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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:GNA13-BMI1 (FusionGDB2 ID:33536)

Fusion Gene Summary for GNA13-BMI1

check button Fusion gene summary
Fusion gene informationFusion gene name: GNA13-BMI1
Fusion gene ID: 33536
HgeneTgene
Gene symbol

GNA13

BMI1

Gene ID

10672

100532731

Gene nameG protein subunit alpha 13COMMD3-BMI1 readthrough
SynonymsG13BMI1|PCGF4|RNF51
Cytomap

17q24.1

10p12.2

Type of geneprotein-codingprotein-coding
Descriptionguanine nucleotide-binding protein subunit alpha-13g alpha-13guanine nucleotide binding protein (G protein), alpha 13COMMD3-BMI1 read-through proteinPolycomb complex protein BMI-1Polycomb group RING finger protein 4RING finger protein 51
Modification date2020031320200313
UniProtAcc.

P35226

Ensembl transtripts involved in fusion geneENST00000439174, ENST00000541118, 
ENST00000376663, 
Fusion gene scores* DoF score11 X 4 X 9=3963 X 2 X 3=18
# samples 163
** MAII scorelog2(16/396*10)=-1.30742852519225
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: GNA13 [Title/Abstract] AND BMI1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGNA13(63049620)-BMI1(22617063), # samples:3
Anticipated loss of major functional domain due to fusion event.GNA13-BMI1 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
GNA13-BMI1 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

check buttonFusion gene breakpoints across GNA13 (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 BMI1 (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 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
ChimerDB4HNSCTCGA-CV-7429-01AGNA13chr17

63049620

-BMI1chr10

22617063

+
ChimerDB4HNSCTCGA-CV-7429GNA13chr17

63049620

-BMI1chr10

22617063

+


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Fusion Gene ORF analysis for GNA13-BMI1

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
Frame-shiftENST00000439174ENST00000376663GNA13chr17

63049620

-BMI1chr10

22617063

+
In-frameENST00000541118ENST00000376663GNA13chr17

63049620

-BMI1chr10

22617063

+

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)
ENST00000541118GNA13chr1763049620-ENST00000376663BMI1chr1022617063+2907409410964184

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
ENST00000541118ENST00000376663GNA13chr1763049620-BMI1chr1022617063+0.0070412860.9929588

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Fusion Genomic Features for GNA13-BMI1


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)
GNA13chr1763049619-BMI1chr1022617062+0.095165590.90483445
GNA13chr1763049619-BMI1chr1022617062+0.095165590.90483445
GNA13chr1763049619-BMI1chr1022617062+0.095165590.90483445
GNA13chr1763049619-BMI1chr1022617062+0.095165590.90483445

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

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.
genomic feature of top 1%

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Fusion Protein Features for GNA13-BMI1


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/chr17:63049620/chr10:22617063)
- 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
.BMI1

P35226

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: Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A 'Lys-119', rendering chromatin heritably changed in its expressibility (PubMed:15386022, PubMed:16359901, PubMed:26151332, PubMed:16714294, PubMed:21772249, PubMed:25355358, PubMed:27827373). The complex composed of RNF2, UB2D3 and BMI1 binds nucleosomes, and has activity only with nucleosomal histone H2A (PubMed:21772249, PubMed:25355358). In the PRC1-like complex, regulates the E3 ubiquitin-protein ligase activity of RNF2/RING2 (PubMed:15386022, PubMed:26151332, PubMed:21772249). {ECO:0000269|PubMed:15386022, ECO:0000269|PubMed:16359901, ECO:0000269|PubMed:16714294, ECO:0000269|PubMed:16882984, ECO:0000269|PubMed:21772249, ECO:0000269|PubMed:25355358, ECO:0000269|PubMed:26151332, ECO:0000269|PubMed:27827373}.

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
HgeneGNA13chr17:63049620chr10:22617063ENST00000439174-2458_63170378.0Nucleotide bindingGTP
HgeneGNA13chr17:63049620chr10:22617063ENST00000439174-2450_63170378.0RegionG1 motif
TgeneBMI1chr17:63049620chr10:22617063ENST00000376663510251_326141327.0Compositional biasNote=Pro/Ser-rich

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneGNA13chr17:63049620chr10:22617063ENST00000439174-2447_377170378.0DomainG-alpha
HgeneGNA13chr17:63049620chr10:22617063ENST00000439174-24197_200170378.0Nucleotide bindingGTP
HgeneGNA13chr17:63049620chr10:22617063ENST00000439174-24291_294170378.0Nucleotide bindingGTP
HgeneGNA13chr17:63049620chr10:22617063ENST00000439174-24195_203170378.0RegionG2 motif
HgeneGNA13chr17:63049620chr10:22617063ENST00000439174-24218_227170378.0RegionG3 motif
HgeneGNA13chr17:63049620chr10:22617063ENST00000439174-24287_294170378.0RegionG4 motif
HgeneGNA13chr17:63049620chr10:22617063ENST00000439174-24347_352170378.0RegionG5 motif
TgeneBMI1chr17:63049620chr10:22617063ENST0000037666351081_95141327.0MotifNuclear localization signal
TgeneBMI1chr17:63049620chr10:22617063ENST0000037666351018_57141327.0Zinc fingerRING-type


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Fusion Gene Sequence for GNA13-BMI1


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.
>33536_33536_1_GNA13-BMI1_GNA13_chr17_63049620_ENST00000541118_BMI1_chr10_22617063_ENST00000376663_length(transcript)=2907nt_BP=409nt
AATAAGGGAACTTTTTGCCCGAGACTTCTTGTCAAGGGCGTAGGGTGACAGCCTCCTTTTGGGCGAGAATATGAAACTTGAGGAGTGTCA
GGTTGACTGTACTGGAATCAGGAGAGAGTGGACCCATACAGTTAGCATGAAAATGTAGCATCTGTGCTTTTTCGCCCCAGTGTCACGGTC
AGGTATGAGGGTGCTGGTTGATGCTCGAGAGAAGCTTCATATTCCCTGGGGAGACAACTCAAACCAACAACATGGAGATAAGATGATGTC
GTTTGATACCCGGGCCCCCATGGCAGCCCAAGGAATGGTGGAAACAAGGGTTTTCTTACAATATCTTCCTGCTATAAGAGCATTATGGGC
AGACAGCGGCATACAGAATGCCTATGACCGGCGTCGAGAATTTCAACTGATTGGATCGGAAAGTAAACAAAGACAAAGAGAAATCTAAGG
AGGAGGTGAATGATAAAAGATACTTACGATGCCCAGCAGCAATGACTGTGATGCACTTAAGAAAGTTTCTCAGAAGTAAAATGGACATAC
CTAATACTTTCCAGATTGATGTCATGTATGAGGAGGAACCTTTAAAGGATTATTATACACTAATGGATATTGCCTACATTTATACCTGGA
GAAGGAATGGTCCACTTCCATTGAAATACAGAGTTCGACCTACTTGTAAAAGAATGAAGATCAGTCACCAGAGAGATGGACTGACAAATG
CTGGAGAACTGGAAAGTGACTCTGGGAGTGACAAGGCCAACAGCCCAGCAGGAGGTATTCCCTCCACCTCTTCTTGTTTGCCTAGCCCCA
GTACTCCAGTGCAGTCTCCTCATCCACAGTTTCCTCACATTTCCAGTACTATGAATGGAACCAGCAACAGCCCCAGCGGTAACCACCAAT
CTTCTTTTGCCAATAGACCTCGAAAATCATCAGTAAATGGGTCATCAGCAACTTCTTCTGGTTGATACCTGAGACTGTTAAGGAAAAAAA
TTTTAAACCCCTGATTTATATAGATATCTTCATGCCATTACAGCTTTCTAGATGCTAATACATGTGACTATCGTCCAATTTGCTTTCTTT
TGTAGTGACATTAAATTTGGCTATAAAAGATGGACTACATGTGATACTCCTATGGACGTTAATTGAAAAGAAAGATTGTTGTTATAAAGA
ATTGGTTTCTTGGAAAGCAGGCAAGACTTTTTCTCTGTGTTAGGAAAGATGGGAAATGGTTTCTGTAACCATTGTTTGGATTTGGAAGTA
CTCTGCAGTGGACATAAGCATTGGGCCATAGTTTGTTAATCTCAACTAACGCCTACATTACATTCTCCTTGATCGTTCTTGTTATTACGC
TGTTTTGTGAACCTGTAGAAAACAAGTGCTTTTTATCTTGAAATTCAACCAACGGAAAGAATATGCATAGAATAATGCATTCTATGTAGC
CATGTCACTGTGAATAACGATTTCTTGCATATTTAGCCATTTTGATTCCTGTTTGATTTATACTTCTCTGTTGCTACGCAAAACCGATCA
AAGAAAAGTGAACTTCAGTTTTACAATCTGTATGCCTAAAAGCGGGTACTACCGTTTATTTTACTGACTTGTTTAAATGATTCGCTTTTG
TAAGAATCAGATGGCATTATGCTTGTTGTACAATGCCATATTGGTATATGACATAACAGGAAACAGTATTGTATGATATATTTATAAATG
CTATAAAGAAATATTGTGTTTCATGCATTCAGAAATGATTGTTAAAATTCTCCCAACTGGTTCGACCTTTGCAGATACCCATAACCTATG
TTGAGCCTTGCTTACCAGCAAAGAATATTTTTAATGTGGATATCTAATTCTAAAGTCTGTTCCATTAGAAGCAATTGGCACATCTTTCTA
TACTTTATATACTTTTCTCCAGTAATACATGTTTACTTTAAAGATTGTTGCAGTGAAGAAAAACCTTTAACTGAGAAATATGGAAACCGT
CTTAATTTTCCATTGGCTATGATGGAATTAATATTGTATTTTAAAAATGCATATTGATCACTATAATTCTAAAACAATTTTTTAAATAAA
CCAGCAGGTTGCTAAAAGAAGGCATTTTATCTAAAGTTATTTTAATAGGTGGTATAGCAGTAATTTTAAATTTAAGAGTTGCTTTTACAG
TTAACAATGGAATATGCCTTCTCTGCTATGTCTGAAAATAGAAGCTATTTATTATGAGCTTCTACAGGTATTTTTAAATAGAGCAAGCAT
GTTGAATTTAAAATATGAATAACCCCACCCAACAATTTTCAGTTTATTTTTTGCTTTGGTCGAACTTGGTGTGTGTTCATCACCCATCAG
TTATTTGTGAGGGTGTTTATTCTATATGAATATTGTTTCATGTTTGTATGGGAAAATTGTAGCTAAACATTTCATTGTCCCCAGTCTGCA
AAAGAAGCACAATTCTATTGCTTTGTCTTGCTTATAGTCATTAAATCATTACTTTTACATATATTGCTGTTACTTCTGCTTTCTTTAAAA
ATATAGTAAAGGATGTTTTATGAAGTCACAAGATACATATATTTTTATTTTGACCTAAATTTGTACAGTCCCATTGTAAGTGTTGTTTCT
AATTATAGATGTAAAATGAAATTTCATTTGTAATTGGAAAAAATCCAATAAAAAGGATATTCATTTAGAAAATAGCTAAGATCTTTAATA
AAAATTTGATATGAAAAGCACAATGTGCAGAAGTTATGGAAAACCTATAGAGGATTACAACAGGTAAACGTTAAAGAGAATACATTGCTG
ACTTATAGTGATGTGGCTAAGAAGTACATGCTTTGTTGTAAAATTGCTTGAAAGCCCATTGAAAGATGTATCTGTTTATTTACAGTCTTT

>33536_33536_1_GNA13-BMI1_GNA13_chr17_63049620_ENST00000541118_BMI1_chr10_22617063_ENST00000376663_length(amino acids)=184AA_BP=1
MDRKVNKDKEKSKEEVNDKRYLRCPAAMTVMHLRKFLRSKMDIPNTFQIDVMYEEEPLKDYYTLMDIAYIYTWRRNGPLPLKYRVRPTCK
RMKISHQRDGLTNAGELESDSGSDKANSPAGGIPSTSSCLPSPSTPVQSPHPQFPHISSTMNGTSNSPSGNHQSSFANRPRKSSVNGSSA

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Fusion Gene PPI Analysis for GNA13-BMI1


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
TgeneBMI1chr17:63049620chr10:22617063ENST00000376663510164_228141.66666666666666327.0E4F1
TgeneBMI1chr17:63049620chr10:22617063ENST00000376663510162_182141.66666666666666327.0PHC2


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 GNA13-BMI1


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 GNA13-BMI1


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