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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:NFIC-RPS3 (FusionGDB2 ID:58922)

Fusion Gene Summary for NFIC-RPS3

Fusion gene summary

Fusion gene information	Fusion gene name: NFIC-RPS3
	Fusion gene ID: 58922
		Hgene	Tgene
	Gene symbol	NFIC	RPS3
	Gene ID	4782	6188
	Gene name	nuclear factor I C	ribosomal protein S3
	Synonyms	CTF\|CTF5\|NF-I\|NFI	S3
	Cytomap	19p13.3	11q13.4
	Type of gene	protein-coding	protein-coding
	Description	nuclear factor 1 C-typeCCAAT-box-binding transcription factorNF-I/CNF1-CTGGCA-binding proteinnuclear factor I/C (CCAAT-binding transcription factor)	40S ribosomal protein S3IMR-90 ribosomal protein S3small ribosomal subunit protein uS3
	Modification date	20200313	20200327
	UniProtAcc	P08651	.
	Ensembl transtripts involved in fusion gene	ENST00000346156, ENST00000589123, ENST00000341919, ENST00000395111, ENST00000443272, ENST00000586919, ENST00000588839, ENST00000590282,	ENST00000527446, ENST00000278572, ENST00000524851, ENST00000526608, ENST00000529285, ENST00000530164, ENST00000531188, ENST00000534440,
Fusion gene scores	* DoF score	30 X 20 X 13=7800	17 X 19 X 5=1615
	# samples	36	22
	** MAII score	log2(36/7800*10)=-4.4374053123073 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(22/1615*10)=-2.87595873605663 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: NFIC [Title/Abstract] AND RPS3 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	NFIC(3463200)-RPS3(75132771), # 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)

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	NFIC	GO:0000122	negative regulation of transcription by RNA polymerase II	19706729
Hgene	NFIC	GO:0045944	positive regulation of transcription by RNA polymerase II	1524678\|19706729
Tgene	RPS3	GO:0006979	response to oxidative stress	23911537
Tgene	RPS3	GO:0017148	negative regulation of translation	20217897
Tgene	RPS3	GO:0031397	negative regulation of protein ubiquitination	19656744
Tgene	RPS3	GO:0032079	positive regulation of endodeoxyribonuclease activity	18973764
Tgene	RPS3	GO:0042769	DNA damage response, detection of DNA damage	23911537
Tgene	RPS3	GO:0045739	positive regulation of DNA repair	23911537
Tgene	RPS3	GO:0061481	response to TNF agonist	20041225
Tgene	RPS3	GO:0070301	cellular response to hydrogen peroxide	23911537
Tgene	RPS3	GO:1901224	positive regulation of NIK/NF-kappaB signaling	20041225
Tgene	RPS3	GO:1902546	positive regulation of DNA N-glycosylase activity	15518571
Tgene	RPS3	GO:1905053	positive regulation of base-excision repair	18973764
Tgene	RPS3	GO:2001235	positive regulation of apoptotic signaling pathway	14988002

Fusion gene breakpoints across NFIC (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across RPS3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	BRCA	TCGA-AQ-A04L-01B	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+

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Fusion Gene ORF analysis for NFIC-RPS3

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
3UTR-3UTR	ENST00000346156	ENST00000527446	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
3UTR-3UTR	ENST00000589123	ENST00000527446	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
3UTR-intron	ENST00000346156	ENST00000278572	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
3UTR-intron	ENST00000346156	ENST00000524851	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
3UTR-intron	ENST00000346156	ENST00000526608	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
3UTR-intron	ENST00000346156	ENST00000529285	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
3UTR-intron	ENST00000346156	ENST00000530164	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
3UTR-intron	ENST00000346156	ENST00000531188	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
3UTR-intron	ENST00000346156	ENST00000534440	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
3UTR-intron	ENST00000589123	ENST00000278572	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
3UTR-intron	ENST00000589123	ENST00000524851	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
3UTR-intron	ENST00000589123	ENST00000526608	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
3UTR-intron	ENST00000589123	ENST00000529285	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
3UTR-intron	ENST00000589123	ENST00000530164	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
3UTR-intron	ENST00000589123	ENST00000531188	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
3UTR-intron	ENST00000589123	ENST00000534440	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-3UTR	ENST00000341919	ENST00000527446	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-3UTR	ENST00000395111	ENST00000527446	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-3UTR	ENST00000443272	ENST00000527446	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-3UTR	ENST00000586919	ENST00000527446	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-3UTR	ENST00000588839	ENST00000527446	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-3UTR	ENST00000590282	ENST00000527446	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000341919	ENST00000278572	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000341919	ENST00000524851	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000341919	ENST00000526608	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000341919	ENST00000529285	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000341919	ENST00000530164	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000341919	ENST00000531188	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000341919	ENST00000534440	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000395111	ENST00000278572	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000395111	ENST00000524851	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000395111	ENST00000526608	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000395111	ENST00000529285	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000395111	ENST00000530164	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000395111	ENST00000531188	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000395111	ENST00000534440	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000443272	ENST00000278572	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000443272	ENST00000524851	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000443272	ENST00000526608	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000443272	ENST00000529285	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000443272	ENST00000530164	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000443272	ENST00000531188	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000443272	ENST00000534440	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000586919	ENST00000278572	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000586919	ENST00000524851	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000586919	ENST00000526608	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000586919	ENST00000529285	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000586919	ENST00000530164	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000586919	ENST00000531188	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000586919	ENST00000534440	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000588839	ENST00000278572	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000588839	ENST00000524851	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000588839	ENST00000526608	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000588839	ENST00000529285	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000588839	ENST00000530164	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000588839	ENST00000531188	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000588839	ENST00000534440	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000590282	ENST00000278572	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000590282	ENST00000524851	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000590282	ENST00000526608	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000590282	ENST00000529285	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000590282	ENST00000530164	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000590282	ENST00000531188	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+
intron-intron	ENST00000590282	ENST00000534440	NFIC	chr19	3463200	+	RPS3	chr11	75132771	+

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 NFIC-RPS3

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)

Distribution 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.

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 NFIC-RPS3

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:3463200/:75132771)
- 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
NFIC P08651	.
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.	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}.

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 NFIC-RPS3

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 NFIC-RPS3

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 NFIC-RPS3

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

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Related Diseases for NFIC-RPS3

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source