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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:ABCC1-NDE1 (FusionGDB2 ID:240)

Fusion Gene Summary for ABCC1-NDE1

check button Fusion gene summary
Fusion gene informationFusion gene name: ABCC1-NDE1
Fusion gene ID: 240
HgeneTgene
Gene symbol

ABCC1

NDE1

Gene ID

4363

54820

Gene nameATP binding cassette subfamily C member 1nudE neurodevelopment protein 1
SynonymsABC29|ABCC|GS-X|MRP|MRP1HOM-TES-87|LIS4|MHAC|NDE|NUDE|NUDE1
Cytomap

16p13.11

16p13.11

Type of geneprotein-codingprotein-coding
Descriptionmultidrug resistance-associated protein 1ATP-binding cassette transporter variant ABCC1delta-ex13ATP-binding cassette transporter variant ABCC1delta-ex13&14ATP-binding cassette transporter variant ABCC1delta-ex25ATP-binding cassette transporter variannuclear 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

P33527

Q9NXR1

Ensembl transtripts involved in fusion geneENST00000576557, ENST00000345148, 
ENST00000346370, ENST00000349029, 
ENST00000351154, ENST00000399408, 
ENST00000399410, 		ENST00000571896, 
ENST00000342673, ENST00000396353, 
ENST00000396354, ENST00000396355, 
Fusion gene scores* DoF score11 X 10 X 6=6609 X 10 X 6=540
# samples 1411
** MAII scorelog2(14/660*10)=-2.23703919730085
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: ABCC1 [Title/Abstract] AND NDE1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointABCC1(16110478)-NDE1(15758593), # 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 ABCC1 (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
ChimerDB4CESCTCGA-VS-A8EC-01AABCC1chr16

16110478

-NDE1chr16

15758593

+
ChimerDB4CESCTCGA-VS-A8EC-01AABCC1chr16

16110478

+NDE1chr16

15758593

+
ChimerDB4STADTCGA-CD-A4MJABCC1chr16

16196574

+NDE1chr16

15818047

+


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Fusion Gene ORF analysis for ABCC1-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-3UTRENST00000576557ENST00000571896ABCC1chr16

16196574

+NDE1chr16

15818047

+
3UTR-intronENST00000576557ENST00000342673ABCC1chr16

16196574

+NDE1chr16

15818047

+
3UTR-intronENST00000576557ENST00000396353ABCC1chr16

16196574

+NDE1chr16

15818047

+
3UTR-intronENST00000576557ENST00000396354ABCC1chr16

16196574

+NDE1chr16

15818047

+
3UTR-intronENST00000576557ENST00000396355ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-3UTRENST00000345148ENST00000571896ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-3UTRENST00000346370ENST00000571896ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-3UTRENST00000349029ENST00000571896ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-3UTRENST00000351154ENST00000571896ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-3UTRENST00000399408ENST00000571896ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-3UTRENST00000399410ENST00000571896ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-5UTRENST00000345148ENST00000342673ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000345148ENST00000396353ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000345148ENST00000396354ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000345148ENST00000396355ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000346370ENST00000342673ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000346370ENST00000396353ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000346370ENST00000396354ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000346370ENST00000396355ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000349029ENST00000342673ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000349029ENST00000396353ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000349029ENST00000396354ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000349029ENST00000396355ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000351154ENST00000342673ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000351154ENST00000396353ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000351154ENST00000396354ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000351154ENST00000396355ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000399408ENST00000342673ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000399408ENST00000396353ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000399408ENST00000396354ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000399408ENST00000396355ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000399410ENST00000342673ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000399410ENST00000396353ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000399410ENST00000396354ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-5UTRENST00000399410ENST00000396355ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-intronENST00000345148ENST00000342673ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000345148ENST00000396353ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000345148ENST00000396354ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000345148ENST00000396355ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000345148ENST00000571896ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-intronENST00000346370ENST00000342673ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000346370ENST00000396353ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000346370ENST00000396354ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000346370ENST00000396355ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000346370ENST00000571896ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-intronENST00000349029ENST00000342673ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000349029ENST00000396353ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000349029ENST00000396354ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000349029ENST00000396355ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000349029ENST00000571896ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-intronENST00000351154ENST00000342673ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000351154ENST00000396353ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000351154ENST00000396354ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000351154ENST00000396355ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000351154ENST00000571896ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-intronENST00000399408ENST00000342673ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000399408ENST00000396353ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000399408ENST00000396354ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000399408ENST00000396355ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000399408ENST00000571896ABCC1chr16

16110478

+NDE1chr16

15758593

+
5CDS-intronENST00000399410ENST00000342673ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000399410ENST00000396353ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000399410ENST00000396354ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000399410ENST00000396355ABCC1chr16

16196574

+NDE1chr16

15818047

+
5CDS-intronENST00000399410ENST00000571896ABCC1chr16

16110478

+NDE1chr16

15758593

+
intron-5UTRENST00000576557ENST00000342673ABCC1chr16

16110478

+NDE1chr16

15758593

+
intron-5UTRENST00000576557ENST00000396353ABCC1chr16

16110478

+NDE1chr16

15758593

+
intron-5UTRENST00000576557ENST00000396354ABCC1chr16

16110478

+NDE1chr16

15758593

+
intron-5UTRENST00000576557ENST00000396355ABCC1chr16

16110478

+NDE1chr16

15758593

+
intron-intronENST00000576557ENST00000571896ABCC1chr16

16110478

+NDE1chr16

15758593

+

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 ABCC1-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)
ABCC1chr1616110478+NDE1chr1615758592+3.18E-070.99999964
ABCC1chr1616196574+NDE1chr1615818047+1.13E-070.9999999
ABCC1chr1616110478+NDE1chr1615758592+3.18E-070.99999964
ABCC1chr1616196574+NDE1chr1615818047+1.13E-070.9999999

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 ABCC1-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/:16110478/:15758593)
- 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
ABCC1

P33527

NDE1

Q9NXR1

FUNCTION: Mediates export of organic anions and drugs from the cytoplasm (PubMed:7961706, PubMed:16230346, PubMed:9281595, PubMed:10064732, PubMed:11114332). Mediates ATP-dependent transport of glutathione and glutathione conjugates, leukotriene C4, estradiol-17-beta-o-glucuronide, methotrexate, antiviral drugs and other xenobiotics (PubMed:7961706, PubMed:16230346, PubMed:9281595, PubMed:10064732, PubMed:11114332). Confers resistance to anticancer drugs by decreasing accumulation of drug in cells, and by mediating ATP- and GSH-dependent drug export (PubMed:9281595). Hydrolyzes ATP with low efficiency (PubMed:16230346). Catalyzes the export of sphingosine 1-phosphate from mast cells independently of their degranulation (PubMed:17050692). Participates in inflammatory response by allowing export of leukotriene C4 from leukotriene C4-synthezing cells (By similarity). {ECO:0000250|UniProtKB:O35379, ECO:0000269|PubMed:10064732, ECO:0000269|PubMed:11114332, ECO:0000269|PubMed:16230346, ECO:0000269|PubMed:17050692, ECO:0000269|PubMed:7961706, ECO:0000269|PubMed:9281595}.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 ABCC1-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 ABCC1-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 ABCC1-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 ABCC1-NDE1


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