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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:NFRKB-APLP2 (FusionGDB2 ID:58992)

Fusion Gene Summary for NFRKB-APLP2

check button Fusion gene summary
Fusion gene informationFusion gene name: NFRKB-APLP2
Fusion gene ID: 58992
HgeneTgene
Gene symbol

NFRKB

APLP2

Gene ID

4798

334

Gene namenuclear factor related to kappaB binding proteinamyloid beta precursor like protein 2
SynonymsINO80GAPLP-2|APPH|APPL2|CDEBP
Cytomap

11q24.3

11q24.3

Type of geneprotein-codingprotein-coding
Descriptionnuclear factor related to kappa-B-binding proteinDNA-binding protein R kappa BINO80 complex subunit Gamyloid-like protein 2CDEI box-binding proteinamyloid beta (A4) precursor-like protein 2amyloid precursor protein homolog HSD-2testicular tissue protein Li 23
Modification date2020031320200313
UniProtAcc

Q6P4R8

Q06481

Ensembl transtripts involved in fusion geneENST00000304521, ENST00000446488, 
ENST00000524746, ENST00000524794, 
ENST00000526940, 		ENST00000263574, 
ENST00000278756, ENST00000338167, 
ENST00000345598, ENST00000528499, 
ENST00000532456, ENST00000539648, 
ENST00000543137, 
Fusion gene scores* DoF score6 X 7 X 6=25211 X 14 X 8=1232
# samples 718
** MAII scorelog2(7/252*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(18/1232*10)=-2.77493344436523
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NFRKB [Title/Abstract] AND APLP2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNFRKB(129765391)-APLP2(130010293), # 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

check buttonFusion gene breakpoints across NFRKB (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 APLP2 (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-8530-01ANFRKBchr11

129765391

-APLP2chr11

130010293

+


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Fusion Gene ORF analysis for NFRKB-APLP2

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-intronENST00000304521ENST00000263574NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000304521ENST00000278756NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000304521ENST00000338167NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000304521ENST00000345598NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000304521ENST00000528499NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000304521ENST00000532456NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000304521ENST00000539648NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000304521ENST00000543137NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000446488ENST00000263574NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000446488ENST00000278756NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000446488ENST00000338167NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000446488ENST00000345598NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000446488ENST00000528499NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000446488ENST00000532456NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000446488ENST00000539648NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000446488ENST00000543137NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000524746ENST00000263574NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000524746ENST00000278756NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000524746ENST00000338167NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000524746ENST00000345598NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000524746ENST00000528499NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000524746ENST00000532456NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000524746ENST00000539648NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000524746ENST00000543137NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000524794ENST00000263574NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000524794ENST00000278756NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000524794ENST00000338167NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000524794ENST00000345598NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000524794ENST00000528499NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000524794ENST00000532456NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000524794ENST00000539648NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000524794ENST00000543137NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000526940ENST00000263574NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000526940ENST00000278756NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000526940ENST00000338167NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000526940ENST00000345598NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000526940ENST00000528499NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000526940ENST00000532456NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000526940ENST00000539648NFRKBchr11

129765391

-APLP2chr11

130010293

+
intron-intronENST00000526940ENST00000543137NFRKBchr11

129765391

-APLP2chr11

130010293

+

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 NFRKB-APLP2


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 NFRKB-APLP2


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/:129765391/:130010293)
- 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
NFRKB

Q6P4R8

APLP2

Q06481

FUNCTION: Binds to the DNA consensus sequence 5'-GGGGAATCTCC-3'. {ECO:0000269|PubMed:18922472}.; FUNCTION: Putative regulatory component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair. Modulates the deubiquitinase activity of UCHL5 in the INO80 complex. {ECO:0000269|PubMed:18922472}.FUNCTION: May play a role in the regulation of hemostasis. The soluble form may have inhibitory properties towards coagulation factors. May interact with cellular G-protein signaling pathways. May bind to the DNA 5'-GTCACATG-3'(CDEI box). Inhibits trypsin, chymotrypsin, plasmin, factor XIA and plasma and glandular kallikrein. Modulates the Cu/Zn nitric oxide-catalyzed autodegradation of GPC1 heparan sulfate side chains in fibroblasts (By similarity). {ECO:0000250, ECO:0000269|PubMed:8307156}.

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 NFRKB-APLP2


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 NFRKB-APLP2


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 NFRKB-APLP2


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 NFRKB-APLP2


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