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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:ATXN1-ATRX (FusionGDB2 ID:HG6310TG546)

Fusion Gene Summary for ATXN1-ATRX

check button Fusion gene summary
Fusion gene informationFusion gene name: ATXN1-ATRX
Fusion gene ID: hg6310tg546
HgeneTgene
Gene symbol

ATXN1

ATRX

Gene ID

6310

546

Gene nameataxin 1ATRX chromatin remodeler
SynonymsATX1|D6S504E|SCA1JMS|MRX52|RAD54|RAD54L|XH2|XNP|ZNF-HX
Cytomap('ATXN1')('ATRX')

6p22.3

Xq21.1

Type of geneprotein-codingprotein-coding
Descriptionataxin-1alternative ataxin1spinocerebellar ataxia type 1 proteintranscriptional regulator ATRXATP-dependent helicase ATRXX-linked helicase IIX-linked nuclear proteinalpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S. cerevisiae)
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000244769, ENST00000436367, 
ENST00000467008, 
Fusion gene scores* DoF score28 X 20 X 12=672010 X 10 X 8=800
# samples 3312
** MAII scorelog2(33/6720*10)=-4.34792330342031
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(12/800*10)=-2.73696559416621
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ATXN1 [Title/Abstract] AND ATRX [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATXN1(16761528)-ATRX(76778879), # 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
HgeneATXN1

GO:0045892

negative regulation of transcription, DNA-templated

15016912

HgeneATXN1

GO:0051168

nuclear export

15615787

TgeneATRX

GO:0006334

nucleosome assembly

20651253

TgeneATRX

GO:0006338

chromatin remodeling

20651253



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
ChimerDB4Non-Cancer43NATXN1chr6

16761528

-ATRXchrX

76778879

-


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Fusion Gene ORF analysis for ATXN1-ATRX

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-3CDSENST00000244769ENST00000373344ATXN1chr6

16761528

-ATRXchrX

76778879

-
5UTR-3CDSENST00000244769ENST00000395603ATXN1chr6

16761528

-ATRXchrX

76778879

-
5UTR-3CDSENST00000436367ENST00000373344ATXN1chr6

16761528

-ATRXchrX

76778879

-
5UTR-3CDSENST00000436367ENST00000395603ATXN1chr6

16761528

-ATRXchrX

76778879

-
5UTR-3CDSENST00000467008ENST00000373344ATXN1chr6

16761528

-ATRXchrX

76778879

-
5UTR-3CDSENST00000467008ENST00000395603ATXN1chr6

16761528

-ATRXchrX

76778879

-
5UTR-5UTRENST00000244769ENST00000480283ATXN1chr6

16761528

-ATRXchrX

76778879

-
5UTR-5UTRENST00000436367ENST00000480283ATXN1chr6

16761528

-ATRXchrX

76778879

-
5UTR-5UTRENST00000467008ENST00000480283ATXN1chr6

16761528

-ATRXchrX

76778879

-
5UTR-intronENST00000244769ENST00000373341ATXN1chr6

16761528

-ATRXchrX

76778879

-
5UTR-intronENST00000436367ENST00000373341ATXN1chr6

16761528

-ATRXchrX

76778879

-
5UTR-intronENST00000467008ENST00000373341ATXN1chr6

16761528

-ATRXchrX

76778879

-

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 ATXN1-ATRX


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 ATXN1-ATRX


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/:16761528/:76778879)
- 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 ATXN1-ATRX


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 ATXN1-ATRX


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 ATXN1-ATRX


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 ATXN1-ATRX


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneATXN1C0752120Spinocerebellar Ataxia Type 15CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneATXN1C0087012Ataxia, Spinocerebellar4CTD_human
HgeneATXN1C0752121Spinocerebellar Ataxia Type 24CTD_human
HgeneATXN1C0752122Spinocerebellar Ataxia Type 44CTD_human
HgeneATXN1C0752123Spinocerebellar Ataxia Type 54CTD_human
HgeneATXN1C0752124Spinocerebellar Ataxia Type 6 (disorder)4CTD_human
HgeneATXN1C0752125Spinocerebellar Ataxia Type 74CTD_human
HgeneATXN1C0004238Atrial Fibrillation2CTD_human
HgeneATXN1C0235480Paroxysmal atrial fibrillation2CTD_human
HgeneATXN1C2585653Persistent atrial fibrillation2CTD_human
HgeneATXN1C3468561familial atrial fibrillation2CTD_human
HgeneATXN1C0035309Retinal Diseases1CTD_human
HgeneATXN1C0270715Degenerative Diseases, Central Nervous System1CTD_human
HgeneATXN1C0524851Neurodegenerative Disorders1CTD_human
HgeneATXN1C0751733Degenerative Diseases, Spinal Cord1CTD_human
HgeneATXN1C2362914clinical depression1PSYGENET
TgeneC0796003Juberg-Marsidi syndrome17CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC1845055ALPHA-THALASSEMIA/MENTAL RETARDATION SYNDROME, NONDELETION TYPE, X-LINKED16CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0017638Glioma2CTD_human
TgeneC0027819Neuroblastoma2CTD_human
TgeneC0259783mixed gliomas2CTD_human
TgeneC0555198Malignant Glioma2CTD_human
TgeneC0010417Cryptorchidism1CTD_human
TgeneC0010606Adenoid Cystic Carcinoma1CTD_human
TgeneC0018273Growth Disorders1CTD_human
TgeneC0030297Pancreatic Neoplasm1CTD_human
TgeneC0030846Penile Diseases1CTD_human
TgeneC0039978Thoracic Diseases1CTD_human
TgeneC0206754Neuroendocrine Tumors1CTD_human
TgeneC0346647Malignant neoplasm of pancreas1CTD_human
TgeneC0376634Craniofacial Abnormalities1CTD_human
TgeneC0431663Bilateral Cryptorchidism1CTD_human
TgeneC0431664Unilateral Cryptorchidism1CTD_human
TgeneC0585216Alpha-Thalassemia Myelodysplasia Syndrome1CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC0796159Mental retardation Smith Fineman Myers type1ORPHANET
TgeneC1136249Mental Retardation, X-Linked1CTD_human
TgeneC1563730Abdominal Cryptorchidism1CTD_human
TgeneC1563731Inguinal Cryptorchidism1CTD_human
TgeneC2713368Hematopoetic Myelodysplasia1CTD_human
TgeneC3463824MYELODYSPLASTIC SYNDROME1CTD_human