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 | Fusion Gene Summary |
| Fusion Gene ORF analysis |
| Fusion Genomic Features |
| Fusion Protein Features |
| Fusion Gene Sequence |
| Fusion Gene PPI analysis |
| Related Drugs |
| Related Diseases |
Fusion gene:LIMA1-ARID2 (FusionGDB2 ID:44682) |
Fusion Gene Summary for LIMA1-ARID2 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: LIMA1-ARID2 | Fusion gene ID: 44682 | Hgene | Tgene | Gene symbol | LIMA1 | ARID2 | Gene ID | 51474 | 196528 |
| Gene name | LIM domain and actin binding 1 | AT-rich interaction domain 2 | |
| Synonyms | EPLIN|LDLCQ8|SREBP3 | BAF200|CSS6|p200 | |
| Cytomap | 12q13.12 | 12q12 | |
| Type of gene | protein-coding | protein-coding | |
| Description | LIM domain and actin-binding protein 11110021C24Rikepithelial protein lost in neoplasm betasterol regulatory element binding protein 3 | AT-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 date | 20200313 | 20200320 | |
| UniProtAcc | Q9UHB6 | Q68CP9 | |
| Ensembl transtripts involved in fusion gene | ENST00000341247, ENST00000394943, ENST00000547825, ENST00000552008, ENST00000552491, ENST00000552783, ENST00000552823, ENST00000552909, | ENST00000444670, ENST00000457135, ENST00000479608, ENST00000334344, ENST00000422737, | |
| Fusion gene scores | * DoF score | 11 X 9 X 7=693 | 8 X 8 X 3=192 |
| # samples | 12 | 8 | |
| ** MAII score | log2(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 breakpoint | LIMA1(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) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Hgene | LIMA1 | GO:0030835 | negative regulation of actin filament depolymerization | 12566430 |
| Hgene | LIMA1 | GO:0031529 | ruffle organization | 12566430 |
| Hgene | LIMA1 | GO:0051017 | actin filament bundle assembly | 12566430 |
| Tgene | ARID2 | GO:0006337 | nucleosome disassembly | 8895581 |
| Tgene | ARID2 | GO:0008285 | negative regulation of cell proliferation | 26169693 |
| Tgene | ARID2 | GO:0030336 | negative regulation of cell migration | 26169693 |
| Fusion gene breakpoints across LIMA1 (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Fusion gene breakpoints across ARID2 (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| 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. |
| Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChimerDB4 | STAD | TCGA-BR-A4J8 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
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Fusion Gene ORF analysis for LIMA1-ARID2 |
| 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. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| 5CDS-3UTR | ENST00000341247 | ENST00000444670 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| 5CDS-3UTR | ENST00000341247 | ENST00000457135 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| 5CDS-3UTR | ENST00000341247 | ENST00000479608 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| 5CDS-3UTR | ENST00000394943 | ENST00000444670 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| 5CDS-3UTR | ENST00000394943 | ENST00000457135 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| 5CDS-3UTR | ENST00000394943 | ENST00000479608 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| Frame-shift | ENST00000341247 | ENST00000334344 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| Frame-shift | ENST00000341247 | ENST00000422737 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| Frame-shift | ENST00000394943 | ENST00000334344 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| Frame-shift | ENST00000394943 | ENST00000422737 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3CDS | ENST00000547825 | ENST00000334344 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3CDS | ENST00000547825 | ENST00000422737 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3CDS | ENST00000552008 | ENST00000334344 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3CDS | ENST00000552008 | ENST00000422737 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3CDS | ENST00000552491 | ENST00000334344 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3CDS | ENST00000552491 | ENST00000422737 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3CDS | ENST00000552783 | ENST00000334344 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3CDS | ENST00000552783 | ENST00000422737 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3CDS | ENST00000552823 | ENST00000334344 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3CDS | ENST00000552823 | ENST00000422737 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3CDS | ENST00000552909 | ENST00000334344 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3CDS | ENST00000552909 | ENST00000422737 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3UTR | ENST00000547825 | ENST00000444670 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3UTR | ENST00000547825 | ENST00000457135 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3UTR | ENST00000547825 | ENST00000479608 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3UTR | ENST00000552008 | ENST00000444670 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3UTR | ENST00000552008 | ENST00000457135 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3UTR | ENST00000552008 | ENST00000479608 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3UTR | ENST00000552491 | ENST00000444670 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3UTR | ENST00000552491 | ENST00000457135 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3UTR | ENST00000552491 | ENST00000479608 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3UTR | ENST00000552783 | ENST00000444670 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3UTR | ENST00000552783 | ENST00000457135 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3UTR | ENST00000552783 | ENST00000479608 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3UTR | ENST00000552823 | ENST00000444670 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3UTR | ENST00000552823 | ENST00000457135 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3UTR | ENST00000552823 | ENST00000479608 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3UTR | ENST00000552909 | ENST00000444670 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3UTR | ENST00000552909 | ENST00000457135 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| intron-3UTR | ENST00000552909 | ENST00000479608 | LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + |
| ORFfinder result based on the fusion transcript sequence of in-frame fusion genes. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
| DeepORF 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. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
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Fusion Genomic Features for LIMA1-ARID2 |
| FusionAI 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. |
| Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | 1-p | p (fusion gene breakpoint) |
| LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + | 7.01E-09 | 1 |
| LIMA1 | chr12 | 50642415 | - | ARID2 | chr12 | 46285562 | + | 7.01E-09 | 1 |
| Distribution 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. |
| Distribution 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. |
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Fusion Protein Features for LIMA1-ARID2 |
| 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. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| LIMA1 | ARID2 |
| FUNCTION: Actin-binding protein involved in actin cytoskeleton regulation and dynamics. Increases the number and size of actin stress fibers and inhibits membrane ruffling. Inhibits actin filament depolymerization. Bundles actin filaments, delays filament nucleation and reduces formation of branched filaments (PubMed:12566430). Plays a role in cholesterol homeostasis. Influences plasma cholesterol levels through regulation of intestinal cholesterol absorption. May act as a scaffold protein by regulating NPC1L1 transportation, an essential protein for cholesterol absorption, to the plasma membrane by recruiting MYO5B to NPC1L1, and thus facilitates cholesterol uptake (By similarity). {ECO:0000250|UniProtKB:Q9ERG0, ECO:0000269|PubMed:12566430}. | FUNCTION: Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Required for the stability of the SWI/SNF chromatin remodeling complex SWI/SNF-B (PBAF). May be involved in targeting the complex to different genes. May be involved in regulating transcriptional activation of cardiac genes. {ECO:0000269|PubMed:16782067, ECO:0000303|PubMed:22952240, ECO:0000303|PubMed:26601204}. |
| Retention 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 * 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. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| - In-frame and not-retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
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Fusion Gene Sequence for LIMA1-ARID2 |
| 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 LIMA1-ARID2 |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in |
| Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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Related Drugs for LIMA1-ARID2 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.8 2021-05-08) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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Related Diseases for LIMA1-ARID2 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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