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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:SYNE2-NAP1L4 (FusionGDB2 ID:88429)

Fusion Gene Summary for SYNE2-NAP1L4

check button Fusion gene summary
Fusion gene informationFusion gene name: SYNE2-NAP1L4
Fusion gene ID: 88429
HgeneTgene
Gene symbol

SYNE2

NAP1L4

Gene ID

23224

4676

Gene namespectrin repeat containing nuclear envelope protein 2nucleosome assembly protein 1 like 4
SynonymsEDMD5|KASH2|NUA|NUANCE|Nesp2|Nesprin-2|SYNE-2|TROPHNAP1L4b|NAP2|NAP2L|hNAP2
Cytomap

14q23.2

11p15.4

Type of geneprotein-codingprotein-coding
Descriptionnesprin-2KASH domain-containing protein 2nesprin 2nuclear envelope spectrin repeat protein 2nucleus and actin connecting element proteinpolytrophinspectrin repeat containing, nuclear envelope 2synaptic nuclear envelope protein 2synaptic nuclei expnucleosome assembly protein 1-like 4NAP-2nucleosome assembly protein 1-like 4bnucleosome assembly protein 2
Modification date2020032020200322
UniProtAcc.

Q99733

Ensembl transtripts involved in fusion geneENST00000341472, ENST00000344113, 
ENST00000356081, ENST00000358025, 
ENST00000554584, ENST00000357395, 
ENST00000394768, ENST00000441438, 
ENST00000458046, ENST00000553455, 
ENST00000554805, ENST00000555002, 
ENST00000555022, ENST00000556725, 
ENST00000469089, ENST00000526115, 
ENST00000380542, 
Fusion gene scores* DoF score20 X 22 X 9=39608 X 8 X 5=320
# samples 2410
** MAII scorelog2(24/3960*10)=-4.04439411935845
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/320*10)=-1.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SYNE2 [Title/Abstract] AND NAP1L4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSYNE2(64375945)-NAP1L4(2981139), # samples:1
Anticipated loss of major functional domain due to fusion event.SYNE2-NAP1L4 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
SYNE2-NAP1L4 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
HgeneSYNE2

GO:0090286

cytoskeletal anchoring at nuclear membrane

18396275

TgeneNAP1L4

GO:0006334

nucleosome assembly

9325046


check buttonFusion gene breakpoints across SYNE2 (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 NAP1L4 (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
ChimerDB4THCATCGA-IM-A3EBSYNE2chr14

64375945

+NAP1L4chr11

2981139

-


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Fusion Gene ORF analysis for SYNE2-NAP1L4

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
5CDS-intronENST00000341472ENST00000469089SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
5CDS-intronENST00000341472ENST00000526115SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
5CDS-intronENST00000344113ENST00000469089SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
5CDS-intronENST00000344113ENST00000526115SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
5CDS-intronENST00000356081ENST00000469089SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
5CDS-intronENST00000356081ENST00000526115SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
5CDS-intronENST00000358025ENST00000469089SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
5CDS-intronENST00000358025ENST00000526115SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
5CDS-intronENST00000554584ENST00000469089SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
5CDS-intronENST00000554584ENST00000526115SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
5UTR-3CDSENST00000357395ENST00000380542SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
5UTR-intronENST00000357395ENST00000469089SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
5UTR-intronENST00000357395ENST00000526115SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
Frame-shiftENST00000341472ENST00000380542SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
Frame-shiftENST00000344113ENST00000380542SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
Frame-shiftENST00000356081ENST00000380542SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
Frame-shiftENST00000358025ENST00000380542SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
Frame-shiftENST00000554584ENST00000380542SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-3CDSENST00000394768ENST00000380542SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-3CDSENST00000441438ENST00000380542SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-3CDSENST00000458046ENST00000380542SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-3CDSENST00000553455ENST00000380542SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-3CDSENST00000554805ENST00000380542SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-3CDSENST00000555002ENST00000380542SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-3CDSENST00000555022ENST00000380542SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-3CDSENST00000556725ENST00000380542SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-intronENST00000394768ENST00000469089SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-intronENST00000394768ENST00000526115SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-intronENST00000441438ENST00000469089SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-intronENST00000441438ENST00000526115SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-intronENST00000458046ENST00000469089SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-intronENST00000458046ENST00000526115SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-intronENST00000553455ENST00000469089SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-intronENST00000553455ENST00000526115SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-intronENST00000554805ENST00000469089SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-intronENST00000554805ENST00000526115SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-intronENST00000555002ENST00000469089SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-intronENST00000555002ENST00000526115SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-intronENST00000555022ENST00000469089SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-intronENST00000555022ENST00000526115SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-intronENST00000556725ENST00000469089SYNE2chr14

64375945

+NAP1L4chr11

2981139

-
intron-intronENST00000556725ENST00000526115SYNE2chr14

64375945

+NAP1L4chr11

2981139

-

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 SYNE2-NAP1L4


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 SYNE2-NAP1L4


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/:64375945/:2981139)
- 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
.NAP1L4

Q99733

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: Acts as histone chaperone in nucleosome assembly. {ECO:0000269|PubMed:9325046}.

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 SYNE2-NAP1L4


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 SYNE2-NAP1L4


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 SYNE2-NAP1L4


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 SYNE2-NAP1L4


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