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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:NBEAL1-CARF (FusionGDB2 ID:57408)

Fusion Gene Summary for NBEAL1-CARF

check button Fusion gene summary
Fusion gene informationFusion gene name: NBEAL1-CARF
Fusion gene ID: 57408
HgeneTgene
Gene symbol

NBEAL1

CARF

Gene ID

65065

79800

Gene nameneurobeachin like 1calcium responsive transcription factor
SynonymsA530083I02Rik|ALS2CR16|ALS2CR17ALS2CR8|NYD-SP24
Cytomap

2q33.2

2q33.2

Type of geneprotein-codingprotein-coding
Descriptionneurobeachin-like protein 1amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17amyotrophic lateral sclerosis 2 chromosomal region candidate gene 16 proteincalcium-responsive transcription factoramyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8 proteincalcium-response factortestis development protein NYD-SP24
Modification date2020031320200313
UniProtAcc

Q6ZS30

Q8N187

Ensembl transtripts involved in fusion geneENST00000478884, ENST00000449802, 
ENST00000320443, ENST00000402905, 
ENST00000414439, ENST00000428585, 
ENST00000434998, ENST00000438828, 
ENST00000444724, ENST00000456821, 
ENST00000471271, ENST00000545253, 
ENST00000545262, 
Fusion gene scores* DoF score11 X 11 X 7=8473 X 4 X 3=36
# samples 124
** MAII scorelog2(12/847*10)=-2.81932756372368
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: NBEAL1 [Title/Abstract] AND CARF [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNBEAL1(204022548)-CARF(203817282), # samples:1
NBEAL1(203922179)-CARF(203850832), # samples:1
Anticipated loss of major functional domain due to fusion event.NBEAL1-CARF seems lost the major protein functional domain in Tgene partner, which is a transcription factor 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
TgeneCARF

GO:0035865

cellular response to potassium ion

22174809

TgeneCARF

GO:0061400

positive regulation of transcription from RNA polymerase II promoter in response to calcium ion

11832226|22174809

TgeneCARF

GO:0071277

cellular response to calcium ion

11832226|22174809


check buttonFusion gene breakpoints across NBEAL1 (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 CARF (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
ChimerDB4LUADTCGA-55-6969-01ANBEAL1chr2

204022548

+CARFchr2

203817282

+
ChiTaRS5.0N/AAK096293NBEAL1chr2

203922179

+CARFchr2

203850832

+


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Fusion Gene ORF analysis for NBEAL1-CARF

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-3UTRENST00000478884ENST00000320443NBEAL1chr2

203922179

+CARFchr2

203850832

+
3UTR-3UTRENST00000478884ENST00000402905NBEAL1chr2

203922179

+CARFchr2

203850832

+
3UTR-intronENST00000478884ENST00000414439NBEAL1chr2

203922179

+CARFchr2

203850832

+
3UTR-intronENST00000478884ENST00000428585NBEAL1chr2

203922179

+CARFchr2

203850832

+
3UTR-intronENST00000478884ENST00000434998NBEAL1chr2

203922179

+CARFchr2

203850832

+
3UTR-intronENST00000478884ENST00000438828NBEAL1chr2

203922179

+CARFchr2

203850832

+
3UTR-intronENST00000478884ENST00000444724NBEAL1chr2

203922179

+CARFchr2

203850832

+
3UTR-intronENST00000478884ENST00000456821NBEAL1chr2

203922179

+CARFchr2

203850832

+
3UTR-intronENST00000478884ENST00000471271NBEAL1chr2

203922179

+CARFchr2

203850832

+
3UTR-intronENST00000478884ENST00000545253NBEAL1chr2

203922179

+CARFchr2

203850832

+
3UTR-intronENST00000478884ENST00000545262NBEAL1chr2

203922179

+CARFchr2

203850832

+
5CDS-3UTRENST00000449802ENST00000320443NBEAL1chr2

204022548

+CARFchr2

203817282

+
5CDS-3UTRENST00000449802ENST00000320443NBEAL1chr2

203922179

+CARFchr2

203850832

+
5CDS-3UTRENST00000449802ENST00000402905NBEAL1chr2

203922179

+CARFchr2

203850832

+
5CDS-3UTRENST00000449802ENST00000414439NBEAL1chr2

204022548

+CARFchr2

203817282

+
5CDS-3UTRENST00000449802ENST00000428585NBEAL1chr2

204022548

+CARFchr2

203817282

+
5CDS-3UTRENST00000449802ENST00000434998NBEAL1chr2

204022548

+CARFchr2

203817282

+
5CDS-3UTRENST00000449802ENST00000438828NBEAL1chr2

204022548

+CARFchr2

203817282

+
5CDS-3UTRENST00000449802ENST00000456821NBEAL1chr2

204022548

+CARFchr2

203817282

+
5CDS-3UTRENST00000449802ENST00000471271NBEAL1chr2

204022548

+CARFchr2

203817282

+
5CDS-3UTRENST00000449802ENST00000545253NBEAL1chr2

204022548

+CARFchr2

203817282

+
5CDS-3UTRENST00000449802ENST00000545262NBEAL1chr2

204022548

+CARFchr2

203817282

+
5CDS-intronENST00000449802ENST00000414439NBEAL1chr2

203922179

+CARFchr2

203850832

+
5CDS-intronENST00000449802ENST00000428585NBEAL1chr2

203922179

+CARFchr2

203850832

+
5CDS-intronENST00000449802ENST00000434998NBEAL1chr2

203922179

+CARFchr2

203850832

+
5CDS-intronENST00000449802ENST00000438828NBEAL1chr2

203922179

+CARFchr2

203850832

+
5CDS-intronENST00000449802ENST00000444724NBEAL1chr2

203922179

+CARFchr2

203850832

+
5CDS-intronENST00000449802ENST00000456821NBEAL1chr2

203922179

+CARFchr2

203850832

+
5CDS-intronENST00000449802ENST00000471271NBEAL1chr2

203922179

+CARFchr2

203850832

+
5CDS-intronENST00000449802ENST00000545253NBEAL1chr2

203922179

+CARFchr2

203850832

+
5CDS-intronENST00000449802ENST00000545262NBEAL1chr2

203922179

+CARFchr2

203850832

+
Frame-shiftENST00000449802ENST00000402905NBEAL1chr2

204022548

+CARFchr2

203817282

+
Frame-shiftENST00000449802ENST00000444724NBEAL1chr2

204022548

+CARFchr2

203817282

+
intron-3CDSENST00000478884ENST00000402905NBEAL1chr2

204022548

+CARFchr2

203817282

+
intron-3CDSENST00000478884ENST00000444724NBEAL1chr2

204022548

+CARFchr2

203817282

+
intron-3UTRENST00000478884ENST00000320443NBEAL1chr2

204022548

+CARFchr2

203817282

+
intron-3UTRENST00000478884ENST00000414439NBEAL1chr2

204022548

+CARFchr2

203817282

+
intron-3UTRENST00000478884ENST00000428585NBEAL1chr2

204022548

+CARFchr2

203817282

+
intron-3UTRENST00000478884ENST00000434998NBEAL1chr2

204022548

+CARFchr2

203817282

+
intron-3UTRENST00000478884ENST00000438828NBEAL1chr2

204022548

+CARFchr2

203817282

+
intron-3UTRENST00000478884ENST00000456821NBEAL1chr2

204022548

+CARFchr2

203817282

+
intron-3UTRENST00000478884ENST00000471271NBEAL1chr2

204022548

+CARFchr2

203817282

+
intron-3UTRENST00000478884ENST00000545253NBEAL1chr2

204022548

+CARFchr2

203817282

+
intron-3UTRENST00000478884ENST00000545262NBEAL1chr2

204022548

+CARFchr2

203817282

+

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 NBEAL1-CARF


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)
NBEAL1chr2204022548+CARFchr2203817281+8.73E-080.9999999
NBEAL1chr2204022548+CARFchr2203817281+8.73E-080.9999999

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 NBEAL1-CARF


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/:204022548/:203817282)
- 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
NBEAL1

Q6ZS30

CARF

Q8N187

FUNCTION: Acts as a transcriptional activator that mediates the calcium- and neuron-selective induction of BDNF exon III transcription. Binds to the consensus calcium-response element CaRE1 5'-CTATTTCGAG-3' sequence. {ECO:0000269|PubMed:11832226, ECO:0000269|PubMed:22174809}.

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 NBEAL1-CARF


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 NBEAL1-CARF


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 NBEAL1-CARF


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 NBEAL1-CARF


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