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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:EIF3K-CIC (FusionGDB2 ID:25882)

Fusion Gene Summary for EIF3K-CIC

check button Fusion gene summary
Fusion gene informationFusion gene name: EIF3K-CIC
Fusion gene ID: 25882
HgeneTgene
Gene symbol

EIF3K

CIC

Gene ID

27335

23152

Gene nameeukaryotic translation initiation factor 3 subunit Kcapicua transcriptional repressor
SynonymsARG134|EIF3-p28|EIF3S12|HSPC029|M9|MSTP001|PLAC-24|PLAC24|PRO1474|PTD001MRD45
Cytomap

19q13.2

19q13.2

Type of geneprotein-codingprotein-coding
Descriptioneukaryotic translation initiation factor 3 subunit KeIF-3 p28eukaryotic translation initiation factor 3, subunit 12muscle specificmuscle-specific gene M9 proteinprotein capicua homolog
Modification date2020032220200313
UniProtAcc

Q9UBQ5

Q96RK0

Ensembl transtripts involved in fusion geneENST00000593062, ENST00000248342, 
ENST00000538434, ENST00000545173, 
ENST00000588934, ENST00000592558, 
ENST00000593149, 		ENST00000572681, 
ENST00000160740, ENST00000575354, 
ENST00000575839, 
Fusion gene scores* DoF score9 X 9 X 4=3245 X 5 X 4=100
# samples 125
** MAII scorelog2(12/324*10)=-1.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/100*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: EIF3K [Title/Abstract] AND CIC [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointEIF3K(39114832)-CIC(42775927), # samples:1
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
HgeneEIF3K

GO:0006413

translational initiation

17581632


check buttonFusion gene breakpoints across EIF3K (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 CIC (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
ChimerDB4GBMTCGA-32-1970-01AEIF3Kchr19

39114832

+CICchr19

42775927

+


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Fusion Gene ORF analysis for EIF3K-CIC

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
3UTR-5UTRENST00000593062ENST00000572681EIF3Kchr19

39114832

+CICchr19

42775927

+
3UTR-intronENST00000593062ENST00000160740EIF3Kchr19

39114832

+CICchr19

42775927

+
3UTR-intronENST00000593062ENST00000575354EIF3Kchr19

39114832

+CICchr19

42775927

+
3UTR-intronENST00000593062ENST00000575839EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-5UTRENST00000248342ENST00000572681EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-5UTRENST00000538434ENST00000572681EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-5UTRENST00000545173ENST00000572681EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-5UTRENST00000588934ENST00000572681EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-5UTRENST00000592558ENST00000572681EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-5UTRENST00000593149ENST00000572681EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-intronENST00000248342ENST00000160740EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-intronENST00000248342ENST00000575354EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-intronENST00000248342ENST00000575839EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-intronENST00000538434ENST00000160740EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-intronENST00000538434ENST00000575354EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-intronENST00000538434ENST00000575839EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-intronENST00000545173ENST00000160740EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-intronENST00000545173ENST00000575354EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-intronENST00000545173ENST00000575839EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-intronENST00000588934ENST00000160740EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-intronENST00000588934ENST00000575354EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-intronENST00000588934ENST00000575839EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-intronENST00000592558ENST00000160740EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-intronENST00000592558ENST00000575354EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-intronENST00000592558ENST00000575839EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-intronENST00000593149ENST00000160740EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-intronENST00000593149ENST00000575354EIF3Kchr19

39114832

+CICchr19

42775927

+
5CDS-intronENST00000593149ENST00000575839EIF3Kchr19

39114832

+CICchr19

42775927

+

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 EIF3K-CIC


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)
EIF3Kchr1939114837+CICchr1942775925+3.92E-091
EIF3Kchr1939114837+CICchr1942775925+3.92E-091

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 EIF3K-CIC


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/:39114832/:42775927)
- 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
EIF3K

Q9UBQ5

CIC

Q96RK0

FUNCTION: Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis (PubMed:17581632, PubMed:25849773, PubMed:27462815). The eIF-3 complex associates with the 40S ribosome and facilitates the recruitment of eIF-1, eIF-1A, eIF-2:GTP:methionyl-tRNAi and eIF-5 to form the 43S pre-initiation complex (43S PIC). The eIF-3 complex stimulates mRNA recruitment to the 43S PIC and scanning of the mRNA for AUG recognition. The eIF-3 complex is also required for disassembly and recycling of post-termination ribosomal complexes and subsequently prevents premature joining of the 40S and 60S ribosomal subunits prior to initiation (PubMed:17581632). The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation, including cell cycling, differentiation and apoptosis, and uses different modes of RNA stem-loop binding to exert either translational activation or repression (PubMed:25849773). {ECO:0000255|HAMAP-Rule:MF_03010, ECO:0000269|PubMed:17581632, ECO:0000269|PubMed:25849773, ECO:0000269|PubMed:27462815}.FUNCTION: Transcriptional repressor which plays a role in development of the central nervous system (CNS). In concert with ATXN1 and ATXN1L, involved in brain development. {ECO:0000250|UniProtKB:Q924A2}.

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 EIF3K-CIC


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 EIF3K-CIC


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 EIF3K-CIC


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 EIF3K-CIC


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