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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:TPRA1-MCM2 (FusionGDB2 ID:93440)

Fusion Gene Summary for TPRA1-MCM2

check button Fusion gene summary
Fusion gene informationFusion gene name: TPRA1-MCM2
Fusion gene ID: 93440
HgeneTgene
Gene symbol

TPRA1

MCM2

Gene ID

131601

4176

Gene nametransmembrane protein adipocyte associated 1minichromosome maintenance complex component 7
SynonymsGPR175|TMEM227|TPRA40CDC47|MCM2|P1.1-MCM3|P1CDC47|P85MCM|PNAS146|PPP1R104
Cytomap

3q21.3

7q22.1

Type of geneprotein-codingprotein-coding
Descriptiontransmembrane protein adipocyte-associated 1G protein-coupled receptor 175integral membrane protein GPR175seven transmembrane domain orphan receptortransmembrane domain protein regulated in adipocytes 40 kDatransmembrane protein 227transmembrane proDNA replication licensing factor MCM7CDC47 homologhomolog of S. cerevisiae Cdc47minichromosome maintenance deficient 7protein phosphatase 1, regulatory subunit 104
Modification date2020031320200320
UniProtAcc.

P49736

Ensembl transtripts involved in fusion geneENST00000296210, ENST00000355552, 
ENST00000489960, ENST00000450633, 
ENST00000465915, 		ENST00000265056, 
ENST00000468414, 
Fusion gene scores* DoF score4 X 5 X 3=603 X 4 X 2=24
# samples 54
** MAII scorelog2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/24*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: TPRA1 [Title/Abstract] AND MCM2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTPRA1(127309252)-MCM2(127334704), # samples:1
TPRA1(127309253)-MCM2(127334705), # samples:1
TPRA1(127310733)-MCM2(127334705), # 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

check buttonFusion gene breakpoints across TPRA1 (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 MCM2 (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
ChimerDB4OVTCGA-31-1951-01ATPRA1chr3

127309253

-MCM2chr3

127334705

+
ChimerDB4OVTCGA-31-1951-01ATPRA1chr3

127310733

-MCM2chr3

127334705

+
ChimerDB4OVTCGA-31-1951TPRA1chr3

127309252

-MCM2chr3

127334704

+


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Fusion Gene ORF analysis for TPRA1-MCM2

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-3CDSENST00000296210ENST00000265056TPRA1chr3

127309253

-MCM2chr3

127334705

+
5UTR-3CDSENST00000296210ENST00000265056TPRA1chr3

127309252

-MCM2chr3

127334704

+
5UTR-3CDSENST00000355552ENST00000265056TPRA1chr3

127309253

-MCM2chr3

127334705

+
5UTR-3CDSENST00000355552ENST00000265056TPRA1chr3

127309252

-MCM2chr3

127334704

+
5UTR-3CDSENST00000489960ENST00000265056TPRA1chr3

127309253

-MCM2chr3

127334705

+
5UTR-3CDSENST00000489960ENST00000265056TPRA1chr3

127309252

-MCM2chr3

127334704

+
5UTR-intronENST00000296210ENST00000468414TPRA1chr3

127309253

-MCM2chr3

127334705

+
5UTR-intronENST00000296210ENST00000468414TPRA1chr3

127309252

-MCM2chr3

127334704

+
5UTR-intronENST00000355552ENST00000468414TPRA1chr3

127309253

-MCM2chr3

127334705

+
5UTR-intronENST00000355552ENST00000468414TPRA1chr3

127309252

-MCM2chr3

127334704

+
5UTR-intronENST00000489960ENST00000468414TPRA1chr3

127309253

-MCM2chr3

127334705

+
5UTR-intronENST00000489960ENST00000468414TPRA1chr3

127309252

-MCM2chr3

127334704

+
intron-3CDSENST00000296210ENST00000265056TPRA1chr3

127310733

-MCM2chr3

127334705

+
intron-3CDSENST00000355552ENST00000265056TPRA1chr3

127310733

-MCM2chr3

127334705

+
intron-3CDSENST00000450633ENST00000265056TPRA1chr3

127309253

-MCM2chr3

127334705

+
intron-3CDSENST00000450633ENST00000265056TPRA1chr3

127310733

-MCM2chr3

127334705

+
intron-3CDSENST00000450633ENST00000265056TPRA1chr3

127309252

-MCM2chr3

127334704

+
intron-3CDSENST00000465915ENST00000265056TPRA1chr3

127309253

-MCM2chr3

127334705

+
intron-3CDSENST00000465915ENST00000265056TPRA1chr3

127310733

-MCM2chr3

127334705

+
intron-3CDSENST00000465915ENST00000265056TPRA1chr3

127309252

-MCM2chr3

127334704

+
intron-3CDSENST00000489960ENST00000265056TPRA1chr3

127310733

-MCM2chr3

127334705

+
intron-intronENST00000296210ENST00000468414TPRA1chr3

127310733

-MCM2chr3

127334705

+
intron-intronENST00000355552ENST00000468414TPRA1chr3

127310733

-MCM2chr3

127334705

+
intron-intronENST00000450633ENST00000468414TPRA1chr3

127309253

-MCM2chr3

127334705

+
intron-intronENST00000450633ENST00000468414TPRA1chr3

127310733

-MCM2chr3

127334705

+
intron-intronENST00000450633ENST00000468414TPRA1chr3

127309252

-MCM2chr3

127334704

+
intron-intronENST00000465915ENST00000468414TPRA1chr3

127309253

-MCM2chr3

127334705

+
intron-intronENST00000465915ENST00000468414TPRA1chr3

127310733

-MCM2chr3

127334705

+
intron-intronENST00000465915ENST00000468414TPRA1chr3

127309252

-MCM2chr3

127334704

+
intron-intronENST00000489960ENST00000468414TPRA1chr3

127310733

-MCM2chr3

127334705

+

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 TPRA1-MCM2


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)
TPRA1chr3127309252-MCM2chr3127334704+0.0017673670.9982326
TPRA1chr3127309252-MCM2chr3127334704+0.0017673670.9982326
TPRA1chr3127309252-MCM2chr3127334704+0.0017673670.9982326
TPRA1chr3127309252-MCM2chr3127334704+0.0017673670.9982326

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 TPRA1-MCM2


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/:127309252/:127334704)
- 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
.MCM2

P49736

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: Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative helicase essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells. The active ATPase sites in the MCM2-7 ring are formed through the interaction surfaces of two neighboring subunits such that a critical structure of a conserved arginine finger motif is provided in trans relative to the ATP-binding site of the Walker A box of the adjacent subunit. The six ATPase active sites, however, are likely to contribute differentially to the complex helicase activity. Required for the entry in S phase and for cell division. Plays a role in terminally differentiated hair cells development of the cochlea and induces cells apoptosis. {ECO:0000269|PubMed:26196677, ECO:0000269|PubMed:8175912}.

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 TPRA1-MCM2


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 TPRA1-MCM2


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 TPRA1-MCM2


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 TPRA1-MCM2


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