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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:LIMS1-RNF185 (FusionGDB2 ID:44739)

Fusion Gene Summary for LIMS1-RNF185

check button Fusion gene summary
Fusion gene informationFusion gene name: LIMS1-RNF185
Fusion gene ID: 44739
HgeneTgene
Gene symbol

LIMS1

RNF185

Gene ID

3987

91445

Gene nameLIM zinc finger domain containing 1ring finger protein 185
SynonymsPINCH|PINCH-1|PINCH1-
Cytomap

2q12.3

22q12.2

Type of geneprotein-codingprotein-coding
DescriptionLIM and senescent cell antigen-like-containing domain protein 1LIM and senescent cell antigen-like domains 1LIM-type zinc finger domains 1particularly interesting new Cys-His protein 1renal carcinoma antigen NY-REN-48senescent cell antigenE3 ubiquitin-protein ligase RNF185BSK65-MONO1BSK65-MONO2BSK65-PANC1BSK65-PANC2BSK65-TEST1BSK65-TEST2BSK65-TEST3RING-type E3 ubiquitin transferase RNF185
Modification date2020032720200313
UniProtAcc

P48059

.
Ensembl transtripts involved in fusion geneENST00000393310, ENST00000332345, 
ENST00000338045, ENST00000393314, 
ENST00000409441, ENST00000410093, 
ENST00000462817, ENST00000542845, 
ENST00000544547, 		ENST00000266252, 
ENST00000326132, ENST00000426256, 
Fusion gene scores* DoF score9 X 4 X 6=2166 X 6 X 1=36
# samples 86
** MAII scorelog2(8/216*10)=-1.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/36*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: LIMS1 [Title/Abstract] AND RNF185 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLIMS1(109205072)-RNF185(31562886), # 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
HgeneLIMS1

GO:0045892

negative regulation of transcription, DNA-templated

21390327

TgeneRNF185

GO:0051865

protein autoubiquitination

24019521|27485036


check buttonFusion gene breakpoints across LIMS1 (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 RNF185 (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
ChiTaRS5.0N/ABX644470LIMS1chr2

109205072

+RNF185chr22

31562886

+


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Fusion Gene ORF analysis for LIMS1-RNF185

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
5UTR-intronENST00000393310ENST00000266252LIMS1chr2

109205072

+RNF185chr22

31562886

+
5UTR-intronENST00000393310ENST00000326132LIMS1chr2

109205072

+RNF185chr22

31562886

+
5UTR-intronENST00000393310ENST00000426256LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000332345ENST00000266252LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000332345ENST00000326132LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000332345ENST00000426256LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000338045ENST00000266252LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000338045ENST00000326132LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000338045ENST00000426256LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000393314ENST00000266252LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000393314ENST00000326132LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000393314ENST00000426256LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000409441ENST00000266252LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000409441ENST00000326132LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000409441ENST00000426256LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000410093ENST00000266252LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000410093ENST00000326132LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000410093ENST00000426256LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000462817ENST00000266252LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000462817ENST00000326132LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000462817ENST00000426256LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000542845ENST00000266252LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000542845ENST00000326132LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000542845ENST00000426256LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000544547ENST00000266252LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000544547ENST00000326132LIMS1chr2

109205072

+RNF185chr22

31562886

+
intron-intronENST00000544547ENST00000426256LIMS1chr2

109205072

+RNF185chr22

31562886

+

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 LIMS1-RNF185


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)

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.

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Fusion Protein Features for LIMS1-RNF185


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/:109205072/:31562886)
- 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
LIMS1

P48059

.
FUNCTION: Adapter protein in a cytoplasmic complex linking beta-integrins to the actin cytoskeleton, bridges the complex to cell surface receptor tyrosine kinases and growth factor receptors. Involved in the regulation of cell survival, cell proliferation and cell differentiation.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 LIMS1-RNF185


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 LIMS1-RNF185


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 LIMS1-RNF185


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 LIMS1-RNF185


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