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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:CPEB1-CRTC3 (FusionGDB2 ID:18950)

Fusion Gene Summary for CPEB1-CRTC3

check button Fusion gene summary
Fusion gene informationFusion gene name: CPEB1-CRTC3
Fusion gene ID: 18950
HgeneTgene
Gene symbol

CPEB1

CRTC3

Gene ID

64506

64784

Gene namecytoplasmic polyadenylation element binding protein 1CREB regulated transcription coactivator 3
SynonymsCPE-BP1|CPEB|CPEB-1|h-CPEB|hCPEB-1TORC-3|TORC3
Cytomap

15q25.2

15q26.1

Type of geneprotein-codingprotein-coding
Descriptioncytoplasmic polyadenylation element-binding protein 1CPE-binding protein 1CREB-regulated transcription coactivator 3transducer of regulated CREB protein 3transducer of regulated cAMP response element-binding protein (CREB) 3
Modification date2020032020200313
UniProtAcc

Q9BZB8

Q6UUV7

Ensembl transtripts involved in fusion geneENST00000568128, ENST00000450751, 
ENST00000568757, ENST00000261723, 
ENST00000398591, ENST00000398592, 
ENST00000423133, ENST00000562019, 
ENST00000563519, ENST00000563800, 
ENST00000564522, 		ENST00000558619, 
ENST00000268184, ENST00000560098, 
ENST00000420329, 
Fusion gene scores* DoF score6 X 7 X 2=848 X 11 X 5=440
# samples 610
** MAII scorelog2(6/84*10)=-0.485426827170242
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/440*10)=-2.13750352374993
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CPEB1 [Title/Abstract] AND CRTC3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCPEB1(83315888)-CRTC3(91147617), # samples:2
Anticipated loss of major functional domain due to fusion event.CPEB1-CRTC3 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
CPEB1-CRTC3 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
CPEB1-CRTC3 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
HgeneCPEB1

GO:0032869

cellular response to insulin stimulus

18752464

HgeneCPEB1

GO:0071456

cellular response to hypoxia

18752464

HgeneCPEB1

GO:1900365

positive regulation of mRNA polyadenylation

28383716


check buttonFusion gene breakpoints across CPEB1 (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 CRTC3 (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
ChimerDB4SKCMTCGA-WE-A8ZM-06ACPEB1chr15

83315888

-CRTC3chr15

91147617

+
ChimerDB4SKCMTCGA-WE-A8ZM-06ACPEB1chr15

83316607

-CRTC3chr15

91150610

+


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Fusion Gene ORF analysis for CPEB1-CRTC3

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
5CDS-3UTRENST00000568128ENST00000558619CPEB1chr15

83316607

-CRTC3chr15

91150610

+
5CDS-intronENST00000568128ENST00000268184CPEB1chr15

83316607

-CRTC3chr15

91150610

+
5CDS-intronENST00000568128ENST00000560098CPEB1chr15

83316607

-CRTC3chr15

91150610

+
5UTR-3CDSENST00000450751ENST00000420329CPEB1chr15

83315888

-CRTC3chr15

91147617

+
5UTR-3CDSENST00000568757ENST00000420329CPEB1chr15

83315888

-CRTC3chr15

91147617

+
5UTR-3UTRENST00000450751ENST00000558619CPEB1chr15

83315888

-CRTC3chr15

91147617

+
5UTR-3UTRENST00000568757ENST00000558619CPEB1chr15

83315888

-CRTC3chr15

91147617

+
5UTR-intronENST00000450751ENST00000268184CPEB1chr15

83315888

-CRTC3chr15

91147617

+
5UTR-intronENST00000450751ENST00000560098CPEB1chr15

83315888

-CRTC3chr15

91147617

+
5UTR-intronENST00000568757ENST00000268184CPEB1chr15

83315888

-CRTC3chr15

91147617

+
5UTR-intronENST00000568757ENST00000560098CPEB1chr15

83315888

-CRTC3chr15

91147617

+
Frame-shiftENST00000568128ENST00000420329CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3CDSENST00000261723ENST00000420329CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-3CDSENST00000261723ENST00000420329CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3CDSENST00000398591ENST00000420329CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-3CDSENST00000398591ENST00000420329CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3CDSENST00000398592ENST00000420329CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-3CDSENST00000398592ENST00000420329CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3CDSENST00000423133ENST00000420329CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-3CDSENST00000423133ENST00000420329CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3CDSENST00000450751ENST00000420329CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3CDSENST00000562019ENST00000420329CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-3CDSENST00000562019ENST00000420329CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3CDSENST00000563519ENST00000420329CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-3CDSENST00000563519ENST00000420329CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3CDSENST00000563800ENST00000420329CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-3CDSENST00000563800ENST00000420329CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3CDSENST00000564522ENST00000420329CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-3CDSENST00000564522ENST00000420329CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3CDSENST00000568128ENST00000420329CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-3CDSENST00000568757ENST00000420329CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3UTRENST00000261723ENST00000558619CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-3UTRENST00000261723ENST00000558619CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3UTRENST00000398591ENST00000558619CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-3UTRENST00000398591ENST00000558619CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3UTRENST00000398592ENST00000558619CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-3UTRENST00000398592ENST00000558619CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3UTRENST00000423133ENST00000558619CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-3UTRENST00000423133ENST00000558619CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3UTRENST00000450751ENST00000558619CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3UTRENST00000562019ENST00000558619CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-3UTRENST00000562019ENST00000558619CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3UTRENST00000563519ENST00000558619CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-3UTRENST00000563519ENST00000558619CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3UTRENST00000563800ENST00000558619CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-3UTRENST00000563800ENST00000558619CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3UTRENST00000564522ENST00000558619CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-3UTRENST00000564522ENST00000558619CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-3UTRENST00000568128ENST00000558619CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-3UTRENST00000568757ENST00000558619CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000261723ENST00000268184CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-intronENST00000261723ENST00000268184CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000261723ENST00000560098CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-intronENST00000261723ENST00000560098CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000398591ENST00000268184CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-intronENST00000398591ENST00000268184CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000398591ENST00000560098CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-intronENST00000398591ENST00000560098CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000398592ENST00000268184CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-intronENST00000398592ENST00000268184CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000398592ENST00000560098CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-intronENST00000398592ENST00000560098CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000423133ENST00000268184CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-intronENST00000423133ENST00000268184CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000423133ENST00000560098CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-intronENST00000423133ENST00000560098CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000450751ENST00000268184CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000450751ENST00000560098CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000562019ENST00000268184CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-intronENST00000562019ENST00000268184CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000562019ENST00000560098CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-intronENST00000562019ENST00000560098CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000563519ENST00000268184CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-intronENST00000563519ENST00000268184CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000563519ENST00000560098CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-intronENST00000563519ENST00000560098CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000563800ENST00000268184CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-intronENST00000563800ENST00000268184CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000563800ENST00000560098CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-intronENST00000563800ENST00000560098CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000564522ENST00000268184CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-intronENST00000564522ENST00000268184CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000564522ENST00000560098CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-intronENST00000564522ENST00000560098CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000568128ENST00000268184CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-intronENST00000568128ENST00000560098CPEB1chr15

83315888

-CRTC3chr15

91147617

+
intron-intronENST00000568757ENST00000268184CPEB1chr15

83316607

-CRTC3chr15

91150610

+
intron-intronENST00000568757ENST00000560098CPEB1chr15

83316607

-CRTC3chr15

91150610

+

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 CPEB1-CRTC3


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)
CPEB1chr1583315887-CRTC3chr1591147616+0.095142660.9048574
CPEB1chr1583316606-CRTC3chr1591150609+0.0124871880.98751277
CPEB1chr1583315887-CRTC3chr1591147616+0.095142660.9048574
CPEB1chr1583316606-CRTC3chr1591150609+0.0124871880.98751277

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 CPEB1-CRTC3


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/:83315888/:91147617)
- 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
CPEB1

Q9BZB8

CRTC3

Q6UUV7

FUNCTION: Sequence-specific RNA-binding protein that regulates mRNA cytoplasmic polyadenylation and translation initiation during oocyte maturation, early development and at postsynapse sites of neurons. Binds to the cytoplasmic polyadenylation element (CPE), an uridine-rich sequence element (consensus sequence 5'-UUUUUAU-3') within the mRNA 3'-UTR. RNA binding results in a clear conformational change analogous to the Venus fly trap mechanism (PubMed:24990967). In absence of phosphorylation and in association with TACC3 is also involved as a repressor of translation of CPE-containing mRNA; a repression that is relieved by phosphorylation or degradation (By similarity). Involved in the transport of CPE-containing mRNA to dendrites; those mRNAs may be transported to dendrites in a translationally dormant form and translationally activated at synapses (By similarity). Its interaction with APLP1 promotes local CPE-containing mRNA polyadenylation and translation activation (By similarity). Induces the assembly of stress granules in the absence of stress. Required for cell cycle progression, specifically for prophase entry (PubMed:26398195). {ECO:0000250|UniProtKB:P70166, ECO:0000269|PubMed:15731006, ECO:0000269|PubMed:15966895, ECO:0000269|PubMed:24990967, ECO:0000269|PubMed:26398195}.FUNCTION: Transcriptional coactivator for CREB1 which activates transcription through both consensus and variant cAMP response element (CRE) sites. Acts as a coactivator, in the SIK/TORC signaling pathway, being active when dephosphorylated and acts independently of CREB1 'Ser-133' phosphorylation. Enhances the interaction of CREB1 with TAF4. Regulates the expression of specific CREB-activated genes such as the steroidogenic gene, StAR. Potent coactivator of PPARGC1A and inducer of mitochondrial biogenesis in muscle cells. Also coactivator for TAX activation of the human T-cell leukemia virus type 1 (HTLV-1) long terminal repeats (LTR). {ECO:0000269|PubMed:14506290, ECO:0000269|PubMed:15454081, ECO:0000269|PubMed:15466468, ECO:0000269|PubMed:16817901, ECO:0000269|PubMed:16980408, ECO:0000269|PubMed:17210223, ECO:0000269|PubMed:17644518}.

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 CPEB1-CRTC3


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 CPEB1-CRTC3


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 CPEB1-CRTC3


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 CPEB1-CRTC3


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