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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:ACAA1-HNRNPU (FusionGDB2 ID:HG30TG3192)

Fusion Gene Summary for ACAA1-HNRNPU

check button Fusion gene summary
Fusion gene informationFusion gene name: ACAA1-HNRNPU
Fusion gene ID: hg30tg3192
HgeneTgene
Gene symbol

ACAA1

HNRNPU

Gene ID

30

3192

Gene nameacetyl-CoA acyltransferase 1heterogeneous nuclear ribonucleoprotein U
SynonymsACAA|PTHIO|THIOEIEE54|GRIP120|HNRNPU-AS1|HNRPU|SAF-A|SAFA|U21.1|hnRNP U|pp120
Cytomap('ACAA1')('HNRNPU')

3p22.2

1q44

Type of geneprotein-codingprotein-coding
Description3-ketoacyl-CoA thiolase, peroxisomalacetyl-Coenzyme A acyltransferase 1beta-ketothiolaseepididymis secretory sperm binding proteinperoxisomal 3-oxoacyl-CoA thiolaseperoxisomal 3-oxoacyl-Coenzyme A thiolasetesticular tissue protein Li 197heterogeneous nuclear ribonucleoprotein UHNRNPU antisense RNA 1heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A)nuclear p120 ribonucleoproteinp120 nuclear protein
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000480865, ENST00000544624, 
ENST00000301810, ENST00000333167, 
ENST00000444607, ENST00000450296, 
Fusion gene scores* DoF score3 X 4 X 2=246 X 10 X 5=300
# samples 410
** MAII scorelog2(4/24*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(10/300*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ACAA1 [Title/Abstract] AND HNRNPU [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointACAA1(38173417)-HNRNPU(245020158), # samples:1
Anticipated loss of major functional domain due to fusion event.ACAA1-HNRNPU seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
ACAA1-HNRNPU seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ACAA1-HNRNPU 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
TgeneHNRNPU

GO:0000381

regulation of alternative mRNA splicing, via spliceosome

22325991

TgeneHNRNPU

GO:0048255

mRNA stabilization

17174306

TgeneHNRNPU

GO:0071385

cellular response to glucocorticoid stimulus

9353307



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
ChimerDB4STADTCGA-BR-A4QI-01AACAA1chr3

38173417

-HNRNPUchr1

245020158

-


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Fusion Gene ORF analysis for ACAA1-HNRNPU

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
5UTR-3CDSENST00000480865ENST00000283179ACAA1chr3

38173417

-HNRNPUchr1

245020158

-
5UTR-3CDSENST00000480865ENST00000444376ACAA1chr3

38173417

-HNRNPUchr1

245020158

-
5UTR-3CDSENST00000544624ENST00000283179ACAA1chr3

38173417

-HNRNPUchr1

245020158

-
5UTR-3CDSENST00000544624ENST00000444376ACAA1chr3

38173417

-HNRNPUchr1

245020158

-
Frame-shiftENST00000301810ENST00000283179ACAA1chr3

38173417

-HNRNPUchr1

245020158

-
Frame-shiftENST00000301810ENST00000444376ACAA1chr3

38173417

-HNRNPUchr1

245020158

-
Frame-shiftENST00000333167ENST00000283179ACAA1chr3

38173417

-HNRNPUchr1

245020158

-
Frame-shiftENST00000333167ENST00000444376ACAA1chr3

38173417

-HNRNPUchr1

245020158

-
Frame-shiftENST00000444607ENST00000283179ACAA1chr3

38173417

-HNRNPUchr1

245020158

-
Frame-shiftENST00000444607ENST00000444376ACAA1chr3

38173417

-HNRNPUchr1

245020158

-
intron-3CDSENST00000450296ENST00000283179ACAA1chr3

38173417

-HNRNPUchr1

245020158

-
intron-3CDSENST00000450296ENST00000444376ACAA1chr3

38173417

-HNRNPUchr1

245020158

-

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 ACAA1-HNRNPU


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 ACAA1-HNRNPU


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/:38173417/:245020158)
- 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
..
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}.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 ACAA1-HNRNPU


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 ACAA1-HNRNPU


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 ACAA1-HNRNPU


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 ACAA1-HNRNPU


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0543888Epileptic encephalopathy2GENOMICS_ENGLAND
TgeneC4479319EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 542CTD_human;GENOMICS_ENGLAND
TgeneC0014544Epilepsy1CTD_human
TgeneC0086237Epilepsy, Cryptogenic1CTD_human
TgeneC0236018Aura1CTD_human
TgeneC0751111Awakening Epilepsy1CTD_human
TgeneC1535926Neurodevelopmental Disorders1CTD_human
TgeneC3714756Intellectual Disability1GENOMICS_ENGLAND
TgeneC43045401q44 microdeletion syndrome1ORPHANET