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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:GDI1-NDUFS2 (FusionGDB2 ID:32856)

Fusion Gene Summary for GDI1-NDUFS2

check button Fusion gene summary
Fusion gene informationFusion gene name: GDI1-NDUFS2
Fusion gene ID: 32856
HgeneTgene
Gene symbol

GDI1

NDUFS2

Gene ID

2664

4720

Gene nameGDP dissociation inhibitor 1NADH:ubiquinone oxidoreductase core subunit S2
Synonyms1A|GDIL|MRX41|MRX48|OPHN2|RABGD1A|RABGDIA|XAP-4CI-49|MC1DN6
Cytomap

Xq28

1q23.3

Type of geneprotein-codingprotein-coding
Descriptionrab GDP dissociation inhibitor alphaGDI-1guanosine diphosphate dissociation inhibitor 1mental retardation, X-linked 48oligophrenin-2protein XAP-4rab GDI alpharab GDP-dissociation inhibitor, alphatestis secretory sperm-binding protein Li 208aNADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialCI-49kDNADH dehydrogenase (ubiquinone) Fe-S protein 2, 49kDa (NADH-coenzyme Q reductase)NADH-ubiquinone oxidoreductase 49 kDa subunitNADH-ubiquinone oxidoreductase NDUFS2 subunitcomp
Modification date2020031320200313
UniProtAcc

P31150

O75306

Ensembl transtripts involved in fusion geneENST00000447750, ENST00000465640, 
ENST00000392179, ENST00000465923, 
ENST00000476409, ENST00000367993, 
Fusion gene scores* DoF score5 X 5 X 3=757 X 8 X 5=280
# samples 69
** MAII scorelog2(6/75*10)=-0.321928094887362
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/280*10)=-1.63742992061529
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: GDI1 [Title/Abstract] AND NDUFS2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGDI1(153669542)-NDUFS2(161183945), # samples:1
GDI1(153669542)-NDUFS2(161183946), # samples:1
Anticipated loss of major functional domain due to fusion event.GDI1-NDUFS2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
GDI1-NDUFS2 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneNDUFS2

GO:0006979

response to oxidative stress

12857734


check buttonFusion gene breakpoints across GDI1 (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 NDUFS2 (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-CD-A4MH-01AGDI1chrX

153669542

+NDUFS2chr1

161183946

+
ChimerDB4STADTCGA-CD-A4MHGDI1chrX

153669542

+NDUFS2chr1

161183945

+


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Fusion Gene ORF analysis for GDI1-NDUFS2

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-3UTRENST00000447750ENST00000392179GDI1chrX

153669542

+NDUFS2chr1

161183946

+
5CDS-3UTRENST00000447750ENST00000392179GDI1chrX

153669542

+NDUFS2chr1

161183945

+
5CDS-3UTRENST00000447750ENST00000465923GDI1chrX

153669542

+NDUFS2chr1

161183946

+
5CDS-3UTRENST00000447750ENST00000465923GDI1chrX

153669542

+NDUFS2chr1

161183945

+
5CDS-intronENST00000447750ENST00000476409GDI1chrX

153669542

+NDUFS2chr1

161183946

+
5CDS-intronENST00000447750ENST00000476409GDI1chrX

153669542

+NDUFS2chr1

161183945

+
Frame-shiftENST00000447750ENST00000367993GDI1chrX

153669542

+NDUFS2chr1

161183946

+
Frame-shiftENST00000447750ENST00000367993GDI1chrX

153669542

+NDUFS2chr1

161183945

+
intron-3CDSENST00000465640ENST00000367993GDI1chrX

153669542

+NDUFS2chr1

161183946

+
intron-3CDSENST00000465640ENST00000367993GDI1chrX

153669542

+NDUFS2chr1

161183945

+
intron-3UTRENST00000465640ENST00000392179GDI1chrX

153669542

+NDUFS2chr1

161183946

+
intron-3UTRENST00000465640ENST00000392179GDI1chrX

153669542

+NDUFS2chr1

161183945

+
intron-3UTRENST00000465640ENST00000465923GDI1chrX

153669542

+NDUFS2chr1

161183946

+
intron-3UTRENST00000465640ENST00000465923GDI1chrX

153669542

+NDUFS2chr1

161183945

+
intron-intronENST00000465640ENST00000476409GDI1chrX

153669542

+NDUFS2chr1

161183946

+
intron-intronENST00000465640ENST00000476409GDI1chrX

153669542

+NDUFS2chr1

161183945

+

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 GDI1-NDUFS2


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)
GDI1chrX153669542+NDUFS2chr1161183945+0.0004440850.9995559
GDI1chrX153669542+NDUFS2chr1161183945+0.0004440850.9995559
GDI1chrX153669542+NDUFS2chr1161183945+0.0004440850.9995559
GDI1chrX153669542+NDUFS2chr1161183945+0.0004440850.9995559

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.
genomic feature of top 1%

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Fusion Protein Features for GDI1-NDUFS2


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/:153669542/:161183945)
- 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
GDI1

P31150

NDUFS2

O75306

FUNCTION: Regulates the GDP/GTP exchange reaction of most Rab proteins by inhibiting the dissociation of GDP from them, and the subsequent binding of GTP to them. Promotes the dissociation of GDP-bound Rab proteins from the membrane and inhibits their activation. Promotes the dissociation of RAB1A, RAB3A, RAB5A and RAB10 from membranes. {ECO:0000269|PubMed:23815289}.FUNCTION: Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor (PubMed:30922174, PubMed:22036843). Essential for the catalytic activity of complex I (PubMed:30922174, PubMed:22036843). Essential for the assembly of complex I (By similarity). Redox-sensitive, critical component of the oxygen-sensing pathway in the pulmonary vasculature which plays a key role in acute pulmonary oxygen-sensing and hypoxic pulmonary vasoconstriction (PubMed:30922174). Plays an important role in carotid body sensing of hypoxia (By similarity). Essential for glia-like neural stem and progenitor cell proliferation, differentiation and subsequent oligodendrocyte or neuronal maturation (By similarity). {ECO:0000250|UniProtKB:Q91WD5, ECO:0000269|PubMed:22036843, ECO:0000269|PubMed:30922174}.

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 GDI1-NDUFS2


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 GDI1-NDUFS2


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 GDI1-NDUFS2


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 GDI1-NDUFS2


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