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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:RNMT-SNCAIP (FusionGDB2 ID:75181)

Fusion Gene Summary for RNMT-SNCAIP

check button Fusion gene summary
Fusion gene informationFusion gene name: RNMT-SNCAIP
Fusion gene ID: 75181
HgeneTgene
Gene symbol

RNMT

SNCAIP

Gene ID

8731

9627

Gene nameRNA guanine-7 methyltransferasesynuclein alpha interacting protein
SynonymsCMT1|CMT1c|MET|Met|RG7MT1|cm1p|hCMT1|hMetSYPH1|Sph1
Cytomap

18p11.21

5q23.2

Type of geneprotein-codingprotein-coding
DescriptionmRNA cap guanine-N7 methyltransferaseRNA (guanine-7-) methyltransferasehcm1pmRNA (guanine-7-)methyltransferasemRNA (guanine-N(7)-)-methyltransferasemRNA cap methyltransferasesynphilin-1
Modification date2020032920200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000383314, ENST00000535051, 
ENST00000543302, ENST00000592764, 
ENST00000262173, ENST00000589866, 
ENST00000591922, 		ENST00000504884, 
ENST00000261367, ENST00000261368, 
ENST00000379533, ENST00000379536, 
ENST00000379538, ENST00000414317, 
ENST00000503116, ENST00000542191, 
Fusion gene scores* DoF score5 X 5 X 3=757 X 6 X 5=210
# samples 59
** MAII scorelog2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/210*10)=-1.22239242133645
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RNMT [Title/Abstract] AND SNCAIP [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRNMT(13726728)-SNCAIP(121776324), # 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
HgeneRNMT

GO:0006370

7-methylguanosine mRNA capping

27422871

TgeneSNCAIP

GO:0008219

cell death

16595633

TgeneSNCAIP

GO:0042417

dopamine metabolic process

14506261

TgeneSNCAIP

GO:0046928

regulation of neurotransmitter secretion

14506261

TgeneSNCAIP

GO:0090083

regulation of inclusion body assembly

15603737


check buttonFusion gene breakpoints across RNMT (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 SNCAIP (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
ChimerDB4SARCTCGA-DX-A7EF-01ARNMTchr18

13726728

+SNCAIPchr5

121776324

+


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Fusion Gene ORF analysis for RNMT-SNCAIP

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-3UTRENST00000383314ENST00000504884RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-3UTRENST00000535051ENST00000504884RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-3UTRENST00000543302ENST00000504884RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-3UTRENST00000592764ENST00000504884RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000383314ENST00000261367RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000383314ENST00000261368RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000383314ENST00000379533RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000383314ENST00000379536RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000383314ENST00000379538RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000383314ENST00000414317RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000383314ENST00000503116RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000383314ENST00000542191RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000535051ENST00000261367RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000535051ENST00000261368RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000535051ENST00000379533RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000535051ENST00000379536RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000535051ENST00000379538RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000535051ENST00000414317RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000535051ENST00000503116RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000535051ENST00000542191RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000543302ENST00000261367RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000543302ENST00000261368RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000543302ENST00000379533RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000543302ENST00000379536RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000543302ENST00000379538RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000543302ENST00000414317RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000543302ENST00000503116RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000543302ENST00000542191RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000592764ENST00000261367RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000592764ENST00000261368RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000592764ENST00000379533RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000592764ENST00000379536RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000592764ENST00000379538RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000592764ENST00000414317RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000592764ENST00000503116RNMTchr18

13726728

+SNCAIPchr5

121776324

+
5UTR-5UTRENST00000592764ENST00000542191RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-3UTRENST00000262173ENST00000504884RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-3UTRENST00000589866ENST00000504884RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-3UTRENST00000591922ENST00000504884RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000262173ENST00000261367RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000262173ENST00000261368RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000262173ENST00000379533RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000262173ENST00000379536RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000262173ENST00000379538RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000262173ENST00000414317RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000262173ENST00000503116RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000262173ENST00000542191RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000589866ENST00000261367RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000589866ENST00000261368RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000589866ENST00000379533RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000589866ENST00000379536RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000589866ENST00000379538RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000589866ENST00000414317RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000589866ENST00000503116RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000589866ENST00000542191RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000591922ENST00000261367RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000591922ENST00000261368RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000591922ENST00000379533RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000591922ENST00000379536RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000591922ENST00000379538RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000591922ENST00000414317RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000591922ENST00000503116RNMTchr18

13726728

+SNCAIPchr5

121776324

+
intron-5UTRENST00000591922ENST00000542191RNMTchr18

13726728

+SNCAIPchr5

121776324

+

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 RNMT-SNCAIP


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)
RNMTchr1813726728+SNCAIPchr5121776323+9.68E-060.99999034
RNMTchr1813726728+SNCAIPchr5121776323+9.68E-060.99999034

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 RNMT-SNCAIP


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/:13726728/:121776324)
- 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


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Fusion Gene Sequence for RNMT-SNCAIP


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 RNMT-SNCAIP


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 RNMT-SNCAIP


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 RNMT-SNCAIP


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