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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:PCCB-EPHB1 (FusionGDB2 ID:63170)

Fusion Gene Summary for PCCB-EPHB1

check button Fusion gene summary
Fusion gene informationFusion gene name: PCCB-EPHB1
Fusion gene ID: 63170
HgeneTgene
Gene symbol

PCCB

EPHB1

Gene ID

5096

2047

Gene namepropionyl-CoA carboxylase subunit betaEPH receptor B1
Synonyms-ELK|EPHT2|Hek6|NET
Cytomap

3q22.3

3q22.2

Type of geneprotein-codingprotein-coding
Descriptionpropionyl-CoA carboxylase beta chain, mitochondrialPCCase subunit betapropanoyl-CoA:carbon dioxide ligase subunit betapropionyl CoA carboxylase, beta polypeptidepropionyl Coenzyme A carboxylase, beta polypeptidepropionyl-CoA carboxylase beta subunitephrin type-B receptor 1EK6EPH-like kinase 6eph tyrosine kinase 2neuronally-expressed EPH-related tyrosine kinasesoluble EPHB1 variant 1tyrosine-protein kinase receptor EPH-2
Modification date2020031320200313
UniProtAcc.

P54762

Ensembl transtripts involved in fusion geneENST00000474833, ENST00000251654, 
ENST00000462637, ENST00000466072, 
ENST00000468777, ENST00000469217, 
ENST00000471595, ENST00000478469, 
ENST00000483687, ENST00000490504, 
ENST00000482086, 		ENST00000398015, 
ENST00000488154, ENST00000493838, 
Fusion gene scores* DoF score8 X 9 X 4=2885 X 5 X 3=75
# samples 85
** MAII scorelog2(8/288*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PCCB [Title/Abstract] AND EPHB1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPCCB(135969400)-EPHB1(134825290), # samples:1
Anticipated loss of major functional domain due to fusion event.PCCB-EPHB1 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
PCCB-EPHB1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
PCCB-EPHB1 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
PCCB-EPHB1 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
PCCB-EPHB1 seems lost the major protein functional domain in Tgene partner, which is a kinase due to the frame-shifted ORF.
* 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
TgeneEPHB1

GO:0001525

angiogenesis

9499402

TgeneEPHB1

GO:0031589

cell-substrate adhesion

9430661

TgeneEPHB1

GO:0046328

regulation of JNK cascade

9430661

TgeneEPHB1

GO:0046777

protein autophosphorylation

18034775

TgeneEPHB1

GO:0048013

ephrin receptor signaling pathway

12925710|18034775

TgeneEPHB1

GO:0060326

cell chemotaxis

12925710

TgeneEPHB1

GO:0070372

regulation of ERK1 and ERK2 cascade

12925710|18034775


check buttonFusion gene breakpoints across PCCB (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 EPHB1 (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
ChimerDB4HNSCTCGA-BA-4075-01APCCBchr3

135969400

+EPHB1chr3

134825290

+


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Fusion Gene ORF analysis for PCCB-EPHB1

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-3CDSENST00000474833ENST00000398015PCCBchr3

135969400

+EPHB1chr3

134825290

+
3UTR-3UTRENST00000474833ENST00000488154PCCBchr3

135969400

+EPHB1chr3

134825290

+
3UTR-5UTRENST00000474833ENST00000493838PCCBchr3

135969400

+EPHB1chr3

134825290

+
5CDS-3UTRENST00000251654ENST00000488154PCCBchr3

135969400

+EPHB1chr3

134825290

+
5CDS-3UTRENST00000462637ENST00000488154PCCBchr3

135969400

+EPHB1chr3

134825290

+
5CDS-3UTRENST00000466072ENST00000488154PCCBchr3

135969400

+EPHB1chr3

134825290

+
5CDS-3UTRENST00000468777ENST00000488154PCCBchr3

135969400

+EPHB1chr3

134825290

+
5CDS-3UTRENST00000469217ENST00000488154PCCBchr3

135969400

+EPHB1chr3

134825290

+
5CDS-3UTRENST00000471595ENST00000488154PCCBchr3

135969400

+EPHB1chr3

134825290

+
5CDS-3UTRENST00000478469ENST00000488154PCCBchr3

135969400

+EPHB1chr3

134825290

+
5CDS-3UTRENST00000483687ENST00000488154PCCBchr3

135969400

+EPHB1chr3

134825290

+
5CDS-3UTRENST00000490504ENST00000488154PCCBchr3

135969400

+EPHB1chr3

134825290

+
5CDS-5UTRENST00000251654ENST00000493838PCCBchr3

135969400

+EPHB1chr3

134825290

+
5CDS-5UTRENST00000462637ENST00000493838PCCBchr3

135969400

+EPHB1chr3

134825290

+
5CDS-5UTRENST00000466072ENST00000493838PCCBchr3

135969400

+EPHB1chr3

134825290

+
5CDS-5UTRENST00000468777ENST00000493838PCCBchr3

135969400

+EPHB1chr3

134825290

+
5CDS-5UTRENST00000469217ENST00000493838PCCBchr3

135969400

+EPHB1chr3

134825290

+
5CDS-5UTRENST00000471595ENST00000493838PCCBchr3

135969400

+EPHB1chr3

134825290

+
5CDS-5UTRENST00000478469ENST00000493838PCCBchr3

135969400

+EPHB1chr3

134825290

+
5CDS-5UTRENST00000483687ENST00000493838PCCBchr3

135969400

+EPHB1chr3

134825290

+
5CDS-5UTRENST00000490504ENST00000493838PCCBchr3

135969400

+EPHB1chr3

134825290

+
Frame-shiftENST00000251654ENST00000398015PCCBchr3

135969400

+EPHB1chr3

134825290

+
Frame-shiftENST00000462637ENST00000398015PCCBchr3

135969400

+EPHB1chr3

134825290

+
Frame-shiftENST00000466072ENST00000398015PCCBchr3

135969400

+EPHB1chr3

134825290

+
Frame-shiftENST00000468777ENST00000398015PCCBchr3

135969400

+EPHB1chr3

134825290

+
Frame-shiftENST00000469217ENST00000398015PCCBchr3

135969400

+EPHB1chr3

134825290

+
Frame-shiftENST00000471595ENST00000398015PCCBchr3

135969400

+EPHB1chr3

134825290

+
Frame-shiftENST00000478469ENST00000398015PCCBchr3

135969400

+EPHB1chr3

134825290

+
Frame-shiftENST00000483687ENST00000398015PCCBchr3

135969400

+EPHB1chr3

134825290

+
Frame-shiftENST00000490504ENST00000398015PCCBchr3

135969400

+EPHB1chr3

134825290

+
intron-3CDSENST00000482086ENST00000398015PCCBchr3

135969400

+EPHB1chr3

134825290

+
intron-3UTRENST00000482086ENST00000488154PCCBchr3

135969400

+EPHB1chr3

134825290

+
intron-5UTRENST00000482086ENST00000493838PCCBchr3

135969400

+EPHB1chr3

134825290

+

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 PCCB-EPHB1


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)
PCCBchr3135969400+EPHB1chr3134825289+8.14E-080.9999999
PCCBchr3135969400+EPHB1chr3134825289+8.14E-080.9999999

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 PCCB-EPHB1


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/:135969400/:134825290)
- 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
.EPHB1

P54762

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: Receptor tyrosine kinase which binds promiscuously transmembrane ephrin-B family ligands residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. The signaling pathway downstream of the receptor is referred to as forward signaling while the signaling pathway downstream of the ephrin ligand is referred to as reverse signaling. Cognate/functional ephrin ligands for this receptor include EFNB1, EFNB2 and EFNB3. During nervous system development, regulates retinal axon guidance redirecting ipsilaterally ventrotemporal retinal ganglion cells axons at the optic chiasm midline. This probably requires repulsive interaction with EFNB2. In the adult nervous system together with EFNB3, regulates chemotaxis, proliferation and polarity of the hippocampus neural progenitors. In addition to its role in axon guidance plays also an important redundant role with other ephrin-B receptors in development and maturation of dendritic spines and synapse formation. May also regulate angiogenesis. More generally, may play a role in targeted cell migration and adhesion. Upon activation by EFNB1 and probably other ephrin-B ligands activates the MAPK/ERK and the JNK signaling cascades to regulate cell migration and adhesion respectively. Involved in the maintenance of the pool of satellite cells (muscle stem cells) by promoting their self-renewal and reducing their activation and differentiation (By similarity). {ECO:0000250|UniProtKB:Q8CBF3, ECO:0000269|PubMed:12223469, ECO:0000269|PubMed:12925710, ECO:0000269|PubMed:18034775, ECO:0000269|PubMed:9430661, ECO:0000269|PubMed:9499402}.

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 PCCB-EPHB1


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 PCCB-EPHB1


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 PCCB-EPHB1


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 PCCB-EPHB1


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