

positive regulation of cell proliferation

10806482

HgenePDGFRA

GO:0010544

negative regulation of platelet activation

8188664

HgenePDGFRA

GO:0018108

peptidyl-tyrosine phosphorylation

1646396|2536956|8188664

HgenePDGFRA

GO:0030335

positive regulation of cell migration

17470632

HgenePDGFRA

GO:0034614

cellular response to reactive oxygen species

24190966

HgenePDGFRA

GO:0038091

positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway

17470632

HgenePDGFRA

GO:0046777

protein autophosphorylation

1646396|2536956|8188664

HgenePDGFRA

GO:0048008

platelet-derived growth factor receptor signaling pathway

2536956|10806482

HgenePDGFRA

GO:0048146

positive regulation of fibroblast proliferation

10806482



check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4BRCATCGA-E2-A14UPDGFRAchr4

55095582

+UBAP2Lchr1

154238976

+


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Fusion Gene ORF analysis for PDGFRA-UBAP2L

check button 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.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5UTR-3UTRENST00000257290ENST00000484819PDGFRAchr4

55095582

+UBAP2Lchr1

154238976

+
5UTR-3UTRENST00000508170ENST00000484819PDGFRAchr4

55095582

+UBAP2Lchr1

154238976

+
5UTR-intronENST00000257290ENST00000271877PDGFRAchr4

55095582

+UBAP2Lchr1

154238976

+
5UTR-intronENST00000257290ENST00000343815PDGFRAchr4

55095582

+UBAP2Lchr1

154238976

+
5UTR-intronENST00000257290ENST00000361546PDGFRAchr4

55095582

+UBAP2Lchr1

154238976

+
5UTR-intronENST00000257290ENST00000428931PDGFRAchr4

55095582

+UBAP2Lchr1

154238976

+
5UTR-intronENST00000508170ENST00000271877PDGFRAchr4

55095582

+UBAP2Lchr1

154238976

+
5UTR-intronENST00000508170ENST00000343815PDGFRAchr4

55095582

+UBAP2Lchr1

154238976

+
5UTR-intronENST00000508170ENST00000361546PDGFRAchr4

55095582

+UBAP2Lchr1

154238976

+
5UTR-intronENST00000508170ENST00000428931PDGFRAchr4

55095582

+UBAP2Lchr1

154238976

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for PDGFRA-UBAP2L


check buttonFusionAI 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.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
PDGFRAchr455095582+UBAP2Lchr1154238976+0.000675730.9993243
PDGFRAchr455095582+UBAP2Lchr1154238976+0.000675730.9993243


check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for PDGFRA-UBAP2L


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:55095582/:154238976)
- 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PDGFRA

P16234

.
FUNCTION: Tyrosine-protein kinase that acts as a cell-surface receptor for PDGFA, PDGFB and PDGFC and plays an essential role in the regulation of embryonic development, cell proliferation, survival and chemotaxis. Depending on the context, promotes or inhibits cell proliferation and cell migration. Plays an important role in the differentiation of bone marrow-derived mesenchymal stem cells. Required for normal skeleton development and cephalic closure during embryonic development. Required for normal development of the mucosa lining the gastrointestinal tract, and for recruitment of mesenchymal cells and normal development of intestinal villi. Plays a role in cell migration and chemotaxis in wound healing. Plays a role in platelet activation, secretion of agonists from platelet granules, and in thrombin-induced platelet aggregation. Binding of its cognate ligands - homodimeric PDGFA, homodimeric PDGFB, heterodimers formed by PDGFA and PDGFB or homodimeric PDGFC -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 PIK3R1, PLCG1, and PTPN11. 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. Phosphorylates PIK3R1, the regulatory subunit of phosphatidylinositol 3-kinase, and thereby mediates activation of the AKT1 signaling pathway. Mediates activation of HRAS and of the MAP kinases MAPK1/ERK2 and/or MAPK3/ERK1. Promotes activation of STAT family members STAT1, STAT3 and STAT5A and/or STAT5B. 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:10734113, ECO:0000269|PubMed:10947961, ECO:0000269|PubMed:11297552, ECO:0000269|PubMed:12522257, ECO:0000269|PubMed:1646396, ECO:0000269|PubMed:17087943, ECO:0000269|PubMed:1709159, ECO:0000269|PubMed:17141222, ECO:0000269|PubMed:20972453, ECO:0000269|PubMed:21224473, ECO:0000269|PubMed:21596750, ECO:0000269|PubMed:2554309, ECO:0000269|PubMed:8188664, ECO:0000269|PubMed:8760137, ECO:0000269|PubMed:8943348}.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}.

check buttonRetention 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

download page


* 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.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for PDGFRA-UBAP2L


check button 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 PDGFRA-UBAP2L


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for PDGFRA-UBAP2L


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgenePDGFRAP16234DB00619ImatinibAntagonistSmall moleculeApproved
HgenePDGFRAP16234DB00619ImatinibAntagonistSmall moleculeApproved
HgenePDGFRAP16234DB00619ImatinibAntagonistSmall moleculeApproved
HgenePDGFRAP16234DB06589PazopanibInhibitorSmall moleculeApproved
HgenePDGFRAP16234DB06589PazopanibInhibitorSmall moleculeApproved
HgenePDGFRAP16234DB06589PazopanibInhibitorSmall moleculeApproved
HgenePDGFRAP16234DB08896RegorafenibInhibitorSmall moleculeApproved
HgenePDGFRAP16234DB08896RegorafenibInhibitorSmall moleculeApproved
HgenePDGFRAP16234DB08896RegorafenibInhibitorSmall moleculeApproved
HgenePDGFRAP16234DB09079NintedanibInhibitorSmall moleculeApproved
HgenePDGFRAP16234DB09079NintedanibInhibitorSmall moleculeApproved
HgenePDGFRAP16234DB09079NintedanibInhibitorSmall moleculeApproved
HgenePDGFRAP16234DB10772Foreskin keratinocyte (neonatal)AgonistBiotechApproved
HgenePDGFRAP16234DB10772Foreskin keratinocyte (neonatal)AgonistBiotechApproved
HgenePDGFRAP16234DB10772Foreskin keratinocyte (neonatal)AgonistBiotechApproved
HgenePDGFRAP16234DB14840RipretinibInhibitorSmall moleculeApproved
HgenePDGFRAP16234DB14840RipretinibInhibitorSmall moleculeApproved
HgenePDGFRAP16234DB14840RipretinibInhibitorSmall moleculeApproved
HgenePDGFRAP16234DB00102BecaplerminBiotechApproved|Investigational
HgenePDGFRAP16234DB00102BecaplerminBiotechApproved|Investigational
HgenePDGFRAP16234DB00102BecaplerminBiotechApproved|Investigational
HgenePDGFRAP16234DB01268SunitinibInhibitorSmall moleculeApproved|Investigational
HgenePDGFRAP16234DB01268SunitinibInhibitorSmall moleculeApproved|Investigational
HgenePDGFRAP16234DB01268SunitinibInhibitorSmall moleculeApproved|Investigational
HgenePDGFRAP16234DB06043OlaratumabAntagonistBiotechApproved|Investigational
HgenePDGFRAP16234DB06043OlaratumabAntagonistBiotechApproved|Investigational
HgenePDGFRAP16234DB06043OlaratumabAntagonistBiotechApproved|Investigational
HgenePDGFRAP16234DB06595MidostaurinAntagonist|InhibitorSmall moleculeApproved|Investigational
HgenePDGFRAP16234DB06595MidostaurinAntagonist|InhibitorSmall moleculeApproved|Investigational
HgenePDGFRAP16234DB06595MidostaurinAntagonist|InhibitorSmall moleculeApproved|Investigational
HgenePDGFRAP16234DB08901PonatinibInhibitorSmall moleculeApproved|Investigational
HgenePDGFRAP16234DB08901PonatinibInhibitorSmall moleculeApproved|Investigational
HgenePDGFRAP16234DB08901PonatinibInhibitorSmall moleculeApproved|Investigational
HgenePDGFRAP16234DB09078LenvatinibInhibitorSmall moleculeApproved|Investigational
HgenePDGFRAP16234DB09078LenvatinibInhibitorSmall moleculeApproved|Investigational
HgenePDGFRAP16234DB09078LenvatinibInhibitorSmall moleculeApproved|Investigational
HgenePDGFRAP16234DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
HgenePDGFRAP16234DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
HgenePDGFRAP16234DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
HgenePDGFRAP16234DB12147ErdafitinibSubstrateSmall moleculeApproved|Investigational
HgenePDGFRAP16234DB12147ErdafitinibSubstrateSmall moleculeApproved|Investigational
HgenePDGFRAP16234DB12147ErdafitinibSubstrateSmall moleculeApproved|Investigational

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Related Diseases for PDGFRA-UBAP2L


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePDGFRAC0238198Gastrointestinal Stromal Tumors10CGI;CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgenePDGFRAC3179349Gastrointestinal Stromal Sarcoma9CLINGEN;CTD_human;ORPHANET
HgenePDGFRAC0346421Chronic eosinophilic leukemia4ORPHANET
HgenePDGFRAC0206141Idiopathic Hypereosinophilic Syndrome3CTD_human;GENOMICS_ENGLAND
HgenePDGFRAC0006413Burkitt Lymphoma2ORPHANET
HgenePDGFRAC0206142Eosinophilic leukemia2CTD_human
HgenePDGFRAC0206143Loeffler's Endocarditis2CTD_human
HgenePDGFRAC1292769Precursor B-cell lymphoblastic leukemia2ORPHANET
HgenePDGFRAC1540912Hypereosinophilic syndrome2CGI;CTD_human
HgenePDGFRAC0008925Cleft Palate1CTD_human
HgenePDGFRAC0015923Fetal Alcohol Syndrome1PSYGENET
HgenePDGFRAC0018801Heart failure1CTD_human
HgenePDGFRAC0018802Congestive heart failure1CTD_human
HgenePDGFRAC0023212Left-Sided Heart Failure1CTD_human
HgenePDGFRAC0023893Liver Cirrhosis, Experimental1CTD_human
HgenePDGFRAC0024115Lung diseases1CTD_human
HgenePDGFRAC0025149Medulloblastoma1CTD_human
HgenePDGFRAC0035238Congenital abnormality of respiratory system1CTD_human
HgenePDGFRAC0038219Status Dysraphicus1CTD_human
HgenePDGFRAC0080178Spina Bifida1CTD_human
HgenePDGFRAC0205833Medullomyoblastoma1CTD_human
HgenePDGFRAC0206637Mesenchymal Chondrosarcoma1CTD_human
HgenePDGFRAC0235527Heart Failure, Right-Sided1CTD_human
HgenePDGFRAC0266508Rachischisis1CTD_human
HgenePDGFRAC0278510Childhood Medulloblastoma1CTD_human
HgenePDGFRAC0278876Adult Medulloblastoma1CTD_human
HgenePDGFRAC0376634Craniofacial Abnormalities1CTD_human
HgenePDGFRAC0751291Desmoplastic Medulloblastoma1CTD_human
HgenePDGFRAC1275668Melanotic medulloblastoma1CTD_human
HgenePDGFRAC1837218Cleft palate, isolated1CTD_human
HgenePDGFRAC1959583Myocardial Failure1CTD_human
HgenePDGFRAC1961112Heart Decompensation1CTD_human
HgenePDGFRAC2718076Fetal Mummification1CTD_human
HgenePDGFRAC2985290Fetal Alcohol Spectrum Disorders1PSYGENET
HgenePDGFRAC4545381Myeloid and/or lymphoid neoplasm associated with platelet derived growth factor receptor alpha rearrangement1ORPHANET