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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:RTN4-SUCLG1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: RTN4-SUCLG1
FusionPDB ID: 78593
FusionGDB2.0 ID: 78593
HgeneTgene
Gene symbol

RTN4

SUCLG1

Gene ID

57142

8802

Gene namereticulon 4succinate-CoA ligase GDP/ADP-forming subunit alpha
SynonymsASY|NI220/250|NOGO|NSP|NSP-CL|Nbla00271|Nbla10545|RTN-X|RTN4-A|RTN4-B1|RTN4-B2|RTN4-CGALPHA|MTDPS9|SUCLA1
Cytomap

2p16.1

2p11.2

Type of geneprotein-codingprotein-coding
Descriptionreticulon-4Human NogoAMy043 proteinfoocenneurite growth inhibitor 220neurite outgrowth inhibitorneuroendocrine-specific protein C homologreticulon 5succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrialSCS-alphasuccinate-CoA ligase alpha subunitsuccinyl-CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrialsuccinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrialsuccinyl-Co
Modification date2020032720200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000317610, ENST00000337526, 
ENST00000357732, ENST00000402434, 
ENST00000354474, ENST00000357376, 
ENST00000394609, ENST00000394611, 
ENST00000404909, ENST00000405240, 
ENST00000486085, 		ENST00000491123, 
ENST00000393868, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score18 X 22 X 7=277210 X 9 X 6=540
# samples 2710
** MAII scorelog2(27/2772*10)=-3.35989594508638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/540*10)=-2.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: RTN4 [Title/Abstract] AND SUCLG1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)RTN4(55276880)-SUCLG1(84676876), # samples:1
Anticipated loss of major functional domain due to fusion event.RTN4-SUCLG1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
RTN4-SUCLG1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
RTN4-SUCLG1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
RTN4-SUCLG1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
RTN4-SUCLG1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
RTN4-SUCLG1 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
RTN4-SUCLG1 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
RTN4-SUCLG1 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
HgeneRTN4

GO:0030517

negative regulation of axon extension

10667797

HgeneRTN4

GO:0071787

endoplasmic reticulum tubular network formation

24262037|25612671

HgeneRTN4

GO:1905552

positive regulation of protein localization to endoplasmic reticulum

27353365


check buttonFusion gene breakpoints across RTN4 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across SUCLG1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4BLCATCGA-2F-A9KWRTN4chr2

55276880

-SUCLG1chr2

84676876

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000402434RTN4chr255276880-ENST00000393868SUCLG1chr284676876-1715548491491480

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
ENST00000402434ENST00000393868RTN4chr255276880-SUCLG1chr284676876-0.0067254740.99327457

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>78593_78593_1_RTN4-SUCLG1_RTN4_chr2_55276880_ENST00000402434_SUCLG1_chr2_84676876_ENST00000393868_length(amino acids)=480AA_BP=166
MQHHLHPPAMEPEDEEEEEEEEEEDEDEDLEELEVLERKPAAGLSAAPVPTAPAAGAPLMDFGNDFVPPAPRGPLPAAPPVAPERQPSWD
PSPVSSTVPAPSPLSAAAVSPSKLPEDDEPPARPPPPPPASVSPQAEPVWTPPAPAPAAPPSTPAAPKRRGSSGSVVPQNGIRHCSYTAS
RQHLYVDKNTKIICQGFTGKQGTFHSQQALEYGTKLVGGTTPGKGGQTHLGLPVFNTVKEAKEQTGATASVIYVPPPFAAAAINEAIEAE
IPLVVCITEGIPQQDMVRVKHKLLRQEKTRLIGPNCPGVINPGECKIGIMPGHIHKKGRIGIVSRSGTLTYEAVHQTTQVGLGQSLCVGI
GGDPFNGTDFIDCLEIFLNDSATEGIILIGEIGGNAEENAAEFLKQHNSGPNSKPVVSFIAGLTAPPGRRMGHAGAIIAGGKGGAKEKIS

--------------------------------------------------------------

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Fusion Protein Functional Features


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/chr2:55276880/chr2:84676876)
- 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
..
FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneRTN4chr2:55276880chr2:84676876ENST00000317610-17143_148185.33333333333334374.0Compositional biasNote=Poly-Pro
HgeneRTN4chr2:55276880chr2:84676876ENST00000317610-1730_47185.33333333333334374.0Compositional biasNote=Poly-Glu
HgeneRTN4chr2:55276880chr2:84676876ENST00000337526-19143_148185.333333333333341193.0Compositional biasNote=Poly-Pro
HgeneRTN4chr2:55276880chr2:84676876ENST00000337526-1930_47185.333333333333341193.0Compositional biasNote=Poly-Glu
HgeneRTN4chr2:55276880chr2:84676876ENST00000357732-18143_148185.33333333333334393.0Compositional biasNote=Poly-Pro
HgeneRTN4chr2:55276880chr2:84676876ENST00000357732-1830_47185.33333333333334393.0Compositional biasNote=Poly-Glu
TgeneSUCLG1chr2:55276880chr2:84676876ENST0000039386809143_14532.333333333333336347.0RegionCoenzyme A binding
TgeneSUCLG1chr2:55276880chr2:84676876ENST000003938680964_6732.333333333333336347.0RegionCoenzyme A binding

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneRTN4chr2:55276880chr2:84676876ENST00000357376-19143_1480987.0Compositional biasNote=Poly-Pro
HgeneRTN4chr2:55276880chr2:84676876ENST00000357376-1930_470987.0Compositional biasNote=Poly-Glu
HgeneRTN4chr2:55276880chr2:84676876ENST00000394609-17143_1480200.0Compositional biasNote=Poly-Pro
HgeneRTN4chr2:55276880chr2:84676876ENST00000394609-1730_470200.0Compositional biasNote=Poly-Glu
HgeneRTN4chr2:55276880chr2:84676876ENST00000394611-19143_1480987.0Compositional biasNote=Poly-Pro
HgeneRTN4chr2:55276880chr2:84676876ENST00000394611-1930_470987.0Compositional biasNote=Poly-Glu
HgeneRTN4chr2:55276880chr2:84676876ENST00000404909-19143_1480987.0Compositional biasNote=Poly-Pro
HgeneRTN4chr2:55276880chr2:84676876ENST00000404909-1930_470987.0Compositional biasNote=Poly-Glu
HgeneRTN4chr2:55276880chr2:84676876ENST00000405240-19143_1480987.0Compositional biasNote=Poly-Pro
HgeneRTN4chr2:55276880chr2:84676876ENST00000405240-1930_470987.0Compositional biasNote=Poly-Glu
HgeneRTN4chr2:55276880chr2:84676876ENST00000317610-171005_1192185.33333333333334374.0DomainReticulon
HgeneRTN4chr2:55276880chr2:84676876ENST00000337526-191005_1192185.333333333333341193.0DomainReticulon
HgeneRTN4chr2:55276880chr2:84676876ENST00000357376-191005_11920987.0DomainReticulon
HgeneRTN4chr2:55276880chr2:84676876ENST00000357732-181005_1192185.33333333333334393.0DomainReticulon
HgeneRTN4chr2:55276880chr2:84676876ENST00000394609-171005_11920200.0DomainReticulon
HgeneRTN4chr2:55276880chr2:84676876ENST00000394611-191005_11920987.0DomainReticulon
HgeneRTN4chr2:55276880chr2:84676876ENST00000404909-191005_11920987.0DomainReticulon
HgeneRTN4chr2:55276880chr2:84676876ENST00000405240-191005_11920987.0DomainReticulon
HgeneRTN4chr2:55276880chr2:84676876ENST00000317610-171040_1133185.33333333333334374.0Topological domainLumenal
HgeneRTN4chr2:55276880chr2:84676876ENST00000317610-171155_1192185.33333333333334374.0Topological domainCytoplasmic
HgeneRTN4chr2:55276880chr2:84676876ENST00000317610-171_1018185.33333333333334374.0Topological domainCytoplasmic
HgeneRTN4chr2:55276880chr2:84676876ENST00000337526-191040_1133185.333333333333341193.0Topological domainLumenal
HgeneRTN4chr2:55276880chr2:84676876ENST00000337526-191155_1192185.333333333333341193.0Topological domainCytoplasmic
HgeneRTN4chr2:55276880chr2:84676876ENST00000337526-191_1018185.333333333333341193.0Topological domainCytoplasmic
HgeneRTN4chr2:55276880chr2:84676876ENST00000357376-191040_11330987.0Topological domainLumenal
HgeneRTN4chr2:55276880chr2:84676876ENST00000357376-191155_11920987.0Topological domainCytoplasmic
HgeneRTN4chr2:55276880chr2:84676876ENST00000357376-191_10180987.0Topological domainCytoplasmic
HgeneRTN4chr2:55276880chr2:84676876ENST00000357732-181040_1133185.33333333333334393.0Topological domainLumenal
HgeneRTN4chr2:55276880chr2:84676876ENST00000357732-181155_1192185.33333333333334393.0Topological domainCytoplasmic
HgeneRTN4chr2:55276880chr2:84676876ENST00000357732-181_1018185.33333333333334393.0Topological domainCytoplasmic
HgeneRTN4chr2:55276880chr2:84676876ENST00000394609-171040_11330200.0Topological domainLumenal
HgeneRTN4chr2:55276880chr2:84676876ENST00000394609-171155_11920200.0Topological domainCytoplasmic
HgeneRTN4chr2:55276880chr2:84676876ENST00000394609-171_10180200.0Topological domainCytoplasmic
HgeneRTN4chr2:55276880chr2:84676876ENST00000394611-191040_11330987.0Topological domainLumenal
HgeneRTN4chr2:55276880chr2:84676876ENST00000394611-191155_11920987.0Topological domainCytoplasmic
HgeneRTN4chr2:55276880chr2:84676876ENST00000394611-191_10180987.0Topological domainCytoplasmic
HgeneRTN4chr2:55276880chr2:84676876ENST00000404909-191040_11330987.0Topological domainLumenal
HgeneRTN4chr2:55276880chr2:84676876ENST00000404909-191155_11920987.0Topological domainCytoplasmic
HgeneRTN4chr2:55276880chr2:84676876ENST00000404909-191_10180987.0Topological domainCytoplasmic
HgeneRTN4chr2:55276880chr2:84676876ENST00000405240-191040_11330987.0Topological domainLumenal
HgeneRTN4chr2:55276880chr2:84676876ENST00000405240-191155_11920987.0Topological domainCytoplasmic
HgeneRTN4chr2:55276880chr2:84676876ENST00000405240-191_10180987.0Topological domainCytoplasmic
HgeneRTN4chr2:55276880chr2:84676876ENST00000317610-171019_1039185.33333333333334374.0TransmembraneHelical
HgeneRTN4chr2:55276880chr2:84676876ENST00000317610-171134_1154185.33333333333334374.0TransmembraneHelical
HgeneRTN4chr2:55276880chr2:84676876ENST00000337526-191019_1039185.333333333333341193.0TransmembraneHelical
HgeneRTN4chr2:55276880chr2:84676876ENST00000337526-191134_1154185.333333333333341193.0TransmembraneHelical
HgeneRTN4chr2:55276880chr2:84676876ENST00000357376-191019_10390987.0TransmembraneHelical
HgeneRTN4chr2:55276880chr2:84676876ENST00000357376-191134_11540987.0TransmembraneHelical
HgeneRTN4chr2:55276880chr2:84676876ENST00000357732-181019_1039185.33333333333334393.0TransmembraneHelical
HgeneRTN4chr2:55276880chr2:84676876ENST00000357732-181134_1154185.33333333333334393.0TransmembraneHelical
HgeneRTN4chr2:55276880chr2:84676876ENST00000394609-171019_10390200.0TransmembraneHelical
HgeneRTN4chr2:55276880chr2:84676876ENST00000394609-171134_11540200.0TransmembraneHelical
HgeneRTN4chr2:55276880chr2:84676876ENST00000394611-191019_10390987.0TransmembraneHelical
HgeneRTN4chr2:55276880chr2:84676876ENST00000394611-191134_11540987.0TransmembraneHelical
HgeneRTN4chr2:55276880chr2:84676876ENST00000404909-191019_10390987.0TransmembraneHelical
HgeneRTN4chr2:55276880chr2:84676876ENST00000404909-191134_11540987.0TransmembraneHelical
HgeneRTN4chr2:55276880chr2:84676876ENST00000405240-191019_10390987.0TransmembraneHelical
HgeneRTN4chr2:55276880chr2:84676876ENST00000405240-191134_11540987.0TransmembraneHelical


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
RTN4
SUCLG1


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to RTN4-SUCLG1


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to RTN4-SUCLG1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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