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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-C3 (FusionGDB2 ID:39448)

Fusion Gene Summary for ILF3-C3

check button Fusion gene summary
Fusion gene informationFusion gene name: ILF3-C3
Fusion gene ID: 39448
HgeneTgene
Gene symbol

ILF3

C3

Gene ID

3609

718

Gene nameinterleukin enhancer binding factor 3complement C3
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|TCP80AHUS5|ARMD9|ASP|C3a|C3b|CPAMD1|HEL-S-62p
Cytomap

19p13.2

19p13.3

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, 90kDinterlecomplement C3C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1C3a anaphylatoxinacylation-stimulating protein cleavage productcomplement component 3complement component C3acomplement component C3bepididymis secretory sperm binding pr
Modification date2020032220200327
UniProtAcc

Q12906

A6NLC5

Ensembl transtripts involved in fusion geneENST00000420083, ENST00000449870, 
ENST00000318511, ENST00000407004, 
ENST00000589998, ENST00000250241, 
ENST00000592763, ENST00000588657, 
ENST00000590261, ENST00000586544, 
ENST00000245907, ENST00000599668, 
Fusion gene scores* DoF score23 X 15 X 11=379522 X 20 X 8=3520
# samples 3022
** MAII scorelog2(30/3795*10)=-3.66106547980695
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(22/3520*10)=-4
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ILF3 [Title/Abstract] AND C3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointILF3(10765163)-C3(6697805), # samples:3
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

TgeneC3

GO:0001934

positive regulation of protein phosphorylation

15833747

TgeneC3

GO:0010575

positive regulation of vascular endothelial growth factor production

16452172

TgeneC3

GO:0010828

positive regulation of glucose transmembrane transport

9059512|15833747

TgeneC3

GO:0010866

regulation of triglyceride biosynthetic process

10432298

TgeneC3

GO:0010884

positive regulation of lipid storage

9555951

TgeneC3

GO:0045745

positive regulation of G protein-coupled receptor signaling pathway

15833747


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 C3 (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-A2-A0YJ-01AILF3chr19

10765163

+C3chr19

6697805

-
ChimerDB4BRCATCGA-A2-A0YJ-01AILF3chr19

10765163

+C3chr19

6697805

-
ChimerDB4BRCATCGA-A2-A0YJ-01AILF3chr19

10765163

-C3chr19

6697805

-


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Fusion Gene ORF analysis for ILF3-C3

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-3CDSENST00000420083ENST00000245907ILF3chr19

10765163

+C3chr19

6697805

-
5UTR-intronENST00000420083ENST00000599668ILF3chr19

10765163

+C3chr19

6697805

-
5UTR-3CDSENST00000449870ENST00000245907ILF3chr19

10765163

+C3chr19

6697805

-
5UTR-intronENST00000449870ENST00000599668ILF3chr19

10765163

+C3chr19

6697805

-
5UTR-3CDSENST00000318511ENST00000245907ILF3chr19

10765163

+C3chr19

6697805

-
5UTR-intronENST00000318511ENST00000599668ILF3chr19

10765163

+C3chr19

6697805

-
5UTR-3CDSENST00000407004ENST00000245907ILF3chr19

10765163

+C3chr19

6697805

-
5UTR-intronENST00000407004ENST00000599668ILF3chr19

10765163

+C3chr19

6697805

-
5UTR-3CDSENST00000589998ENST00000245907ILF3chr19

10765163

+C3chr19

6697805

-
5UTR-intronENST00000589998ENST00000599668ILF3chr19

10765163

+C3chr19

6697805

-
intron-3CDSENST00000250241ENST00000245907ILF3chr19

10765163

+C3chr19

6697805

-
intron-intronENST00000250241ENST00000599668ILF3chr19

10765163

+C3chr19

6697805

-
intron-3CDSENST00000592763ENST00000245907ILF3chr19

10765163

+C3chr19

6697805

-
intron-intronENST00000592763ENST00000599668ILF3chr19

10765163

+C3chr19

6697805

-
intron-3CDSENST00000588657ENST00000245907ILF3chr19

10765163

+C3chr19

6697805

-
intron-intronENST00000588657ENST00000599668ILF3chr19

10765163

+C3chr19

6697805

-
intron-3CDSENST00000590261ENST00000245907ILF3chr19

10765163

+C3chr19

6697805

-
intron-intronENST00000590261ENST00000599668ILF3chr19

10765163

+C3chr19

6697805

-
intron-3CDSENST00000586544ENST00000245907ILF3chr19

10765163

+C3chr19

6697805

-
intron-intronENST00000586544ENST00000599668ILF3chr19

10765163

+C3chr19

6697805

-

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-C3


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-C3


check button Go to

FGviewer for the breakpoints of :-:

.
- 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
ILF3

Q12906

C3

A6NLC5

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: May play a role in neuronal and neurobehavioral development. {ECO:0000250|UniProtKB:Q1LY84}.

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-C3


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-C3


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-C3


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-C3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC3C3151071COMPLEMENT COMPONENT 3 DEFICIENCY, AUTOSOMAL RECESSIVE5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC3C0242383Age related macular degeneration4CTD_human;GENOMICS_ENGLAND
TgeneC3C2752037HEMOLYTIC UREMIC SYNDROME, ATYPICAL, SUSCEPTIBILITY TO, 54GENOMICS_ENGLAND;UNIPROT
TgeneC3C1969651Macular Degeneration, Age-Related, 92CTD_human;UNIPROT
TgeneC3C0003257Antibody Deficiency Syndrome1CTD_human
TgeneC3C0007787Transient Ischemic Attack1CTD_human
TgeneC3C0011860Diabetes Mellitus, Non-Insulin-Dependent1CTD_human
TgeneC3C0013221Drug toxicity1CTD_human
TgeneC3C0017665Membranous glomerulonephritis1CTD_human
TgeneC3C0019061Hemolytic-Uremic Syndrome1GENOMICS_ENGLAND
TgeneC3C0019193Hepatitis, Toxic1CTD_human
TgeneC3C0021051Immunologic Deficiency Syndromes1CTD_human
TgeneC3C0021655Insulin Resistance1CTD_human
TgeneC3C0022660Kidney Failure, Acute1CTD_human
TgeneC3C0030524Paratuberculosis1CTD_human
TgeneC3C0030807Pemphigus1CTD_human
TgeneC3C0030809Pemphigus Vulgaris1CTD_human
TgeneC3C0034152Henoch-Schoenlein Purpura1CTD_human
TgeneC3C0041755Adverse reaction to drug1CTD_human
TgeneC3C0042386Vasculitis, Hemorrhagic1CTD_human
TgeneC3C0086445Idiopathic Membranous Glomerulonephritis1CTD_human
TgeneC3C0086922Rheumatoid Purpura1CTD_human
TgeneC3C0238281Middle Cerebral Artery Syndrome1CTD_human
TgeneC3C0242461Purpura, Nonthrombocytopenic1CTD_human
TgeneC3C0263313Pemphigus Foliaceus1CTD_human
TgeneC3C0272242Complement deficiency disease1GENOMICS_ENGLAND
TgeneC3C0376362Purpura Hemorrhagica1CTD_human
TgeneC3C0472381Posterior Circulation Transient Ischemic Attack1CTD_human
TgeneC3C0740376Middle Cerebral Artery Thrombosis1CTD_human
TgeneC3C0740391Middle Cerebral Artery Occlusion1CTD_human
TgeneC3C0740392Infarction, Middle Cerebral Artery1CTD_human
TgeneC3C0751019Carotid Circulation Transient Ischemic Attack1CTD_human
TgeneC3C0751020Transient Ischemic Attack, Vertebrobasilar Circulation1CTD_human
TgeneC3C0751021Crescendo Transient Ischemic Attacks1CTD_human
TgeneC3C0751022Brain Stem Ischemia, Transient1CTD_human
TgeneC3C0751845Middle Cerebral Artery Embolus1CTD_human
TgeneC3C0751846Left Middle Cerebral Artery Infarction1CTD_human
TgeneC3C0751847Embolic Infarction, Middle Cerebral Artery1CTD_human
TgeneC3C0751848Thrombotic Infarction, Middle Cerebral Artery1CTD_human
TgeneC3C0751849Right Middle Cerebral Artery Infarction1CTD_human
TgeneC3C0860207Drug-Induced Liver Disease1CTD_human
TgeneC3C0917805Transient Cerebral Ischemia1CTD_human
TgeneC3C0920563Insulin Sensitivity1CTD_human
TgeneC3C1262760Hepatitis, Drug-Induced1CTD_human
TgeneC3C1332655Complement component 3 deficiency1GENOMICS_ENGLAND
TgeneC3C1527335Transient Ischemic Attack, Anterior Circulation1CTD_human
TgeneC3C1565662Acute Kidney Insufficiency1CTD_human
TgeneC3C1704378Heymann Nephritis1CTD_human
TgeneC3C2609414Acute kidney injury1CTD_human
TgeneC3C2931788Atypical Hemolytic Uremic Syndrome1CTD_human;GENOMICS_ENGLAND
TgeneC3C3658290Drug-Induced Acute Liver Injury1CTD_human
TgeneC3C4087273C3 glomerulopathy1GENOMICS_ENGLAND
TgeneC3C4277682Chemical and Drug Induced Liver Injury1CTD_human
TgeneC3C4279912Chemically-Induced Liver Toxicity1CTD_human