Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:LIMA1-ARID2 (FusionGDB2 ID:HG51474TG196528)

Fusion Gene Summary for LIMA1-ARID2

check button Fusion gene summary
Fusion gene informationFusion gene name: LIMA1-ARID2
Fusion gene ID: hg51474tg196528
HgeneTgene
Gene symbol

LIMA1

ARID2

Gene ID

51474

196528

Gene nameLIM domain and actin binding 1AT-rich interaction domain 2
SynonymsEPLIN|LDLCQ8|SREBP3BAF200|CSS6|p200
Cytomap('LIMA1')('ARID2')

12q13.12

12q12

Type of geneprotein-codingprotein-coding
DescriptionLIM domain and actin-binding protein 11110021C24Rikepithelial protein lost in neoplasm betasterol regulatory element binding protein 3AT-rich interactive domain-containing protein 2ARID domain-containing protein 2AT rich interactive domain 2 (ARID, RFX-like)BRG1-associated factor 200zinc finger protein with activation potentialzipzap/p200
Modification date2020031320200320
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000341247, ENST00000394943, 
ENST00000547825, ENST00000552008, 
ENST00000552491, ENST00000552783, 
ENST00000552823, ENST00000552909, 
Fusion gene scores* DoF score11 X 9 X 7=6938 X 8 X 3=192
# samples 128
** MAII scorelog2(12/693*10)=-2.5298209465287
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/192*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LIMA1 [Title/Abstract] AND ARID2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLIMA1(50642415)-ARID2(46285562), # samples:1
Anticipated loss of major functional domain due to fusion event.LIMA1-ARID2 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
LIMA1-ARID2 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
LIMA1-ARID2 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
LIMA1-ARID2 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
LIMA1-ARID2 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
LIMA1-ARID2 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
HgeneLIMA1

GO:0030835

negative regulation of actin filament depolymerization

12566430

HgeneLIMA1

GO:0031529

ruffle organization

12566430

HgeneLIMA1

GO:0051017

actin filament bundle assembly

12566430

TgeneARID2

GO:0006337

nucleosome disassembly

8895581

TgeneARID2

GO:0008285

negative regulation of cell proliferation

26169693

TgeneARID2

GO:0030336

negative regulation of cell migration

26169693



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-A4J8LIMA1chr12

50642415

-ARID2chr12

46285562

+


Top

Fusion Gene ORF analysis for LIMA1-ARID2

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-3UTRENST00000341247ENST00000444670LIMA1chr12

50642415

-ARID2chr12

46285562

+
5CDS-3UTRENST00000341247ENST00000457135LIMA1chr12

50642415

-ARID2chr12

46285562

+
5CDS-3UTRENST00000341247ENST00000479608LIMA1chr12

50642415

-ARID2chr12

46285562

+
5CDS-3UTRENST00000394943ENST00000444670LIMA1chr12

50642415

-ARID2chr12

46285562

+
5CDS-3UTRENST00000394943ENST00000457135LIMA1chr12

50642415

-ARID2chr12

46285562

+
5CDS-3UTRENST00000394943ENST00000479608LIMA1chr12

50642415

-ARID2chr12

46285562

+
Frame-shiftENST00000341247ENST00000334344LIMA1chr12

50642415

-ARID2chr12

46285562

+
Frame-shiftENST00000341247ENST00000422737LIMA1chr12

50642415

-ARID2chr12

46285562

+
Frame-shiftENST00000394943ENST00000334344LIMA1chr12

50642415

-ARID2chr12

46285562

+
Frame-shiftENST00000394943ENST00000422737LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3CDSENST00000547825ENST00000334344LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3CDSENST00000547825ENST00000422737LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3CDSENST00000552008ENST00000334344LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3CDSENST00000552008ENST00000422737LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3CDSENST00000552491ENST00000334344LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3CDSENST00000552491ENST00000422737LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3CDSENST00000552783ENST00000334344LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3CDSENST00000552783ENST00000422737LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3CDSENST00000552823ENST00000334344LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3CDSENST00000552823ENST00000422737LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3CDSENST00000552909ENST00000334344LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3CDSENST00000552909ENST00000422737LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3UTRENST00000547825ENST00000444670LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3UTRENST00000547825ENST00000457135LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3UTRENST00000547825ENST00000479608LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3UTRENST00000552008ENST00000444670LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3UTRENST00000552008ENST00000457135LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3UTRENST00000552008ENST00000479608LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3UTRENST00000552491ENST00000444670LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3UTRENST00000552491ENST00000457135LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3UTRENST00000552491ENST00000479608LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3UTRENST00000552783ENST00000444670LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3UTRENST00000552783ENST00000457135LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3UTRENST00000552783ENST00000479608LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3UTRENST00000552823ENST00000444670LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3UTRENST00000552823ENST00000457135LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3UTRENST00000552823ENST00000479608LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3UTRENST00000552909ENST00000444670LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3UTRENST00000552909ENST00000457135LIMA1chr12

50642415

-ARID2chr12

46285562

+
intron-3UTRENST00000552909ENST00000479608LIMA1chr12

50642415

-ARID2chr12

46285562

+

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

Top

Fusion Genomic Features for LIMA1-ARID2


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)
LIMA1chr1250642415-ARID2chr1246285562+7.01E-091
LIMA1chr1250642415-ARID2chr1246285562+7.01E-091


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%

Top

Fusion Protein Features for LIMA1-ARID2


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/:50642415/:46285562)
- 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


Top

Fusion Gene Sequence for LIMA1-ARID2


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.

Top

Fusion Gene PPI Analysis for LIMA1-ARID2


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


Top

Related Drugs for LIMA1-ARID2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for LIMA1-ARID2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC2239176Liver carcinoma2CGI;CTD_human
TgeneC0033578Prostatic Neoplasms1CTD_human
TgeneC0265338Coffin-Siris syndrome1ORPHANET
TgeneC0376358Malignant neoplasm of prostate1CTD_human