Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:GABPA-ATP5J (FusionGDB2 ID:HG2551TG522)

Fusion Gene Summary for GABPA-ATP5J

check button Fusion gene summary
Fusion gene informationFusion gene name: GABPA-ATP5J
Fusion gene ID: hg2551tg522
HgeneTgene
Gene symbol

GABPA

ATP5J

Gene ID

2551

522

Gene nameGA binding protein transcription factor subunit alphaATP synthase peripheral stalk subunit F6
SynonymsE4TF1-60|E4TF1A|NFT2|NRF2|NRF2A|RCH04A07ATP5|ATP5A|ATP5J|ATPM|CF6|F6
Cytomap('GABPA')('ATP5J')

21q21.3

21q21.3

Type of geneprotein-codingprotein-coding
DescriptionGA-binding protein alpha chainGA binding protein transcription factor alpha subunit 60kDaGABP subunit alphahuman nuclear respiratory factor-2 subunit alphanuclear respiratory factor 2 alpha subunitnuclear respiratory factor 2 subunit alphatranscriptATP synthase-coupling factor 6, mitochondrialATP synthase, H+ transporting, mitochondrial F0 complex, subunit F6ATP synthase, H+ transporting, mitochondrial Fo complex subunit F6ATPase subunit F6coupling factor 6mitochondrial ATP synthase, coupling f
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000487266, ENST00000400075, 
ENST00000354828, 
Fusion gene scores* DoF score7 X 6 X 4=1681 X 1 X 1=1
# samples 81
** MAII scorelog2(8/168*10)=-1.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Context

PubMed: GABPA [Title/Abstract] AND ATP5J [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGABPA(27107889)-ATP5J(27107965), # samples:1
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
HgeneGABPA

GO:0045944

positive regulation of transcription by RNA polymerase II

9857059|12750007|22306510|24501276

TgeneATP5J

GO:0042776

mitochondrial ATP synthesis coupled proton transport

12110673



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-A4PDGABPAchr21

27107889

+ATP5Jchr21

27107965

-


Top

Fusion Gene ORF analysis for GABPA-ATP5J

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
3UTR-5UTRENST00000487266ENST00000400093GABPAchr21

27107889

+ATP5Jchr21

27107965

-
3UTR-intronENST00000487266ENST00000284971GABPAchr21

27107889

+ATP5Jchr21

27107965

-
3UTR-intronENST00000487266ENST00000400087GABPAchr21

27107889

+ATP5Jchr21

27107965

-
3UTR-intronENST00000487266ENST00000400090GABPAchr21

27107889

+ATP5Jchr21

27107965

-
3UTR-intronENST00000487266ENST00000400094GABPAchr21

27107889

+ATP5Jchr21

27107965

-
3UTR-intronENST00000487266ENST00000400099GABPAchr21

27107889

+ATP5Jchr21

27107965

-
3UTR-intronENST00000487266ENST00000457143GABPAchr21

27107889

+ATP5Jchr21

27107965

-
5UTR-5UTRENST00000400075ENST00000400093GABPAchr21

27107889

+ATP5Jchr21

27107965

-
5UTR-intronENST00000400075ENST00000284971GABPAchr21

27107889

+ATP5Jchr21

27107965

-
5UTR-intronENST00000400075ENST00000400087GABPAchr21

27107889

+ATP5Jchr21

27107965

-
5UTR-intronENST00000400075ENST00000400090GABPAchr21

27107889

+ATP5Jchr21

27107965

-
5UTR-intronENST00000400075ENST00000400094GABPAchr21

27107889

+ATP5Jchr21

27107965

-
5UTR-intronENST00000400075ENST00000400099GABPAchr21

27107889

+ATP5Jchr21

27107965

-
5UTR-intronENST00000400075ENST00000457143GABPAchr21

27107889

+ATP5Jchr21

27107965

-
intron-5UTRENST00000354828ENST00000400093GABPAchr21

27107889

+ATP5Jchr21

27107965

-
intron-intronENST00000354828ENST00000284971GABPAchr21

27107889

+ATP5Jchr21

27107965

-
intron-intronENST00000354828ENST00000400087GABPAchr21

27107889

+ATP5Jchr21

27107965

-
intron-intronENST00000354828ENST00000400090GABPAchr21

27107889

+ATP5Jchr21

27107965

-
intron-intronENST00000354828ENST00000400094GABPAchr21

27107889

+ATP5Jchr21

27107965

-
intron-intronENST00000354828ENST00000400099GABPAchr21

27107889

+ATP5Jchr21

27107965

-
intron-intronENST00000354828ENST00000457143GABPAchr21

27107889

+ATP5Jchr21

27107965

-

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

Top

Fusion Genomic Features for GABPA-ATP5J


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)


Top

Fusion Protein Features for GABPA-ATP5J


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/:27107889/:27107965)
- 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


Top

Fusion Gene Sequence for GABPA-ATP5J


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.

Top

Fusion Gene PPI Analysis for GABPA-ATP5J


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


Top

Related Drugs for GABPA-ATP5J


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for GABPA-ATP5J


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneGABPAC0011581Depressive disorder1PSYGENET
HgeneGABPAC0015923Fetal Alcohol Syndrome1PSYGENET
HgeneGABPAC2985290Fetal Alcohol Spectrum Disorders1PSYGENET