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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:BCAR3-PIBF1 (FusionGDB2 ID:9169)

Fusion Gene Summary for BCAR3-PIBF1

Fusion gene summary

Fusion gene information	Fusion gene name: BCAR3-PIBF1
	Fusion gene ID: 9169
		Hgene	Tgene
	Gene symbol	BCAR3	PIBF1
	Gene ID	8412	10464
	Gene name	BCAR3 adaptor protein, NSP family member	progesterone immunomodulatory binding factor 1
	Synonyms	AND-34\|NSP2\|SH2D3B	C13orf24\|CEP90\|JBTS33\|PIBF
	Cytomap	1p22.1	13q21.33-q22.1
	Type of gene	protein-coding	protein-coding
	Description	breast cancer anti-estrogen resistance protein 3BCAR3, NSP family adaptor proteinSH2 domain-containing protein 3Bbreast cancer anti-estrogen resistance 3breast cancer antiestrogen resistance 3 proteindJ1033H22.2 (breast cancer anti-estrogen resistanc	progesterone-induced-blocking factor 1centrosomal protein of 90 kDa
	Modification date	20200313	20200313
	UniProtAcc	O75815	.
	Ensembl transtripts involved in fusion gene	ENST00000260502, ENST00000370243, ENST00000370244, ENST00000370247, ENST00000466632, ENST00000539242,	ENST00000489922, ENST00000326291,
Fusion gene scores	* DoF score	11 X 12 X 9=1188	16 X 13 X 13=2704
	# samples	12	23
	** MAII score	log2(12/1188*10)=-3.30742852519225 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(23/2704*10)=-3.55538938533781 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: BCAR3 [Title/Abstract] AND PIBF1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	BCAR3(94107859)-PIBF1(73572959), # samples:1
Anticipated loss of major functional domain due to fusion event.	BCAR3-PIBF1 seems lost the major protein functional domain in Hgene partner, which is a essential gene 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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Tgene	PIBF1	GO:0031393	negative regulation of prostaglandin biosynthetic process	3863495
Tgene	PIBF1	GO:0032695	negative regulation of interleukin-12 production	14634107
Tgene	PIBF1	GO:0032733	positive regulation of interleukin-10 production	14634107
Tgene	PIBF1	GO:0032815	negative regulation of natural killer cell activation	12516630
Tgene	PIBF1	GO:0042531	positive regulation of tyrosine phosphorylation of STAT protein	16393965
Tgene	PIBF1	GO:0042532	negative regulation of tyrosine phosphorylation of STAT protein	16393965
Tgene	PIBF1	GO:0042976	activation of Janus kinase activity	16393965

Fusion gene breakpoints across BCAR3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across PIBF1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	STAD	TCGA-D7-6518	BCAR3	chr1	94107859	-	PIBF1	chr13	73572959	+

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Fusion Gene ORF analysis for BCAR3-PIBF1

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
5CDS-3UTR	ENST00000260502	ENST00000489922	BCAR3	chr1	94107859	-	PIBF1	chr13	73572959	+
5CDS-3UTR	ENST00000370243	ENST00000489922	BCAR3	chr1	94107859	-	PIBF1	chr13	73572959	+
5CDS-3UTR	ENST00000370244	ENST00000489922	BCAR3	chr1	94107859	-	PIBF1	chr13	73572959	+
Frame-shift	ENST00000260502	ENST00000326291	BCAR3	chr1	94107859	-	PIBF1	chr13	73572959	+
Frame-shift	ENST00000370244	ENST00000326291	BCAR3	chr1	94107859	-	PIBF1	chr13	73572959	+
In-frame	ENST00000370243	ENST00000326291	BCAR3	chr1	94107859	-	PIBF1	chr13	73572959	+
intron-3CDS	ENST00000370247	ENST00000326291	BCAR3	chr1	94107859	-	PIBF1	chr13	73572959	+
intron-3CDS	ENST00000466632	ENST00000326291	BCAR3	chr1	94107859	-	PIBF1	chr13	73572959	+
intron-3CDS	ENST00000539242	ENST00000326291	BCAR3	chr1	94107859	-	PIBF1	chr13	73572959	+
intron-3UTR	ENST00000370247	ENST00000489922	BCAR3	chr1	94107859	-	PIBF1	chr13	73572959	+
intron-3UTR	ENST00000466632	ENST00000489922	BCAR3	chr1	94107859	-	PIBF1	chr13	73572959	+
intron-3UTR	ENST00000539242	ENST00000489922	BCAR3	chr1	94107859	-	PIBF1	chr13	73572959	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

Seq length
(transcript)

BP loci
(transcript)

Predicted start
(transcript)

Predicted stop
(transcript)

Seq length
(amino acids)

ENST00000370243

BCAR3

chr1

94107859

ENST00000326291

PIBF1

chr13

73572959

1391

632

856

262

DeepORF 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.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000370243	ENST00000326291	BCAR3	chr1	94107859	-	PIBF1	chr13	73572959	+	0.00427567	0.9957243

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Fusion Genomic Features for BCAR3-PIBF1

FusionAI 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.

Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	1-p	p (fusion gene breakpoint)
BCAR3	chr1	94107859	-	PIBF1	chr13	73572959	+	3.86E-05	0.9999615
BCAR3	chr1	94107859	-	PIBF1	chr13	73572959	+	3.86E-05	0.9999615

Distribution 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.

Distribution 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 BCAR3-PIBF1

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:94107859/chr13:73572959)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
BCAR3 O75815	.
FUNCTION: Acts as an adapter protein downstream of several growth factor receptors to promote cell proliferation, migration, and redistribution of actin fibers (PubMed:24216110). Specifically involved in INS/insulin signaling pathway by mediating MAPK1/ERK2-MAPK3/ERK1 activation and DNA synthesis (PubMed:24216110). Promotes insulin-mediated membrane ruffling (By similarity). In response to vasoconstrictor peptide EDN1, involved in the activation of RAP1 downstream of PTK2B via interaction with phosphorylated BCAR1 (PubMed:19086031). Inhibits cell migration and invasion via regulation of TGFB-mediated matrix digestion, actin filament rearrangement, and inhibition of invadopodia activity (By similarity). May inhibit TGFB-SMAD signaling, via facilitating BCAR1 and SMAD2 and/or SMAD3 interaction (By similarity). Regulates EGF-induced DNA synthesis (PubMed:18722344). Required for the maintenance of ocular lens morphology and structural integrity, potentially via regulation of focal adhesion complex signaling (By similarity). Acts upstream of PTPRA to regulate the localization of BCAR1 and PTPRA to focal adhesions, via regulation of SRC-mediated phosphorylation of PTPRA (By similarity). Positively regulates integrin-induced tyrosine phosphorylation of BCAR1 (By similarity). Acts as a guanine nucleotide exchange factor (GEF) for small GTPases RALA, RAP1A and RRAS (By similarity). However, in a contrasting study, lacks GEF activity towards RAP1 (PubMed:22081014). {ECO:0000250\|UniProtKB:D3ZAZ5, ECO:0000250\|UniProtKB:Q9QZK2, ECO:0000269\|PubMed:18722344, ECO:0000269\|PubMed:19086031, ECO:0000269\|PubMed:22081014, ECO:0000269\|PubMed:24216110}.	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}.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- In-frame and not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

BCAR3

chr1:94107859

chr13:73572959

ENST00000260502

479_482

119

826.0

Compositional bias

Note=Poly-Asp

Hgene

BCAR3

chr1:94107859

chr13:73572959

ENST00000370243

479_482

119

826.0

Compositional bias

Note=Poly-Asp

Hgene

BCAR3

chr1:94107859

chr13:73572959

ENST00000370244

479_482

119

826.0

Compositional bias

Note=Poly-Asp

Hgene

BCAR3

chr1:94107859

chr13:73572959

ENST00000370247

479_482

735.0

Compositional bias

Note=Poly-Asp

Hgene

BCAR3

chr1:94107859

chr13:73572959

ENST00000539242

479_482

502.0

Compositional bias

Note=Poly-Asp

Hgene

BCAR3

chr1:94107859

chr13:73572959

ENST00000260502

154_253

119

826.0

Domain

SH2

Hgene

BCAR3

chr1:94107859

chr13:73572959

ENST00000260502

548_818

119

826.0

Domain

Ras-GEF

Hgene

BCAR3

chr1:94107859

chr13:73572959

ENST00000370243

154_253

119

826.0

Domain

SH2

Hgene

BCAR3

chr1:94107859

chr13:73572959

ENST00000370243

548_818

119

826.0

Domain

Ras-GEF

Hgene

BCAR3

chr1:94107859

chr13:73572959

ENST00000370244

154_253

119

826.0

Domain

SH2

Hgene

BCAR3

chr1:94107859

chr13:73572959

ENST00000370244

548_818

119

826.0

Domain

Ras-GEF

Hgene

BCAR3

chr1:94107859

chr13:73572959

ENST00000370247

154_253

735.0

Domain

SH2

Hgene

BCAR3

chr1:94107859

chr13:73572959

ENST00000370247

548_818

735.0

Domain

Ras-GEF

Hgene

BCAR3

chr1:94107859

chr13:73572959

ENST00000539242

154_253

502.0

Domain

SH2

Hgene

BCAR3

chr1:94107859

chr13:73572959

ENST00000539242

548_818

502.0

Domain

Ras-GEF

Tgene

PIBF1

chr1:94107859

chr13:73572959

ENST00000326291

1_184

683

758.0

Region

Sufficient for NK inhibitory function

Tgene

PIBF1

chr1:94107859

chr13:73572959

ENST00000326291

1_419

683

758.0

Region

Mediates modulation of Th2 dominant cytokine production

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Fusion Gene Sequence for BCAR3-PIBF1

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.

>9169_9169_1_BCAR3-PIBF1_BCAR3_chr1_94107859_ENST00000370243_PIBF1_chr13_73572959_ENST00000326291_length(transcript)=1391nt_BP=632nt
GAGCGCGCTGGGACTCCCCGAGACGTGGCCCACGGCGGGGAGCGCTCAGCGATTGGCGGCCAGGCATCTTGCTCGGTGGCACTCGAGCGG
CATCTTCCCGGGCGCTGGCCTCGCCCGACCCCCTGCCCGTCGGAGCTGCTCTGCCGGCCACCCCGCCCTGTCCCGCCCGTCCCCTCTTCG
CAGAAGCCGGCCGGGGTCGGGCAGATGCGAGGGCCCAGAGCGCTCTGGTGGAAGCCCAAGGCTCCGAGGAGGCGAGTTTCTCCGAGTTGA
GAATTATGGCTGCAGGAAAATTTGCAAGCCTTCCCAGAAACATGCCGGTGAATCACCAGTTCCCCCTGGCCTCATCCATGGACCTTCTGA
GCAGCAGGTCCCCTCTCGCTGAGCATCGCCCAGATGCCTATCAAGATGTGTCTATACATGGCACCCTTCCACGGAAGAAAAAAGGTCCTC
CTCCCATAAGGTCCTGTGATGACTTCAGTCACATGGGCACCCTCCCCCACTCCAAATCCCCACGGCAGAACTCGCCTGTGACCCAGGATG
GCATCCAGGAGAGCCCATGGCAGGACCGGCACGGCGAAACCTTCACCTTCAGGGATCCACATCTTCTGGACCCAACTGTGGAATATGTGA
AGGAATTGGCAGCAATGAAACAGATTCTCGTTAAGATGCATAGTAAACATTCTGAGAACAGCTTACTTCTCACTAAAACAGAACCAAAAC
ATGTGACAGAAAATCAGAAATCAAAGACTTTGAATGTGCCTAAAGAGCATGAAGACAATATATTTACACCTAAACCAACACTCTTTACTA
AAAAAGAAGCACCTGAGTGGTCTAAGAAACAAAAGATGAAGACCTAGTGTTTTGGATGGGAAGCACCTGTAGACCATTATATACTCCTGA
AGTTCTTTTTCTGATGGAAAACAAAATTCAGCTTAATCGTGTACTCAGCATTTTTTAAATAACAATGTTTATTTGAACTAATATTAAATT
AACAAATTCAGTGTAATCAAAATGTGTAAAGAACAATCAATATACTTTATTTTTTTTTCTATTTTATAAAATAAATATATATGCTATGCT
TTAAATTTTGGAGCTTTCATAAATGTTCAATGCATTTTAAGTGTGTGGCTTATAAATATTTTGGTATTTTTCTATACTACGTAAATTCTG
AGTTTAAATGTCATACACAAATACTAAGACACTTTGCATTTTTAAAAATTAAGAATCATTTGTGAAGTCCACTACGAGGTACTTCAAAAG
CCCAGTAATGGTGGTCAGATACCATGTAGATGGATACAGATTGTTGACTCTTTTGAAGTTGTTTTTTTCTTATATTTTATATTACCATTA

>9169_9169_1_BCAR3-PIBF1_BCAR3_chr1_94107859_ENST00000370243_PIBF1_chr13_73572959_ENST00000326291_length(amino acids)=262AA_BP=188
MLGGTRAASSRALASPDPLPVGAALPATPPCPARPLFAEAGRGRADARAQSALVEAQGSEEASFSELRIMAAGKFASLPRNMPVNHQFPL
ASSMDLLSSRSPLAEHRPDAYQDVSIHGTLPRKKKGPPPIRSCDDFSHMGTLPHSKSPRQNSPVTQDGIQESPWQDRHGETFTFRDPHLL

--------------------------------------------------------------

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Fusion Gene PPI Analysis for BCAR3-PIBF1

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for BCAR3-PIBF1

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for BCAR3-PIBF1

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source