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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:E2F3-FARS2 (FusionGDB2 ID:24755)

Fusion Gene Summary for E2F3-FARS2

check button Fusion gene summary
Fusion gene informationFusion gene name: E2F3-FARS2
Fusion gene ID: 24755
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 geneENST00000346618, ENST00000535432, 
ENST00000324331, ENST00000274680, 
Fusion gene scores* 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

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

Most frequent breakpointE2F3(20404063)-FARS2(5404774), # samples:2
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
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.

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.

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

+
ChimerDB4THCATCGA-DJ-A2PUE2F3chr6

20404063

+FARS2chr6

5404774

+


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Fusion Gene ORF analysis for E2F3-FARS2

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-3CDSENST00000346618ENST00000324331E2F3chr6

20404063

+FARS2chr6

5404774

+
intron-3CDSENST00000346618ENST00000274680E2F3chr6

20404063

+FARS2chr6

5404774

+
In-frameENST00000535432ENST00000324331E2F3chr6

20404063

+FARS2chr6

5404774

+
In-frameENST00000535432ENST00000274680E2F3chr6

20404063

+FARS2chr6

5404774

+

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)
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 Genomic Features for E2F3-FARS2


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)
E2F3chr620404063+FARS2chr65404774+1.88E-050.9999813
E2F3chr620404063+FARS2chr65404774+1.88E-050.9999813

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 E2F3-FARS2


check button Go to

FGviewer for the breakpoints of 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.
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.
- In-frame and 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

- In-frame and 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 Gene Sequence for E2F3-FARS2


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.
>In-frame_ENST00000535432_ENST00000324331_TCGA-DJ-A2PU_E2F3_chr6_20404063_+_FARS2_chr6_5404774_length(transcript)=774nt_BP=30nt
CTGGTTTCGGAAATGCCCTTACAGCAGCAGTTATTTGCTGGTATAAAGGATGGAGAAAGCCTGCAGCTCTTTGAACAAAGTTCTCGCTCT
GCGCATAAACAAGAGACACACACCATGGAGGCCGTGAAGCTTGTAGAGTTTGATCTTAAGCAAACGCTTACCAGGCTCATGGCACATCTT
TTTGGAGATGAGCTGGAGATAAGATGGGTAGACTGCTACTTCCCTTTTACACATCCTTCCTTTGAGATGGAGATCAACTTTCATGGAGAA
TGGCTGGAAGTTCTTGGCTGCGGGGTGATGGAACAACAACTGGTCAATTCAGCTGGTGCTCAAGACCGAATCGGCTGGGCTTTTGGCCTA
GGATTAGAAAGGCTAGCCATGATCCTCTACGACATCCCTGATATCCGTCTCTTCTGGTGTGAGGACGAGCGCTTCCTGAAGCAGTTCTGT
GTATCCAACATTAATCAGAAGGTGAAGTTTCAGCCTCTTAGCAAATATCCGGCTGTGATCAATGATATTTCATTCTGGTTGCCCTCTGAG
AATTACGCAGAAAATGATTTCTATGACTTAGTCCGAACAATTGGAGGAGACCTGGTGGAAAAGGTTGATCTCATAGACAAGTTTGTACAT
CCAAAGACGCACAAGACCAGCCACTGCTACCGCATCACGTACCGCCACATGGAACGGACTCTGTCCCAGAGAGAGGTCAGGCACATCCAC

>In-frame_ENST00000535432_ENST00000324331_TCGA-DJ-A2PU_E2F3_chr6_20404063_+_FARS2_chr6_5404774_length(amino acids)=257AA_start in transcript=0_stop in transcript=773
LVSEMPLQQQLFAGIKDGESLQLFEQSSRSAHKQETHTMEAVKLVEFDLKQTLTRLMAHLFGDELEIRWVDCYFPFTHPSFEMEINFHGE
WLEVLGCGVMEQQLVNSAGAQDRIGWAFGLGLERLAMILYDIPDIRLFWCEDERFLKQFCVSNINQKVKFQPLSKYPAVINDISFWLPSE

--------------------------------------------------------------
>In-frame_ENST00000535432_ENST00000274680_TCGA-DJ-A2PU_E2F3_chr6_20404063_+_FARS2_chr6_5404774_length(transcript)=925nt_BP=30nt
CTGGTTTCGGAAATGCCCTTACAGCAGCAGTTATTTGCTGGTATAAAGGATGGAGAAAGCCTGCAGCTCTTTGAACAAAGTTCTCGCTCT
GCGCATAAACAAGAGACACACACCATGGAGGCCGTGAAGCTTGTAGAGTTTGATCTTAAGCAAACGCTTACCAGGCTCATGGCACATCTT
TTTGGAGATGAGCTGGAGATAAGATGGGTAGACTGCTACTTCCCTTTTACACATCCTTCCTTTGAGATGGAGATCAACTTTCATGGAGAA
TGGCTGGAAGTTCTTGGCTGCGGGGTGATGGAACAACAACTGGTCAATTCAGCTGGTGCTCAAGACCGAATCGGCTGGGCTTTTGGCCTA
GGATTAGAAAGGCTAGCCATGATCCTCTACGACATCCCTGATATCCGTCTCTTCTGGTGTGAGGACGAGCGCTTCCTGAAGCAGTTCTGT
GTATCCAACATTAATCAGAAGGTGAAGTTTCAGCCTCTTAGCAAATATCCGGCTGTGATCAATGATATTTCATTCTGGTTGCCCTCTGAG
AATTACGCAGAAAATGATTTCTATGACTTAGTCCGAACAATTGGAGGAGACCTGGTGGAAAAGGTTGATCTCATAGACAAGTTTGTACAT
CCAAAGACGCACAAGACCAGCCACTGCTACCGCATCACGTACCGCCACATGGAACGGACTCTGTCCCAGAGAGAGGTCAGGCACATCCAC
CAGGCCTTGCAGGAGGCTGCAGTCCAGCTGTTGGGTGTGGAGGGCAGGTTCTGATGTCACCACTTCACTCAGGCTGCAGCCCTCTTGGGG
CTCCAGGATTTGCTGAAAGAGAAAAAGATATGGTTTGTGAACTGGGGCATCAATCATCTTTTGATAAATGGATCAGTTTTAGGACTTTCA

>In-frame_ENST00000535432_ENST00000274680_TCGA-DJ-A2PU_E2F3_chr6_20404063_+_FARS2_chr6_5404774_length(amino acids)=257AA_start in transcript=0_stop in transcript=773
LVSEMPLQQQLFAGIKDGESLQLFEQSSRSAHKQETHTMEAVKLVEFDLKQTLTRLMAHLFGDELEIRWVDCYFPFTHPSFEMEINFHGE
WLEVLGCGVMEQQLVNSAGAQDRIGWAFGLGLERLAMILYDIPDIRLFWCEDERFLKQFCVSNINQKVKFQPLSKYPAVINDISFWLPSE

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Fusion Gene PPI Analysis for E2F3-FARS2


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 E2F3-FARS2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneFARS2O95363DB00120PhenylalanineSmall moleculeApproved|Investigational|Nutraceutical
TgeneFARS2O95363DB00120PhenylalanineSmall moleculeApproved|Investigational|Nutraceutical
TgeneFARS2O95363DB00120PhenylalanineSmall moleculeApproved|Investigational|Nutraceutical

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Related Diseases for E2F3-FARS2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneE2F3C0007131Non-Small Cell Lung Carcinoma1CTD_human
HgeneE2F3C0017668Focal glomerulosclerosis1GENOMICS_ENGLAND
HgeneE2F3C3714756Intellectual Disability1GENOMICS_ENGLAND
HgeneE2F3C4049702Focal Segmental Glomerulosclerosis, Not Otherwise Specified1GENOMICS_ENGLAND
TgeneFARS2C0023264Leigh Disease7CLINGEN
TgeneFARS2C1838951LEIGH SYNDROME DUE TO MITOCHONDRIAL COMPLEX I DEFICIENCY7CLINGEN
TgeneFARS2C1850597Leigh Syndrome Due To Mitochondrial Complex II Deficiency7CLINGEN
TgeneFARS2C1850598Leigh Syndrome due to Mitochondrial Complex III Deficiency7CLINGEN
TgeneFARS2C1850599Leigh Syndrome due to Mitochondrial Complex IV Deficiency7CLINGEN
TgeneFARS2C1850600Leigh Syndrome due to Mitochondrial Complex V Deficiency7CLINGEN
TgeneFARS2C2931891Necrotizing encephalopathy, infantile subacute, of Leigh7CLINGEN
TgeneFARS2C3554168COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 144CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneFARS2C4310750SPASTIC PARAPLEGIA 77, AUTOSOMAL RECESSIVE3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT