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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:RTN4IP1-QRSL1 (FusionGDB2 ID:78113)

Fusion Gene Summary for RTN4IP1-QRSL1

check button Fusion gene summary
Fusion gene informationFusion gene name: RTN4IP1-QRSL1
Fusion gene ID: 78113
HgeneTgene
Gene symbol

RTN4IP1

QRSL1

Gene ID

84816

55278

Gene namereticulon 4 interacting protein 1glutaminyl-tRNA amidotransferase subunit QRSL1
SynonymsNIMP|OPA10GatA
Cytomap

6q21

6q21

Type of geneprotein-codingprotein-coding
Descriptionreticulon-4-interacting protein 1, mitochondrialNOGO-interacting mitochondrial proteinglutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrialQRSL1, glutaminyl-tRNA amidotransferase subunit Aglu-AdT subunit Aglutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1glutaminyl-tRNA synthase-like protein 1glutamyl-tRNA(Gln) amidotransf
Modification date2020032720200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000539449, ENST00000369063, 
ENST00000498091, 		ENST00000369046, 
ENST00000467262, ENST00000369044, 
Fusion gene scores* DoF score3 X 4 X 3=369 X 9 X 5=405
# samples 413
** MAII scorelog2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(13/405*10)=-1.63941028474353
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RTN4IP1 [Title/Abstract] AND QRSL1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRTN4IP1(107076623)-QRSL1(107088224), # samples:1
RTN4IP1(107067077)-QRSL1(107110855), # samples:1
Anticipated loss of major functional domain due to fusion event.RTN4IP1-QRSL1 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
RTN4IP1-QRSL1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
RTN4IP1-QRSL1 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
TgeneQRSL1

GO:0070681

glutaminyl-tRNAGln biosynthesis via transamidation

19805282


check buttonFusion gene breakpoints across RTN4IP1 (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 QRSL1 (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
ChimerDB4LUSCTCGA-77-A5G6-01ARTN4IP1chr6

107076623

-QRSL1chr6

107088224

+
ChimerDB4STADTCGA-BR-8060-01ARTN4IP1chr6

107067077

-QRSL1chr6

107110855

+


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Fusion Gene ORF analysis for RTN4IP1-QRSL1

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
In-frameENST00000539449ENST00000369046RTN4IP1chr6

107076623

-QRSL1chr6

107088224

+
5CDS-3UTRENST00000539449ENST00000467262RTN4IP1chr6

107076623

-QRSL1chr6

107088224

+
5CDS-3UTRENST00000539449ENST00000369044RTN4IP1chr6

107076623

-QRSL1chr6

107088224

+
In-frameENST00000369063ENST00000369046RTN4IP1chr6

107076623

-QRSL1chr6

107088224

+
5CDS-3UTRENST00000369063ENST00000467262RTN4IP1chr6

107076623

-QRSL1chr6

107088224

+
5CDS-3UTRENST00000369063ENST00000369044RTN4IP1chr6

107076623

-QRSL1chr6

107088224

+
intron-3CDSENST00000498091ENST00000369046RTN4IP1chr6

107076623

-QRSL1chr6

107088224

+
intron-3UTRENST00000498091ENST00000467262RTN4IP1chr6

107076623

-QRSL1chr6

107088224

+
intron-3UTRENST00000498091ENST00000369044RTN4IP1chr6

107076623

-QRSL1chr6

107088224

+
Frame-shiftENST00000539449ENST00000369046RTN4IP1chr6

107067077

-QRSL1chr6

107110855

+
5CDS-intronENST00000539449ENST00000467262RTN4IP1chr6

107067077

-QRSL1chr6

107110855

+
5CDS-intronENST00000539449ENST00000369044RTN4IP1chr6

107067077

-QRSL1chr6

107110855

+
In-frameENST00000369063ENST00000369046RTN4IP1chr6

107067077

-QRSL1chr6

107110855

+
5CDS-intronENST00000369063ENST00000467262RTN4IP1chr6

107067077

-QRSL1chr6

107110855

+
5CDS-intronENST00000369063ENST00000369044RTN4IP1chr6

107067077

-QRSL1chr6

107110855

+
intron-3CDSENST00000498091ENST00000369046RTN4IP1chr6

107067077

-QRSL1chr6

107110855

+
intron-intronENST00000498091ENST00000467262RTN4IP1chr6

107067077

-QRSL1chr6

107110855

+
intron-intronENST00000498091ENST00000369044RTN4IP1chr6

107067077

-QRSL1chr6

107110855

+

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 RTN4IP1-QRSL1


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)
RTN4IP1chr6107067076-QRSL1chr6107110854+1.10E-050.99998903
RTN4IP1chr6107076622-QRSL1chr6107088223+7.78E-070.99999917
RTN4IP1chr6107067076-QRSL1chr6107110854+1.10E-050.99998903
RTN4IP1chr6107076622-QRSL1chr6107088223+7.78E-070.99999917

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 RTN4IP1-QRSL1


check button Go to

FGviewer for the breakpoints of chr6:107076623-chr6:107088224

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
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.
- 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 RTN4IP1-QRSL1


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 RTN4IP1-QRSL1


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 RTN4IP1-QRSL1


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 RTN4IP1-QRSL1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRTN4IP1C4225227OPTIC ATROPHY 10 WITH OR WITHOUT ATAXIA, MENTAL RETARDATION, AND SEIZURES3CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneQRSL1C3532239Mitochondrial cardiomyopathy1GENOMICS_ENGLAND