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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:RABGAP1-NFE2L1 (FusionGDB2 ID:71573)

Fusion Gene Summary for RABGAP1-NFE2L1

check button Fusion gene summary
Fusion gene informationFusion gene name: RABGAP1-NFE2L1
Fusion gene ID: 71573
HgeneTgene
Gene symbol

RABGAP1

NFE2L1

Gene ID

23637

4779

Gene nameRAB GTPase activating protein 1nuclear factor, erythroid 2 like 1
SynonymsGAPCENA|TBC1D11LCR-F1|NRF1|TCF11
Cytomap

9q33.2-q33.3

17q21.32

Type of geneprotein-codingprotein-coding
Descriptionrab GTPase-activating protein 1GAP and centrosome-associated proteinRab6 GTPase activating protein, GAPCenATBC1 domain family, member 11rab6 GTPase activating protein (GAP and centrosome-associated)rab6 GTPase-activating protein GAPCenAendoplasmic 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 fa
Modification date2020031320200313
UniProtAcc.

Q14494

Ensembl transtripts involved in fusion geneENST00000373643, ENST00000373647, 
ENST00000493854, 		ENST00000585291, 
ENST00000357480, ENST00000361665, 
ENST00000362042, ENST00000536222, 
ENST00000579481, ENST00000582155, 
ENST00000583378, 
Fusion gene scores* DoF score13 X 10 X 7=91011 X 9 X 5=495
# samples 1311
** MAII scorelog2(13/910*10)=-2.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/495*10)=-2.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RABGAP1 [Title/Abstract] AND NFE2L1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRABGAP1(125720610)-NFE2L1(46138842), # 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
HgeneRABGAP1

GO:0043087

regulation of GTPase activity

17562788


check buttonFusion gene breakpoints across RABGAP1 (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 NFE2L1 (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/ABM970024RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
ChiTaRS5.0N/ABM970334RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-


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Fusion Gene ORF analysis for RABGAP1-NFE2L1

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-3UTRENST00000373643ENST00000585291RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-3UTRENST00000373647ENST00000585291RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-3UTRENST00000493854ENST00000585291RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000373643ENST00000357480RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000373643ENST00000361665RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000373643ENST00000362042RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000373643ENST00000536222RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000373643ENST00000579481RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000373643ENST00000582155RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000373643ENST00000583378RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000373647ENST00000357480RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000373647ENST00000361665RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000373647ENST00000362042RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000373647ENST00000536222RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000373647ENST00000579481RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000373647ENST00000582155RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000373647ENST00000583378RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000493854ENST00000357480RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000493854ENST00000361665RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000493854ENST00000362042RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000493854ENST00000536222RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000493854ENST00000579481RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000493854ENST00000582155RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-
intron-intronENST00000493854ENST00000583378RABGAP1chr9

125720610

+NFE2L1chr17

46138842

-

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 RABGAP1-NFE2L1


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 RABGAP1-NFE2L1


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/:125720610/:46138842)
- 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

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.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}.

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 RABGAP1-NFE2L1


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 RABGAP1-NFE2L1


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 RABGAP1-NFE2L1


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 RABGAP1-NFE2L1


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