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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:BAD-STX5 (FusionGDB2 ID:HG572TG6811)

Fusion Gene Summary for BAD-STX5

check button Fusion gene summary
Fusion gene informationFusion gene name: BAD-STX5
Fusion gene ID: hg572tg6811
HgeneTgene
Gene symbol

BAD

STX5

Gene ID

572

6811

Gene nameBCL2 associated agonist of cell deathsyntaxin 5
SynonymsBBC2|BCL2L8SED5|STX5A
Cytomap('BAD')('STX5')

11q13.1

11q12.3

Type of geneprotein-codingprotein-coding
Descriptionbcl2-associated agonist of cell deathBCL-X/BCL-2 binding proteinBCL2-antagonist of cell death proteinBCL2-binding component 6BCL2-binding proteinbcl-2-binding component 6bcl-2-like protein 8bcl-XL/Bcl-2-associated death promoterbcl2 antagonist of syntaxin-5syntaxin 5A
Modification date2020032720200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000394531, ENST00000309032, 
ENST00000394532, ENST00000544785, 
Fusion gene scores* DoF score6 X 5 X 5=1506 X 2 X 7=84
# samples 79
** MAII scorelog2(7/150*10)=-1.09953567355091
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(9/84*10)=0.0995356735509144
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: BAD [Title/Abstract] AND STX5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBAD(64039085)-STX5(62575100), # samples:2
Anticipated loss of major functional domain due to fusion event.BAD-STX5 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
BAD-STX5 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
BAD-STX5 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
BAD-STX5 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
BAD-STX5 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
HgeneBAD

GO:0006915

apoptotic process

19667065

HgeneBAD

GO:0043065

positive regulation of apoptotic process

9388232

HgeneBAD

GO:0043280

positive regulation of cysteine-type endopeptidase activity involved in apoptotic process

18402937

HgeneBAD

GO:0045862

positive regulation of proteolysis

18387192

HgeneBAD

GO:0046931

pore complex assembly

19667065|21081150

HgeneBAD

GO:0071316

cellular response to nicotine

18676776

HgeneBAD

GO:0097202

activation of cysteine-type endopeptidase activity

18387192

TgeneSTX5

GO:0042147

retrograde transport, endosome to Golgi

15215310

TgeneSTX5

GO:0090166

Golgi disassembly

16081076

TgeneSTX5

GO:1903358

regulation of Golgi organization

16081076


check buttonFusion gene breakpoints across BAD (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure
check buttonFusion gene breakpoints across STX5 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4LUADTCGA-53-7813-01ABADchr11

64039085

-STX5chr11

62575100

-


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Fusion Gene ORF analysis for BAD-STX5

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
3UTR-3CDSENST00000394531ENST00000294179BADchr11

64039085

-STX5chr11

62575100

-
3UTR-3CDSENST00000394531ENST00000377897BADchr11

64039085

-STX5chr11

62575100

-
3UTR-3CDSENST00000394531ENST00000394690BADchr11

64039085

-STX5chr11

62575100

-
3UTR-3CDSENST00000394531ENST00000541317BADchr11

64039085

-STX5chr11

62575100

-
Frame-shiftENST00000309032ENST00000377897BADchr11

64039085

-STX5chr11

62575100

-
Frame-shiftENST00000309032ENST00000394690BADchr11

64039085

-STX5chr11

62575100

-
Frame-shiftENST00000309032ENST00000541317BADchr11

64039085

-STX5chr11

62575100

-
Frame-shiftENST00000394532ENST00000294179BADchr11

64039085

-STX5chr11

62575100

-
Frame-shiftENST00000394532ENST00000377897BADchr11

64039085

-STX5chr11

62575100

-
Frame-shiftENST00000394532ENST00000394690BADchr11

64039085

-STX5chr11

62575100

-
Frame-shiftENST00000394532ENST00000541317BADchr11

64039085

-STX5chr11

62575100

-
In-frameENST00000309032ENST00000294179BADchr11

64039085

-STX5chr11

62575100

-
intron-3CDSENST00000544785ENST00000294179BADchr11

64039085

-STX5chr11

62575100

-
intron-3CDSENST00000544785ENST00000377897BADchr11

64039085

-STX5chr11

62575100

-
intron-3CDSENST00000544785ENST00000394690BADchr11

64039085

-STX5chr11

62575100

-
intron-3CDSENST00000544785ENST00000541317BADchr11

64039085

-STX5chr11

62575100

-

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)
ENST00000309032BADchr1164039085-ENST00000294179STX5chr1162575100-1157425778140212

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
ENST00000309032ENST00000294179BADchr1164039085-STX5chr1162575100-0.2457170.75428295

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Fusion Genomic Features for BAD-STX5


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.
genomic feature

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Fusion Protein Features for BAD-STX5


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/chr11:64039085/chr11:62575100)
- 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
HgeneBADchr11:64039085chr11:62575100ENST00000309032-34110_124126169.0MotifNote=BH3
HgeneBADchr11:64039085chr11:62575100ENST00000394532-23110_124126169.0MotifNote=BH3
TgeneSTX5chr11:64039085chr11:62575100ENST00000394690911287_318248302.0Coiled coilOntology_term=ECO:0000255
TgeneSTX5chr11:64039085chr11:62575100ENST00000394690911263_325248302.0Domaint-SNARE coiled-coil homology
TgeneSTX5chr11:64039085chr11:62575100ENST00000294179911355_355302356.0Topological domainVesicular
TgeneSTX5chr11:64039085chr11:62575100ENST00000394690911355_355248302.0Topological domainVesicular
TgeneSTX5chr11:64039085chr11:62575100ENST00000294179911334_354302356.0TransmembraneHelical%3B Anchor for type IV membrane protein
TgeneSTX5chr11:64039085chr11:62575100ENST00000394690911334_354248302.0TransmembraneHelical%3B Anchor for type IV membrane protein

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneSTX5chr11:64039085chr11:62575100ENST00000294179911287_318302356.0Coiled coilOntology_term=ECO:0000255
TgeneSTX5chr11:64039085chr11:62575100ENST00000294179911263_325302356.0Domaint-SNARE coiled-coil homology
TgeneSTX5chr11:64039085chr11:62575100ENST00000294179911245_247302356.0MotifIxM motif%3B signal for cargo packaging into COPII-coated vesicles
TgeneSTX5chr11:64039085chr11:62575100ENST00000394690911245_247248302.0MotifIxM motif%3B signal for cargo packaging into COPII-coated vesicles
TgeneSTX5chr11:64039085chr11:62575100ENST000002941799111_333302356.0Topological domainCytoplasmic
TgeneSTX5chr11:64039085chr11:62575100ENST000003946909111_333248302.0Topological domainCytoplasmic


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Fusion Gene Sequence for BAD-STX5


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.
>8842_8842_1_BAD-STX5_BAD_chr11_64039085_ENST00000309032_STX5_chr11_62575100_ENST00000294179_length(transcript)=1157nt_BP=425nt
CGGCAGGCCCGGGTCAGGGGCCTCGAGATCGGGCTTGGGCCCAGAGCATGTTCCAGATCCCAGAGTTTGAGCCGAGTGAGCAGGAAGACT
CCAGCTCTGCAGAGAGGGGCCTGGGCCCCAGCCCCGCAGGGGACGGGCCCTCAGGCTCCGGCAAGCATCATCGCCAGGCCCCAGGCCTCC
TGTGGGACGCCAGTCACCAGCAGGAGCAGCCAACCAGCAGCAGCCATCATGGAGGCGCTGGGGCTGTGGAGATCCGGAGTCGCCACAGCT
CCTACCCCGCGGGGACGGAGGACGACGAAGGGATGGGGGAGGAGCCCAGCCCCTTTCGGGGCCGCTCGCGCTCGGCGCCCCCCAACCTCT
GGGCAGCACAGCGCTATGGCCGCGAGCTCCGGAGGATGAGTGACGAGTTTGTGGACTCCTTTAAGGATCGACGAGAACGTGCTAGGAGCC
CAGCTGGACGTTGAGGCCGCCCATTCAGAGATCCTCAAGTACTTCCAGTCTGTCACCTCCAACCGGTGGCTCATGGTCAAAATCTTCCTC
ATCCTCATTGTCTTCTTCATCATCTTTGTGGTCTTCCTTGCTTGAACCCTCTCTACTCTGAGGCACTCTGTTGGGGTTTGGGACCCTCCT
GGGAAGGCAAGTGGCCAGTGCTGCCACTGAGCCTGTGCAGGGTACTTGGGAGAAAGGCCCTGTTTCCCTGGAACTGCTAAGAATGACCAC
TGCCCCTGATCCCCCACCCCTTGCCTCTGGCCACCCTGTCCTCCCCCCACCACCCTCAGGCCTATGAAACACACAGGGTTCTAGATTTGA
ACTCTGCTGTGAAGTGACTGGAAGGGAGCAGAGGCCAGCTGGGGGCCAGTGGGGGAGGTTGTTTCCACTAGGAGATTTTTATAAACCCTC
TCCAGCCTCTCCCAAAGGAAGCGTTGGCAGCAAAGGGAGATGATGCCCTTACCCACCTTCCTGTGAGTGAAGAGAGGAAGCAGCCCCAGG
GACCAATTTTCCCAATTGACCTCTTTCTTCCTCTTTCACCATGTGAGGCAGGGAGCCCTGAGCCCTTCAGCTGCCTGCACAACCCCTGAC

>8842_8842_1_BAD-STX5_BAD_chr11_64039085_ENST00000309032_STX5_chr11_62575100_ENST00000294179_length(amino acids)=212AA_BP=1
MRVVGGGQGGQRQGVGDQGQWSFLAVPGKQGLSPKYPAQAQWQHWPLAFPGGSQTPTECLRVERVQARKTTKMMKKTMRMRKILTMSHRL
EVTDWKYLRISEWAASTSSWAPSTFSSILKGVHKLVTHPPELAAIALCCPEVGGRRARAAPKGAGLLPHPFVVLRPRGVGAVATPDLHSP

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

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Fusion Gene PPI Analysis for BAD-STX5


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 BAD-STX5


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 BAD-STX5


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneBADC0033578Prostatic Neoplasms2CTD_human
HgeneBADC0376358Malignant neoplasm of prostate2CTD_human
HgeneBADC0007787Transient Ischemic Attack1CTD_human
HgeneBADC0023418leukemia1CTD_human
HgeneBADC0472381Posterior Circulation Transient Ischemic Attack1CTD_human
HgeneBADC0751019Carotid Circulation Transient Ischemic Attack1CTD_human
HgeneBADC0751020Transient Ischemic Attack, Vertebrobasilar Circulation1CTD_human
HgeneBADC0751021Crescendo Transient Ischemic Attacks1CTD_human
HgeneBADC0751022Brain Stem Ischemia, Transient1CTD_human
HgeneBADC0917805Transient Cerebral Ischemia1CTD_human
HgeneBADC1527335Transient Ischemic Attack, Anterior Circulation1CTD_human