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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:NPAS3-LONP1 (FusionGDB2 ID:59837)

Fusion Gene Summary for NPAS3-LONP1

Fusion gene summary

Fusion gene information	Fusion gene name: NPAS3-LONP1
	Fusion gene ID: 59837
		Hgene	Tgene
	Gene symbol	NPAS3	LONP1
	Gene ID	64067	9361
	Gene name	neuronal PAS domain protein 3	lon peptidase 1, mitochondrial
	Synonyms	MOP6\|PASD6\|bHLHe12	CODASS\|LON\|LONP\|LonHS\|PIM1\|PRSS15\|hLON
	Cytomap	14q13.1	19p13.3
	Type of gene	protein-coding	protein-coding
	Description	neuronal PAS domain-containing protein 3PAS domain-containing protein 6basic-helix-loop-helix-PAS protein MOP6class E basic helix-loop-helix protein 12member of PAS protein 6neuronal PAS3	lon protease homolog, mitochondrialhLON ATP-dependent proteaselon protease-like proteinmitochondrial ATP-dependent protease Lonmitochondrial lon protease-like proteinserine protease 15
	Modification date	20200313	20200313
	UniProtAcc	Q8IXF0	P36776
	Ensembl transtripts involved in fusion gene	ENST00000341321, ENST00000346562, ENST00000356141, ENST00000357798, ENST00000547068, ENST00000548645, ENST00000550662, ENST00000551008, ENST00000551492,	ENST00000360614, ENST00000540670, ENST00000585374, ENST00000590511, ENST00000590729, ENST00000593119,
Fusion gene scores	* DoF score	10 X 9 X 4=360	3 X 4 X 3=36
	# samples	13	5
	** MAII score	log2(13/360*10)=-1.46948528330122 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(5/36*10)=0.473931188332412 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context	PubMed: NPAS3 [Title/Abstract] AND LONP1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	NPAS3(34003419)-LONP1(5691845), # 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
Tgene	LONP1	GO:0034599	cellular response to oxidative stress	17420247
Tgene	LONP1	GO:0051603	proteolysis involved in cellular protein catabolic process	8248235\|17420247

Fusion gene breakpoints across NPAS3 (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 LONP1 (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	BU859918	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+

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Fusion Gene ORF analysis for NPAS3-LONP1

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
intron-intron	ENST00000341321	ENST00000360614	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000341321	ENST00000540670	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000341321	ENST00000585374	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000341321	ENST00000590511	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000341321	ENST00000590729	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000341321	ENST00000593119	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000346562	ENST00000360614	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000346562	ENST00000540670	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000346562	ENST00000585374	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000346562	ENST00000590511	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000346562	ENST00000590729	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000346562	ENST00000593119	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000356141	ENST00000360614	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000356141	ENST00000540670	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000356141	ENST00000585374	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000356141	ENST00000590511	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000356141	ENST00000590729	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000356141	ENST00000593119	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000357798	ENST00000360614	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000357798	ENST00000540670	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000357798	ENST00000585374	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000357798	ENST00000590511	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000357798	ENST00000590729	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000357798	ENST00000593119	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000547068	ENST00000360614	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000547068	ENST00000540670	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000547068	ENST00000585374	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000547068	ENST00000590511	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000547068	ENST00000590729	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000547068	ENST00000593119	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000548645	ENST00000360614	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000548645	ENST00000540670	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000548645	ENST00000585374	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000548645	ENST00000590511	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000548645	ENST00000590729	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000548645	ENST00000593119	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000550662	ENST00000360614	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000550662	ENST00000540670	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000550662	ENST00000585374	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000550662	ENST00000590511	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000550662	ENST00000590729	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000550662	ENST00000593119	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000551008	ENST00000360614	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000551008	ENST00000540670	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000551008	ENST00000585374	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000551008	ENST00000590511	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000551008	ENST00000590729	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000551008	ENST00000593119	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000551492	ENST00000360614	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000551492	ENST00000540670	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000551492	ENST00000585374	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000551492	ENST00000590511	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000551492	ENST00000590729	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+
intron-intron	ENST00000551492	ENST00000593119	NPAS3	chr14	34003419	-	LONP1	chr19	5691845	+

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 NPAS3-LONP1

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 NPAS3-LONP1

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:34003419/:5691845)
- 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
NPAS3 Q8IXF0	LONP1 P36776
FUNCTION: May play a broad role in neurogenesis. May control regulatory pathways relevant to schizophrenia and to psychotic illness (By similarity). {ECO:0000250}.	FUNCTION: ATP-dependent serine protease that mediates the selective degradation of misfolded, unassembled or oxidatively damaged polypeptides as well as certain short-lived regulatory proteins in the mitochondrial matrix. May also have a chaperone function in the assembly of inner membrane protein complexes. Participates in the regulation of mitochondrial gene expression and in the maintenance of the integrity of the mitochondrial genome. Binds to mitochondrial promoters and RNA in a single-stranded, site-specific, and strand-specific manner. May regulate mitochondrial DNA replication and/or gene expression using site-specific, single-stranded DNA binding to target the degradation of regulatory proteins binding to adjacent sites in mitochondrial promoters (PubMed:12198491, PubMed:15870080, PubMed:17420247, PubMed:8248235). Endogenous substrates include mitochondrial steroidogenic acute regulatory (StAR) protein, helicase Twinkle (TWNK) and the large ribosomal subunit protein bL32m. bL32m is protected from degradation by LONP1 when it is bound to a nucleic acid (RNA), but TWNK is not (PubMed:17579211, PubMed:28377575). {ECO:0000255\|HAMAP-Rule:MF_03120, ECO:0000269\|PubMed:12198491, ECO:0000269\|PubMed:15870080, ECO:0000269\|PubMed:17420247, ECO:0000269\|PubMed:17579211, ECO:0000269\|PubMed:28377575, ECO:0000269\|PubMed:8248235}.

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 NPAS3-LONP1

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 NPAS3-LONP1

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 NPAS3-LONP1

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 NPAS3-LONP1

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source