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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:AFF1-RBFOX1 (FusionGDB2 ID:HG4299TG54715)

Fusion Gene Summary for AFF1-RBFOX1

check button Fusion gene summary
Fusion gene informationFusion gene name: AFF1-RBFOX1
Fusion gene ID: hg4299tg54715
HgeneTgene
Gene symbol

AFF1

RBFOX1

Gene ID

4299

54715

Gene nameAF4/FMR2 family member 1RNA binding fox-1 homolog 1
SynonymsAF4|MLLT2|PBM12BP1|A2BP1|FOX-1|FOX1|HRNBP1
Cytomap('AFF1')('RBFOX1')

4q21.3-q22.1

16p13.3

Type of geneprotein-codingprotein-coding
DescriptionAF4/FMR2 family member 1ALL1-fused gene from chromosome 4 proteinmyeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 2pre-B-cell monocytic leukemia partner 1proto-oncogene AF4RNA binding protein fox-1 homolog 1RNA binding protein, fox-1 homolog 1ataxin 2-binding protein 1fox-1 homolog Afox-1-like RNA-binding protein 1hexaribonucleotide binding protein 1 isoform alphahexaribonucleotide binding protein 1 isoform betahexar
Modification date2020031320200313
UniProtAcc

P51825

.
Ensembl transtripts involved in fusion geneENST00000307808, ENST00000395146, 
ENST00000511996, ENST00000544085, 
Fusion gene scores* DoF score27 X 51 X 13=1790136 X 34 X 8=9792
# samples 6839
** MAII scorelog2(68/17901*10)=-4.71836162613835
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(39/9792*10)=-4.65005752894304
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: AFF1 [Title/Abstract] AND RBFOX1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAFF1(87968746)-RBFOX1(7102058), # 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 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
ChimerDB4PRADTCGA-KC-A4BV-01AAFF1chr4

87968746

-RBFOX1chr16

7102058

+
ChimerDB4PRADTCGA-KC-A4BV-01AAFF1chr4

87968746

+RBFOX1chr16

7102058

+
ChimerDB4PRADTCGA-KC-A4BVAFF1chr4

87968746

+RBFOX1chr16

7102058

+


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Fusion Gene ORF analysis for AFF1-RBFOX1

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
5CDS-3UTRENST00000307808ENST00000547427AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-3UTRENST00000307808ENST00000552089AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-3UTRENST00000395146ENST00000547427AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-3UTRENST00000395146ENST00000552089AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-5UTRENST00000307808ENST00000422070AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-5UTRENST00000307808ENST00000535565AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-5UTRENST00000307808ENST00000547338AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-5UTRENST00000307808ENST00000547372AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-5UTRENST00000307808ENST00000550418AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-5UTRENST00000307808ENST00000553186AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-5UTRENST00000395146ENST00000422070AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-5UTRENST00000395146ENST00000535565AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-5UTRENST00000395146ENST00000547338AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-5UTRENST00000395146ENST00000547372AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-5UTRENST00000395146ENST00000550418AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-5UTRENST00000395146ENST00000553186AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-intronENST00000307808ENST00000311745AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-intronENST00000307808ENST00000340209AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-intronENST00000307808ENST00000355637AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-intronENST00000307808ENST00000436368AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-intronENST00000395146ENST00000311745AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-intronENST00000395146ENST00000340209AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-intronENST00000395146ENST00000355637AFF1chr4

87968746

+RBFOX1chr16

7102058

+
5CDS-intronENST00000395146ENST00000436368AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-3UTRENST00000511996ENST00000547427AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-3UTRENST00000511996ENST00000552089AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-3UTRENST00000544085ENST00000547427AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-3UTRENST00000544085ENST00000552089AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-5UTRENST00000511996ENST00000422070AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-5UTRENST00000511996ENST00000535565AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-5UTRENST00000511996ENST00000547338AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-5UTRENST00000511996ENST00000547372AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-5UTRENST00000511996ENST00000550418AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-5UTRENST00000511996ENST00000553186AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-5UTRENST00000544085ENST00000422070AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-5UTRENST00000544085ENST00000535565AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-5UTRENST00000544085ENST00000547338AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-5UTRENST00000544085ENST00000547372AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-5UTRENST00000544085ENST00000550418AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-5UTRENST00000544085ENST00000553186AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-intronENST00000511996ENST00000311745AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-intronENST00000511996ENST00000340209AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-intronENST00000511996ENST00000355637AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-intronENST00000511996ENST00000436368AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-intronENST00000544085ENST00000311745AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-intronENST00000544085ENST00000340209AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-intronENST00000544085ENST00000355637AFF1chr4

87968746

+RBFOX1chr16

7102058

+
intron-intronENST00000544085ENST00000436368AFF1chr4

87968746

+RBFOX1chr16

7102058

+

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 AFF1-RBFOX1


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)
AFF1chr487968746+RBFOX1chr167102057+0.0039643930.99603564
AFF1chr487968746+RBFOX1chr167102057+0.0039643930.99603564
AFF1chr487968746+RBFOX1chr167102057+0.0039643930.99603564
AFF1chr487968746+RBFOX1chr167102057+0.0039643930.99603564


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.
genomic feature of top 1%

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Fusion Protein Features for AFF1-RBFOX1


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/:87968746/:7102058)
- 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
AFF1

P51825

.
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 AFF1-RBFOX1


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 AFF1-RBFOX1


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 AFF1-RBFOX1


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 AFF1-RBFOX1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0004352Autistic Disorder2CTD_human
TgeneC0022333Jacksonian Seizure1CTD_human
TgeneC0036572Seizures1CTD_human
TgeneC0149958Complex partial seizures1CTD_human
TgeneC0234533Generalized seizures1CTD_human
TgeneC0234535Clonic Seizures1CTD_human
TgeneC0270824Visual seizure1CTD_human
TgeneC0270844Tonic Seizures1CTD_human
TgeneC0270846Epileptic drop attack1CTD_human
TgeneC0422850Seizures, Somatosensory1CTD_human
TgeneC0422852Seizures, Auditory1CTD_human
TgeneC0422853Olfactory seizure1CTD_human
TgeneC0422854Gustatory seizure1CTD_human
TgeneC0422855Vertiginous seizure1CTD_human
TgeneC0494475Tonic - clonic seizures1CTD_human
TgeneC0751056Non-epileptic convulsion1CTD_human
TgeneC0751110Single Seizure1CTD_human
TgeneC0751123Atonic Absence Seizures1CTD_human
TgeneC0751494Convulsive Seizures1CTD_human
TgeneC0751495Seizures, Focal1CTD_human
TgeneC0751496Seizures, Sensory1CTD_human
TgeneC3495874Nonepileptic Seizures1CTD_human
TgeneC4048158Convulsions1CTD_human
TgeneC4316903Absence Seizures1CTD_human
TgeneC4317109Epileptic Seizures1CTD_human
TgeneC4317123Myoclonic Seizures1CTD_human
TgeneC4505436Generalized Absence Seizures1CTD_human