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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:FBXL20-HMGA1 (FusionGDB2 ID:HG84961TG3159)

Fusion Gene Summary for FBXL20-HMGA1

check button Fusion gene summary
Fusion gene informationFusion gene name: FBXL20-HMGA1
Fusion gene ID: hg84961tg3159
HgeneTgene
Gene symbol

FBXL20

HMGA1

Gene ID

84961

3159

Gene nameF-box and leucine rich repeat protein 20high mobility group AT-hook 1
SynonymsFbl2|Fbl20HMG-R|HMGA1A|HMGIY
Cytomap('FBXL20')('HMGA1')

17q12

6p21.31

Type of geneprotein-codingprotein-coding
DescriptionF-box/LRR-repeat protein 20F-box protein FBL2high mobility group protein HMG-I/HMG-Yhigh mobility group protein A1high mobility group protein Rhigh-mobility group (nonhistone chromosomal) protein isoforms I and Ynonhistone chromosomal high-mobility group protein HMG-I/HMG-Y
Modification date2020031320200315
UniProtAcc.

P17096

Ensembl transtripts involved in fusion geneENST00000264658, ENST00000394294, 
ENST00000577399, ENST00000583610, 
Fusion gene scores* DoF score58 X 21 X 16=194886 X 5 X 3=90
# samples 616
** MAII scorelog2(61/19488*10)=-4.99763298545608
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/90*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: FBXL20 [Title/Abstract] AND HMGA1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFBXL20(37499432)-HMGA1(34208513), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
TgeneHMGA1

GO:0035986

senescence-associated heterochromatin focus assembly

16901784

TgeneHMGA1

GO:0090402

oncogene-induced cell senescence

16901784



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
ChimerDB4STADTCGA-BR-7197FBXL20chr17

37499432

-HMGA1chr6

34208513

+


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Fusion Gene ORF analysis for FBXL20-HMGA1

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-3UTRENST00000264658ENST00000478214FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-3UTRENST00000394294ENST00000478214FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-3UTRENST00000577399ENST00000478214FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-3UTRENST00000583610ENST00000478214FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000264658ENST00000311487FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000264658ENST00000347617FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000264658ENST00000374116FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000264658ENST00000395004FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000264658ENST00000401473FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000264658ENST00000447654FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000394294ENST00000311487FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000394294ENST00000347617FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000394294ENST00000374116FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000394294ENST00000395004FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000394294ENST00000401473FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000394294ENST00000447654FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000577399ENST00000311487FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000577399ENST00000347617FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000577399ENST00000374116FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000577399ENST00000395004FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000577399ENST00000401473FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000577399ENST00000447654FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000583610ENST00000311487FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000583610ENST00000347617FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000583610ENST00000374116FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000583610ENST00000395004FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000583610ENST00000401473FBXL20chr17

37499432

-HMGA1chr6

34208513

+
5CDS-5UTRENST00000583610ENST00000447654FBXL20chr17

37499432

-HMGA1chr6

34208513

+

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 FBXL20-HMGA1


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)
FBXL20chr1737499432-HMGA1chr634208513+0.0027897470.9972102
FBXL20chr1737499432-HMGA1chr634208513+0.0027897470.9972102


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 FBXL20-HMGA1


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/:37499432/:34208513)
- 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
.HMGA1

P17096

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: HMG-I/Y bind preferentially to the minor groove of A+T rich regions in double-stranded DNA. It is suggested that these proteins could function in nucleosome phasing and in the 3'-end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to A+T-rich regions.

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 FBXL20-HMGA1


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 FBXL20-HMGA1


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 FBXL20-HMGA1


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 FBXL20-HMGA1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0011860Diabetes Mellitus, Non-Insulin-Dependent1CTD_human
TgeneC0020456Hyperglycemia1CTD_human
TgeneC0021655Insulin Resistance1CTD_human
TgeneC0023269leiomyosarcoma1CTD_human
TgeneC0036341Schizophrenia1PSYGENET
TgeneC0042138Uterine Neoplasms1CTD_human
TgeneC0153567Uterine Cancer1CTD_human
TgeneC0205815Leiomyosarcoma, Epithelioid1CTD_human
TgeneC0205816Leiomyosarcoma, Myxoid1CTD_human
TgeneC0524620Metabolic Syndrome X1CTD_human
TgeneC0920563Insulin Sensitivity1CTD_human
TgeneC1855520Hyperglycemia, Postprandial1CTD_human