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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:NPTN-NEO1 (FusionGDB2 ID:60031)

Fusion Gene Summary for NPTN-NEO1

check button Fusion gene summary
Fusion gene informationFusion gene name: NPTN-NEO1
Fusion gene ID: 60031
HgeneTgene
Gene symbol

NPTN

NEO1

Gene ID

27020

4756

Gene nameneuroplastinneogenin 1
SynonymsGP55|GP65|SDFR1|SDR1|np55|np65IGDCC2|NGN|NTN1R2
Cytomap

15q24.1

15q24.1

Type of geneprotein-codingprotein-coding
DescriptionneuroplastinSDR-1stromal cell derived factor receptor 1stromal cell-derived receptor 1neogeninimmunoglobulin superfamily DCC subclass member 2neogenin homolog 1
Modification date2020031320200313
UniProtAcc

Q9Y639

Q92859

Ensembl transtripts involved in fusion geneENST00000287226, ENST00000345330, 
ENST00000351217, ENST00000542234, 
ENST00000545878, ENST00000562924, 
ENST00000563691, ENST00000564551, 
ENST00000261908, ENST00000339362, 
ENST00000558964, ENST00000560262, 
ENST00000560352, 
Fusion gene scores* DoF score11 X 10 X 7=7708 X 8 X 4=256
# samples 138
** MAII scorelog2(13/770*10)=-2.56634682255381
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/256*10)=-1.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NPTN [Title/Abstract] AND NEO1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNEO1(73418911)-NPTN(73866136), # samples:1
NPTN(73925466)-NEO1(73528628), # samples:1
Anticipated loss of major functional domain due to fusion event.NEO1-NPTN seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
NEO1-NPTN seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
NEO1-NPTN seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID

check buttonFusion gene breakpoints across NPTN (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 NEO1 (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
ChimerDB4Non-CancerTCGA-CG-5734-11ANPTNchr15

73925466

-NEO1chr15

73528628

+


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Fusion Gene ORF analysis for NPTN-NEO1

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-intronENST00000287226ENST00000261908NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000287226ENST00000339362NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000287226ENST00000558964NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000287226ENST00000560262NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000287226ENST00000560352NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000345330ENST00000261908NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000345330ENST00000339362NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000345330ENST00000558964NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000345330ENST00000560262NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000345330ENST00000560352NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000351217ENST00000261908NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000351217ENST00000339362NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000351217ENST00000558964NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000351217ENST00000560262NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000351217ENST00000560352NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000542234ENST00000261908NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000542234ENST00000339362NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000542234ENST00000558964NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000542234ENST00000560262NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000542234ENST00000560352NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000545878ENST00000261908NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000545878ENST00000339362NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000545878ENST00000558964NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000545878ENST00000560262NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000545878ENST00000560352NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000562924ENST00000261908NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000562924ENST00000339362NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000562924ENST00000558964NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000562924ENST00000560262NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000562924ENST00000560352NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000563691ENST00000261908NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000563691ENST00000339362NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000563691ENST00000558964NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000563691ENST00000560262NPTNchr15

73925466

-NEO1chr15

73528628

+
5CDS-intronENST00000563691ENST00000560352NPTNchr15

73925466

-NEO1chr15

73528628

+
5UTR-intronENST00000564551ENST00000261908NPTNchr15

73925466

-NEO1chr15

73528628

+
5UTR-intronENST00000564551ENST00000339362NPTNchr15

73925466

-NEO1chr15

73528628

+
5UTR-intronENST00000564551ENST00000558964NPTNchr15

73925466

-NEO1chr15

73528628

+
5UTR-intronENST00000564551ENST00000560262NPTNchr15

73925466

-NEO1chr15

73528628

+
5UTR-intronENST00000564551ENST00000560352NPTNchr15

73925466

-NEO1chr15

73528628

+

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 NPTN-NEO1


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 NPTN-NEO1


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/:73418911/:73866136)
- 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
NPTN

Q9Y639

NEO1

Q92859

FUNCTION: Probable homophilic and heterophilic cell adhesion molecule involved in long term potentiation at hippocampal excitatory synapses through activation of p38MAPK. May also regulate neurite outgrowth by activating the FGFR1 signaling pathway. May play a role in synaptic plasticity (By similarity). {ECO:0000250}.FUNCTION: Multi-functional cell surface receptor regulating cell adhesion in many diverse developmental processes, including neural tube and mammary gland formation, myogenesis and angiogenesis. Receptor for members of the BMP, netrin, and repulsive guidance molecule (RGM) families. Netrin-Neogenin interactions result in a chemoattractive axon guidance response and cell-cell adhesion, the interaction between NEO1/Neogenin and RGMa and RGMb induces a chemorepulsive response. {ECO:0000269|PubMed:21149453}.

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 NPTN-NEO1


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 NPTN-NEO1


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 NPTN-NEO1


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 NPTN-NEO1


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