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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:EDF1-CLN3 (FusionGDB2 ID:HG8721TG1201)

Fusion Gene Summary for EDF1-CLN3

check button Fusion gene summary
Fusion gene informationFusion gene name: EDF1-CLN3
Fusion gene ID: hg8721tg1201
HgeneTgene
Gene symbol

EDF1

CLN3

Gene ID

8721

1201

Gene nameendothelial differentiation related factor 1CLN3 lysosomal/endosomal transmembrane protein, battenin
SynonymsCFAP280|EDF-1|MBF1BTN1|BTS|JNCL
Cytomap('EDF1')('CLN3')

9q34.3

16p12.1

Type of geneprotein-codingprotein-coding
Descriptionendothelial differentiation-related factor 1multiprotein bridging factor 1batteninCLN3, batteninbatten disease proteinceroid-lipofuscinosis, neuronal 3
Modification date2020031320200328
UniProtAcc

O60869

.
Ensembl transtripts involved in fusion geneENST00000224073, ENST00000371649, 
ENST00000371648, 
Fusion gene scores* DoF score12 X 9 X 8=8648 X 8 X 3=192
# samples 148
** MAII scorelog2(14/864*10)=-2.6256044852185
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/192*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: EDF1 [Title/Abstract] AND CLN3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointEDF1(139757358)-CLN3(28478223), # 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
HgeneEDF1

GO:0043388

positive regulation of DNA binding

10567391

TgeneCLN3

GO:0015809

arginine transport

16251196

TgeneCLN3

GO:0035752

lysosomal lumen pH elevation

10924275

TgeneCLN3

GO:0042987

amyloid precursor protein catabolic process

10924275



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
ChimerDB4UCECTCGA-AX-A0IU-01AEDF1chr9

139757358

-CLN3chr16

28478223

-


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Fusion Gene ORF analysis for EDF1-CLN3

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
5CDS-3UTRENST00000224073ENST00000535392EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-3UTRENST00000224073ENST00000568224EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-3UTRENST00000371649ENST00000535392EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-3UTRENST00000371649ENST00000568224EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000224073ENST00000333496EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000224073ENST00000354630EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000224073ENST00000355477EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000224073ENST00000357076EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000224073ENST00000357806EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000224073ENST00000357857EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000224073ENST00000359984EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000224073ENST00000360019EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000224073ENST00000395653EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000224073ENST00000565316EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000224073ENST00000567160EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000224073ENST00000567963EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000224073ENST00000569430EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000371649ENST00000333496EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000371649ENST00000354630EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000371649ENST00000355477EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000371649ENST00000357076EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000371649ENST00000357806EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000371649ENST00000357857EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000371649ENST00000359984EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000371649ENST00000360019EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000371649ENST00000395653EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000371649ENST00000565316EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000371649ENST00000567160EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000371649ENST00000567963EDF1chr9

139757358

-CLN3chr16

28478223

-
5CDS-intronENST00000371649ENST00000569430EDF1chr9

139757358

-CLN3chr16

28478223

-
intron-3UTRENST00000371648ENST00000535392EDF1chr9

139757358

-CLN3chr16

28478223

-
intron-3UTRENST00000371648ENST00000568224EDF1chr9

139757358

-CLN3chr16

28478223

-
intron-intronENST00000371648ENST00000333496EDF1chr9

139757358

-CLN3chr16

28478223

-
intron-intronENST00000371648ENST00000354630EDF1chr9

139757358

-CLN3chr16

28478223

-
intron-intronENST00000371648ENST00000355477EDF1chr9

139757358

-CLN3chr16

28478223

-
intron-intronENST00000371648ENST00000357076EDF1chr9

139757358

-CLN3chr16

28478223

-
intron-intronENST00000371648ENST00000357806EDF1chr9

139757358

-CLN3chr16

28478223

-
intron-intronENST00000371648ENST00000357857EDF1chr9

139757358

-CLN3chr16

28478223

-
intron-intronENST00000371648ENST00000359984EDF1chr9

139757358

-CLN3chr16

28478223

-
intron-intronENST00000371648ENST00000360019EDF1chr9

139757358

-CLN3chr16

28478223

-
intron-intronENST00000371648ENST00000395653EDF1chr9

139757358

-CLN3chr16

28478223

-
intron-intronENST00000371648ENST00000565316EDF1chr9

139757358

-CLN3chr16

28478223

-
intron-intronENST00000371648ENST00000567160EDF1chr9

139757358

-CLN3chr16

28478223

-
intron-intronENST00000371648ENST00000567963EDF1chr9

139757358

-CLN3chr16

28478223

-
intron-intronENST00000371648ENST00000569430EDF1chr9

139757358

-CLN3chr16

28478223

-

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 EDF1-CLN3


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 EDF1-CLN3


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/:139757358/:28478223)
- 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
EDF1

O60869

.
FUNCTION: Transcriptional coactivator stimulating NR5A1 and ligand-dependent NR1H3/LXRA and PPARG transcriptional activities. Enhances the DNA-binding activity of ATF1, ATF2, CREB1 and NR5A1. Regulates nitric oxid synthase activity probably by sequestering calmodulin in the cytoplasm. May function in endothelial cells differentiation, hormone-induced cardiomyocytes hypertrophy and lipid metabolism. {ECO:0000269|PubMed:10567391, ECO:0000269|PubMed:12040021, ECO:0000269|PubMed:15112053, ECO:0000269|PubMed:9813014}.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 EDF1-CLN3


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 EDF1-CLN3


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 EDF1-CLN3


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 EDF1-CLN3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0751383Juvenile Neuronal Ceroid Lipofuscinosis7CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0024623Malignant neoplasm of stomach1CTD_human
TgeneC0038356Stomach Neoplasms1CTD_human
TgeneC0235874Disease Exacerbation1CTD_human
TgeneC1708349Hereditary Diffuse Gastric Cancer1CTD_human