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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:GTF2IRD1-BCAS3 (FusionGDB2 ID:35246)

Fusion Gene Summary for GTF2IRD1-BCAS3

check button Fusion gene summary
Fusion gene informationFusion gene name: GTF2IRD1-BCAS3
Fusion gene ID: 35246
HgeneTgene
Gene symbol

GTF2IRD1

BCAS3

Gene ID

9569

54828

Gene nameGTF2I repeat domain containing 1BCAS3 microtubule associated cell migration factor
SynonymsBEN|CREAM1|GTF3|MUSTRD1|RBAP2|WBS|WBSCR11|WBSCR12|hMusTRD1alpha1GAOB1|MAAB
Cytomap

7q11.23

17q23.2

Type of geneprotein-codingprotein-coding
Descriptiongeneral transcription factor II-I repeat domain-containing protein 1USE B1-binding proteinWilliams-Beuren syndrome chromosome region 11binding factor for early enhancergeneral transcription factor 3general transcription factor IIImuscle TFII-I repeabreast carcinoma-amplified sequence 3BCAS4/BCAS3 fusionRudhirabreast carcinoma amplified sequence 4/3 fusion proteinmetastasis associated antigen of breast cancerprotein Maab1
Modification date2020031320200313
UniProtAcc

Q9UHL9

Q9H6U6

Ensembl transtripts involved in fusion geneENST00000265755, ENST00000424337, 
ENST00000455841, ENST00000476977, 
ENST00000489094, 		ENST00000390652, 
ENST00000407086, ENST00000408905, 
ENST00000585744, ENST00000585812, 
ENST00000588462, ENST00000588874, 
ENST00000589222, 
Fusion gene scores* DoF score11 X 6 X 9=59445 X 32 X 19=27360
# samples 1253
** MAII scorelog2(12/594*10)=-2.30742852519225
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(53/27360*10)=-5.6899320603227
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: GTF2IRD1 [Title/Abstract] AND BCAS3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGTF2IRD1(73924873)-BCAS3(59369957), # 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
TgeneBCAS3

GO:0043085

positive regulation of catalytic activity

17505058

TgeneBCAS3

GO:0045944

positive regulation of transcription by RNA polymerase II

17505058

TgeneBCAS3

GO:0071391

cellular response to estrogen stimulus

17505058


check buttonFusion gene breakpoints across GTF2IRD1 (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 BCAS3 (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/AAA729070GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-


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Fusion Gene ORF analysis for GTF2IRD1-BCAS3

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
intron-intronENST00000265755ENST00000390652GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000265755ENST00000407086GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000265755ENST00000408905GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000265755ENST00000585744GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000265755ENST00000585812GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000265755ENST00000588462GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000265755ENST00000588874GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000265755ENST00000589222GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000424337ENST00000390652GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000424337ENST00000407086GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000424337ENST00000408905GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000424337ENST00000585744GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000424337ENST00000585812GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000424337ENST00000588462GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000424337ENST00000588874GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000424337ENST00000589222GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000455841ENST00000390652GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000455841ENST00000407086GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000455841ENST00000408905GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000455841ENST00000585744GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000455841ENST00000585812GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000455841ENST00000588462GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000455841ENST00000588874GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000455841ENST00000589222GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000476977ENST00000390652GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000476977ENST00000407086GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000476977ENST00000408905GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000476977ENST00000585744GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000476977ENST00000585812GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000476977ENST00000588462GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000476977ENST00000588874GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000476977ENST00000589222GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000489094ENST00000390652GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000489094ENST00000407086GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000489094ENST00000408905GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000489094ENST00000585744GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000489094ENST00000585812GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000489094ENST00000588462GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000489094ENST00000588874GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-
intron-intronENST00000489094ENST00000589222GTF2IRD1chr7

73924873

+BCAS3chr17

59369957

-

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 GTF2IRD1-BCAS3


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 GTF2IRD1-BCAS3


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/:73924873/:59369957)
- 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
GTF2IRD1

Q9UHL9

BCAS3

Q9H6U6

FUNCTION: May be a transcription regulator involved in cell-cycle progression and skeletal muscle differentiation. May repress GTF2I transcriptional functions, by preventing its nuclear residency, or by inhibiting its transcriptional activation. May contribute to slow-twitch fiber type specificity during myogenesis and in regenerating muscles. Binds troponin I slow-muscle fiber enhancer (USE B1). Binds specifically and with high affinity to the EFG sequences derived from the early enhancer of HOXC8 (By similarity). {ECO:0000250, ECO:0000269|PubMed:11438732}.FUNCTION: Plays a role in angiogenesis. Participates in the regulation of cell polarity and directional endothelial cell migration by mediating both the activation and recruitment of CDC42 and the reorganization of the actin cytoskeleton at the cell leading edge. Promotes filipodia formation (By similarity). Functions synergistically with PELP1 as a transcriptional coactivator of estrogen receptor-responsive genes. Stimulates histone acetyltransferase activity. Binds to chromatin. {ECO:0000250|UniProtKB:Q8CCN5, ECO:0000269|PubMed:17505058}.

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 GTF2IRD1-BCAS3


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 GTF2IRD1-BCAS3


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 GTF2IRD1-BCAS3


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 GTF2IRD1-BCAS3


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