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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:LIMA1-ANO6 (FusionGDB2 ID:44681)

Fusion Gene Summary for LIMA1-ANO6

check button Fusion gene summary
Fusion gene informationFusion gene name: LIMA1-ANO6
Fusion gene ID: 44681
HgeneTgene
Gene symbol

LIMA1

ANO6

Gene ID

51474

196527

Gene nameLIM domain and actin binding 1anoctamin 6
SynonymsEPLIN|LDLCQ8|SREBP3BDPLT7|SCTS|TMEM16F
Cytomap

12q13.12

12q12

Type of geneprotein-codingprotein-coding
DescriptionLIM domain and actin-binding protein 11110021C24Rikepithelial protein lost in neoplasm betasterol regulatory element binding protein 3anoctamin-6SCAN channelsmall-conductance calcium-activated nonselective cation channeltransmembrane protein 16F
Modification date2020031320200313
UniProtAcc

Q9UHB6

Q4KMQ2

Ensembl transtripts involved in fusion geneENST00000341247, ENST00000394943, 
ENST00000547825, ENST00000552008, 
ENST00000552491, ENST00000552783, 
ENST00000552823, ENST00000552909, 
ENST00000320560, ENST00000423947, 
ENST00000425752, ENST00000426898, 
ENST00000435642, ENST00000441606, 
Fusion gene scores* DoF score11 X 9 X 7=6939 X 9 X 7=567
# samples 129
** MAII scorelog2(12/693*10)=-2.5298209465287
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/567*10)=-2.65535182861255
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LIMA1 [Title/Abstract] AND ANO6 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLIMA1(50642416)-ANO6(45695797), # samples:2
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
HgeneLIMA1

GO:0030835

negative regulation of actin filament depolymerization

12566430

HgeneLIMA1

GO:0031529

ruffle organization

12566430

HgeneLIMA1

GO:0051017

actin filament bundle assembly

12566430

TgeneANO6

GO:0006812

cation transport

22946059


check buttonFusion 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.

check buttonFusion gene breakpoints across ANO6 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4UCECTCGA-AJ-A3NF-01ALIMA1chr12

50642416

-ANO6chr12

45695797

+


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Fusion Gene ORF analysis for LIMA1-ANO6

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-intronENST00000341247ENST00000320560LIMA1chr12

50642416

-ANO6chr12

45695797

+
5CDS-intronENST00000341247ENST00000423947LIMA1chr12

50642416

-ANO6chr12

45695797

+
5CDS-intronENST00000341247ENST00000425752LIMA1chr12

50642416

-ANO6chr12

45695797

+
5CDS-intronENST00000341247ENST00000426898LIMA1chr12

50642416

-ANO6chr12

45695797

+
5CDS-intronENST00000341247ENST00000435642LIMA1chr12

50642416

-ANO6chr12

45695797

+
5CDS-intronENST00000341247ENST00000441606LIMA1chr12

50642416

-ANO6chr12

45695797

+
5CDS-intronENST00000394943ENST00000320560LIMA1chr12

50642416

-ANO6chr12

45695797

+
5CDS-intronENST00000394943ENST00000423947LIMA1chr12

50642416

-ANO6chr12

45695797

+
5CDS-intronENST00000394943ENST00000425752LIMA1chr12

50642416

-ANO6chr12

45695797

+
5CDS-intronENST00000394943ENST00000426898LIMA1chr12

50642416

-ANO6chr12

45695797

+
5CDS-intronENST00000394943ENST00000435642LIMA1chr12

50642416

-ANO6chr12

45695797

+
5CDS-intronENST00000394943ENST00000441606LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000547825ENST00000320560LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000547825ENST00000423947LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000547825ENST00000425752LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000547825ENST00000426898LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000547825ENST00000435642LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000547825ENST00000441606LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552008ENST00000320560LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552008ENST00000423947LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552008ENST00000425752LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552008ENST00000426898LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552008ENST00000435642LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552008ENST00000441606LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552491ENST00000320560LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552491ENST00000423947LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552491ENST00000425752LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552491ENST00000426898LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552491ENST00000435642LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552491ENST00000441606LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552783ENST00000320560LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552783ENST00000423947LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552783ENST00000425752LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552783ENST00000426898LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552783ENST00000435642LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552783ENST00000441606LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552823ENST00000320560LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552823ENST00000423947LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552823ENST00000425752LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552823ENST00000426898LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552823ENST00000435642LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552823ENST00000441606LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552909ENST00000320560LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552909ENST00000423947LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552909ENST00000425752LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552909ENST00000426898LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552909ENST00000435642LIMA1chr12

50642416

-ANO6chr12

45695797

+
intron-intronENST00000552909ENST00000441606LIMA1chr12

50642416

-ANO6chr12

45695797

+

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 LIMA1-ANO6


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-ANO6chr1245695796+1.21E-060.9999988
LIMA1chr1250642415-ANO6chr1245695796+1.21E-060.9999988

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.

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 LIMA1-ANO6


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/:50642416/:45695797)
- 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
LIMA1

Q9UHB6

ANO6

Q4KMQ2

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: Small-conductance calcium-activated nonselective cation (SCAN) channel which acts as a regulator of phospholipid scrambling in platelets and osteoblasts. Phospholipid scrambling results in surface exposure of phosphatidylserine which in platelets is essential to trigger the clotting system whereas in osteoblasts is essential for the deposition of hydroxyapatite during bone mineralization. Has calcium-dependent phospholipid scramblase activity; scrambles phosphatidylserine, phosphatidylcholine and galactosylceramide (By similarity). Can generate outwardly rectifying chloride channel currents in airway epithelial cells and Jurkat T lymphocytes. {ECO:0000250|UniProtKB:Q6P9J9, ECO:0000269|PubMed:20056604, ECO:0000269|PubMed:21107324, ECO:0000269|PubMed:21908539, ECO:0000269|PubMed:22006324, ECO:0000269|PubMed:22946059}.

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 LIMA1-ANO6


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 LIMA1-ANO6


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 LIMA1-ANO6


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 LIMA1-ANO6


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