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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:BANP-SF3A3 (FusionGDB2 ID:HG54971TG10946)

Fusion Gene Summary for BANP-SF3A3

check button Fusion gene summary
Fusion gene informationFusion gene name: BANP-SF3A3
Fusion gene ID: hg54971tg10946
HgeneTgene
Gene symbol

BANP

SF3A3

Gene ID

54971

10946

Gene nameBTG3 associated nuclear proteinsplicing factor 3a subunit 3
SynonymsBEND1|SMAR1|SMARBP1PRP9|PRPF9|SAP61|SF3a60
Cytomap('BANP')('SF3A3')

16q24.2

1p34.3

Type of geneprotein-codingprotein-coding
Descriptionprotein BANPBEN domain-containing protein 1scaffold/matrix-associated region-1-binding proteinsplicing factor 3A subunit 3SAP 61pre-mRNA splicing factor SF3a (60kD)spliceosome associated protein 61splicing factor 3a, subunit 3, 60kDsplicing factor 3a, subunit 3, 60kDa
Modification date2020031520200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000286122, ENST00000355022, 
ENST00000355163, ENST00000393207, 
ENST00000393208, ENST00000479780, 
ENST00000538234, ENST00000481948, 
Fusion gene scores* DoF score8 X 7 X 8=4487 X 8 X 5=280
# samples 811
** MAII scorelog2(8/448*10)=-2.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(11/280*10)=-1.34792330342031
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BANP [Title/Abstract] AND SF3A3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBANP(88061256)-SF3A3(38450451), # samples:2
Anticipated loss of major functional domain due to fusion event.BANP-SF3A3 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
BANP-SF3A3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
BANP-SF3A3 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
BANP-SF3A3 seems lost the major protein functional domain in Tgene 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneSF3A3

GO:0000398

mRNA splicing, via spliceosome

29360106

TgeneSF3A3

GO:1903241

U2-type prespliceosome assembly

11533230



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
ChimerDB4PRADTCGA-HC-A8CY-01ABANPchr16

88061256

+SF3A3chr1

38450451

-
ChimerDB4PRADTCGA-HC-A8CYBANPchr16

88061256

+SF3A3chr1

38450451

-


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Fusion Gene ORF analysis for BANP-SF3A3

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-5UTRENST00000286122ENST00000489537BANPchr16

88061256

+SF3A3chr1

38450451

-
5CDS-5UTRENST00000355022ENST00000489537BANPchr16

88061256

+SF3A3chr1

38450451

-
5CDS-5UTRENST00000355163ENST00000489537BANPchr16

88061256

+SF3A3chr1

38450451

-
5CDS-5UTRENST00000393207ENST00000489537BANPchr16

88061256

+SF3A3chr1

38450451

-
5CDS-5UTRENST00000393208ENST00000489537BANPchr16

88061256

+SF3A3chr1

38450451

-
5CDS-5UTRENST00000479780ENST00000489537BANPchr16

88061256

+SF3A3chr1

38450451

-
5CDS-5UTRENST00000538234ENST00000489537BANPchr16

88061256

+SF3A3chr1

38450451

-
Frame-shiftENST00000286122ENST00000373019BANPchr16

88061256

+SF3A3chr1

38450451

-
Frame-shiftENST00000286122ENST00000448721BANPchr16

88061256

+SF3A3chr1

38450451

-
Frame-shiftENST00000355022ENST00000373019BANPchr16

88061256

+SF3A3chr1

38450451

-
Frame-shiftENST00000355022ENST00000448721BANPchr16

88061256

+SF3A3chr1

38450451

-
Frame-shiftENST00000355163ENST00000373019BANPchr16

88061256

+SF3A3chr1

38450451

-
Frame-shiftENST00000355163ENST00000448721BANPchr16

88061256

+SF3A3chr1

38450451

-
Frame-shiftENST00000393207ENST00000373019BANPchr16

88061256

+SF3A3chr1

38450451

-
Frame-shiftENST00000393207ENST00000448721BANPchr16

88061256

+SF3A3chr1

38450451

-
Frame-shiftENST00000393208ENST00000373019BANPchr16

88061256

+SF3A3chr1

38450451

-
Frame-shiftENST00000393208ENST00000448721BANPchr16

88061256

+SF3A3chr1

38450451

-
Frame-shiftENST00000479780ENST00000373019BANPchr16

88061256

+SF3A3chr1

38450451

-
Frame-shiftENST00000479780ENST00000448721BANPchr16

88061256

+SF3A3chr1

38450451

-
Frame-shiftENST00000538234ENST00000373019BANPchr16

88061256

+SF3A3chr1

38450451

-
Frame-shiftENST00000538234ENST00000448721BANPchr16

88061256

+SF3A3chr1

38450451

-
intron-3CDSENST00000481948ENST00000373019BANPchr16

88061256

+SF3A3chr1

38450451

-
intron-3CDSENST00000481948ENST00000448721BANPchr16

88061256

+SF3A3chr1

38450451

-
intron-5UTRENST00000481948ENST00000489537BANPchr16

88061256

+SF3A3chr1

38450451

-

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 BANP-SF3A3


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 BANP-SF3A3


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/:88061256/:38450451)
- 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 BANP-SF3A3


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 BANP-SF3A3


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 BANP-SF3A3


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 BANP-SF3A3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0019693HIV Infections1CTD_human
TgeneC4505456HIV Coinfection1CTD_human