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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:NFE2L1-CDK5RAP3 (FusionGDB2 ID:58815)

Fusion Gene Summary for NFE2L1-CDK5RAP3

check button Fusion gene summary
Fusion gene informationFusion gene name: NFE2L1-CDK5RAP3
Fusion gene ID: 58815
HgeneTgene
Gene symbol

NFE2L1

CDK5RAP3

Gene ID

4779

80279

Gene namenuclear factor, erythroid 2 like 1CDK5 regulatory subunit associated protein 3
SynonymsLCR-F1|NRF1|TCF11C53|HSF-27|IC53|LZAP|MST016|OK/SW-cl.114|PP1553
Cytomap

17q21.32

17q21.32

Type of geneprotein-codingprotein-coding
Descriptionendoplasmic reticulum membrane sensor NFE2L1NF-E2-related factor 1NFE2-related factor 1TCF-11locus control region-factor 1nuclear factor erythroid 2-related factor 1nuclear factor, erythroid derived 2, like 1protein NRF1, p120 formtranscription faCDK5 regulatory subunit-associated protein 3CDK5 regulatory subunit associated protein IC53-2LXXLL/leucine-zipper-containing ARF-binding proteinLXXLL/leucine-zipper-containing ARFbinding proteinischemic heart CDK5 activator-binding protein C53
Modification date2020031320200320
UniProtAcc

Q14494

Q96JB5

Ensembl transtripts involved in fusion geneENST00000579481, ENST00000357480, 
ENST00000361665, ENST00000362042, 
ENST00000585291, ENST00000536222, 
ENST00000582155, ENST00000583378, 
ENST00000338399, ENST00000536708, 
ENST00000578663, 
Fusion gene scores* DoF score18 X 12 X 13=28089 X 8 X 8=576
# samples 2010
** MAII scorelog2(20/2808*10)=-3.81147103052984
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/576*10)=-2.52606881166759
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NFE2L1 [Title/Abstract] AND CDK5RAP3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNFE2L1(46125824)-CDK5RAP3(46050884), # samples:1
NFE2L1(46126226)-CDK5RAP3(46050885), # samples:1
NFE2L1(46125824)-CDK5RAP3(46050885), # 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
TgeneCDK5RAP3

GO:0008283

cell proliferation

12054757

TgeneCDK5RAP3

GO:0031398

positive regulation of protein ubiquitination

16173922

TgeneCDK5RAP3

GO:0071569

protein ufmylation

23152784

TgeneCDK5RAP3

GO:1900182

positive regulation of protein localization to nucleus

16173922

TgeneCDK5RAP3

GO:1901798

positive regulation of signal transduction by p53 class mediator

16173922

TgeneCDK5RAP3

GO:1903363

negative regulation of cellular protein catabolic process

16173922

TgeneCDK5RAP3

GO:2000060

positive regulation of ubiquitin-dependent protein catabolic process

16173922


check buttonFusion gene breakpoints across NFE2L1 (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 CDK5RAP3 (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-VQ-AA6D-01ANFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
ChimerDB4STADTCGA-VQ-AA6D-01ANFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
ChimerDB4STADTCGA-VQ-AA6DNFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+


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Fusion Gene ORF analysis for NFE2L1-CDK5RAP3

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-3CDSENST00000579481ENST00000338399NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
3UTR-3CDSENST00000579481ENST00000536708NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
3UTR-intronENST00000579481ENST00000578663NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
5UTR-3CDSENST00000357480ENST00000338399NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
5UTR-3CDSENST00000357480ENST00000338399NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
5UTR-3CDSENST00000357480ENST00000536708NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
5UTR-3CDSENST00000357480ENST00000536708NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
5UTR-3CDSENST00000361665ENST00000338399NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
5UTR-3CDSENST00000361665ENST00000536708NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
5UTR-3CDSENST00000362042ENST00000338399NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
5UTR-3CDSENST00000362042ENST00000338399NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
5UTR-3CDSENST00000362042ENST00000536708NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
5UTR-3CDSENST00000362042ENST00000536708NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
5UTR-3CDSENST00000585291ENST00000338399NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
5UTR-3CDSENST00000585291ENST00000338399NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
5UTR-3CDSENST00000585291ENST00000536708NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
5UTR-3CDSENST00000585291ENST00000536708NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
5UTR-intronENST00000357480ENST00000578663NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
5UTR-intronENST00000357480ENST00000578663NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
5UTR-intronENST00000361665ENST00000578663NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
5UTR-intronENST00000362042ENST00000578663NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
5UTR-intronENST00000362042ENST00000578663NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
5UTR-intronENST00000585291ENST00000578663NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
5UTR-intronENST00000585291ENST00000578663NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
intron-3CDSENST00000357480ENST00000338399NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000357480ENST00000536708NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000361665ENST00000338399NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000361665ENST00000338399NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
intron-3CDSENST00000361665ENST00000536708NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000361665ENST00000536708NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
intron-3CDSENST00000362042ENST00000338399NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000362042ENST00000536708NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000536222ENST00000338399NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000536222ENST00000338399NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000536222ENST00000338399NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
intron-3CDSENST00000536222ENST00000536708NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000536222ENST00000536708NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000536222ENST00000536708NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
intron-3CDSENST00000579481ENST00000338399NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000579481ENST00000338399NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
intron-3CDSENST00000579481ENST00000536708NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000579481ENST00000536708NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
intron-3CDSENST00000582155ENST00000338399NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000582155ENST00000338399NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000582155ENST00000338399NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
intron-3CDSENST00000582155ENST00000536708NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000582155ENST00000536708NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000582155ENST00000536708NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
intron-3CDSENST00000583378ENST00000338399NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000583378ENST00000338399NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000583378ENST00000338399NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
intron-3CDSENST00000583378ENST00000536708NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000583378ENST00000536708NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000583378ENST00000536708NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
intron-3CDSENST00000585291ENST00000338399NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
intron-3CDSENST00000585291ENST00000536708NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
intron-intronENST00000357480ENST00000578663NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
intron-intronENST00000361665ENST00000578663NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
intron-intronENST00000361665ENST00000578663NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
intron-intronENST00000362042ENST00000578663NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
intron-intronENST00000536222ENST00000578663NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
intron-intronENST00000536222ENST00000578663NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
intron-intronENST00000536222ENST00000578663NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
intron-intronENST00000579481ENST00000578663NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
intron-intronENST00000579481ENST00000578663NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
intron-intronENST00000582155ENST00000578663NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
intron-intronENST00000582155ENST00000578663NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
intron-intronENST00000582155ENST00000578663NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
intron-intronENST00000583378ENST00000578663NFE2L1chr17

46125824

+CDK5RAP3chr17

46050885

+
intron-intronENST00000583378ENST00000578663NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+
intron-intronENST00000583378ENST00000578663NFE2L1chr17

46125824

+CDK5RAP3chr17

46050884

+
intron-intronENST00000585291ENST00000578663NFE2L1chr17

46126226

+CDK5RAP3chr17

46050885

+

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 NFE2L1-CDK5RAP3


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)
NFE2L1chr1746126226+CDK5RAP3chr1746050884+4.12E-070.99999964
NFE2L1chr1746125824+CDK5RAP3chr1746050884+4.06E-091
NFE2L1chr1746125824+CDK5RAP3chr1746050884+4.06E-091
NFE2L1chr1746126226+CDK5RAP3chr1746050884+4.12E-070.99999964
NFE2L1chr1746125824+CDK5RAP3chr1746050884+4.06E-091
NFE2L1chr1746125824+CDK5RAP3chr1746050884+4.06E-091

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 NFE2L1-CDK5RAP3


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/:46125824/:46050884)
- 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
NFE2L1

Q14494

CDK5RAP3

Q96JB5

FUNCTION: [Endoplasmic reticulum membrane sensor NFE2L1]: Endoplasmic reticulum membrane sensor that translocates into the nucleus in response to various stresses to act as a transcription factor (PubMed:20932482, PubMed:24448410). Constitutes a precursor of the transcription factor NRF1 (By similarity). Able to detect various cellular stresses, such as cholesterol excess, oxidative stress or proteasome inhibition (PubMed:20932482). In response to stress, it is released from the endoplasmic reticulum membrane following cleavage by the protease DDI2 and translocates into the nucleus to form the transcription factor NRF1 (By similarity). Acts as a key sensor of cholesterol excess: in excess cholesterol conditions, the endoplasmic reticulum membrane form of the protein directly binds cholesterol via its CRAC motif, preventing cleavage and release of the transcription factor NRF1, thereby allowing expression of genes promoting cholesterol removal, such as CD36 (By similarity). Involved in proteasome homeostasis: in response to proteasome inhibition, it is released from the endoplasmic reticulum membrane, translocates to the nucleus and activates expression of genes encoding proteasome subunits (PubMed:20932482). {ECO:0000250|UniProtKB:Q61985, ECO:0000269|PubMed:20932482, ECO:0000269|PubMed:24448410}.; FUNCTION: [Transcription factor NRF1]: CNC-type bZIP family transcription factor that translocates to the nucleus and regulates expression of target genes in response to various stresses (PubMed:8932385, PubMed:9421508). Heterodimerizes with small-Maf proteins (MAFF, MAFG or MAFK) and binds DNA motifs including the antioxidant response elements (AREs), which regulate expression of genes involved in oxidative stress response (PubMed:8932385, PubMed:9421508). Activates or represses expression of target genes, depending on the context (PubMed:8932385, PubMed:9421508). Plays a key role in cholesterol homeostasis by acting as a sensor of cholesterol excess: in low cholesterol conditions, translocates into the nucleus and represses expression of genes involved in defense against cholesterol excess, such as CD36 (By similarity). In excess cholesterol conditions, the endoplasmic reticulum membrane form of the protein directly binds cholesterol via its CRAC motif, preventing cleavage and release of the transcription factor NRF1, thereby allowing expression of genes promoting cholesterol removal (By similarity). Critical for redox balance in response to oxidative stress: acts by binding the AREs motifs on promoters and mediating activation of oxidative stress response genes, such as GCLC, GCLM, GSS, MT1 and MT2 (By similarity). Plays an essential role during fetal liver hematopoiesis: probably has a protective function against oxidative stress and is involved in lipid homeostasis in the liver (By similarity). Involved in proteasome homeostasis: in response to proteasome inhibition, mediates the 'bounce-back' of proteasome subunits by translocating into the nucleus and activating expression of genes encoding proteasome subunits (PubMed:20932482). Also involved in regulating glucose flux (By similarity). Together with CEBPB; represses expression of DSPP during odontoblast differentiation (PubMed:15308669). In response to ascorbic acid induction, activates expression of SP7/Osterix in osteoblasts. {ECO:0000250|UniProtKB:Q61985, ECO:0000269|PubMed:15308669, ECO:0000269|PubMed:20932482, ECO:0000269|PubMed:8932385, ECO:0000269|PubMed:9421508}.FUNCTION: Substrate adapter for ufmylation, the covalent attachment of the ubiquitin-like modifier UFM1 to substrate proteins, in response to endoplasmic reticulum stress (PubMed:23152784, PubMed:30635284). Negatively regulates NF-kappa-B-mediated gene transcription through the control of RELA phosphorylation (PubMed:17785205, PubMed:20228063). Probable tumor suppressor initially identified as a CDK5R1 interactor controlling cell proliferation (PubMed:12054757, PubMed:12737517). Also regulates mitotic G2/M transition checkpoint and mitotic G2 DNA damage checkpoint (PubMed:15790566, PubMed:19223857). Through its interaction with CDKN2A/ARF and MDM2 may induce MDM2-dependent p53/TP53 ubiquitination, stabilization and activation in the nucleus, thereby promoting G1 cell cycle arrest and inhibition of cell proliferation (PubMed:16173922). May also play a role in the rupture of the nuclear envelope during apoptosis (PubMed:23478299). May regulate MAPK14 activity by regulating its dephosphorylation by PPM1D/WIP1 (PubMed:21283629). Required for liver development (By similarity). {ECO:0000250|UniProtKB:Q99LM2, ECO:0000269|PubMed:12054757, ECO:0000269|PubMed:12737517, ECO:0000269|PubMed:15790566, ECO:0000269|PubMed:16173922, ECO:0000269|PubMed:17785205, ECO:0000269|PubMed:19223857, ECO:0000269|PubMed:20228063, ECO:0000269|PubMed:21283629, ECO:0000269|PubMed:23152784, ECO:0000269|PubMed:23478299, ECO:0000269|PubMed:30635284}.; FUNCTION: (Microbial infection) May be negatively regulated by hepatitis B virus large envelope protein mutant pre-s2 to promote mitotic entry. {ECO:0000269|PubMed:21971960}.

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 NFE2L1-CDK5RAP3


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 NFE2L1-CDK5RAP3


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 NFE2L1-CDK5RAP3


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 NFE2L1-CDK5RAP3


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