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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:AFF4-RPL34 (FusionGDB2 ID:HG27125TG6164)

Fusion Gene Summary for AFF4-RPL34

check button Fusion gene summary
Fusion gene informationFusion gene name: AFF4-RPL34
Fusion gene ID: hg27125tg6164
HgeneTgene
Gene symbol

AFF4

RPL34

Gene ID

27125

6164

Gene nameAF4/FMR2 family member 4ribosomal protein L34
SynonymsAF5Q31|CHOPS|MCEFL34
Cytomap('AFF4')('RPL34')

5q31.1

4q25

Type of geneprotein-codingprotein-coding
DescriptionAF4/FMR2 family member 4ALL1-fused gene from chromosome 5q31 proteinmajor CDK9 elongation factor-associated protein60S ribosomal protein L34large ribosomal subunit protein eL34leukemia-associated protein
Modification date2020031520200313
UniProtAcc

Q9UHB7

.
Ensembl transtripts involved in fusion geneENST00000265343, ENST00000378595, 
ENST00000491831, 
Fusion gene scores* DoF score12 X 10 X 6=72011 X 13 X 3=429
# samples 1413
** MAII scorelog2(14/720*10)=-2.36257007938471
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(13/429*10)=-1.72246602447109
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: AFF4 [Title/Abstract] AND RPL34 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAFF4(132215369)-RPL34(109541732), # samples:2
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 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
ChimerDB4ESCATCGA-L5-A4OF-01AAFF4chr5

132215369

-RPL34chr4

109541732

+
ChimerDB4ESCATCGA-L5-A4OFAFF4chr5

132215369

-RPL34chr4

109541732

+


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Fusion Gene ORF analysis for AFF4-RPL34

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-5UTRENST00000265343ENST00000394667AFF4chr5

132215369

-RPL34chr4

109541732

+
intron-5UTRENST00000265343ENST00000502534AFF4chr5

132215369

-RPL34chr4

109541732

+
intron-5UTRENST00000378595ENST00000394667AFF4chr5

132215369

-RPL34chr4

109541732

+
intron-5UTRENST00000378595ENST00000502534AFF4chr5

132215369

-RPL34chr4

109541732

+
intron-5UTRENST00000491831ENST00000394667AFF4chr5

132215369

-RPL34chr4

109541732

+
intron-5UTRENST00000491831ENST00000502534AFF4chr5

132215369

-RPL34chr4

109541732

+
intron-intronENST00000265343ENST00000394665AFF4chr5

132215369

-RPL34chr4

109541732

+
intron-intronENST00000265343ENST00000394668AFF4chr5

132215369

-RPL34chr4

109541732

+
intron-intronENST00000265343ENST00000506397AFF4chr5

132215369

-RPL34chr4

109541732

+
intron-intronENST00000378595ENST00000394665AFF4chr5

132215369

-RPL34chr4

109541732

+
intron-intronENST00000378595ENST00000394668AFF4chr5

132215369

-RPL34chr4

109541732

+
intron-intronENST00000378595ENST00000506397AFF4chr5

132215369

-RPL34chr4

109541732

+
intron-intronENST00000491831ENST00000394665AFF4chr5

132215369

-RPL34chr4

109541732

+
intron-intronENST00000491831ENST00000394668AFF4chr5

132215369

-RPL34chr4

109541732

+
intron-intronENST00000491831ENST00000506397AFF4chr5

132215369

-RPL34chr4

109541732

+

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 AFF4-RPL34


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 AFF4-RPL34


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/:132215369/:109541732)
- 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
AFF4

Q9UHB7

.
FUNCTION: Key component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA. In the SEC complex, AFF4 acts as a central scaffold that recruits other factors through direct interactions with ELL proteins (ELL, ELL2 or ELL3) and the P-TEFb complex. In case of infection by HIV-1 virus, the SEC complex is recruited by the viral Tat protein to stimulate viral gene expression. {ECO:0000269|PubMed:20159561, ECO:0000269|PubMed:20471948, ECO:0000269|PubMed:23251033}.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 AFF4-RPL34


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 AFF4-RPL34


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 AFF4-RPL34


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 AFF4-RPL34


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneAFF4C0000772Multiple congenital anomalies1CTD_human
HgeneAFF4C0005941Bone Diseases, Developmental1CTD_human
HgeneAFF4C0009241Cognition Disorders1CTD_human
HgeneAFF4C0018273Growth Disorders1CTD_human
HgeneAFF4C0018798Congenital Heart Defects1CTD_human
HgeneAFF4C0024115Lung diseases1CTD_human
HgeneAFF4C0028754Obesity1CTD_human
HgeneAFF4C0282631Facies1CTD_human
HgeneAFF4C4085597CHOPS SYNDROME1CTD_human;ORPHANET;UNIPROT