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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:NAV2-USB1 (FusionGDB2 ID:57351)

Fusion Gene Summary for NAV2-USB1

check button Fusion gene summary
Fusion gene informationFusion gene name: NAV2-USB1
Fusion gene ID: 57351
HgeneTgene
Gene symbol

NAV2

USB1

Gene ID

89797

79650

Gene nameneuron navigator 2U6 snRNA biogenesis phosphodiesterase 1
SynonymsHELAD1|POMFIL2|RAINB1|STEERIN2|UNC53H2C16orf57|HVSL1|Mpn1|PN|hUsb1
Cytomap

11p15.1

16q21

Type of geneprotein-codingprotein-coding
Descriptionneuron navigator 2helicase, APC down-regulated 1pore membrane and/or filament-interacting-like protein 2retinoic acid inducible gene in neuroblastoma 1steerin-2unc-53 homolog 2U6 snRNA phosphodiesteraseHVSL motif containing 1U six biogenesis 1U6 snRNA biogenesis 1UPF0406 protein C16orf57mutated in poikiloderma with neutropenia protein 1putative U6 snRNA phosphodiesterase
Modification date2020031320200328
UniProtAcc

Q8IVL1

Q9BQ65

Ensembl transtripts involved in fusion geneENST00000311043, ENST00000349880, 
ENST00000360655, ENST00000396085, 
ENST00000527559, ENST00000540292, 
ENST00000396087, ENST00000533917, 
ENST00000534229, 		ENST00000219281, 
ENST00000539737, ENST00000423271, 
ENST00000561743, ENST00000563149, 
ENST00000565662, 
Fusion gene scores* DoF score16 X 19 X 6=18242 X 3 X 2=12
# samples 193
** MAII scorelog2(19/1824*10)=-3.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/12*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: NAV2 [Title/Abstract] AND USB1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNAV2(20142993)-USB1(58054472), # samples:3
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 NAV2 (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 USB1 (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
ChimerDB4HNSCTCGA-BA-5149NAV2chr11

20142987

+USB1chr16

58054466

+
ChimerDB4HNSCTCGA-CV-7095NAV2chr11

20142993

+USB1chr16

58054472

+
ChimerDB4HNSCTCGA-D6-8569NAV2chr11

20142993

+USB1chr16

58054472

+
ChimerDB4LUSCTCGA-63-6202NAV2chr11

20142993

+USB1chr16

58054472

+


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Fusion Gene ORF analysis for NAV2-USB1

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-3UTRENST00000311043ENST00000219281NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-3UTRENST00000311043ENST00000219281NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-3UTRENST00000311043ENST00000539737NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-3UTRENST00000311043ENST00000539737NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-3UTRENST00000349880ENST00000219281NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-3UTRENST00000349880ENST00000219281NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-3UTRENST00000349880ENST00000539737NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-3UTRENST00000349880ENST00000539737NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-3UTRENST00000360655ENST00000219281NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-3UTRENST00000360655ENST00000219281NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-3UTRENST00000360655ENST00000539737NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-3UTRENST00000360655ENST00000539737NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-3UTRENST00000396085ENST00000219281NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-3UTRENST00000396085ENST00000219281NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-3UTRENST00000396085ENST00000539737NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-3UTRENST00000396085ENST00000539737NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-3UTRENST00000527559ENST00000219281NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-3UTRENST00000527559ENST00000219281NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-3UTRENST00000527559ENST00000539737NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-3UTRENST00000527559ENST00000539737NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-3UTRENST00000540292ENST00000219281NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-3UTRENST00000540292ENST00000219281NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-3UTRENST00000540292ENST00000539737NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-3UTRENST00000540292ENST00000539737NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000311043ENST00000423271NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000311043ENST00000423271NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000311043ENST00000561743NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000311043ENST00000561743NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000311043ENST00000563149NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000311043ENST00000563149NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000311043ENST00000565662NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000311043ENST00000565662NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000349880ENST00000423271NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000349880ENST00000423271NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000349880ENST00000561743NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000349880ENST00000561743NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000349880ENST00000563149NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000349880ENST00000563149NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000349880ENST00000565662NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000349880ENST00000565662NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000360655ENST00000423271NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000360655ENST00000423271NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000360655ENST00000561743NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000360655ENST00000561743NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000360655ENST00000563149NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000360655ENST00000563149NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000360655ENST00000565662NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000360655ENST00000565662NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000396085ENST00000423271NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000396085ENST00000423271NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000396085ENST00000561743NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000396085ENST00000561743NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000396085ENST00000563149NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000396085ENST00000563149NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000396085ENST00000565662NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000396085ENST00000565662NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000527559ENST00000423271NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000527559ENST00000423271NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000527559ENST00000561743NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000527559ENST00000561743NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000527559ENST00000563149NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000527559ENST00000563149NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000527559ENST00000565662NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000527559ENST00000565662NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000540292ENST00000423271NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000540292ENST00000423271NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000540292ENST00000561743NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000540292ENST00000561743NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000540292ENST00000563149NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000540292ENST00000563149NAV2chr11

20142993

+USB1chr16

58054472

+
3UTR-intronENST00000540292ENST00000565662NAV2chr11

20142987

+USB1chr16

58054466

+
3UTR-intronENST00000540292ENST00000565662NAV2chr11

20142993

+USB1chr16

58054472

+
intron-3UTRENST00000396087ENST00000219281NAV2chr11

20142987

+USB1chr16

58054466

+
intron-3UTRENST00000396087ENST00000219281NAV2chr11

20142993

+USB1chr16

58054472

+
intron-3UTRENST00000396087ENST00000539737NAV2chr11

20142987

+USB1chr16

58054466

+
intron-3UTRENST00000396087ENST00000539737NAV2chr11

20142993

+USB1chr16

58054472

+
intron-3UTRENST00000533917ENST00000219281NAV2chr11

20142987

+USB1chr16

58054466

+
intron-3UTRENST00000533917ENST00000219281NAV2chr11

20142993

+USB1chr16

58054472

+
intron-3UTRENST00000533917ENST00000539737NAV2chr11

20142987

+USB1chr16

58054466

+
intron-3UTRENST00000533917ENST00000539737NAV2chr11

20142993

+USB1chr16

58054472

+
intron-3UTRENST00000534229ENST00000219281NAV2chr11

20142987

+USB1chr16

58054466

+
intron-3UTRENST00000534229ENST00000219281NAV2chr11

20142993

+USB1chr16

58054472

+
intron-3UTRENST00000534229ENST00000539737NAV2chr11

20142987

+USB1chr16

58054466

+
intron-3UTRENST00000534229ENST00000539737NAV2chr11

20142993

+USB1chr16

58054472

+
intron-intronENST00000396087ENST00000423271NAV2chr11

20142987

+USB1chr16

58054466

+
intron-intronENST00000396087ENST00000423271NAV2chr11

20142993

+USB1chr16

58054472

+
intron-intronENST00000396087ENST00000561743NAV2chr11

20142987

+USB1chr16

58054466

+
intron-intronENST00000396087ENST00000561743NAV2chr11

20142993

+USB1chr16

58054472

+
intron-intronENST00000396087ENST00000563149NAV2chr11

20142987

+USB1chr16

58054466

+
intron-intronENST00000396087ENST00000563149NAV2chr11

20142993

+USB1chr16

58054472

+
intron-intronENST00000396087ENST00000565662NAV2chr11

20142987

+USB1chr16

58054466

+
intron-intronENST00000396087ENST00000565662NAV2chr11

20142993

+USB1chr16

58054472

+
intron-intronENST00000533917ENST00000423271NAV2chr11

20142987

+USB1chr16

58054466

+
intron-intronENST00000533917ENST00000423271NAV2chr11

20142993

+USB1chr16

58054472

+
intron-intronENST00000533917ENST00000561743NAV2chr11

20142987

+USB1chr16

58054466

+
intron-intronENST00000533917ENST00000561743NAV2chr11

20142993

+USB1chr16

58054472

+
intron-intronENST00000533917ENST00000563149NAV2chr11

20142987

+USB1chr16

58054466

+
intron-intronENST00000533917ENST00000563149NAV2chr11

20142993

+USB1chr16

58054472

+
intron-intronENST00000533917ENST00000565662NAV2chr11

20142987

+USB1chr16

58054466

+
intron-intronENST00000533917ENST00000565662NAV2chr11

20142993

+USB1chr16

58054472

+
intron-intronENST00000534229ENST00000423271NAV2chr11

20142987

+USB1chr16

58054466

+
intron-intronENST00000534229ENST00000423271NAV2chr11

20142993

+USB1chr16

58054472

+
intron-intronENST00000534229ENST00000561743NAV2chr11

20142987

+USB1chr16

58054466

+
intron-intronENST00000534229ENST00000561743NAV2chr11

20142993

+USB1chr16

58054472

+
intron-intronENST00000534229ENST00000563149NAV2chr11

20142987

+USB1chr16

58054466

+
intron-intronENST00000534229ENST00000563149NAV2chr11

20142993

+USB1chr16

58054472

+
intron-intronENST00000534229ENST00000565662NAV2chr11

20142987

+USB1chr16

58054466

+
intron-intronENST00000534229ENST00000565662NAV2chr11

20142993

+USB1chr16

58054472

+

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 NAV2-USB1


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 NAV2-USB1


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/:20142993/:58054472)
- 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
NAV2

Q8IVL1

USB1

Q9BQ65

FUNCTION: Possesses 3' to 5' helicase activity and exonuclease activity. Involved in neuronal development, specifically in the development of different sensory organs. {ECO:0000269|PubMed:12214280, ECO:0000269|PubMed:15158073}.FUNCTION: Phosphodiesterase responsible for the U6 snRNA 3' end processing. Acts as an exoribonuclease (RNase) responsible for trimming the poly(U) tract of the last nucleotides in the pre-U6 snRNA molecule, leading to the formation of mature U6 snRNA 3' end-terminated with a 2',3'-cyclic phosphate. {ECO:0000255|HAMAP-Rule:MF_03040, ECO:0000269|PubMed:22899009, ECO:0000269|PubMed:23190533}.

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 NAV2-USB1


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 NAV2-USB1


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 NAV2-USB1


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 NAV2-USB1


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