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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-ATG10 (FusionGDB2 ID:30699)

Fusion Gene Summary for FLT1-ATG10

check button Fusion gene summary
Fusion gene informationFusion gene name: FLT1-ATG10
Fusion gene ID: 30699
HgeneTgene
Gene symbol

FLT1

ATG10

Gene ID

2321

83734

Gene namefms related receptor tyrosine kinase 1autophagy related 10
SynonymsFLT|FLT-1|VEGFR-1|VEGFR1APG10|APG10L|pp12616
Cytomap

13q12.3

5q14.1-q14.2

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 kiubiquitin-like-conjugating enzyme ATG10APG10 autophagy 10-likeATG10 autophagy related 10 homologautophagy-related protein 10
Modification date2020032220200313
UniProtAcc

P17948

Q9BSB4

Ensembl transtripts involved in fusion geneENST00000282397, ENST00000539099, 
ENST00000540678, ENST00000541932, 
ENST00000543394, 		ENST00000282185, 
ENST00000355178, ENST00000458350, 
ENST00000513443, ENST00000513634, 
ENST00000514253, 
Fusion gene scores* DoF score3 X 3 X 1=910 X 9 X 7=630
# samples 311
** MAII scorelog2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(11/630*10)=-2.51784830486262
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: FLT1 [Title/Abstract] AND ATG10 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFLT1(28995889)-ATG10(81471544), # 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

TgeneATG10

GO:0032446

protein modification by small protein conjugation

16963840


check buttonFusion gene breakpoints across FLT1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across ATG10 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS5.0N/AAY516568FLT1chr13

28995889

+ATG10chr5

81471544

-


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Fusion Gene ORF analysis for FLT1-ATG10

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
intron-intronENST00000282397ENST00000282185FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000282397ENST00000355178FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000282397ENST00000458350FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000282397ENST00000513443FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000282397ENST00000513634FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000282397ENST00000514253FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000539099ENST00000282185FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000539099ENST00000355178FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000539099ENST00000458350FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000539099ENST00000513443FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000539099ENST00000513634FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000539099ENST00000514253FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000540678ENST00000282185FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000540678ENST00000355178FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000540678ENST00000458350FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000540678ENST00000513443FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000540678ENST00000513634FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000540678ENST00000514253FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000541932ENST00000282185FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000541932ENST00000355178FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000541932ENST00000458350FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000541932ENST00000513443FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000541932ENST00000513634FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000541932ENST00000514253FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000543394ENST00000282185FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000543394ENST00000355178FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000543394ENST00000458350FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000543394ENST00000513443FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000543394ENST00000513634FLT1chr13

28995889

+ATG10chr5

81471544

-
intron-intronENST00000543394ENST00000514253FLT1chr13

28995889

+ATG10chr5

81471544

-

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-ATG10


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)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

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.

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Fusion Protein Features for FLT1-ATG10


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/:28995889/:81471544)
- 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
FLT1

P17948

ATG10

Q9BSB4

FUNCTION: Tyrosine-protein kinase that acts as a cell-surface receptor for VEGFA, VEGFB and PGF, and plays an essential role in the development of embryonic vasculature, the regulation of angiogenesis, cell survival, cell migration, macrophage function, chemotaxis, and cancer cell invasion. Acts as a positive regulator of postnatal retinal hyaloid vessel regression (Ref.11). May play an essential role as a negative regulator of embryonic angiogenesis by inhibiting excessive proliferation of endothelial cells. Can promote endothelial cell proliferation, survival and angiogenesis in adulthood. Its function in promoting cell proliferation seems to be cell-type specific. Promotes PGF-mediated proliferation of endothelial cells, proliferation of some types of cancer cells, but does not promote proliferation of normal fibroblasts (in vitro). Has very high affinity for VEGFA and relatively low protein kinase activity; may function as a negative regulator of VEGFA signaling by limiting the amount of free VEGFA and preventing its binding to KDR. Modulates KDR signaling by forming heterodimers with KDR. Ligand binding leads to the activation of several signaling cascades. Activation of PLCG leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate and the activation of protein kinase C. Mediates phosphorylation of PIK3R1, the regulatory subunit of phosphatidylinositol 3-kinase, leading to activation of phosphatidylinositol kinase and the downstream signaling pathway. Mediates activation of MAPK1/ERK2, MAPK3/ERK1 and the MAP kinase signaling pathway, as well as of the AKT1 signaling pathway. Phosphorylates SRC and YES1, and may also phosphorylate CBL. Promotes phosphorylation of AKT1 at 'Ser-473'. Promotes phosphorylation of PTK2/FAK1 (PubMed:16685275). {ECO:0000269|PubMed:11141500, ECO:0000269|PubMed:11312102, ECO:0000269|PubMed:11811792, ECO:0000269|PubMed:12796773, ECO:0000269|PubMed:14633857, ECO:0000269|PubMed:15735759, ECO:0000269|PubMed:16685275, ECO:0000269|PubMed:18079407, ECO:0000269|PubMed:18515749, ECO:0000269|PubMed:18583712, ECO:0000269|PubMed:18593464, ECO:0000269|PubMed:20512933, ECO:0000269|PubMed:20551949, ECO:0000269|PubMed:21752276, ECO:0000269|PubMed:7824266, ECO:0000269|PubMed:8248162, ECO:0000269|PubMed:8605350, ECO:0000269|PubMed:9299537, ECO:0000269|Ref.11}.; FUNCTION: [Isoform 1]: Phosphorylates PLCG. {ECO:0000269|PubMed:9299537}.; FUNCTION: [Isoform 2]: May function as decoy receptor for VEGFA. {ECO:0000269|PubMed:21752276}.; FUNCTION: [Isoform 3]: May function as decoy receptor for VEGFA. {ECO:0000269|PubMed:21752276}.; FUNCTION: [Isoform 4]: May function as decoy receptor for VEGFA. {ECO:0000269|PubMed:21752276}.; FUNCTION: [Isoform 7]: Has a truncated kinase domain; it increases phosphorylation of SRC at 'Tyr-418' by unknown means and promotes tumor cell invasion. {ECO:0000269|PubMed:20512933}.FUNCTION: Autophagy factor required for autophagosome formation. Stabilizes ATG13, protecting it from proteasomal degradation. {ECO:0000269|PubMed:19287211, ECO:0000269|PubMed:19597335}.

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-ATG10


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-ATG10


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-ATG10


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-ATG10


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource