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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:ILF3-ATG4D (FusionGDB2 ID:39614)

Fusion Gene Summary for ILF3-ATG4D

check button Fusion gene summary
Fusion gene informationFusion gene name: ILF3-ATG4D
Fusion gene ID: 39614
HgeneTgene
Gene symbol

ILF3

ATG4D

Gene ID

3609

84971

Gene nameinterleukin enhancer binding factor 3autophagy related 4D cysteine peptidase
SynonymsCBTF|DRBF|DRBP76|MMP4|MPHOSPH4|MPP4|MPP4110|NF-AT-90|NF110|NF110b|NF90|NF90a|NF90b|NF90c|NF90ctv|NFAR|NFAR-1|NFAR-2|NFAR110|NFAR2|NFAR90|TCP110|TCP80APG4-D|APG4D|AUTL4
Cytomap

19p13.2

19p13.2

Type of geneprotein-codingprotein-coding
Descriptioninterleukin enhancer-binding factor 3M phase phosphoprotein 4, nuclear factor associated with DS RNAM-phase phosphoprotein 4double-stranded RNA-binding protein, 76 kDdsRNA binding protein NFAR-2/MPP4interleukin enhancer binding factor 3, 90kDinterlecysteine protease ATG4DAPG4 autophagy 4 homolog DATG4 autophagy related 4 homolog DAUT-like 4 cysteine endopeptidaseautophagin-4autophagy-related cysteine endopeptidase 4autophagy-related protein 4 homolog Dcysteine protease involved in autophagy
Modification date2020032220200313
UniProtAcc

Q12906

Q86TL0

Ensembl transtripts involved in fusion geneENST00000318511, ENST00000407004, 
ENST00000420083, ENST00000449870, 
ENST00000589998, ENST00000250241, 
ENST00000586544, ENST00000588657, 
ENST00000590261, ENST00000592763, 
ENST00000309469, ENST00000540862, 
Fusion gene scores* DoF score23 X 15 X 11=37953 X 3 X 3=27
# samples 303
** MAII scorelog2(30/3795*10)=-3.66106547980695
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: ILF3 [Title/Abstract] AND ATG4D [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointILF3(10765163)-ATG4D(10662573), # 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
HgeneILF3

GO:0006468

protein phosphorylation

21123651

HgeneILF3

GO:0045892

negative regulation of transcription, DNA-templated

11739746

HgeneILF3

GO:0045893

positive regulation of transcription, DNA-templated

11739746


check buttonFusion gene breakpoints across ILF3 (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 ATG4D (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
ChimerDB4BLCATCGA-XF-A9SI-01AILF3chr19

10765163

-ATG4Dchr19

10662573

+
ChimerDB4BLCATCGA-XF-A9SIILF3chr19

10765163

+ATG4Dchr19

10662572

+
ChimerDB4BLCATCGA-XF-A9SIILF3chr19

10765163

+ATG4Dchr19

10662573

+


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Fusion Gene ORF analysis for ILF3-ATG4D

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
5UTR-3CDSENST00000318511ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662572

+
5UTR-3CDSENST00000318511ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662573

+
5UTR-3CDSENST00000407004ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662572

+
5UTR-3CDSENST00000407004ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662573

+
5UTR-3CDSENST00000420083ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662572

+
5UTR-3CDSENST00000420083ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662573

+
5UTR-3CDSENST00000449870ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662572

+
5UTR-3CDSENST00000449870ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662573

+
5UTR-3CDSENST00000589998ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662572

+
5UTR-3CDSENST00000589998ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662573

+
5UTR-5UTRENST00000318511ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662572

+
5UTR-5UTRENST00000318511ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662573

+
5UTR-5UTRENST00000407004ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662572

+
5UTR-5UTRENST00000407004ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662573

+
5UTR-5UTRENST00000420083ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662572

+
5UTR-5UTRENST00000420083ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662573

+
5UTR-5UTRENST00000449870ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662572

+
5UTR-5UTRENST00000449870ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662573

+
5UTR-5UTRENST00000589998ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662572

+
5UTR-5UTRENST00000589998ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662573

+
intron-3CDSENST00000250241ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662572

+
intron-3CDSENST00000250241ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662573

+
intron-3CDSENST00000586544ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662572

+
intron-3CDSENST00000586544ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662573

+
intron-3CDSENST00000588657ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662572

+
intron-3CDSENST00000588657ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662573

+
intron-3CDSENST00000590261ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662572

+
intron-3CDSENST00000590261ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662573

+
intron-3CDSENST00000592763ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662572

+
intron-3CDSENST00000592763ENST00000309469ILF3chr19

10765163

+ATG4Dchr19

10662573

+
intron-5UTRENST00000250241ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662572

+
intron-5UTRENST00000250241ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662573

+
intron-5UTRENST00000586544ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662572

+
intron-5UTRENST00000586544ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662573

+
intron-5UTRENST00000588657ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662572

+
intron-5UTRENST00000588657ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662573

+
intron-5UTRENST00000590261ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662572

+
intron-5UTRENST00000590261ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662573

+
intron-5UTRENST00000592763ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662572

+
intron-5UTRENST00000592763ENST00000540862ILF3chr19

10765163

+ATG4Dchr19

10662573

+

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 ILF3-ATG4D


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)
ILF3chr1910765163+ATG4Dchr1910662572+4.16E-070.99999964
ILF3chr1910765163+ATG4Dchr1910662572+4.16E-070.99999964

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.
genomic feature of top 1%

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Fusion Protein Features for ILF3-ATG4D


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/:10765163/:10662573)
- 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
ILF3

Q12906

ATG4D

Q86TL0

FUNCTION: RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. Within the nucleus, promotes circRNAs processing by stabilizing the regulatory elements residing in the flanking introns of the circularized exons. Plays thereby a role in the back-splicing of a subset of circRNAs (PubMed:28625552). As a consequence, participates in a wide range of transcriptional and post-transcriptional processes. Binds to poly-U elements and AU-rich elements (AREs) in the 3'-UTR of target mRNAs (PubMed:14731398). Upon viral infection, ILF3 accumulates in the cytoplasm and participates in the innate antiviral response (PubMed:21123651). Mechanistically, ILF3 becomes phosphorylated and activated by the double-stranded RNA-activated protein kinase/PKR which releases ILF3 from cellular mature circRNAs. In turn, unbound ILF3 molecules are able to interact with and thus inhibit viral mRNAs (PubMed:21123651, PubMed:28625552). {ECO:0000269|PubMed:14731398, ECO:0000269|PubMed:21123651, ECO:0000269|PubMed:28625552, ECO:0000269|PubMed:9442054}.FUNCTION: [Cysteine protease ATG4D]: Cysteine protease required for the cytoplasm to vacuole transport (Cvt) and autophagy. Cleaves the C-terminal amino acid of ATG8 family proteins MAP1LC3 and GABARAPL2, to reveal a C-terminal glycine. Exposure of the glycine at the C-terminus is essential for ATG8 proteins conjugation to phosphatidylethanolamine (PE) and insertion to membranes, which is necessary for autophagy. Has also an activity of delipidating enzyme for the PE-conjugated forms.; FUNCTION: [Cysteine protease ATG4D, mitochondrial]: Plays a role as an autophagy regulator that links mitochondrial dysfunction with apoptosis. The mitochondrial import of ATG4D during cellular stress and differentiation may play important roles in the regulation of mitochondrial physiology, ROS, mitophagy and cell viability.

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 ILF3-ATG4D


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 ILF3-ATG4D


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 ILF3-ATG4D


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 ILF3-ATG4D


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