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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:NRDE2-GRIN1 (FusionGDB2 ID:60245)

Fusion Gene Summary for NRDE2-GRIN1

check button Fusion gene summary
Fusion gene informationFusion gene name: NRDE2-GRIN1
Fusion gene ID: 60245
HgeneTgene
Gene symbol

NRDE2

GRIN1

Gene ID

55051

114787

Gene nameNRDE-2, necessary for RNA interference, domain containingG protein regulated inducer of neurite outgrowth 1
SynonymsC14orf102GRIN1
Cytomap

14q32.11

5q35.2

Type of geneprotein-codingprotein-coding
Descriptionnuclear exosome regulator NRDE2UPF0614 protein C14orf102protein NRDE2 homologG protein-regulated inducer of neurite outgrowth 1
Modification date2020031320200313
UniProtAcc

Q9H7Z3

Q05586

Ensembl transtripts involved in fusion geneENST00000354366, ENST00000357904, 
ENST00000557106, 		ENST00000315048, 
ENST00000371561, ENST00000350902, 
ENST00000371546, ENST00000371550, 
ENST00000371553, ENST00000371555, 
ENST00000371559, ENST00000371560, 
ENST00000471122, 
Fusion gene scores* DoF score5 X 4 X 4=805 X 5 X 5=125
# samples 56
** MAII scorelog2(5/80*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/125*10)=-1.05889368905357
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NRDE2 [Title/Abstract] AND GRIN1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNRDE2(90770600)-GRIN1(140052831), # 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)

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 NRDE2 (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 GRIN1 (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
ChimerDB4STADTCGA-FP-8211-01ANRDE2chr14

90770600

-GRIN1chr9

140052831

+


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Fusion Gene ORF analysis for NRDE2-GRIN1

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
intron-3CDSENST00000354366ENST00000315048NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3CDSENST00000354366ENST00000371561NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3CDSENST00000357904ENST00000315048NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3CDSENST00000357904ENST00000371561NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3CDSENST00000557106ENST00000315048NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3CDSENST00000557106ENST00000371561NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000354366ENST00000350902NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000354366ENST00000371546NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000354366ENST00000371550NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000354366ENST00000371553NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000354366ENST00000371555NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000354366ENST00000371559NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000354366ENST00000371560NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000354366ENST00000471122NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000357904ENST00000350902NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000357904ENST00000371546NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000357904ENST00000371550NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000357904ENST00000371553NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000357904ENST00000371555NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000357904ENST00000371559NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000357904ENST00000371560NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000357904ENST00000471122NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000557106ENST00000350902NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000557106ENST00000371546NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000557106ENST00000371550NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000557106ENST00000371553NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000557106ENST00000371555NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000557106ENST00000371559NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000557106ENST00000371560NRDE2chr14

90770600

-GRIN1chr9

140052831

+
intron-3UTRENST00000557106ENST00000471122NRDE2chr14

90770600

-GRIN1chr9

140052831

+

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 NRDE2-GRIN1


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 NRDE2-GRIN1


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/:90770600/:140052831)
- 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
NRDE2

Q9H7Z3

GRIN1

Q05586

FUNCTION: Protein of the nuclear speckles that regulates RNA degradation and export from the nucleus through its interaction with MTREX an essential factor directing various RNAs to exosomal degradation (PubMed:30842217). Changes the conformation of MTREX, precluding its association with the nuclear exosome and interaction with proteins required for its function in RNA exosomal degradation (PubMed:30842217). Negatively regulates, for instance, the degradation of mRNAs and lncRNAs by inhibiting their MTREX-mediated recruitment to nuclear exosome (PubMed:30842217). By preventing the degradation of RNAs in the nucleus, it promotes their export to the cytoplasm (PubMed:30842217). U5 snRNP-associated RNA splicing factor which is required for efficient splicing of CEP131 pre-mRNA and plays an important role in centrosome maturation, integrity and function during mitosis (PubMed:30538148). Suppresses intron retention in a subset of pre-mRNAs containing short, GC-rich introns with relatively weak 5' and 3' splice sites (PubMed:30538148). Plays a role in DNA damage response (PubMed:29902117). {ECO:0000269|PubMed:29902117, ECO:0000269|PubMed:30538148, ECO:0000269|PubMed:30842217}.FUNCTION: Component of NMDA receptor complexes that function as heterotetrameric, ligand-gated ion channels with high calcium permeability and voltage-dependent sensitivity to magnesium. Channel activation requires binding of the neurotransmitter glutamate to the epsilon subunit, glycine binding to the zeta subunit, plus membrane depolarization to eliminate channel inhibition by Mg(2+) (PubMed:7685113, PubMed:28126851, PubMed:26919761, PubMed:26875626, PubMed:28105280). Sensitivity to glutamate and channel kinetics depend on the subunit composition (PubMed:26919761). {ECO:0000269|PubMed:26875626, ECO:0000269|PubMed:26919761, ECO:0000269|PubMed:28105280, ECO:0000269|PubMed:28126851, ECO:0000269|PubMed:7685113}.

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 NRDE2-GRIN1


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 NRDE2-GRIN1


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 NRDE2-GRIN1


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 NRDE2-GRIN1


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