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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:C11orf49-RTN4 (FusionGDB2 ID:HG79096TG57142)

Fusion Gene Summary for C11orf49-RTN4

check button Fusion gene summary
Fusion gene informationFusion gene name: C11orf49-RTN4
Fusion gene ID: hg79096tg57142
HgeneTgene
Gene symbol

C11orf49

RTN4

Gene ID

79096

57142

Gene namechromosome 11 open reading frame 49reticulon 4
Synonyms-ASY|NI220/250|NOGO|NSP|NSP-CL|Nbla00271|Nbla10545|RTN-X|RTN4-A|RTN4-B1|RTN4-B2|RTN4-C
Cytomap('C11orf49')('RTN4')

11p11.2

2p16.1

Type of geneprotein-codingprotein-coding
DescriptionUPF0705 protein C11orf49reticulon-4Human NogoAMy043 proteinfoocenneurite growth inhibitor 220neurite outgrowth inhibitorneuroendocrine-specific protein C homologreticulon 5
Modification date2020031320200327
UniProtAcc

Q9H6J7

.
Ensembl transtripts involved in fusion geneENST00000278460, ENST00000378615, 
ENST00000378618, ENST00000395460, 
ENST00000536126, ENST00000543718, 
ENST00000527268, 
Fusion gene scores* DoF score26 X 14 X 9=327627 X 28 X 9=6804
# samples 2735
** MAII scorelog2(27/3276*10)=-3.60090404459018
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(35/6804*10)=-4.28095631383106
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: C11orf49 [Title/Abstract] AND RTN4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointC11orf49(46958402)-RTN4(55201900), # samples:1
Anticipated loss of major functional domain due to fusion event.C11orf49-RTN4 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
C11orf49-RTN4 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
TgeneRTN4

GO:0030517

negative regulation of axon extension

10667797

TgeneRTN4

GO:0071787

endoplasmic reticulum tubular network formation

24262037|25612671

TgeneRTN4

GO:1905552

positive regulation of protein localization to endoplasmic reticulum

27353365



check button Fusion gene information
* 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
ChimerDB4BRCATCGA-BH-A0WA-01AC11orf49chr11

46958402

+RTN4chr2

55201900

-


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Fusion Gene ORF analysis for C11orf49-RTN4

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-intronENST00000278460ENST00000354474C11orf49chr11

46958402

+RTN4chr2

55201900

-
5CDS-intronENST00000278460ENST00000402434C11orf49chr11

46958402

+RTN4chr2

55201900

-
5CDS-intronENST00000278460ENST00000486085C11orf49chr11

46958402

+RTN4chr2

55201900

-
5CDS-intronENST00000378615ENST00000354474C11orf49chr11

46958402

+RTN4chr2

55201900

-
5CDS-intronENST00000378615ENST00000402434C11orf49chr11

46958402

+RTN4chr2

55201900

-
5CDS-intronENST00000378615ENST00000486085C11orf49chr11

46958402

+RTN4chr2

55201900

-
5CDS-intronENST00000378618ENST00000354474C11orf49chr11

46958402

+RTN4chr2

55201900

-
5CDS-intronENST00000378618ENST00000402434C11orf49chr11

46958402

+RTN4chr2

55201900

-
5CDS-intronENST00000378618ENST00000486085C11orf49chr11

46958402

+RTN4chr2

55201900

-
5CDS-intronENST00000395460ENST00000354474C11orf49chr11

46958402

+RTN4chr2

55201900

-
5CDS-intronENST00000395460ENST00000402434C11orf49chr11

46958402

+RTN4chr2

55201900

-
5CDS-intronENST00000395460ENST00000486085C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-3CDSENST00000536126ENST00000317610C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-3CDSENST00000536126ENST00000337526C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-3CDSENST00000536126ENST00000357376C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-3CDSENST00000536126ENST00000357732C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-3CDSENST00000536126ENST00000394609C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-3CDSENST00000536126ENST00000394611C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-3CDSENST00000536126ENST00000404909C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-3CDSENST00000536126ENST00000405240C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-3CDSENST00000543718ENST00000317610C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-3CDSENST00000543718ENST00000337526C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-3CDSENST00000543718ENST00000357376C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-3CDSENST00000543718ENST00000357732C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-3CDSENST00000543718ENST00000394609C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-3CDSENST00000543718ENST00000394611C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-3CDSENST00000543718ENST00000404909C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-3CDSENST00000543718ENST00000405240C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-intronENST00000536126ENST00000354474C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-intronENST00000536126ENST00000402434C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-intronENST00000536126ENST00000486085C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-intronENST00000543718ENST00000354474C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-intronENST00000543718ENST00000402434C11orf49chr11

46958402

+RTN4chr2

55201900

-
5UTR-intronENST00000543718ENST00000486085C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000278460ENST00000317610C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000278460ENST00000337526C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000278460ENST00000357376C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000278460ENST00000357732C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000278460ENST00000394609C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000278460ENST00000394611C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000278460ENST00000404909C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000278460ENST00000405240C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000378615ENST00000317610C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000378615ENST00000337526C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000378615ENST00000357376C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000378615ENST00000357732C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000378615ENST00000394609C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000378615ENST00000394611C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000378615ENST00000404909C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000378615ENST00000405240C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000378618ENST00000317610C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000378618ENST00000337526C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000378618ENST00000357376C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000378618ENST00000357732C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000378618ENST00000394609C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000378618ENST00000394611C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000378618ENST00000404909C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000378618ENST00000405240C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000395460ENST00000317610C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000395460ENST00000337526C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000395460ENST00000357376C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000395460ENST00000357732C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000395460ENST00000394609C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000395460ENST00000394611C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000395460ENST00000404909C11orf49chr11

46958402

+RTN4chr2

55201900

-
Frame-shiftENST00000395460ENST00000405240C11orf49chr11

46958402

+RTN4chr2

55201900

-
intron-3CDSENST00000527268ENST00000317610C11orf49chr11

46958402

+RTN4chr2

55201900

-
intron-3CDSENST00000527268ENST00000337526C11orf49chr11

46958402

+RTN4chr2

55201900

-
intron-3CDSENST00000527268ENST00000357376C11orf49chr11

46958402

+RTN4chr2

55201900

-
intron-3CDSENST00000527268ENST00000357732C11orf49chr11

46958402

+RTN4chr2

55201900

-
intron-3CDSENST00000527268ENST00000394609C11orf49chr11

46958402

+RTN4chr2

55201900

-
intron-3CDSENST00000527268ENST00000394611C11orf49chr11

46958402

+RTN4chr2

55201900

-
intron-3CDSENST00000527268ENST00000404909C11orf49chr11

46958402

+RTN4chr2

55201900

-
intron-3CDSENST00000527268ENST00000405240C11orf49chr11

46958402

+RTN4chr2

55201900

-
intron-intronENST00000527268ENST00000354474C11orf49chr11

46958402

+RTN4chr2

55201900

-
intron-intronENST00000527268ENST00000402434C11orf49chr11

46958402

+RTN4chr2

55201900

-
intron-intronENST00000527268ENST00000486085C11orf49chr11

46958402

+RTN4chr2

55201900

-

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 C11orf49-RTN4


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)


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Fusion Protein Features for C11orf49-RTN4


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/:46958402/:55201900)
- 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
C11orf49

Q9H6J7

.
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}.

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 C11orf49-RTN4


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 C11orf49-RTN4


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 C11orf49-RTN4


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 C11orf49-RTN4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneC0036341Schizophrenia1CTD_human