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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:E2F3-FARS2

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: E2F3-FARS2
FusionPDB ID: 24777
FusionGDB2.0 ID: 24777
HgeneTgene
Gene symbol

E2F3

FARS2

Gene ID

1871

10667

Gene nameE2F transcription factor 3phenylalanyl-tRNA synthetase 2, mitochondrial
SynonymsE2F-3COXPD14|FARS1|HSPC320|PheRS|SPG77|mtPheRS
Cytomap

6p22.3

6p25.1

Type of geneprotein-codingprotein-coding
Descriptiontranscription factor E2F3phenylalanine--tRNA ligase, mitochondrialdJ236A3.1 (phenylalanine-tRNA synthetase)dJ520B18.2 (FARS1 (phenylalanine-tRNA synthetase))mitochondrial PHERSphenylalanine tRNA ligase 2, mitochondrialphenylalanine translasephenylalanine-tRNA synthetase 1 (
Modification date2020032220200313
UniProtAcc

O00716

O95363

Ensembl transtripts involved in fusion geneENST idsENST00000535432, ENST00000346618, 
ENST00000274680, ENST00000324331, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score8 X 3 X 5=12015 X 13 X 10=1950
# samples 1221
** MAII scorelog2(12/120*10)=0log2(21/1950*10)=-3.21501289097085
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: E2F3 [Title/Abstract] AND FARS2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)E2F3(20404063)-FARS2(5404774), # samples:2
Anticipated loss of major functional domain due to fusion event.E2F3-FARS2 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.
E2F3-FARS2 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.
E2F3-FARS2 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.
E2F3-FARS2 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneE2F3

GO:0000082

G1/S transition of mitotic cell cycle

17062573

HgeneE2F3

GO:0006606

protein import into nucleus

17062573

HgeneE2F3

GO:0045944

positive regulation of transcription by RNA polymerase II

7739537

TgeneFARS2

GO:0006432

phenylalanyl-tRNA aminoacylation

10329163

TgeneFARS2

GO:0008033

tRNA processing

10329163


check buttonFusion gene breakpoints across E2F3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across FARS2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4THCATCGA-DJ-A2PUE2F3chr6

20404063

+FARS2chr6

5404774

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000535432E2F3chr620404063+ENST00000324331FARS2chr65404774+774300773257
ENST00000535432E2F3chr620404063+ENST00000274680FARS2chr65404774+925300773257

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
ENST00000535432ENST00000324331E2F3chr620404063+FARS2chr65404774+0.0011360520.99886394
ENST00000535432ENST00000274680E2F3chr620404063+FARS2chr65404774+0.0016101920.99838984

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Fusion Amino Acid Sequences


check button 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

>24777_24777_1_E2F3-FARS2_E2F3_chr6_20404063_ENST00000535432_FARS2_chr6_5404774_ENST00000274680_length(amino acids)=257AA_BP=9
LVSEMPLQQQLFAGIKDGESLQLFEQSSRSAHKQETHTMEAVKLVEFDLKQTLTRLMAHLFGDELEIRWVDCYFPFTHPSFEMEINFHGE
WLEVLGCGVMEQQLVNSAGAQDRIGWAFGLGLERLAMILYDIPDIRLFWCEDERFLKQFCVSNINQKVKFQPLSKYPAVINDISFWLPSE

--------------------------------------------------------------

>24777_24777_2_E2F3-FARS2_E2F3_chr6_20404063_ENST00000535432_FARS2_chr6_5404774_ENST00000324331_length(amino acids)=257AA_BP=9
LVSEMPLQQQLFAGIKDGESLQLFEQSSRSAHKQETHTMEAVKLVEFDLKQTLTRLMAHLFGDELEIRWVDCYFPFTHPSFEMEINFHGE
WLEVLGCGVMEQQLVNSAGAQDRIGWAFGLGLERLAMILYDIPDIRLFWCEDERFLKQFCVSNINQKVKFQPLSKYPAVINDISFWLPSE

--------------------------------------------------------------

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Fusion Protein Functional Features


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/chr6:20404063/chr6:5404774)
- 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
E2F3

O00716

FARS2

O95363

FUNCTION: Transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from G1 to S phase. E2F3 binds specifically to RB1 in a cell-cycle dependent manner. Inhibits adipogenesis, probably through the repression of CEBPA binding to its target gene promoters (By similarity). {ECO:0000250|UniProtKB:O35261}.FUNCTION: Is responsible for the charging of tRNA(Phe) with phenylalanine in mitochondrial translation. To a lesser extent, also catalyzes direct attachment of m-Tyr (an oxidized version of Phe) to tRNA(Phe), thereby opening the way for delivery of the misacylated tRNA to the ribosome and incorporation of ROS-damaged amino acid into proteins. {ECO:0000269|PubMed:19549855, ECO:0000269|PubMed:22833457}.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneFARS2chr6:20404063chr6:5404774ENST0000027468017358_450204.0452.0DomainFDX-ACB
TgeneFARS2chr6:20404063chr6:5404774ENST0000032433117358_450204.0452.0DomainFDX-ACB

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneE2F3chr6:20404063chr6:5404774ENST00000346618+17120_1290466.0Compositional biasNote=Poly-Gly
HgeneE2F3chr6:20404063chr6:5404774ENST00000346618+1726_310466.0Compositional biasNote=Poly-Ala
HgeneE2F3chr6:20404063chr6:5404774ENST00000346618+1745_530466.0Compositional biasNote=Poly-Ala
HgeneE2F3chr6:20404063chr6:5404774ENST00000535432+17120_1296.0335.0Compositional biasNote=Poly-Gly
HgeneE2F3chr6:20404063chr6:5404774ENST00000535432+1726_316.0335.0Compositional biasNote=Poly-Ala
HgeneE2F3chr6:20404063chr6:5404774ENST00000535432+1745_536.0335.0Compositional biasNote=Poly-Ala
HgeneE2F3chr6:20404063chr6:5404774ENST00000346618+17155_2450466.0DNA bindingOntology_term=ECO:0000255
HgeneE2F3chr6:20404063chr6:5404774ENST00000535432+17155_2456.0335.0DNA bindingOntology_term=ECO:0000255
HgeneE2F3chr6:20404063chr6:5404774ENST00000346618+17209_2450466.0MotifNote=DEF box
HgeneE2F3chr6:20404063chr6:5404774ENST00000535432+17209_2456.0335.0MotifNote=DEF box
HgeneE2F3chr6:20404063chr6:5404774ENST00000346618+17101_1530466.0RegionCyclin A/CDK2 binding
HgeneE2F3chr6:20404063chr6:5404774ENST00000346618+17204_2250466.0RegionNote=Leucine-zipper
HgeneE2F3chr6:20404063chr6:5404774ENST00000346618+17246_3370466.0RegionDimerization
HgeneE2F3chr6:20404063chr6:5404774ENST00000346618+17391_4650466.0RegionTransactivation
HgeneE2F3chr6:20404063chr6:5404774ENST00000346618+17432_4490466.0RegionRetinoblastoma protein binding
HgeneE2F3chr6:20404063chr6:5404774ENST00000535432+17101_1536.0335.0RegionCyclin A/CDK2 binding
HgeneE2F3chr6:20404063chr6:5404774ENST00000535432+17204_2256.0335.0RegionNote=Leucine-zipper
HgeneE2F3chr6:20404063chr6:5404774ENST00000535432+17246_3376.0335.0RegionDimerization
HgeneE2F3chr6:20404063chr6:5404774ENST00000535432+17391_4656.0335.0RegionTransactivation
HgeneE2F3chr6:20404063chr6:5404774ENST00000535432+17432_4496.0335.0RegionRetinoblastoma protein binding
TgeneFARS2chr6:20404063chr6:5404774ENST0000027468017157_160204.0452.0RegionNote=Substrate binding
TgeneFARS2chr6:20404063chr6:5404774ENST0000027468017186_188204.0452.0RegionNote=Substrate binding
TgeneFARS2chr6:20404063chr6:5404774ENST0000027468017193_195204.0452.0RegionNote=Substrate binding
TgeneFARS2chr6:20404063chr6:5404774ENST0000032433117157_160204.0452.0RegionNote=Substrate binding
TgeneFARS2chr6:20404063chr6:5404774ENST0000032433117186_188204.0452.0RegionNote=Substrate binding
TgeneFARS2chr6:20404063chr6:5404774ENST0000032433117193_195204.0452.0RegionNote=Substrate binding


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
E2F3
FARS2


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to E2F3-FARS2


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to E2F3-FARS2


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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