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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:PEX7-MED23 (FusionGDB2 ID:64388)

Fusion Gene Summary for PEX7-MED23

check button Fusion gene summary
Fusion gene informationFusion gene name: PEX7-MED23
Fusion gene ID: 64388
HgeneTgene
Gene symbol

PEX7

MED23

Gene ID

5191

9439

Gene nameperoxisomal biogenesis factor 7mediator complex subunit 23
SynonymsPBD9B|PTS2R|RCDP1|RDARC130|CRSP130|CRSP133|CRSP3|DRIP130|MRT18|SUR-2|SUR2
Cytomap

6q23.3

6q23.2

Type of geneprotein-codingprotein-coding
Descriptionperoxisomal biogenesis factor 7PTS2 receptorperoxin-7peroxisomal PTS2 receptorperoxisomal targeting signal 2 receptorperoxisome targeting signal 2 receptormediator of RNA polymerase II transcription subunit 23130 kDa transcriptional co-activator133 kDa transcriptional co-activatoractivator-recruited cofactor 130 kDa componentcofactor required for Sp1 transcriptional activation subunit 3mental retardati
Modification date2020031320200313
UniProtAcc.

Q9ULK4

Ensembl transtripts involved in fusion geneENST00000541292, ENST00000318471, 
ENST00000367756, 		ENST00000354577, 
ENST00000368053, ENST00000368058, 
ENST00000368060, ENST00000368068, 
ENST00000403834, ENST00000479213, 
ENST00000539158, ENST00000540546, 
ENST00000545957, 
Fusion gene scores* DoF score5 X 5 X 4=1004 X 6 X 3=72
# samples 56
** MAII scorelog2(5/100*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/72*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PEX7 [Title/Abstract] AND MED23 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPEX7(137219379)-MED23(131895435), # 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
HgenePEX7

GO:0016558

protein import into peroxisome matrix

9090381

TgeneMED23

GO:0006355

regulation of transcription, DNA-templated

9989412


check buttonFusion gene breakpoints across PEX7 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across MED23 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4BRCATCGA-B6-A0IQ-01APEX7chr6

137219379

-MED23chr6

131895435

-
ChimerDB4BRCATCGA-B6-A0IQ-01APEX7chr6

137219379

+MED23chr6

131895435

-


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Fusion Gene ORF analysis for PEX7-MED23

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
3UTR-3CDSENST00000541292ENST00000354577PEX7chr6

137219379

+MED23chr6

131895435

-
3UTR-intronENST00000541292ENST00000368053PEX7chr6

137219379

+MED23chr6

131895435

-
3UTR-intronENST00000541292ENST00000368058PEX7chr6

137219379

+MED23chr6

131895435

-
3UTR-intronENST00000541292ENST00000368060PEX7chr6

137219379

+MED23chr6

131895435

-
3UTR-intronENST00000541292ENST00000368068PEX7chr6

137219379

+MED23chr6

131895435

-
3UTR-intronENST00000541292ENST00000403834PEX7chr6

137219379

+MED23chr6

131895435

-
3UTR-intronENST00000541292ENST00000479213PEX7chr6

137219379

+MED23chr6

131895435

-
3UTR-intronENST00000541292ENST00000539158PEX7chr6

137219379

+MED23chr6

131895435

-
3UTR-intronENST00000541292ENST00000540546PEX7chr6

137219379

+MED23chr6

131895435

-
3UTR-intronENST00000541292ENST00000545957PEX7chr6

137219379

+MED23chr6

131895435

-
5CDS-intronENST00000318471ENST00000368053PEX7chr6

137219379

+MED23chr6

131895435

-
5CDS-intronENST00000318471ENST00000368058PEX7chr6

137219379

+MED23chr6

131895435

-
5CDS-intronENST00000318471ENST00000368060PEX7chr6

137219379

+MED23chr6

131895435

-
5CDS-intronENST00000318471ENST00000368068PEX7chr6

137219379

+MED23chr6

131895435

-
5CDS-intronENST00000318471ENST00000403834PEX7chr6

137219379

+MED23chr6

131895435

-
5CDS-intronENST00000318471ENST00000479213PEX7chr6

137219379

+MED23chr6

131895435

-
5CDS-intronENST00000318471ENST00000539158PEX7chr6

137219379

+MED23chr6

131895435

-
5CDS-intronENST00000318471ENST00000540546PEX7chr6

137219379

+MED23chr6

131895435

-
5CDS-intronENST00000318471ENST00000545957PEX7chr6

137219379

+MED23chr6

131895435

-
In-frameENST00000318471ENST00000354577PEX7chr6

137219379

+MED23chr6

131895435

-
intron-3CDSENST00000367756ENST00000354577PEX7chr6

137219379

+MED23chr6

131895435

-
intron-intronENST00000367756ENST00000368053PEX7chr6

137219379

+MED23chr6

131895435

-
intron-intronENST00000367756ENST00000368058PEX7chr6

137219379

+MED23chr6

131895435

-
intron-intronENST00000367756ENST00000368060PEX7chr6

137219379

+MED23chr6

131895435

-
intron-intronENST00000367756ENST00000368068PEX7chr6

137219379

+MED23chr6

131895435

-
intron-intronENST00000367756ENST00000403834PEX7chr6

137219379

+MED23chr6

131895435

-
intron-intronENST00000367756ENST00000479213PEX7chr6

137219379

+MED23chr6

131895435

-
intron-intronENST00000367756ENST00000539158PEX7chr6

137219379

+MED23chr6

131895435

-
intron-intronENST00000367756ENST00000540546PEX7chr6

137219379

+MED23chr6

131895435

-
intron-intronENST00000367756ENST00000545957PEX7chr6

137219379

+MED23chr6

131895435

-

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)
ENST00000318471PEX7chr6137219379+ENST00000354577MED23chr6131895435-131498481986301

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
ENST00000318471ENST00000354577PEX7chr6137219379+MED23chr6131895435-0.021451890.97854817

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Fusion Genomic Features for PEX7-MED23


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.
genomic feature

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 PEX7-MED23


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/chr6:137219379/chr6:131895435)
- 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
.MED23

Q9ULK4

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: Required for transcriptional activation subsequent to the assembly of the pre-initiation complex (By similarity). Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional pre-initiation complex with RNA polymerase II and the general transcription factors. Required for transcriptional activation by adenovirus E1A protein. Required for ELK1-dependent transcriptional activation in response to activated Ras signaling. {ECO:0000250, ECO:0000269|PubMed:10353252, ECO:0000269|PubMed:14759369, ECO:0000269|PubMed:16595664}.

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
HgenePEX7chr6:137219379chr6:131895435ENST00000318471+910109_141301324.0RepeatNote=WD 2
HgenePEX7chr6:137219379chr6:131895435ENST00000318471+910153_184301324.0RepeatNote=WD 3
HgenePEX7chr6:137219379chr6:131895435ENST00000318471+910196_227301324.0RepeatNote=WD 4
HgenePEX7chr6:137219379chr6:131895435ENST00000318471+910240_271301324.0RepeatNote=WD 5
HgenePEX7chr6:137219379chr6:131895435ENST00000318471+91065_96301324.0RepeatNote=WD 1

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePEX7chr6:137219379chr6:131895435ENST00000318471+910284_315301324.0RepeatNote=WD 6


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Fusion Gene Sequence for PEX7-MED23


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.
>64388_64388_1_PEX7-MED23_PEX7_chr6_137219379_ENST00000318471_MED23_chr6_131895435_ENST00000354577_length(transcript)=1314nt_BP=984nt
TCTCTCTAACCGCGCCAGTGTGCCTCCGACTCGGAACGGCTTCCGCGGCCGGGGCAGCGAGGGCCGGGGGCGGCGGGCGGGATGAGTGCG
GTGTGCGGTGGAGCGGCGCGGATGCTGCGGACGCCGGGACGCCACGGCTACGCCGCCGAGTTCTCCCCGTACCTGCCGGGCCGCCTGGCC
TGCGCCACCGCGCAGCACTACGGCATCGCGGGCTGTGGAACCCTACTAATATTGGATCCAGATGAAGCTGGGCTAAGGCTTTTTAGAAGC
TTTGACTGGAATGATGGTTTGTTTGATGTGACTTGGAGTGAGAACAACGAACATGTCCTCATCACCTGTAGTGGCGATGGCTCGCTGCAG
CTCTGGGACACTGCCAAAGCTGCAGGGCCACTGCAAGTCTATAAAGAACACGCTCAGGAGGTGTATAGTGTTGATTGGAGCCAAACCAGA
GGTGAACAGCTTGTGGTGTCTGGCTCATGGGATCAAACTGTCAAATTGTGGGATCCAACTGTTGGAAAGTCTCTGTGCACCTTTAGAGGC
CATGAAAGTATTATTTATAGCACAATCTGGTCTCCCCACATCCCTGGTTGTTTTGCTTCAGCCTCAGGTGATCAGACTCTGAGAATATGG
GATGTGAAGGCAGCAGGAGTAAGAATCGTGATTCCTGCACATCAGGCAGAAATCTTGAGTTGTGACTGGTGTAAATACAATGAGAATTTG
CTGGTGACCGGGGCGGTTGACTGTAGTTTGAGAGGCTGGGACTTAAGGAATGTACGACAACCAGTGTTTGAACTTCTTGGTCATACCTAT
GCTATTAGGAGGGTGAAATTTTCACCATTTCATGCTTCTGTGCTGGCCTCTTGCTCGTATGATTTTACTGTAAGATTCTGGAACTTTTCA
AAGCCTGACTCTCTTCTTGAAACAGTGGAGCATCATACAGAGTTTACTTGTGGTTTAGACTTCAGTCTTCAGAGCCCCACTCAGTAAAAA
GTCAGAGTACACAGCAAGGGTTCCAAATTAAGAGGAAGCAAAACGCTGCCCAGATCCTGAGAAACCTGGAGAAAATCAACCTTAGTAGTT
TCAACTCATACATTGTCTTGTTTGATTTTGTTCTTTGTTTTTTATCCTCTTTAAGCACAGATGCGTGTTGAAGTCTAAGGTGTTCTGTCA
TCACACTCTCTTTACTAGAATAAGTGTGCCCAGGCAGAAAAAAAAGTGTATTCAATGTTGCTGGCATGTGTGGATTCACAGCTCGTGGCT

>64388_64388_1_PEX7-MED23_PEX7_chr6_137219379_ENST00000318471_MED23_chr6_131895435_ENST00000354577_length(amino acids)=301AA_BP=
MSAVCGGAARMLRTPGRHGYAAEFSPYLPGRLACATAQHYGIAGCGTLLILDPDEAGLRLFRSFDWNDGLFDVTWSENNEHVLITCSGDG
SLQLWDTAKAAGPLQVYKEHAQEVYSVDWSQTRGEQLVVSGSWDQTVKLWDPTVGKSLCTFRGHESIIYSTIWSPHIPGCFASASGDQTL
RIWDVKAAGVRIVIPAHQAEILSCDWCKYNENLLVTGAVDCSLRGWDLRNVRQPVFELLGHTYAIRRVKFSPFHASVLASCSYDFTVRFW

--------------------------------------------------------------

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Fusion Gene PPI Analysis for PEX7-MED23


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 PEX7-MED23


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 PEX7-MED23


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