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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:NRXN2-BCR (FusionGDB2 ID:60374)

Fusion Gene Summary for NRXN2-BCR

check button Fusion gene summary
Fusion gene informationFusion gene name: NRXN2-BCR
Fusion gene ID: 60374
HgeneTgene
Gene symbol

NRXN2

BCR

Gene ID

9379

613

Gene nameneurexin 2BCR activator of RhoGEF and GTPase
Synonyms-ALL|BCR1|CML|D22S11|D22S662|PHL
Cytomap

11q13.1

22q11.23

Type of geneprotein-codingprotein-coding
Descriptionneurexin-2-betaneurexin IIbreakpoint cluster region proteinBCR, RhoGEF and GTPase activating proteinBCR/FGFR1 chimera proteinFGFR1/BCR chimera proteinbreakpoint cluster regionrenal carcinoma antigen NY-REN-26
Modification date2020031320200313
UniProtAcc

Q9P2S2

P11274

Ensembl transtripts involved in fusion geneENST00000265459, ENST00000301894, 
ENST00000377551, ENST00000377559, 
ENST00000409571, ENST00000496291, 
ENST00000305877, ENST00000359540, 
ENST00000398512, ENST00000436990, 
Fusion gene scores* DoF score4 X 4 X 3=4815 X 58 X 7=6090
# samples 461
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(61/6090*10)=-3.31956108034345
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NRXN2 [Title/Abstract] AND BCR [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNRXN2(64433145)-BCR(23355537), # 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
TgeneBCR

GO:0090630

activation of GTPase activity

7479768


check buttonFusion gene breakpoints across NRXN2 (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 BCR (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/AAF045533NRXN2chr11

64433145

+BCRchr22

23355537

+


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Fusion Gene ORF analysis for NRXN2-BCR

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-intronENST00000265459ENST00000305877NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000265459ENST00000359540NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000265459ENST00000398512NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000265459ENST00000436990NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000301894ENST00000305877NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000301894ENST00000359540NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000301894ENST00000398512NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000301894ENST00000436990NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000377551ENST00000305877NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000377551ENST00000359540NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000377551ENST00000398512NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000377551ENST00000436990NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000377559ENST00000305877NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000377559ENST00000359540NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000377559ENST00000398512NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000377559ENST00000436990NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000409571ENST00000305877NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000409571ENST00000359540NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000409571ENST00000398512NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000409571ENST00000436990NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000496291ENST00000305877NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000496291ENST00000359540NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000496291ENST00000398512NRXN2chr11

64433145

+BCRchr22

23355537

+
intron-intronENST00000496291ENST00000436990NRXN2chr11

64433145

+BCRchr22

23355537

+

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 NRXN2-BCR


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 NRXN2-BCR


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/:64433145/:23355537)
- 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
NRXN2

Q9P2S2

BCR

P11274

FUNCTION: Neuronal cell surface protein that may be involved in cell recognition and cell adhesion. May mediate intracellular signaling.FUNCTION: Protein with a unique structure having two opposing regulatory activities toward small GTP-binding proteins. The C-terminus is a GTPase-activating protein (GAP) domain which stimulates GTP hydrolysis by RAC1, RAC2 and CDC42. Accelerates the intrinsic rate of GTP hydrolysis of RAC1 or CDC42, leading to down-regulation of the active GTP-bound form (PubMed:7479768, PubMed:1903516, PubMed:17116687). The central Dbl homology (DH) domain functions as guanine nucleotide exchange factor (GEF) that modulates the GTPases CDC42, RHOA and RAC1. Promotes the conversion of CDC42, RHOA and RAC1 from the GDP-bound to the GTP-bound form (PubMed:7479768, PubMed:23940119). The amino terminus contains an intrinsic kinase activity (PubMed:1657398). Functions as an important negative regulator of neuronal RAC1 activity (By similarity). Regulates macrophage functions such as CSF1-directed motility and phagocytosis through the modulation of RAC1 activity (PubMed:17116687). Plays a major role as a RHOA GEF in keratinocytes being involved in focal adhesion formation and keratinocyte differentiation (PubMed:23940119). {ECO:0000250|UniProtKB:Q6PAJ1, ECO:0000269|PubMed:1657398, ECO:0000269|PubMed:17116687, ECO:0000269|PubMed:1903516, ECO:0000269|PubMed:23940119, ECO:0000269|PubMed:7479768}.

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 NRXN2-BCR


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 NRXN2-BCR


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 NRXN2-BCR


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 NRXN2-BCR


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