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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:CELF1-NDUFS3 (FusionGDB2 ID:HG10658TG4722)

Fusion Gene Summary for CELF1-NDUFS3

Fusion gene summary

Fusion gene information	Fusion gene name: CELF1-NDUFS3
	Fusion gene ID: hg10658tg4722
		Hgene	Tgene
	Gene symbol	CELF1	NDUFS3
	Gene ID	10658	4722
	Gene name	CUGBP Elav-like family member 1	NADH:ubiquinone oxidoreductase core subunit S3
	Synonyms	BRUNOL2\|CUG-BP\|CUGBP\|CUGBP1\|EDEN-BP\|NAB50\|NAPOR\|hNab50	CI-30\|MC1DN8
	Cytomap	('CELF1')('NDUFS3') 11p11.2	11p11.2
	Type of gene	protein-coding	protein-coding
	Description	CUGBP Elav-like family member 150 kDa nuclear polyadenylated RNA-binding proteinCUG RNA-binding proteinCUG triplet repeat RNA-binding protein 1CUG-BP- and ETR-3-like factor 1EDEN-BP homologRNA-binding protein BRUNOL-2bruno-like 2bruno-like protein	NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialCI-30kDNADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase)NADH dehydrogenase-ubiquinone 30 kDa subunitNADH-ubiquinone oxidoreductase 30 kDa subunitcompl
	Modification date	20200313	20200313
	UniProtAcc	.	O75489
	Ensembl transtripts involved in fusion gene	ENST00000310513, ENST00000531165, ENST00000358597, ENST00000361904, ENST00000395290, ENST00000395292, ENST00000532048, ENST00000539455,
Fusion gene scores	* DoF score	23 X 21 X 14=6762	6 X 7 X 4=168
	# samples	35	7
	** MAII score	log2(35/6762*10)=-4.27202318906105 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(7/168*10)=-1.26303440583379 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: CELF1 [Title/Abstract] AND NDUFS3 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	CELF1(47574544)-NDUFS3(47587458), # 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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	CELF1	GO:0006376	mRNA splice site selection	11158314
Hgene	CELF1	GO:0043484	regulation of RNA splicing	16946708

Fusion gene information
* 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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	LUSC	TCGA-63-A5MT	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+

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Fusion Gene ORF analysis for CELF1-NDUFS3

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
5UTR-3UTR	ENST00000310513	ENST00000533507	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
5UTR-3UTR	ENST00000531165	ENST00000533507	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
5UTR-intron	ENST00000310513	ENST00000263774	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
5UTR-intron	ENST00000310513	ENST00000528192	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
5UTR-intron	ENST00000310513	ENST00000529276	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
5UTR-intron	ENST00000310513	ENST00000534208	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
5UTR-intron	ENST00000310513	ENST00000534716	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
5UTR-intron	ENST00000531165	ENST00000263774	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
5UTR-intron	ENST00000531165	ENST00000528192	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
5UTR-intron	ENST00000531165	ENST00000529276	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
5UTR-intron	ENST00000531165	ENST00000534208	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
5UTR-intron	ENST00000531165	ENST00000534716	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-3UTR	ENST00000358597	ENST00000533507	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-3UTR	ENST00000361904	ENST00000533507	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-3UTR	ENST00000395290	ENST00000533507	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-3UTR	ENST00000395292	ENST00000533507	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-3UTR	ENST00000532048	ENST00000533507	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-3UTR	ENST00000539455	ENST00000533507	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000358597	ENST00000263774	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000358597	ENST00000528192	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000358597	ENST00000529276	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000358597	ENST00000534208	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000358597	ENST00000534716	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000361904	ENST00000263774	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000361904	ENST00000528192	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000361904	ENST00000529276	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000361904	ENST00000534208	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000361904	ENST00000534716	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000395290	ENST00000263774	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000395290	ENST00000528192	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000395290	ENST00000529276	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000395290	ENST00000534208	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000395290	ENST00000534716	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000395292	ENST00000263774	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000395292	ENST00000528192	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000395292	ENST00000529276	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000395292	ENST00000534208	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000395292	ENST00000534716	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000532048	ENST00000263774	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000532048	ENST00000528192	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000532048	ENST00000529276	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000532048	ENST00000534208	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000532048	ENST00000534716	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000539455	ENST00000263774	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000539455	ENST00000528192	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000539455	ENST00000529276	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000539455	ENST00000534208	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+
intron-intron	ENST00000539455	ENST00000534716	CELF1	chr11	47574544	-	NDUFS3	chr11	47587458	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

Seq length
(transcript)

BP loci
(transcript)

Predicted start
(transcript)

Predicted stop
(transcript)

Seq length
(amino acids)

DeepORF 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.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

No-coding score

Coding score

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Fusion Genomic Features for CELF1-NDUFS3

FusionAI 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.

Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	1-p	p (fusion gene breakpoint)
CELF1	chr11	47574543	-	NDUFS3	chr11	47587457	+	1.26E-11	1
CELF1	chr11	47574543	-	NDUFS3	chr11	47587457	+	1.26E-11	1

Distribution 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 CELF1-NDUFS3

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:47574544/:47587458)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
.	NDUFS3 O75489
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.	FUNCTION: Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor (PubMed:14729820, PubMed:30140060). Essential for the catalytic activity and assembly of complex I (PubMed:14729820, PubMed:24028823, PubMed:30140060). {ECO:0000269\|PubMed:14729820, ECO:0000269\|PubMed:24028823, ECO:0000269\|PubMed:30140060}.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- In-frame and not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

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Fusion Gene Sequence for CELF1-NDUFS3

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 CELF1-NDUFS3

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for CELF1-NDUFS3

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner	Gene	UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
Tgene	NDUFS3	O75489	DB00157	NADH		Small molecule	Approved\|Nutraceutical

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Related Diseases for CELF1-NDUFS3

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Tgene		C0023264	Leigh Disease	11	CLINGEN;CTD_human;GENOMICS_ENGLAND
Tgene		C1838951	LEIGH SYNDROME DUE TO MITOCHONDRIAL COMPLEX I DEFICIENCY	10	CLINGEN;GENOMICS_ENGLAND
Tgene		C1850597	Leigh Syndrome Due To Mitochondrial Complex II Deficiency	10	CLINGEN
Tgene		C1850598	Leigh Syndrome due to Mitochondrial Complex III Deficiency	10	CLINGEN
Tgene		C1850599	Leigh Syndrome due to Mitochondrial Complex IV Deficiency	10	CLINGEN
Tgene		C1850600	Leigh Syndrome due to Mitochondrial Complex V Deficiency	10	CLINGEN
Tgene		C2931891	Necrotizing encephalopathy, infantile subacute, of Leigh	10	CLINGEN
Tgene		C4748766	MITOCHONDRIAL COMPLEX I DEFICIENCY, NUCLEAR TYPE 8	4	GENOMICS_ENGLAND;UNIPROT
Tgene		C1838979	MITOCHONDRIAL COMPLEX I DEFICIENCY	3	GENOMICS_ENGLAND;ORPHANET
Tgene		C0006142	Malignant neoplasm of breast	1	CTD_human
Tgene		C0019193	Hepatitis, Toxic	1	CTD_human
Tgene		C0029124	Optic Atrophy	1	CTD_human
Tgene		C0678222	Breast Carcinoma	1	CTD_human
Tgene		C0751267	Encephalopathy, Subacute Necrotizing, Infantile	1	CTD_human
Tgene		C0751268	Encephalopathy, Subacute Necrotizing, Juvenile	1	CTD_human
Tgene		C0751651	Mitochondrial Diseases	1	GENOMICS_ENGLAND
Tgene		C0860207	Drug-Induced Liver Disease	1	CTD_human
Tgene		C1257931	Mammary Neoplasms, Human	1	CTD_human
Tgene		C1262760	Hepatitis, Drug-Induced	1	CTD_human
Tgene		C1458155	Mammary Neoplasms	1	CTD_human
Tgene		C3658290	Drug-Induced Acute Liver Injury	1	CTD_human
Tgene		C4277682	Chemical and Drug Induced Liver Injury	1	CTD_human
Tgene		C4279912	Chemically-Induced Liver Toxicity	1	CTD_human
Tgene		C4704874	Mammary Carcinoma, Human	1	CTD_human

Fusion Gene Studies in Kim Lab

Fusion gene:CELF1-NDUFS3 (FusionGDB2 ID:HG10658TG4722)

Fusion Gene Summary for CELF1-NDUFS3

Fusion Gene ORF analysis for CELF1-NDUFS3

Fusion Genomic Features for CELF1-NDUFS3

Fusion Protein Features for CELF1-NDUFS3

Fusion Gene Sequence for CELF1-NDUFS3

Fusion Gene PPI Analysis for CELF1-NDUFS3

Related Drugs for CELF1-NDUFS3

Related Diseases for CELF1-NDUFS3

Fusion Gene Studies
in Kim Lab