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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:BCAT1-INTS3 (FusionGDB2 ID:9271)

Fusion Gene Summary for BCAT1-INTS3

check button Fusion gene summary
Fusion gene informationFusion gene name: BCAT1-INTS3
Fusion gene ID: 9271
HgeneTgene
Gene symbol

BCAT1

INTS3

Gene ID

586

65123

Gene namebranched chain amino acid transaminase 1integrator complex subunit 3
SynonymsBCATC|BCT1|ECA39|MECA39|PNAS121|PP18C1orf193|C1orf60|INT3|SOSS-A|SOSSA
Cytomap

12p12.1

1q21.3

Type of geneprotein-codingprotein-coding
Descriptionbranched-chain-amino-acid aminotransferase, cytosolicbranched chain amino-acid transaminase 1, cytosolicbranched chain aminotransferase 1, cytosolicplacental protein 18integrator complex subunit 3SOSS complex subunit Asensor of single-strand DNA complex subunit Asensor of ssDNA subunit A
Modification date2020032920200313
UniProtAcc

P54687

Q68E01

Ensembl transtripts involved in fusion geneENST00000342945, ENST00000261192, 
ENST00000538118, ENST00000539282, 
ENST00000539780, ENST00000544418, 
ENST00000512605, ENST00000318967, 
ENST00000435409, ENST00000456435, 
ENST00000476843, 
Fusion gene scores* DoF score18 X 18 X 4=12967 X 5 X 2=70
# samples 207
** MAII scorelog2(20/1296*10)=-2.6959938131099
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/70*10)=0
Context

PubMed: BCAT1 [Title/Abstract] AND INTS3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointINTS3(153723459)-BCAT1(24967757), # samples:1
BCAT1(24967757)-INTS3(153723459), # 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
TgeneINTS3

GO:0016180

snRNA processing

16239144


check buttonFusion gene breakpoints across BCAT1 (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 INTS3 (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
ChiTaRS5.0N/ACB049369BCAT1chr12

24967757

+INTS3chr1

153723459

+


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Fusion Gene ORF analysis for BCAT1-INTS3

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-5UTRENST00000342945ENST00000512605BCAT1chr12

24967757

+INTS3chr1

153723459

+
5CDS-intronENST00000342945ENST00000318967BCAT1chr12

24967757

+INTS3chr1

153723459

+
5CDS-intronENST00000342945ENST00000435409BCAT1chr12

24967757

+INTS3chr1

153723459

+
5CDS-intronENST00000342945ENST00000456435BCAT1chr12

24967757

+INTS3chr1

153723459

+
5CDS-intronENST00000342945ENST00000476843BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-5UTRENST00000261192ENST00000512605BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-5UTRENST00000538118ENST00000512605BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-5UTRENST00000539282ENST00000512605BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-5UTRENST00000539780ENST00000512605BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-5UTRENST00000544418ENST00000512605BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000261192ENST00000318967BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000261192ENST00000435409BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000261192ENST00000456435BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000261192ENST00000476843BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000538118ENST00000318967BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000538118ENST00000435409BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000538118ENST00000456435BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000538118ENST00000476843BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000539282ENST00000318967BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000539282ENST00000435409BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000539282ENST00000456435BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000539282ENST00000476843BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000539780ENST00000318967BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000539780ENST00000435409BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000539780ENST00000456435BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000539780ENST00000476843BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000544418ENST00000318967BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000544418ENST00000435409BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000544418ENST00000456435BCAT1chr12

24967757

+INTS3chr1

153723459

+
intron-intronENST00000544418ENST00000476843BCAT1chr12

24967757

+INTS3chr1

153723459

+

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 BCAT1-INTS3


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)

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 BCAT1-INTS3


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/:153723459/:24967757)
- 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
BCAT1

P54687

INTS3

Q68E01

FUNCTION: Catalyzes the first reaction in the catabolism of the essential branched chain amino acids leucine, isoleucine, and valine.FUNCTION: Component of the Integrator (INT) complex. The Integrator complex is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. The Integrator complex is associated with the C-terminal domain (CTD) of RNA polymerase II largest subunit (POLR2A) and is recruited to the U1 and U2 snRNAs genes (Probable). Mediates recruitment of cytoplasmic dynein to the nuclear envelope, probably as component of the INT complex (PubMed:23904267). {ECO:0000269|PubMed:23904267, ECO:0000305|PubMed:16239144}.; FUNCTION: Component of the SOSS complex, a multiprotein complex that functions downstream of the MRN complex to promote DNA repair and G2/M checkpoint. The SOSS complex associates with single-stranded DNA at DNA lesions and influences diverse endpoints in the cellular DNA damage response including cell-cycle checkpoint activation, recombinational repair and maintenance of genomic stability. The SOSS complex is required for efficient homologous recombination-dependent repair of double-strand breaks (DSBs) and ATM-dependent signaling pathways. In the SOSS complex, it is required for the assembly of the complex and for stabilization of the complex at DNA damage sites. {ECO:0000269|PubMed:19605351, ECO:0000269|PubMed:19683501}.

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 BCAT1-INTS3


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 BCAT1-INTS3


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 BCAT1-INTS3


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 BCAT1-INTS3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource