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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 1019

FusionGeneSummary for AFF3_RTN4

check button Fusion gene summary
Fusion gene informationFusion gene name: AFF3_RTN4
Fusion gene ID: 1019
HgeneTgene
Gene symbol

AFF3

RTN4

Gene ID

3899

57142

Gene nameAF4/FMR2 family member 3reticulon 4
SynonymsLAF4|MLLT2-likeASY|NI220/250|NOGO|NSP|NSP-CL|Nbla00271|Nbla10545|RTN-X|RTN4-A|RTN4-B1|RTN4-B2|RTN4-C
Cytomap

2q11.2

2p16.1

Type of geneprotein-codingprotein-coding
DescriptionAF4/FMR2 family member 3MLLT2-related proteinlymphoid nuclear protein 4lymphoid nuclear protein related to AF4protein LAF-4reticulon-4Human NogoAMy043 proteinfoocenneurite growth inhibitor 220neurite outgrowth inhibitorneuroendocrine-specific protein C homologreticulon 5
Modification date2018052320180523
UniProtAcc

P51826

Q9NQC3

Ensembl transtripts involved in fusion geneENST00000409236, ENST00000356421, 
ENST00000317233, ENST00000409579, 
ENST00000483600, 
ENST00000394609, 
ENST00000405240, ENST00000357376, 
ENST00000317610, ENST00000357732, 
ENST00000337526, ENST00000394611, 
ENST00000404909, ENST00000486085, 
ENST00000354474, ENST00000402434, 
Fusion gene scores* DoF score12 X 9 X 5=54013 X 19 X 5=1235
# samples 1223
** MAII scorelog2(12/540*10)=-2.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(23/1235*10)=-2.42480527552766
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: AFF3 [Title/Abstract] AND RTN4 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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 from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS3.1T06959AFF3chr2

100163863

+RTN4chr2

55252550

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
intron-intronENST00000409236ENST00000394609AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409236ENST00000405240AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409236ENST00000357376AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409236ENST00000317610AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409236ENST00000357732AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409236ENST00000337526AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409236ENST00000394611AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409236ENST00000404909AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409236ENST00000486085AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409236ENST00000354474AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409236ENST00000402434AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000356421ENST00000394609AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000356421ENST00000405240AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000356421ENST00000357376AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000356421ENST00000317610AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000356421ENST00000357732AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000356421ENST00000337526AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000356421ENST00000394611AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000356421ENST00000404909AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000356421ENST00000486085AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000356421ENST00000354474AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000356421ENST00000402434AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000317233ENST00000394609AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000317233ENST00000405240AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000317233ENST00000357376AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000317233ENST00000317610AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000317233ENST00000357732AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000317233ENST00000337526AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000317233ENST00000394611AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000317233ENST00000404909AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000317233ENST00000486085AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000317233ENST00000354474AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000317233ENST00000402434AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409579ENST00000394609AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409579ENST00000405240AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409579ENST00000357376AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409579ENST00000317610AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409579ENST00000357732AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409579ENST00000337526AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409579ENST00000394611AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409579ENST00000404909AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409579ENST00000486085AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409579ENST00000354474AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000409579ENST00000402434AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000483600ENST00000394609AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000483600ENST00000405240AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000483600ENST00000357376AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000483600ENST00000317610AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000483600ENST00000357732AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000483600ENST00000337526AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000483600ENST00000394611AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000483600ENST00000404909AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000483600ENST00000486085AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000483600ENST00000354474AFF3chr2

100163863

+RTN4chr2

55252550

+
intron-intronENST00000483600ENST00000402434AFF3chr2

100163863

+RTN4chr2

55252550

+

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FusionProtFeatures for AFF3_RTN4


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
AFF3

P51826

RTN4

Q9NQC3


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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FusionGeneSequence for AFF3_RTN4


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for AFF3_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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RelatedDrugs for AFF3_RTN4


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for AFF3_RTN4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneAFF3C0003873Rheumatoid Arthritis2CTD_human
HgeneAFF3C0236969Substance-Related Disorders1CTD_human
TgeneRTN4C0005586Bipolar Disorder1PSYGENET
TgeneRTN4C0023893Liver Cirrhosis, Experimental1CTD_human
TgeneRTN4C0036341Schizophrenia1CTD_human