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Center for Computational Systems Medicine
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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:FLT1-CTNND1 (FusionGDB2 ID:HG2321TG1500)

Fusion Gene Summary for FLT1-CTNND1

check button Fusion gene summary
Fusion gene informationFusion gene name: FLT1-CTNND1
Fusion gene ID: hg2321tg1500
HgeneTgene
Gene symbol

FLT1

CTNND1

Gene ID

2321

1500

Gene namefms related receptor tyrosine kinase 1catenin delta 1
SynonymsFLT|FLT-1|VEGFR-1|VEGFR1BCDS2|CAS|CTNND|P120CAS|P120CTN|p120|p120(CAS)|p120(CTN)
Cytomap('FLT1')('CTNND1')

13q12.3

11q12.1

Type of geneprotein-codingprotein-coding
Descriptionvascular endothelial growth factor receptor 1fms related tyrosine kinase 1fms-like tyrosine kinase 1fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)tyrosine-protein kinase FRTtyrosine-protein kicatenin delta-1cadherin-associated Src substratecatenin (cadherin-associated protein), delta 1p120 catenin
Modification date2020032220200327
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000282397, ENST00000539099, 
ENST00000540678, ENST00000541932, 
ENST00000543394, 
Fusion gene scores* DoF score3 X 3 X 1=917 X 21 X 10=3570
# samples 325
** MAII scorelog2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(25/3570*10)=-3.83592407425437
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: FLT1 [Title/Abstract] AND CTNND1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFLT1(28964014)-CTNND1(57545740), # 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
HgeneFLT1

GO:0002548

monocyte chemotaxis

8605350|18079407

HgeneFLT1

GO:0018108

peptidyl-tyrosine phosphorylation

9299537|11513746

HgeneFLT1

GO:0030335

positive regulation of cell migration

8605350

HgeneFLT1

GO:0030949

positive regulation of vascular endothelial growth factor receptor signaling pathway

1312256

HgeneFLT1

GO:0035924

cellular response to vascular endothelial growth factor stimulus

8605350

HgeneFLT1

GO:0036323

vascular endothelial growth factor receptor-1 signaling pathway

15952180

HgeneFLT1

GO:0043406

positive regulation of MAP kinase activity

9299537

HgeneFLT1

GO:0043410

positive regulation of MAPK cascade

9299537

HgeneFLT1

GO:0046777

protein autophosphorylation

9299537|11513746

HgeneFLT1

GO:0048010

vascular endothelial growth factor receptor signaling pathway

9299537

TgeneCTNND1

GO:0099072

regulation of postsynaptic membrane neurotransmitter receptor levels

18602475



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


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Fusion Gene ORF analysis for FLT1-CTNND1

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

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 FLT1-CTNND1


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)


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Fusion Protein Features for FLT1-CTNND1


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/:28964014/:57545740)
- 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
..
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: 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 FLT1-CTNND1


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 FLT1-CTNND1


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 FLT1-CTNND1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for FLT1-CTNND1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneFLT1C0006142Malignant neoplasm of breast2CTD_human
HgeneFLT1C0032914Pre-Eclampsia2CTD_human;ORPHANET
HgeneFLT1C0678222Breast Carcinoma2CTD_human
HgeneFLT1C1257931Mammary Neoplasms, Human2CTD_human
HgeneFLT1C1458155Mammary Neoplasms2CTD_human
HgeneFLT1C4704874Mammary Carcinoma, Human2CTD_human
HgeneFLT1C0007114Malignant neoplasm of skin1CTD_human
HgeneFLT1C0007134Renal Cell Carcinoma1CTD_human
HgeneFLT1C0013366Dyschondroplasias1CTD_human
HgeneFLT1C0018923Hemangiosarcoma1CTD_human
HgeneFLT1C0019193Hepatitis, Toxic1CTD_human
HgeneFLT1C0023890Liver Cirrhosis1CTD_human
HgeneFLT1C0025202melanoma1CTD_human
HgeneFLT1C0025237Melnick-Needles Syndrome1CTD_human
HgeneFLT1C0026760Multiple Epiphyseal Dysplasia1CTD_human
HgeneFLT1C0027627Neoplasm Metastasis1CTD_human
HgeneFLT1C0029422Osteochondrodysplasias1CTD_human
HgeneFLT1C0036391Schwartz-Jampel Syndrome1CTD_human
HgeneFLT1C0037286Skin Neoplasms1CTD_human
HgeneFLT1C0038015Spondyloepiphyseal Dysplasia1CTD_human
HgeneFLT1C0041948Uremia1CTD_human
HgeneFLT1C0235874Disease Exacerbation1CTD_human
HgeneFLT1C0239946Fibrosis, Liver1CTD_human
HgeneFLT1C0279702Conventional (Clear Cell) Renal Cell Carcinoma1CTD_human
HgeneFLT1C0432272Van Buchem disease1CTD_human
HgeneFLT1C0860207Drug-Induced Liver Disease1CTD_human
HgeneFLT1C1262760Hepatitis, Drug-Induced1CTD_human
HgeneFLT1C1266042Chromophobe Renal Cell Carcinoma1CTD_human
HgeneFLT1C1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
HgeneFLT1C1266044Collecting Duct Carcinoma of the Kidney1CTD_human
HgeneFLT1C1306837Papillary Renal Cell Carcinoma1CTD_human
HgeneFLT1C2937358Cerebral Hemorrhage1CTD_human
HgeneFLT1C3541456Spondyloepiphyseal Dysplasia Tarda, X-Linked1CTD_human
HgeneFLT1C3658290Drug-Induced Acute Liver Injury1CTD_human
HgeneFLT1C4277682Chemical and Drug Induced Liver Injury1CTD_human
HgeneFLT1C4279912Chemically-Induced Liver Toxicity1CTD_human
HgeneFLT1C4551479Schwartz-Jampel Syndrome, Type 11CTD_human
TgeneC0008925Cleft Palate1GENOMICS_ENGLAND
TgeneC1861536Blepharo-cheilo-dontic syndrome1ORPHANET