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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:CNN3-LINC01057 (FusionGDB2 ID:HG1266TG101928079)

Fusion Gene Summary for CNN3-LINC01057

check button Fusion gene summary
Fusion gene informationFusion gene name: CNN3-LINC01057
Fusion gene ID: hg1266tg101928079
HgeneTgene
Gene symbol

CNN3

LINC01057

Gene ID

1266

101928079

Gene namecalponin 3SLC44A3 antisense RNA 1
Synonyms-LINC01057|XLOC_000303
Cytomap('CNN3')('LINC01057')

1p21.3

1p21.3

Type of geneprotein-codingncRNA
Descriptioncalponin-3calponin 3, acidiccalponin, acidic isoformdJ639P13.2.2 (acidic calponin 3)long intergenic non-protein coding RNA 1057
Modification date2020031320200313
UniProtAcc

Q15417

.
Ensembl transtripts involved in fusion geneENST00000370206, ENST00000394202, 
ENST00000538964, ENST00000487539, 
ENST00000545882, 
ENST00000370206, 
ENST00000394202, ENST00000538964, 
ENST00000545882, ENST00000487539, 
Fusion gene scores* DoF score5 X 6 X 5=1504 X 5 X 3=60
# samples 94
** MAII scorelog2(9/150*10)=-0.736965594166206
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/60*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CNN3 [Title/Abstract] AND LINC01057 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCNN3(95392394)-LINC01057(95145163), # 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


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-CD-A486-01ACNN3chr1

95392394

-LINC01057chr1

95145163

-
ChimerDB4STADTCGA-CD-A486-01ACNN3chr1

95392394

-LINC01057chr1

95171113

-
ChimerDB4STADTCGA-CD-A486-01ACNN3chr1

95392394

-LINC01057chr1

95197993

-
ChimerDB4TGCTTCGA-2G-AAGWCNN3chr1

95392394

-LINC01057chr1

95145163

-


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Fusion Gene ORF analysis for CNN3-LINC01057

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-5UTRENST00000370206ENST00000452922CNN3chr1

95392394

-LINC01057chr1

95145163

-
5CDS-5UTRENST00000370206ENST00000452922CNN3chr1

95392394

-LINC01057chr1

95171113

-
5CDS-5UTRENST00000370206ENST00000452922CNN3chr1

95392394

-LINC01057chr1

95197993

-
5CDS-5UTRENST00000394202ENST00000452922CNN3chr1

95392394

-LINC01057chr1

95145163

-
5CDS-5UTRENST00000394202ENST00000452922CNN3chr1

95392394

-LINC01057chr1

95171113

-
5CDS-5UTRENST00000394202ENST00000452922CNN3chr1

95392394

-LINC01057chr1

95197993

-
5CDS-5UTRENST00000538964ENST00000452922CNN3chr1

95392394

-LINC01057chr1

95145163

-
5CDS-5UTRENST00000538964ENST00000452922CNN3chr1

95392394

-LINC01057chr1

95171113

-
5CDS-5UTRENST00000538964ENST00000452922CNN3chr1

95392394

-LINC01057chr1

95197993

-
intron-5UTRENST00000487539ENST00000452922CNN3chr1

95392394

-LINC01057chr1

95145163

-
intron-5UTRENST00000487539ENST00000452922CNN3chr1

95392394

-LINC01057chr1

95171113

-
intron-5UTRENST00000487539ENST00000452922CNN3chr1

95392394

-LINC01057chr1

95197993

-
intron-5UTRENST00000545882ENST00000452922CNN3chr1

95392394

-LINC01057chr1

95145163

-
intron-5UTRENST00000545882ENST00000452922CNN3chr1

95392394

-LINC01057chr1

95171113

-
intron-5UTRENST00000545882ENST00000452922CNN3chr1

95392394

-LINC01057chr1

95197993

-

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 CNN3-LINC01057


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)


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Fusion Protein Features for CNN3-LINC01057


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/:95392394/:95145163)
- 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
CNN3

Q15417

.
FUNCTION: Thin filament-associated protein that is implicated in the regulation and modulation of smooth muscle contraction. It is capable of binding to actin, calmodulin and tropomyosin. The interaction of calponin with actin inhibits the actomyosin Mg-ATPase activity.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 CNN3-LINC01057


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 CNN3-LINC01057


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 CNN3-LINC01057


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 CNN3-LINC01057


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCNN3C0007097Carcinoma1CTD_human
HgeneCNN3C0024667Animal Mammary Neoplasms1CTD_human
HgeneCNN3C0024668Mammary Neoplasms, Experimental1CTD_human
HgeneCNN3C0033578Prostatic Neoplasms1CTD_human
HgeneCNN3C0205696Anaplastic carcinoma1CTD_human
HgeneCNN3C0205697Carcinoma, Spindle-Cell1CTD_human
HgeneCNN3C0205698Undifferentiated carcinoma1CTD_human
HgeneCNN3C0205699Carcinomatosis1CTD_human
HgeneCNN3C0376358Malignant neoplasm of prostate1CTD_human
HgeneCNN3C1257925Mammary Carcinoma, Animal1CTD_human