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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:ARID1A-UBE2U (FusionGDB2 ID:6493)

Fusion Gene Summary for ARID1A-UBE2U

check button Fusion gene summary
Fusion gene informationFusion gene name: ARID1A-UBE2U
Fusion gene ID: 6493
HgeneTgene
Gene symbol

ARID1A

UBE2U

Gene ID

8289

148581

Gene nameAT-rich interaction domain 1Aubiquitin conjugating enzyme E2 U
SynonymsB120|BAF250|BAF250a|BM029|C1orf4|CSS2|ELD|MRD14|OSA1|P270|SMARCF1|hELD|hOSA1-
Cytomap

1p36.11

1p31.3

Type of geneprotein-codingprotein-coding
DescriptionAT-rich interactive domain-containing protein 1AARID domain-containing protein 1AAT rich interactive domain 1A (SWI-like)BRG1-associated factor 250aOSA1 nuclear proteinSWI-like proteinSWI/SNF complex protein p270SWI/SNF-related, matrix-associated, ubiquitin-conjugating enzyme E2 UE2 ubiquitin-conjugating enzyme Utesticular tissue protein Li 216ubiquitin carrier protein Uubiquitin conjugating enzyme E2 U (putative)ubiquitin conjugating enzyme E2U (putative)ubiquitin-protein ligase U
Modification date2020032920200313
UniProtAcc

O14497

.
Ensembl transtripts involved in fusion geneENST00000324856, ENST00000457599, 
ENST00000374152, ENST00000540690, 
ENST00000371076, ENST00000464349, 
Fusion gene scores* DoF score29 X 19 X 15=82653 X 3 X 2=18
# samples 454
** MAII scorelog2(45/8265*10)=-4.19901791296264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/18*10)=1.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: ARID1A [Title/Abstract] AND UBE2U [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointARID1A(27059283)-UBE2U(64686542), # samples:2
Anticipated loss of major functional domain due to fusion event.ARID1A-UBE2U seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
ARID1A-UBE2U seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
ARID1A-UBE2U seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ARID1A-UBE2U seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor 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
HgeneARID1A

GO:0006337

nucleosome disassembly

8895581

HgeneARID1A

GO:0006338

chromatin remodeling

11726552

HgeneARID1A

GO:0030520

intracellular estrogen receptor signaling pathway

12200431

HgeneARID1A

GO:0030521

androgen receptor signaling pathway

12200431

HgeneARID1A

GO:0042921

glucocorticoid receptor signaling pathway

12200431

HgeneARID1A

GO:0045893

positive regulation of transcription, DNA-templated

12200431


check buttonFusion gene breakpoints across ARID1A (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across UBE2U (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4STADTCGA-BR-8679ARID1Achr1

27059283

+UBE2Uchr1

64686541

+
ChimerDB4STADTCGA-BR-8679-01AARID1Achr1

27059283

+UBE2Uchr1

64686542

+
ChimerDB4STADTCGA-BR-8679-01AARID1Achr1

27059283

-UBE2Uchr1

64686542

+


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Fusion Gene ORF analysis for ARID1A-UBE2U

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
Frame-shiftENST00000324856ENST00000371076ARID1Achr1

27059283

+UBE2Uchr1

64686541

+
5CDS-3UTRENST00000324856ENST00000464349ARID1Achr1

27059283

+UBE2Uchr1

64686541

+
Frame-shiftENST00000457599ENST00000371076ARID1Achr1

27059283

+UBE2Uchr1

64686541

+
5CDS-3UTRENST00000457599ENST00000464349ARID1Achr1

27059283

+UBE2Uchr1

64686541

+
Frame-shiftENST00000374152ENST00000371076ARID1Achr1

27059283

+UBE2Uchr1

64686541

+
5CDS-3UTRENST00000374152ENST00000464349ARID1Achr1

27059283

+UBE2Uchr1

64686541

+
intron-3CDSENST00000540690ENST00000371076ARID1Achr1

27059283

+UBE2Uchr1

64686541

+
intron-3UTRENST00000540690ENST00000464349ARID1Achr1

27059283

+UBE2Uchr1

64686541

+
Frame-shiftENST00000324856ENST00000371076ARID1Achr1

27059283

+UBE2Uchr1

64686542

+
5CDS-3UTRENST00000324856ENST00000464349ARID1Achr1

27059283

+UBE2Uchr1

64686542

+
Frame-shiftENST00000457599ENST00000371076ARID1Achr1

27059283

+UBE2Uchr1

64686542

+
5CDS-3UTRENST00000457599ENST00000464349ARID1Achr1

27059283

+UBE2Uchr1

64686542

+
Frame-shiftENST00000374152ENST00000371076ARID1Achr1

27059283

+UBE2Uchr1

64686542

+
5CDS-3UTRENST00000374152ENST00000464349ARID1Achr1

27059283

+UBE2Uchr1

64686542

+
intron-3CDSENST00000540690ENST00000371076ARID1Achr1

27059283

+UBE2Uchr1

64686542

+
intron-3UTRENST00000540690ENST00000464349ARID1Achr1

27059283

+UBE2Uchr1

64686542

+

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 ARID1A-UBE2U


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)
ARID1Achr127059283+UBE2Uchr164686541+0.006183580.99381644
ARID1Achr127059283+UBE2Uchr164686541+0.006183580.99381644
ARID1Achr127059283+UBE2Uchr164686541+0.006183580.99381644
ARID1Achr127059283+UBE2Uchr164686541+0.006183580.99381644

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

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.

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Fusion Protein Features for ARID1A-UBE2U


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
ARID1A

O14497

.
FUNCTION: Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Component of SWI/SNF chromatin remodeling complexes that carry out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner. Binds DNA non-specifically. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a postmitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to postmitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). {ECO:0000250|UniProtKB:A2BH40, ECO:0000303|PubMed:12672490, ECO:0000303|PubMed:22952240, ECO:0000303|PubMed:26601204}.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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 ARID1A-UBE2U


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 ARID1A-UBE2U


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 ARID1A-UBE2U


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 ARID1A-UBE2U


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneARID1AC0024623Malignant neoplasm of stomach3CTD_human
HgeneARID1AC0038356Stomach Neoplasms3CTD_human
HgeneARID1AC1708349Hereditary Diffuse Gastric Cancer3CTD_human
HgeneARID1AC2239176Liver carcinoma3CTD_human
HgeneARID1AC0033578Prostatic Neoplasms2CTD_human
HgeneARID1AC0376358Malignant neoplasm of prostate2CTD_human
HgeneARID1AC0001418Adenocarcinoma1CTD_human
HgeneARID1AC0005684Malignant neoplasm of urinary bladder1CTD_human
HgeneARID1AC0005695Bladder Neoplasm1CTD_human
HgeneARID1AC0006413Burkitt Lymphoma1CTD_human
HgeneARID1AC0007138Carcinoma, Transitional Cell1CTD_human
HgeneARID1AC0009402Colorectal Carcinoma1CTD_human
HgeneARID1AC0009404Colorectal Neoplasms1CTD_human
HgeneARID1AC0010606Adenoid Cystic Carcinoma1CTD_human
HgeneARID1AC0014170Endometrial Neoplasms1CTD_human
HgeneARID1AC0027708Nephroblastoma1CTD_human
HgeneARID1AC0027819Neuroblastoma1CTD_human
HgeneARID1AC0036920Sezary Syndrome1CTD_human
HgeneARID1AC0079772T-Cell Lymphoma1CTD_human
HgeneARID1AC0079773Lymphoma, T-Cell, Cutaneous1CTD_human
HgeneARID1AC0205641Adenocarcinoma, Basal Cell1CTD_human
HgeneARID1AC0205642Adenocarcinoma, Oxyphilic1CTD_human
HgeneARID1AC0205643Carcinoma, Cribriform1CTD_human
HgeneARID1AC0205644Carcinoma, Granular Cell1CTD_human
HgeneARID1AC0205645Adenocarcinoma, Tubular1CTD_human
HgeneARID1AC0206656Embryonal Rhabdomyosarcoma1CTD_human
HgeneARID1AC0206698Cholangiocarcinoma1CTD_human
HgeneARID1AC0265338Coffin-Siris syndrome1CTD_human;GENOMICS_ENGLAND
HgeneARID1AC0279628Adenocarcinoma Of Esophagus1CTD_human
HgeneARID1AC0343640African Burkitt's lymphoma1CTD_human
HgeneARID1AC0345905Intrahepatic Cholangiocarcinoma1CTD_human
HgeneARID1AC0376407Granulomatous Slack Skin1CTD_human
HgeneARID1AC0476089Endometrial Carcinoma1CTD_human
HgeneARID1AC0920269Microsatellite Instability1CTD_human
HgeneARID1AC1721098Replication Error Phenotype1CTD_human
HgeneARID1AC2930471Bilateral Wilms Tumor1CTD_human
HgeneARID1AC2931822Nasopharyngeal carcinoma1CTD_human
HgeneARID1AC3805278Extrahepatic Cholangiocarcinoma1CTD_human
HgeneARID1AC4721444Burkitt Leukemia1CTD_human