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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:NONO-RPL28 (FusionGDB2 ID:59613)

Fusion Gene Summary for NONO-RPL28

Fusion gene summary

Fusion gene information	Fusion gene name: NONO-RPL28
	Fusion gene ID: 59613
		Hgene	Tgene
	Gene symbol	NONO	RPL28
	Gene ID	4841	6158
	Gene name	non-POU domain containing octamer binding	ribosomal protein L28
	Synonyms	MRXS34\|NMT55\|NRB54\|P54\|P54NRB\|PPP1R114	L28
	Cytomap	Xq13.1	19q13.42
	Type of gene	protein-coding	protein-coding
	Description	non-POU domain-containing octamer-binding protein54 kDa nuclear RNA- and DNA-binding protein55 kDa nuclear proteinDNA-binding p52/p100 complex, 52 kDa subunitnon-POU domain-containing octamer (ATGCAAAT) binding proteinp54(nrb)protein phosphatase 1,	60S ribosomal protein L28large ribosomal subunit protein eL28
	Modification date	20200313	20200313
	UniProtAcc	Q15233	.
	Ensembl transtripts involved in fusion gene	ENST00000490044, ENST00000276079, ENST00000373841, ENST00000373856, ENST00000535149,	ENST00000344063, ENST00000558131, ENST00000560583, ENST00000428193, ENST00000431533, ENST00000458349, ENST00000558752, ENST00000558815, ENST00000559463, ENST00000560055,
Fusion gene scores	* DoF score	8 X 8 X 2=128	22 X 19 X 8=3344
	# samples	8	26
	** MAII score	log2(8/128*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(26/3344*10)=-3.68499131905243 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: NONO [Title/Abstract] AND RPL28 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	NONO(70517282)-RPL28(55899686), # samples:1
Anticipated loss of major functional domain due to fusion event.	NONO-RPL28 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF. NONO-RPL28 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. NONO-RPL28 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF. NONO-RPL28 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.

* 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	NONO	GO:0002218	activation of innate immune response	28712728
Hgene	NONO	GO:1903377	negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway	15790595

Fusion gene breakpoints across NONO (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 RPL28 (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
ChiTaRS5.0	N/A	BQ653766	NONO	chrX	70517282	+	RPL28	chr19	55899686	+

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Fusion Gene ORF analysis for NONO-RPL28

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-3CDS	ENST00000490044	ENST00000344063	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
3UTR-3UTR	ENST00000490044	ENST00000558131	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
3UTR-3UTR	ENST00000490044	ENST00000560583	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
3UTR-intron	ENST00000490044	ENST00000428193	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
3UTR-intron	ENST00000490044	ENST00000431533	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
3UTR-intron	ENST00000490044	ENST00000458349	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
3UTR-intron	ENST00000490044	ENST00000558752	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
3UTR-intron	ENST00000490044	ENST00000558815	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
3UTR-intron	ENST00000490044	ENST00000559463	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
3UTR-intron	ENST00000490044	ENST00000560055	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-3UTR	ENST00000276079	ENST00000558131	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-3UTR	ENST00000276079	ENST00000560583	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-3UTR	ENST00000373841	ENST00000558131	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-3UTR	ENST00000373841	ENST00000560583	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-3UTR	ENST00000373856	ENST00000558131	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-3UTR	ENST00000373856	ENST00000560583	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-3UTR	ENST00000535149	ENST00000558131	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-3UTR	ENST00000535149	ENST00000560583	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000276079	ENST00000428193	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000276079	ENST00000431533	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000276079	ENST00000458349	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000276079	ENST00000558752	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000276079	ENST00000558815	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000276079	ENST00000559463	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000276079	ENST00000560055	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000373841	ENST00000428193	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000373841	ENST00000431533	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000373841	ENST00000458349	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000373841	ENST00000558752	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000373841	ENST00000558815	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000373841	ENST00000559463	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000373841	ENST00000560055	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000373856	ENST00000428193	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000373856	ENST00000431533	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000373856	ENST00000458349	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000373856	ENST00000558752	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000373856	ENST00000558815	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000373856	ENST00000559463	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000373856	ENST00000560055	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000535149	ENST00000428193	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000535149	ENST00000431533	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000535149	ENST00000458349	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000535149	ENST00000558752	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000535149	ENST00000558815	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000535149	ENST00000559463	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
5CDS-intron	ENST00000535149	ENST00000560055	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
Frame-shift	ENST00000276079	ENST00000344063	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
Frame-shift	ENST00000373841	ENST00000344063	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
Frame-shift	ENST00000373856	ENST00000344063	NONO	chrX	70517282	+	RPL28	chr19	55899686	+
Frame-shift	ENST00000535149	ENST00000344063	NONO	chrX	70517282	+	RPL28	chr19	55899686	+

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 NONO-RPL28

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 NONO-RPL28

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:70517282/:55899686)
- 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
NONO Q15233	.
FUNCTION: DNA- and RNA binding protein, involved in several nuclear processes. Binds the conventional octamer sequence in double-stranded DNA. Also binds single-stranded DNA and RNA at a site independent of the duplex site. Involved in pre-mRNA splicing, probably as a heterodimer with SFPQ. Interacts with U5 snRNA, probably by binding to a purine-rich sequence located on the 3' side of U5 snRNA stem 1b. Together with PSPC1, required for the formation of nuclear paraspeckles. The SFPQ-NONO heteromer associated with MATR3 may play a role in nuclear retention of defective RNAs. The SFPQ-NONO heteromer may be involved in DNA unwinding by modulating the function of topoisomerase I/TOP1. The SFPQ-NONO heteromer may be involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination and may stabilize paired DNA ends. In vitro, the complex strongly stimulates DNA end joining, binds directly to the DNA substrates and cooperates with the Ku70/G22P1-Ku80/XRCC5 (Ku) dimer to establish a functional preligation complex. NONO is involved in transcriptional regulation. The SFPQ-NONO-NR5A1 complex binds to the CYP17 promoter and regulates basal and cAMP-dependent transcriptional activity. NONO binds to an enhancer element in long terminal repeats of endogenous intracisternal A particles (IAPs) and activates transcription. Regulates the circadian clock by repressing the transcriptional activator activity of the CLOCK-ARNTL/BMAL1 heterodimer. Important for the functional organization of GABAergic synapses. Plays a specific and important role in the regulation of synaptic RNAs and GPHN/gephyrin scaffold structure, through the regulation of GABRA2 transcript. Plays a role in the regulation of DNA virus-mediated innate immune response by assembling into the HDP-RNP complex, a complex that serves as a platform for IRF3 phosphorylation and subsequent innate immune response activation through the cGAS-STING pathway (PubMed:28712728). {ECO:0000250\|UniProtKB:Q99K48, ECO:0000269\|PubMed:10858305, ECO:0000269\|PubMed:11525732, ECO:0000269\|PubMed:11897684, ECO:0000269\|PubMed:15590677, ECO:0000269\|PubMed:22416126, ECO:0000269\|PubMed:26571461, ECO:0000269\|PubMed:28712728}.	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 NONO-RPL28

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 NONO-RPL28

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 NONO-RPL28

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 NONO-RPL28

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source