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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:TRAF3-BMP3 (FusionGDB2 ID:93005)

Fusion Gene Summary for TRAF3-BMP3

check button Fusion gene summary
Fusion gene informationFusion gene name: TRAF3-BMP3
Fusion gene ID: 93005
HgeneTgene
Gene symbol

TRAF3

BMP3

Gene ID

7187

651

Gene nameTNF receptor associated factor 3bone morphogenetic protein 3
SynonymsCAP-1|CAP1|CD40bp|CRAF1|IIAE5|LAP1|RNF118BMP-3A
Cytomap

14q32.32

4q21.21

Type of geneprotein-codingprotein-coding
DescriptionTNF receptor-associated factor 3CD40 associated protein 1CD40 binding proteinCD40 receptor associated factor 1LMP1-associated protein 1RING-type E3 ubiquitin transferase TRAF3bone morphogenetic protein 3bone morphogenetic protein 3 (osteogenic)bone morphogenetic protein 3Aosteogenin
Modification date2020032720200329
UniProtAcc

Q13114

.
Ensembl transtripts involved in fusion geneENST00000560371, ENST00000347662, 
ENST00000392745, ENST00000539721, 
ENST00000351691, 
ENST00000282701, 
Fusion gene scores* DoF score15 X 11 X 11=18152 X 1 X 2=4
# samples 203
** MAII scorelog2(20/1815*10)=-3.18189764310839
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/4*10)=2.90689059560852
Context

PubMed: TRAF3 [Title/Abstract] AND BMP3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTRAF3(103296809)-BMP3(81966892), # 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 TRAF3 (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 BMP3 (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-39-5030-01ATRAF3chr14

103296809

+BMP3chr4

81966892

+
ChimerDB4LUSCTCGA-39-5030TRAF3chr14

103296809

+BMP3chr4

81966892

+
ChimerDB4LUSCTCGA-39-5030TRAF3chr14

103244012

+BMP3chr4

81966892

+
ChimerDB4LUSCTCGA-39-5030-01ATRAF3chr14

103296809

-BMP3chr4

81966892

+


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Fusion Gene ORF analysis for TRAF3-BMP3

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-3CDSENST00000560371ENST00000282701TRAF3chr14

103296809

+BMP3chr4

81966892

+
5UTR-3CDSENST00000347662ENST00000282701TRAF3chr14

103296809

+BMP3chr4

81966892

+
5UTR-3CDSENST00000392745ENST00000282701TRAF3chr14

103296809

+BMP3chr4

81966892

+
intron-3CDSENST00000539721ENST00000282701TRAF3chr14

103296809

+BMP3chr4

81966892

+
5UTR-3CDSENST00000351691ENST00000282701TRAF3chr14

103296809

+BMP3chr4

81966892

+
5UTR-3CDSENST00000560371ENST00000282701TRAF3chr14

103244012

+BMP3chr4

81966892

+
5UTR-3CDSENST00000347662ENST00000282701TRAF3chr14

103244012

+BMP3chr4

81966892

+
5UTR-3CDSENST00000392745ENST00000282701TRAF3chr14

103244012

+BMP3chr4

81966892

+
5UTR-3CDSENST00000539721ENST00000282701TRAF3chr14

103244012

+BMP3chr4

81966892

+
intron-3CDSENST00000351691ENST00000282701TRAF3chr14

103244012

+BMP3chr4

81966892

+

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 TRAF3-BMP3


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)
TRAF3chr14103296809+BMP3chr481966891+0.0068135280.9931865
TRAF3chr14103296809+BMP3chr481966891+0.0068135280.9931865
TRAF3chr14103244012+BMP3chr481966891+5.90E-101
TRAF3chr14103296809+BMP3chr481966891+0.0068135280.9931865
TRAF3chr14103296809+BMP3chr481966891+0.0068135280.9931865
TRAF3chr14103244012+BMP3chr481966891+5.90E-101

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 TRAF3-BMP3


check button Go to

FGviewer for the breakpoints of :-:

.
- 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
TRAF3

Q13114

.
FUNCTION: Regulates pathways leading to the activation of NF-kappa-B and MAP kinases, and plays a central role in the regulation of B-cell survival. Part of signaling pathways leading to the production of cytokines and interferon. Required for normal antibody isotype switching from IgM to IgG. Plays a role T-cell dependent immune responses. Plays a role in the regulation of antiviral responses. Is an essential constituent of several E3 ubiquitin-protein ligase complexes. May have E3 ubiquitin-protein ligase activity and promote 'Lys-63'-linked ubiquitination of target proteins. Inhibits activation of NF-kappa-B in response to LTBR stimulation. Inhibits TRAF2-mediated activation of NF-kappa-B. Down-regulates proteolytic processing of NFKB2, and thereby inhibits non-canonical activation of NF-kappa-B. Promotes ubiquitination and proteasomal degradation of MAP3K14. {ECO:0000269|PubMed:15084608, ECO:0000269|PubMed:15383523, ECO:0000269|PubMed:17991829, ECO:0000269|PubMed:19937093, ECO:0000269|PubMed:20097753, ECO:0000269|PubMed:20185819, ECO:0000269|PubMed:32562145}.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 TRAF3-BMP3


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 TRAF3-BMP3


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 TRAF3-BMP3


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 TRAF3-BMP3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTRAF3C3553868ENCEPHALOPATHY, ACUTE, INFECTION-INDUCED (HERPES-SPECIFIC), SUSCEPTIBILITY TO, 52GENOMICS_ENGLAND;UNIPROT
HgeneTRAF3C0019385Herpetic meningoencephalitis1CTD_human;ORPHANET
HgeneTRAF3C0276226Herpes encephalitis1CTD_human;ORPHANET