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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:NDE1-NDE1 (FusionGDB2 ID:57927)

Fusion Gene Summary for NDE1-NDE1

check button Fusion gene summary
Fusion gene informationFusion gene name: NDE1-NDE1
Fusion gene ID: 57927
HgeneTgene
Gene symbol

NDE1

NDE1

Gene ID

54820

54820

Gene namenudE neurodevelopment protein 1nudE neurodevelopment protein 1
SynonymsHOM-TES-87|LIS4|MHAC|NDE|NUDE|NUDE1HOM-TES-87|LIS4|MHAC|NDE|NUDE|NUDE1
Cytomap

16p13.11

16p13.11

Type of geneprotein-codingprotein-coding
Descriptionnuclear distribution protein nudE homolog 1LIS1-interacting protein NUDE1, rat homologepididymis secretory sperm binding proteinnudE nuclear distribution E homolog 1nudE nuclear distribution gene E homolog 1nuclear distribution protein nudE homolog 1LIS1-interacting protein NUDE1, rat homologepididymis secretory sperm binding proteinnudE nuclear distribution E homolog 1nudE nuclear distribution gene E homolog 1
Modification date2020031320200313
UniProtAcc

Q9NXR1

Q9NXR1

Ensembl transtripts involved in fusion geneENST00000342673, ENST00000396354, 
ENST00000396355, ENST00000571896, 
ENST00000396353, 		ENST00000342673, 
ENST00000396353, ENST00000396354, 
ENST00000396355, ENST00000571896, 
Fusion gene scores* DoF score13 X 15 X 5=9759 X 10 X 6=540
# samples 1611
** MAII scorelog2(16/975*10)=-2.60733031374961
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/540*10)=-2.29545588352617
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NDE1 [Title/Abstract] AND NDE1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNDE1(15818594)-NDE1(15814858), # 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)

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 NDE1 (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 NDE1 (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
ChiTaRS5.0N/AAA516440NDE1chr16

15802694

+NDE1chr16

15797691

+
ChiTaRS5.0N/AAI695545NDE1chr16

15818594

+NDE1chr16

15814858

+
ChiTaRS5.0N/AAI700249NDE1chr16

15818594

+NDE1chr16

15814858

+


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Fusion Gene ORF analysis for NDE1-NDE1

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
3UTR-intronENST00000342673ENST00000342673NDE1chr16

15818594

+NDE1chr16

15814858

+
3UTR-intronENST00000342673ENST00000396353NDE1chr16

15818594

+NDE1chr16

15814858

+
3UTR-intronENST00000342673ENST00000396354NDE1chr16

15818594

+NDE1chr16

15814858

+
3UTR-intronENST00000342673ENST00000396355NDE1chr16

15818594

+NDE1chr16

15814858

+
3UTR-intronENST00000342673ENST00000571896NDE1chr16

15818594

+NDE1chr16

15814858

+
3UTR-intronENST00000396354ENST00000342673NDE1chr16

15818594

+NDE1chr16

15814858

+
3UTR-intronENST00000396354ENST00000396353NDE1chr16

15818594

+NDE1chr16

15814858

+
3UTR-intronENST00000396354ENST00000396354NDE1chr16

15818594

+NDE1chr16

15814858

+
3UTR-intronENST00000396354ENST00000396355NDE1chr16

15818594

+NDE1chr16

15814858

+
3UTR-intronENST00000396354ENST00000571896NDE1chr16

15818594

+NDE1chr16

15814858

+
3UTR-intronENST00000396355ENST00000342673NDE1chr16

15818594

+NDE1chr16

15814858

+
3UTR-intronENST00000396355ENST00000396353NDE1chr16

15818594

+NDE1chr16

15814858

+
3UTR-intronENST00000396355ENST00000396354NDE1chr16

15818594

+NDE1chr16

15814858

+
3UTR-intronENST00000396355ENST00000396355NDE1chr16

15818594

+NDE1chr16

15814858

+
3UTR-intronENST00000396355ENST00000571896NDE1chr16

15818594

+NDE1chr16

15814858

+
3UTR-intronENST00000571896ENST00000342673NDE1chr16

15818594

+NDE1chr16

15814858

+
3UTR-intronENST00000571896ENST00000396353NDE1chr16

15818594

+NDE1chr16

15814858

+
3UTR-intronENST00000571896ENST00000396354NDE1chr16

15818594

+NDE1chr16

15814858

+
3UTR-intronENST00000571896ENST00000396355NDE1chr16

15818594

+NDE1chr16

15814858

+
3UTR-intronENST00000571896ENST00000571896NDE1chr16

15818594

+NDE1chr16

15814858

+
intron-intronENST00000342673ENST00000342673NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000342673ENST00000396353NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000342673ENST00000396354NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000342673ENST00000396355NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000342673ENST00000571896NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000396353ENST00000342673NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000396353ENST00000342673NDE1chr16

15818594

+NDE1chr16

15814858

+
intron-intronENST00000396353ENST00000396353NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000396353ENST00000396353NDE1chr16

15818594

+NDE1chr16

15814858

+
intron-intronENST00000396353ENST00000396354NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000396353ENST00000396354NDE1chr16

15818594

+NDE1chr16

15814858

+
intron-intronENST00000396353ENST00000396355NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000396353ENST00000396355NDE1chr16

15818594

+NDE1chr16

15814858

+
intron-intronENST00000396353ENST00000571896NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000396353ENST00000571896NDE1chr16

15818594

+NDE1chr16

15814858

+
intron-intronENST00000396354ENST00000342673NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000396354ENST00000396353NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000396354ENST00000396354NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000396354ENST00000396355NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000396354ENST00000571896NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000396355ENST00000342673NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000396355ENST00000396353NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000396355ENST00000396354NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000396355ENST00000396355NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000396355ENST00000571896NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000571896ENST00000342673NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000571896ENST00000396353NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000571896ENST00000396354NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000571896ENST00000396355NDE1chr16

15802694

+NDE1chr16

15797691

+
intron-intronENST00000571896ENST00000571896NDE1chr16

15802694

+NDE1chr16

15797691

+

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 NDE1-NDE1


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 NDE1-NDE1


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/:15818594/:15814858)
- 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
NDE1

Q9NXR1

NDE1

Q9NXR1

FUNCTION: Required for centrosome duplication and formation and function of the mitotic spindle. Essential for the development of the cerebral cortex. May regulate the production of neurons by controlling the orientation of the mitotic spindle during division of cortical neuronal progenitors of the proliferative ventricular zone of the brain. Orientation of the division plane perpendicular to the layers of the cortex gives rise to two proliferative neuronal progenitors whereas parallel orientation of the division plane yields one proliferative neuronal progenitor and a post-mitotic neuron. A premature shift towards a neuronal fate within the progenitor population may result in an overall reduction in the final number of neurons and an increase in the number of neurons in the deeper layers of the cortex. {ECO:0000269|PubMed:17600710, ECO:0000269|PubMed:21529752}.FUNCTION: Required for centrosome duplication and formation and function of the mitotic spindle. Essential for the development of the cerebral cortex. May regulate the production of neurons by controlling the orientation of the mitotic spindle during division of cortical neuronal progenitors of the proliferative ventricular zone of the brain. Orientation of the division plane perpendicular to the layers of the cortex gives rise to two proliferative neuronal progenitors whereas parallel orientation of the division plane yields one proliferative neuronal progenitor and a post-mitotic neuron. A premature shift towards a neuronal fate within the progenitor population may result in an overall reduction in the final number of neurons and an increase in the number of neurons in the deeper layers of the cortex. {ECO:0000269|PubMed:17600710, ECO:0000269|PubMed:21529752}.

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 NDE1-NDE1


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 NDE1-NDE1


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 NDE1-NDE1


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 NDE1-NDE1


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