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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:PMEPA1-RAB6A (FusionGDB2 ID:66621)

Fusion Gene Summary for PMEPA1-RAB6A

check button Fusion gene summary
Fusion gene informationFusion gene name: PMEPA1-RAB6A
Fusion gene ID: 66621
HgeneTgene
Gene symbol

PMEPA1

RAB6A

Gene ID

56937

5870

Gene nameprostate transmembrane protein, androgen induced 1RAB6A, member RAS oncogene family
SynonymsSTAG1|TMEPAIRAB6
Cytomap

20q13.31

11q13.4

Type of geneprotein-codingprotein-coding
Descriptionprotein TMEPAIsolid tumor-associated 1 proteintransmembrane, prostate androgen induced RNAras-related protein Rab-6ARAB6, member RAS oncogene familyRab GTPase
Modification date2020031320200313
UniProtAcc.

RGP1

Ensembl transtripts involved in fusion geneENST00000265626, ENST00000341744, 
ENST00000347215, ENST00000395814, 
ENST00000395816, ENST00000472841, 
ENST00000310653, ENST00000336083, 
ENST00000536566, ENST00000541588, 
Fusion gene scores* DoF score15 X 12 X 5=90020 X 15 X 10=3000
# samples 1729
** MAII scorelog2(17/900*10)=-2.40439025507934
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(29/3000*10)=-3.37083769536831
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PMEPA1 [Title/Abstract] AND RAB6A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPMEPA1(56226891)-RAB6A(73447844), # 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
HgenePMEPA1

GO:0010991

negative regulation of SMAD protein complex assembly

20129061

HgenePMEPA1

GO:0030512

negative regulation of transforming growth factor beta receptor signaling pathway

24627487

HgenePMEPA1

GO:0060394

negative regulation of pathway-restricted SMAD protein phosphorylation

24627487

TgeneRAB6A

GO:0018125

peptidyl-cysteine methylation

11121396

TgeneRAB6A

GO:0034067

protein localization to Golgi apparatus

12447383|18243103


check buttonFusion gene breakpoints across PMEPA1 (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 RAB6A (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/ACB049800PMEPA1chr20

56226891

-RAB6Achr11

73447844

+


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Fusion Gene ORF analysis for PMEPA1-RAB6A

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
intron-intronENST00000265626ENST00000310653PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000265626ENST00000336083PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000265626ENST00000536566PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000265626ENST00000541588PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000341744ENST00000310653PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000341744ENST00000336083PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000341744ENST00000536566PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000341744ENST00000541588PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000347215ENST00000310653PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000347215ENST00000336083PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000347215ENST00000536566PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000347215ENST00000541588PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000395814ENST00000310653PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000395814ENST00000336083PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000395814ENST00000536566PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000395814ENST00000541588PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000395816ENST00000310653PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000395816ENST00000336083PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000395816ENST00000536566PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000395816ENST00000541588PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000472841ENST00000310653PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000472841ENST00000336083PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000472841ENST00000536566PMEPA1chr20

56226891

-RAB6Achr11

73447844

+
intron-intronENST00000472841ENST00000541588PMEPA1chr20

56226891

-RAB6Achr11

73447844

+

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 PMEPA1-RAB6A


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 PMEPA1-RAB6A


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/:56226891/:73447844)
- 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
.RAB6A

RGP1

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}.1748

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 PMEPA1-RAB6A


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 PMEPA1-RAB6A


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 PMEPA1-RAB6A


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 PMEPA1-RAB6A


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