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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-TP53 (FusionGDB2 ID:39632)

Fusion Gene Summary for ILF3-TP53

check button Fusion gene summary
Fusion gene informationFusion gene name: ILF3-TP53
Fusion gene ID: 39632
HgeneTgene
Gene symbol

ILF3

TP53

Gene ID

3609

7157

Gene nameinterleukin enhancer binding factor 3tumor protein p53
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|TCP80BCC7|BMFS5|LFS1|P53|TRP53
Cytomap

19p13.2

17p13.1

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, 90kDinterlecellular tumor antigen p53antigen NY-CO-13mutant tumor protein 53p53 tumor suppressorphosphoprotein p53transformation-related protein 53tumor protein 53tumor supressor p53
Modification date2020032220200329
UniProtAcc

Q12906

Q12888

Ensembl transtripts involved in fusion geneENST00000318511, ENST00000407004, 
ENST00000420083, ENST00000449870, 
ENST00000589998, ENST00000250241, 
ENST00000586544, ENST00000588657, 
ENST00000590261, ENST00000592763, 
ENST00000269305, ENST00000420246, 
ENST00000445888, ENST00000455263, 
ENST00000359597, ENST00000413465, 
ENST00000574684, 
Fusion gene scores* DoF score23 X 15 X 11=37957 X 7 X 4=196
# samples 309
** MAII scorelog2(30/3795*10)=-3.66106547980695
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/196*10)=-1.12285674778553
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ILF3 [Title/Abstract] AND TP53 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointILF3(10765163)-TP53(7579940), # 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

TgeneTP53

GO:0000733

DNA strand renaturation

8183576

TgeneTP53

GO:0006355

regulation of transcription, DNA-templated

7587074

TgeneTP53

GO:0006974

cellular response to DNA damage stimulus

14744935|15710329|17938203

TgeneTP53

GO:0006978

DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator

16213212

TgeneTP53

GO:0006983

ER overload response

14744935

TgeneTP53

GO:0007050

cell cycle arrest

15149599

TgeneTP53

GO:0008104

protein localization

16507995

TgeneTP53

GO:0008285

negative regulation of cell proliferation

22783376

TgeneTP53

GO:0010628

positive regulation of gene expression

15314173|20332243

TgeneTP53

GO:0030330

DNA damage response, signal transduction by p53 class mediator

15149599

TgeneTP53

GO:0031497

chromatin assembly

16322561

TgeneTP53

GO:0034644

cellular response to UV

16213212|23629966

TgeneTP53

GO:0036003

positive regulation of transcription from RNA polymerase II promoter in response to stress

30089260

TgeneTP53

GO:0042149

cellular response to glucose starvation

14744935|21471221

TgeneTP53

GO:0042771

intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator

14654789|14744935|17403783

TgeneTP53

GO:0042981

regulation of apoptotic process

14744935

TgeneTP53

GO:0043065

positive regulation of apoptotic process

12667443|15565177|20959462

TgeneTP53

GO:0045892

negative regulation of transcription, DNA-templated

24051492

TgeneTP53

GO:0045893

positive regulation of transcription, DNA-templated

16322561|17403783|18549481|20378837

TgeneTP53

GO:0045899

positive regulation of RNA polymerase II transcriptional preinitiation complex assembly

24289924

TgeneTP53

GO:0045944

positive regulation of transcription by RNA polymerase II

11672523|17145718|17310983|17599062|18549481|20959462|24652652

TgeneTP53

GO:0051123

RNA polymerase II preinitiation complex assembly

24289924

TgeneTP53

GO:0051974

negative regulation of telomerase activity

10597287

TgeneTP53

GO:0065003

protein-containing complex assembly

12915590

TgeneTP53

GO:0071158

positive regulation of cell cycle arrest

15314173

TgeneTP53

GO:0071480

cellular response to gamma radiation

16213212

TgeneTP53

GO:0072331

signal transduction by p53 class mediator

15314173

TgeneTP53

GO:0072717

cellular response to actinomycin D

15314173

TgeneTP53

GO:0090200

positive regulation of release of cytochrome c from mitochondria

14963330

TgeneTP53

GO:0097252

oligodendrocyte apoptotic process

7720704

TgeneTP53

GO:1902895

positive regulation of pri-miRNA transcription by RNA polymerase II

20546595

TgeneTP53

GO:1903800

positive regulation of production of miRNAs involved in gene silencing by miRNA

26100857

TgeneTP53

GO:1990248

regulation of transcription from RNA polymerase II promoter in response to DNA damage

30089260


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 TP53 (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
ChimerDB4BRCATCGA-AR-A256-01AILF3chr19

10765163

+TP53chr17

7579940

-


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Fusion Gene ORF analysis for ILF3-TP53

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-5UTRENST00000318511ENST00000269305ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-5UTRENST00000318511ENST00000420246ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-5UTRENST00000318511ENST00000445888ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-5UTRENST00000318511ENST00000455263ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-5UTRENST00000407004ENST00000269305ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-5UTRENST00000407004ENST00000420246ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-5UTRENST00000407004ENST00000445888ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-5UTRENST00000407004ENST00000455263ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-5UTRENST00000420083ENST00000269305ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-5UTRENST00000420083ENST00000420246ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-5UTRENST00000420083ENST00000445888ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-5UTRENST00000420083ENST00000455263ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-5UTRENST00000449870ENST00000269305ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-5UTRENST00000449870ENST00000420246ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-5UTRENST00000449870ENST00000445888ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-5UTRENST00000449870ENST00000455263ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-5UTRENST00000589998ENST00000269305ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-5UTRENST00000589998ENST00000420246ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-5UTRENST00000589998ENST00000445888ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-5UTRENST00000589998ENST00000455263ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-intronENST00000318511ENST00000359597ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-intronENST00000318511ENST00000413465ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-intronENST00000318511ENST00000574684ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-intronENST00000407004ENST00000359597ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-intronENST00000407004ENST00000413465ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-intronENST00000407004ENST00000574684ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-intronENST00000420083ENST00000359597ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-intronENST00000420083ENST00000413465ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-intronENST00000420083ENST00000574684ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-intronENST00000449870ENST00000359597ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-intronENST00000449870ENST00000413465ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-intronENST00000449870ENST00000574684ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-intronENST00000589998ENST00000359597ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-intronENST00000589998ENST00000413465ILF3chr19

10765163

+TP53chr17

7579940

-
5UTR-intronENST00000589998ENST00000574684ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000250241ENST00000269305ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000250241ENST00000420246ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000250241ENST00000445888ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000250241ENST00000455263ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000586544ENST00000269305ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000586544ENST00000420246ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000586544ENST00000445888ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000586544ENST00000455263ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000588657ENST00000269305ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000588657ENST00000420246ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000588657ENST00000445888ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000588657ENST00000455263ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000590261ENST00000269305ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000590261ENST00000420246ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000590261ENST00000445888ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000590261ENST00000455263ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000592763ENST00000269305ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000592763ENST00000420246ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000592763ENST00000445888ILF3chr19

10765163

+TP53chr17

7579940

-
intron-5UTRENST00000592763ENST00000455263ILF3chr19

10765163

+TP53chr17

7579940

-
intron-intronENST00000250241ENST00000359597ILF3chr19

10765163

+TP53chr17

7579940

-
intron-intronENST00000250241ENST00000413465ILF3chr19

10765163

+TP53chr17

7579940

-
intron-intronENST00000250241ENST00000574684ILF3chr19

10765163

+TP53chr17

7579940

-
intron-intronENST00000586544ENST00000359597ILF3chr19

10765163

+TP53chr17

7579940

-
intron-intronENST00000586544ENST00000413465ILF3chr19

10765163

+TP53chr17

7579940

-
intron-intronENST00000586544ENST00000574684ILF3chr19

10765163

+TP53chr17

7579940

-
intron-intronENST00000588657ENST00000359597ILF3chr19

10765163

+TP53chr17

7579940

-
intron-intronENST00000588657ENST00000413465ILF3chr19

10765163

+TP53chr17

7579940

-
intron-intronENST00000588657ENST00000574684ILF3chr19

10765163

+TP53chr17

7579940

-
intron-intronENST00000590261ENST00000359597ILF3chr19

10765163

+TP53chr17

7579940

-
intron-intronENST00000590261ENST00000413465ILF3chr19

10765163

+TP53chr17

7579940

-
intron-intronENST00000590261ENST00000574684ILF3chr19

10765163

+TP53chr17

7579940

-
intron-intronENST00000592763ENST00000359597ILF3chr19

10765163

+TP53chr17

7579940

-
intron-intronENST00000592763ENST00000413465ILF3chr19

10765163

+TP53chr17

7579940

-
intron-intronENST00000592763ENST00000574684ILF3chr19

10765163

+TP53chr17

7579940

-

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-TP53


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 ILF3-TP53


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/:7579940)
- 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

TP53

Q12888

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: Double-strand break (DSB) repair protein involved in response to DNA damage, telomere dynamics and class-switch recombination (CSR) during antibody genesis (PubMed:12364621, PubMed:22553214, PubMed:23333306, PubMed:17190600, PubMed:21144835, PubMed:27153538, PubMed:28241136). Plays a key role in the repair of double-strand DNA breaks (DSBs) in response to DNA damage by promoting non-homologous end joining (NHEJ)-mediated repair of DSBs and specifically counteracting the function of the homologous recombination (HR) repair protein BRCA1 (PubMed:22553214, PubMed:23727112, PubMed:23333306, PubMed:27153538). In response to DSBs, phosphorylation by ATM promotes interaction with RIF1 and dissociation from NUDT16L1/TIRR, leading to recruitment to DSBs sites (PubMed:28241136). Recruited to DSBs sites by recognizing and binding histone H2A monoubiquitinated at 'Lys-15' (H2AK15Ub) and histone H4 dimethylated at 'Lys-20' (H4K20me2), two histone marks that are present at DSBs sites (PubMed:23760478, PubMed:27153538, PubMed:28241136, PubMed:17190600). Required for immunoglobulin class-switch recombination (CSR) during antibody genesis, a process that involves the generation of DNA DSBs (PubMed:23345425). Participates in the repair and the orientation of the broken DNA ends during CSR (By similarity). In contrast, it is not required for classic NHEJ and V(D)J recombination (By similarity). Promotes NHEJ of dysfunctional telomeres via interaction with PAXIP1 (PubMed:23727112). {ECO:0000250|UniProtKB:P70399, ECO:0000269|PubMed:12364621, ECO:0000269|PubMed:17190600, ECO:0000269|PubMed:21144835, ECO:0000269|PubMed:22553214, ECO:0000269|PubMed:23333306, ECO:0000269|PubMed:23345425, ECO:0000269|PubMed:23727112, ECO:0000269|PubMed:23760478, ECO:0000269|PubMed:27153538, ECO:0000269|PubMed:28241136}.

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-TP53


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-TP53


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-TP53


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-TP53


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