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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:EXT2-ALKBH3 (FusionGDB2 ID:HG2132TG221120)

Fusion Gene Summary for EXT2-ALKBH3

check button Fusion gene summary
Fusion gene informationFusion gene name: EXT2-ALKBH3
Fusion gene ID: hg2132tg221120
HgeneTgene
Gene symbol

EXT2

ALKBH3

Gene ID

2132

221120

Gene nameexostosin glycosyltransferase 2alkB homolog 3, alpha-ketoglutaratedependent dioxygenase
SynonymsSOTV|SSMSABH3|DEPC-1|DEPC1|PCA1|hABH3
Cytomap('EXT2')('ALKBH3')

11p11.2

11p11.2

Type of geneprotein-codingprotein-coding
Descriptionexostosin-2N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferaseglucuronosyl-N-acetylglucosaminyl-proteoglycan/N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferasemultiple exostoses protein 2multiple exostosis 2putativalpha-ketoglutarate-dependent dioxygenase alkB homolog 3alkB homolog 3, alpha-ketoglutarate-dependent dioxygenasealkB, alkylation repair homolog 3alkylated DNA repair protein alkB homolog 3prostate cancer antigen-1
Modification date2020031320200327
UniProtAcc

Q93063

.
Ensembl transtripts involved in fusion geneENST00000529186, ENST00000343631, 
ENST00000358681, ENST00000395673, 
ENST00000533608, 
Fusion gene scores* DoF score8 X 6 X 8=3846 X 5 X 7=210
# samples 98
** MAII scorelog2(9/384*10)=-2.09310940439148
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/210*10)=-1.39231742277876
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: EXT2 [Title/Abstract] AND ALKBH3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointEXT2(44135851)-ALKBH3(43940588), # samples:3
Anticipated loss of major functional domain due to fusion event.EXT2-ALKBH3 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
EXT2-ALKBH3 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
EXT2-ALKBH3 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
EXT2-ALKBH3 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
HgeneEXT2

GO:0006024

glycosaminoglycan biosynthetic process

12907669

HgeneEXT2

GO:0033692

cellular polysaccharide biosynthetic process

12907669

TgeneALKBH3

GO:0006281

DNA repair

16858410

TgeneALKBH3

GO:0006307

DNA dealkylation involved in DNA repair

16858410|22055184

TgeneALKBH3

GO:0035552

oxidative single-stranded DNA demethylation

16858410

TgeneALKBH3

GO:0035553

oxidative single-stranded RNA demethylation

26863196|26863410



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
ChimerDB4PCPGTCGA-QR-A6GW-01AEXT2chr11

44219568

-ALKBH3chr11

43940588

+
ChimerDB4SKCMTCGA-ER-A194-01AEXT2chr11

44135851

-ALKBH3chr11

43940588

+
ChimerDB4SKCMTCGA-ER-A194-01AEXT2chr11

44135851

+ALKBH3chr11

43940588

+


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Fusion Gene ORF analysis for EXT2-ALKBH3

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-3CDSENST00000529186ENST00000302708EXT2chr11

44135851

+ALKBH3chr11

43940588

+
3UTR-3UTRENST00000529186ENST00000532410EXT2chr11

44135851

+ALKBH3chr11

43940588

+
3UTR-intronENST00000529186ENST00000378840EXT2chr11

44135851

+ALKBH3chr11

43940588

+
5CDS-3UTRENST00000343631ENST00000532410EXT2chr11

44219568

-ALKBH3chr11

43940588

+
5CDS-3UTRENST00000343631ENST00000532410EXT2chr11

44135851

+ALKBH3chr11

43940588

+
5CDS-3UTRENST00000358681ENST00000532410EXT2chr11

44219568

-ALKBH3chr11

43940588

+
5CDS-3UTRENST00000358681ENST00000532410EXT2chr11

44135851

+ALKBH3chr11

43940588

+
5CDS-3UTRENST00000395673ENST00000532410EXT2chr11

44219568

-ALKBH3chr11

43940588

+
5CDS-3UTRENST00000395673ENST00000532410EXT2chr11

44135851

+ALKBH3chr11

43940588

+
5CDS-3UTRENST00000533608ENST00000532410EXT2chr11

44219568

-ALKBH3chr11

43940588

+
5CDS-3UTRENST00000533608ENST00000532410EXT2chr11

44135851

+ALKBH3chr11

43940588

+
5CDS-intronENST00000343631ENST00000378840EXT2chr11

44219568

-ALKBH3chr11

43940588

+
5CDS-intronENST00000343631ENST00000378840EXT2chr11

44135851

+ALKBH3chr11

43940588

+
5CDS-intronENST00000358681ENST00000378840EXT2chr11

44219568

-ALKBH3chr11

43940588

+
5CDS-intronENST00000358681ENST00000378840EXT2chr11

44135851

+ALKBH3chr11

43940588

+
5CDS-intronENST00000395673ENST00000378840EXT2chr11

44219568

-ALKBH3chr11

43940588

+
5CDS-intronENST00000395673ENST00000378840EXT2chr11

44135851

+ALKBH3chr11

43940588

+
5CDS-intronENST00000533608ENST00000378840EXT2chr11

44219568

-ALKBH3chr11

43940588

+
5CDS-intronENST00000533608ENST00000378840EXT2chr11

44135851

+ALKBH3chr11

43940588

+
Frame-shiftENST00000343631ENST00000302708EXT2chr11

44219568

-ALKBH3chr11

43940588

+
Frame-shiftENST00000343631ENST00000302708EXT2chr11

44135851

+ALKBH3chr11

43940588

+
Frame-shiftENST00000358681ENST00000302708EXT2chr11

44219568

-ALKBH3chr11

43940588

+
Frame-shiftENST00000358681ENST00000302708EXT2chr11

44135851

+ALKBH3chr11

43940588

+
Frame-shiftENST00000395673ENST00000302708EXT2chr11

44219568

-ALKBH3chr11

43940588

+
Frame-shiftENST00000395673ENST00000302708EXT2chr11

44135851

+ALKBH3chr11

43940588

+
Frame-shiftENST00000533608ENST00000302708EXT2chr11

44219568

-ALKBH3chr11

43940588

+
Frame-shiftENST00000533608ENST00000302708EXT2chr11

44135851

+ALKBH3chr11

43940588

+
intron-3CDSENST00000529186ENST00000302708EXT2chr11

44219568

-ALKBH3chr11

43940588

+
intron-3UTRENST00000529186ENST00000532410EXT2chr11

44219568

-ALKBH3chr11

43940588

+
intron-intronENST00000529186ENST00000378840EXT2chr11

44219568

-ALKBH3chr11

43940588

+

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 EXT2-ALKBH3


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)
EXT2chr1144135851+ALKBH3chr1143940587+0.0002404170.9997596
EXT2chr1144135851+ALKBH3chr1143940587+0.0002404170.9997596


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 EXT2-ALKBH3


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/:44135851/:43940588)
- 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
EXT2

Q93063

.
FUNCTION: Glycosyltransferase required for the biosynthesis of heparan-sulfate. The EXT1/EXT2 complex possesses substantially higher glycosyltransferase activity than EXT1 or EXT2 alone. Appears to be a tumor suppressor. Required for the exosomal release of SDCBP, CD63 and syndecan (PubMed:22660413). {ECO:0000269|PubMed:22660413}.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 EXT2-ALKBH3


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 EXT2-ALKBH3


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 EXT2-ALKBH3


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 EXT2-ALKBH3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneEXT2C1851413EXOSTOSES, MULTIPLE, TYPE II18CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneEXT2C4225248SEIZURES, SCOLIOSIS, AND MACROCEPHALY SYNDROME4GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneEXT2C0015306Hereditary Multiple Exostoses1CTD_human
HgeneEXT2C1832588Chromosome 11p11.2 Deletion Syndrome1ORPHANET