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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:EML4-NFIC (FusionGDB2 ID:26467)

Fusion Gene Summary for EML4-NFIC

check button Fusion gene summary
Fusion gene informationFusion gene name: EML4-NFIC
Fusion gene ID: 26467
HgeneTgene
Gene symbol

EML4

NFIC

Gene ID

27436

4782

Gene nameEMAP like 4nuclear factor I C
SynonymsC2orf2|ELP120|EMAP-4|EMAPL4|ROPP120CTF|CTF5|NF-I|NFI
Cytomap

2p21

19p13.3

Type of geneprotein-codingprotein-coding
Descriptionechinoderm microtubule-associated protein-like 4echinoderm microtubule associated protein like 4restrictedly overexpressed proliferation-associated proteinropp 120nuclear factor 1 C-typeCCAAT-box-binding transcription factorNF-I/CNF1-CTGGCA-binding proteinnuclear factor I/C (CCAAT-binding transcription factor)
Modification date2020031320200313
UniProtAcc

Q9HC35

P08651

Ensembl transtripts involved in fusion geneENST00000318522, ENST00000401738, 
ENST00000402711, ENST00000453191, 
ENST00000482660, 		ENST00000589123, 
ENST00000341919, ENST00000346156, 
ENST00000395111, ENST00000443272, 
ENST00000586919, ENST00000588839, 
ENST00000590282, 
Fusion gene scores* DoF score22 X 32 X 18=1267224 X 21 X 9=4536
# samples 4327
** MAII scorelog2(43/12672*10)=-4.88116377049015
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(27/4536*10)=-4.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: EML4 [Title/Abstract] AND NFIC [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointEML4(42559688)-NFIC(3465353), # 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
TgeneNFIC

GO:0000122

negative regulation of transcription by RNA polymerase II

19706729

TgeneNFIC

GO:0045944

positive regulation of transcription by RNA polymerase II

1524678|19706729


check buttonFusion gene breakpoints across EML4 (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 NFIC (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
ChiTaRS5.0N/ANM_001145076EML4chr2

42559688

+NFICchr19

3465353

+


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Fusion Gene ORF analysis for EML4-NFIC

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-3UTRENST00000318522ENST00000589123EML4chr2

42559688

+NFICchr19

3465353

+
5CDS-intronENST00000318522ENST00000341919EML4chr2

42559688

+NFICchr19

3465353

+
5CDS-intronENST00000318522ENST00000346156EML4chr2

42559688

+NFICchr19

3465353

+
5CDS-intronENST00000318522ENST00000395111EML4chr2

42559688

+NFICchr19

3465353

+
5CDS-intronENST00000318522ENST00000443272EML4chr2

42559688

+NFICchr19

3465353

+
5CDS-intronENST00000318522ENST00000586919EML4chr2

42559688

+NFICchr19

3465353

+
5CDS-intronENST00000318522ENST00000588839EML4chr2

42559688

+NFICchr19

3465353

+
5CDS-intronENST00000318522ENST00000590282EML4chr2

42559688

+NFICchr19

3465353

+
intron-3UTRENST00000401738ENST00000589123EML4chr2

42559688

+NFICchr19

3465353

+
intron-3UTRENST00000402711ENST00000589123EML4chr2

42559688

+NFICchr19

3465353

+
intron-3UTRENST00000453191ENST00000589123EML4chr2

42559688

+NFICchr19

3465353

+
intron-3UTRENST00000482660ENST00000589123EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000401738ENST00000341919EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000401738ENST00000346156EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000401738ENST00000395111EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000401738ENST00000443272EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000401738ENST00000586919EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000401738ENST00000588839EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000401738ENST00000590282EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000402711ENST00000341919EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000402711ENST00000346156EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000402711ENST00000395111EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000402711ENST00000443272EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000402711ENST00000586919EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000402711ENST00000588839EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000402711ENST00000590282EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000453191ENST00000341919EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000453191ENST00000346156EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000453191ENST00000395111EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000453191ENST00000443272EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000453191ENST00000586919EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000453191ENST00000588839EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000453191ENST00000590282EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000482660ENST00000341919EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000482660ENST00000346156EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000482660ENST00000395111EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000482660ENST00000443272EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000482660ENST00000586919EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000482660ENST00000588839EML4chr2

42559688

+NFICchr19

3465353

+
intron-intronENST00000482660ENST00000590282EML4chr2

42559688

+NFICchr19

3465353

+

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 EML4-NFIC


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 EML4-NFIC


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/:42559688/:3465353)
- 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
EML4

Q9HC35

NFIC

P08651

FUNCTION: Essential for the formation and stability of microtubules (MTs) (PubMed:16890222, PubMed:31409757). Required for the organization of the mitotic spindle and for the proper attachment of kinetochores to MTs (PubMed:25789526). Promotes the recruitment of NUDC to the mitotic spindle for mitotic progression (PubMed:25789526). {ECO:0000269|PubMed:16890222, ECO:0000269|PubMed:25789526, ECO:0000269|PubMed:31409757}.FUNCTION: Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication.

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 EML4-NFIC


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 EML4-NFIC


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 EML4-NFIC


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 EML4-NFIC


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