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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:SMG5-CCT3 (FusionGDB2 ID:84107)

Fusion Gene Summary for SMG5-CCT3

check button Fusion gene summary
Fusion gene informationFusion gene name: SMG5-CCT3
Fusion gene ID: 84107
HgeneTgene
Gene symbol

SMG5

CCT3

Gene ID

23381

7203

Gene nameSMG5 nonsense mediated mRNA decay factorchaperonin containing TCP1 subunit 3
SynonymsEST1B|LPTS-RP1|LPTSRP1|SMG-5CCT-gamma|CCTG|PIG48|TCP-1-gamma|TRIC5
Cytomap

1q22

1q22

Type of geneprotein-codingprotein-coding
Descriptionprotein SMG5EST1 telomerase component homolog BEST1-like protein BEst1p-like protein BLPTS interacting proteinever shorter telomeres 1Bsmg-5 homolog, nonsense mediated mRNA decay factorT-complex protein 1 subunit gammaT-complex protein 1, gamma subunitTCP1 (t-complex-1) ring complex, polypeptide 5chaperonin containing TCP1, subunit 3 (gamma)hTRiC5
Modification date2020031320200327
UniProtAcc.

P49368

Ensembl transtripts involved in fusion geneENST00000361813, ENST00000368267, 
ENST00000489907, 		ENST00000368256, 
ENST00000295688, ENST00000368259, 
ENST00000368261, ENST00000472765, 
Fusion gene scores* DoF score11 X 13 X 4=57217 X 9 X 10=1530
# samples 1318
** MAII scorelog2(13/572*10)=-2.13750352374993
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(18/1530*10)=-3.08746284125034
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SMG5 [Title/Abstract] AND CCT3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSMG5(156228795)-CCT3(156288808), # samples:2
SMG5(156228796)-CCT3(156288808), # samples:2
CCT3(156307944)-SMG5(156220787), # samples:1
Anticipated loss of major functional domain due to fusion event.CCT3-SMG5 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
CCT3-SMG5 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CCT3-SMG5 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
CCT3-SMG5 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
SMG5-CCT3 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
SMG5-CCT3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
SMG5-CCT3 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
SMG5-CCT3 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

check buttonFusion gene breakpoints across SMG5 (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 CCT3 (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
ChimerDB4ESCATCGA-L5-A8NISMG5chr1

156230241

-CCT3chr1

156290816

-
ChimerDB4ESCATCGA-L5-A8NISMG5chr1

156230242

-CCT3chr1

156290816

-
ChimerDB4ESCATCGA-Z6-AAPN-01ASMG5chr1

156228796

-CCT3chr1

156288808

-
ChimerDB4ESCATCGA-Z6-AAPNSMG5chr1

156228795

-CCT3chr1

156288808

-
ChimerDB4ESCATCGA-Z6-AAPNSMG5chr1

156228796

-CCT3chr1

156288808

-


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Fusion Gene ORF analysis for SMG5-CCT3

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-intronENST00000361813ENST00000368256SMG5chr1

156230241

-CCT3chr1

156290816

-
5CDS-intronENST00000361813ENST00000368256SMG5chr1

156230242

-CCT3chr1

156290816

-
5CDS-intronENST00000361813ENST00000368256SMG5chr1

156228795

-CCT3chr1

156288808

-
5CDS-intronENST00000361813ENST00000368256SMG5chr1

156228796

-CCT3chr1

156288808

-
Frame-shiftENST00000361813ENST00000295688SMG5chr1

156230241

-CCT3chr1

156290816

-
Frame-shiftENST00000361813ENST00000295688SMG5chr1

156230242

-CCT3chr1

156290816

-
Frame-shiftENST00000361813ENST00000368259SMG5chr1

156230241

-CCT3chr1

156290816

-
Frame-shiftENST00000361813ENST00000368259SMG5chr1

156230242

-CCT3chr1

156290816

-
Frame-shiftENST00000361813ENST00000368261SMG5chr1

156230241

-CCT3chr1

156290816

-
Frame-shiftENST00000361813ENST00000368261SMG5chr1

156230242

-CCT3chr1

156290816

-
Frame-shiftENST00000361813ENST00000472765SMG5chr1

156230241

-CCT3chr1

156290816

-
Frame-shiftENST00000361813ENST00000472765SMG5chr1

156230242

-CCT3chr1

156290816

-
In-frameENST00000361813ENST00000295688SMG5chr1

156228795

-CCT3chr1

156288808

-
In-frameENST00000361813ENST00000295688SMG5chr1

156228796

-CCT3chr1

156288808

-
In-frameENST00000361813ENST00000368259SMG5chr1

156228795

-CCT3chr1

156288808

-
In-frameENST00000361813ENST00000368259SMG5chr1

156228796

-CCT3chr1

156288808

-
In-frameENST00000361813ENST00000368261SMG5chr1

156228795

-CCT3chr1

156288808

-
In-frameENST00000361813ENST00000368261SMG5chr1

156228796

-CCT3chr1

156288808

-
In-frameENST00000361813ENST00000472765SMG5chr1

156228795

-CCT3chr1

156288808

-
In-frameENST00000361813ENST00000472765SMG5chr1

156228796

-CCT3chr1

156288808

-
intron-3CDSENST00000368267ENST00000295688SMG5chr1

156230241

-CCT3chr1

156290816

-
intron-3CDSENST00000368267ENST00000295688SMG5chr1

156230242

-CCT3chr1

156290816

-
intron-3CDSENST00000368267ENST00000295688SMG5chr1

156228795

-CCT3chr1

156288808

-
intron-3CDSENST00000368267ENST00000295688SMG5chr1

156228796

-CCT3chr1

156288808

-
intron-3CDSENST00000368267ENST00000368259SMG5chr1

156230241

-CCT3chr1

156290816

-
intron-3CDSENST00000368267ENST00000368259SMG5chr1

156230242

-CCT3chr1

156290816

-
intron-3CDSENST00000368267ENST00000368259SMG5chr1

156228795

-CCT3chr1

156288808

-
intron-3CDSENST00000368267ENST00000368259SMG5chr1

156228796

-CCT3chr1

156288808

-
intron-3CDSENST00000368267ENST00000368261SMG5chr1

156230241

-CCT3chr1

156290816

-
intron-3CDSENST00000368267ENST00000368261SMG5chr1

156230242

-CCT3chr1

156290816

-
intron-3CDSENST00000368267ENST00000368261SMG5chr1

156228795

-CCT3chr1

156288808

-
intron-3CDSENST00000368267ENST00000368261SMG5chr1

156228796

-CCT3chr1

156288808

-
intron-3CDSENST00000368267ENST00000472765SMG5chr1

156230241

-CCT3chr1

156290816

-
intron-3CDSENST00000368267ENST00000472765SMG5chr1

156230242

-CCT3chr1

156290816

-
intron-3CDSENST00000368267ENST00000472765SMG5chr1

156228795

-CCT3chr1

156288808

-
intron-3CDSENST00000368267ENST00000472765SMG5chr1

156228796

-CCT3chr1

156288808

-
intron-3CDSENST00000489907ENST00000295688SMG5chr1

156230241

-CCT3chr1

156290816

-
intron-3CDSENST00000489907ENST00000295688SMG5chr1

156230242

-CCT3chr1

156290816

-
intron-3CDSENST00000489907ENST00000295688SMG5chr1

156228795

-CCT3chr1

156288808

-
intron-3CDSENST00000489907ENST00000295688SMG5chr1

156228796

-CCT3chr1

156288808

-
intron-3CDSENST00000489907ENST00000368259SMG5chr1

156230241

-CCT3chr1

156290816

-
intron-3CDSENST00000489907ENST00000368259SMG5chr1

156230242

-CCT3chr1

156290816

-
intron-3CDSENST00000489907ENST00000368259SMG5chr1

156228795

-CCT3chr1

156288808

-
intron-3CDSENST00000489907ENST00000368259SMG5chr1

156228796

-CCT3chr1

156288808

-
intron-3CDSENST00000489907ENST00000368261SMG5chr1

156230241

-CCT3chr1

156290816

-
intron-3CDSENST00000489907ENST00000368261SMG5chr1

156230242

-CCT3chr1

156290816

-
intron-3CDSENST00000489907ENST00000368261SMG5chr1

156228795

-CCT3chr1

156288808

-
intron-3CDSENST00000489907ENST00000368261SMG5chr1

156228796

-CCT3chr1

156288808

-
intron-3CDSENST00000489907ENST00000472765SMG5chr1

156230241

-CCT3chr1

156290816

-
intron-3CDSENST00000489907ENST00000472765SMG5chr1

156230242

-CCT3chr1

156290816

-
intron-3CDSENST00000489907ENST00000472765SMG5chr1

156228795

-CCT3chr1

156288808

-
intron-3CDSENST00000489907ENST00000472765SMG5chr1

156228796

-CCT3chr1

156288808

-
intron-intronENST00000368267ENST00000368256SMG5chr1

156230241

-CCT3chr1

156290816

-
intron-intronENST00000368267ENST00000368256SMG5chr1

156230242

-CCT3chr1

156290816

-
intron-intronENST00000368267ENST00000368256SMG5chr1

156228795

-CCT3chr1

156288808

-
intron-intronENST00000368267ENST00000368256SMG5chr1

156228796

-CCT3chr1

156288808

-
intron-intronENST00000489907ENST00000368256SMG5chr1

156230241

-CCT3chr1

156290816

-
intron-intronENST00000489907ENST00000368256SMG5chr1

156230242

-CCT3chr1

156290816

-
intron-intronENST00000489907ENST00000368256SMG5chr1

156228795

-CCT3chr1

156288808

-
intron-intronENST00000489907ENST00000368256SMG5chr1

156228796

-CCT3chr1

156288808

-

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 SMG5-CCT3


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 SMG5-CCT3


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/chr1:156228795/chr1:156288808)
- 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
.CCT3

P49368

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: Component of the chaperonin-containing T-complex (TRiC), a molecular chaperone complex that assists the folding of proteins upon ATP hydrolysis (PubMed:25467444). The TRiC complex mediates the folding of WRAP53/TCAB1, thereby regulating telomere maintenance (PubMed:25467444). As part of the TRiC complex may play a role in the assembly of BBSome, a complex involved in ciliogenesis regulating transports vesicles to the cilia (PubMed:20080638). The TRiC complex plays a role in the folding of actin and tubulin (Probable). {ECO:0000269|PubMed:20080638, ECO:0000269|PubMed:25467444, ECO:0000305}.

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
HgeneSMG5chr1:156228795chr1:156288808ENST00000361813-1622460_4638141017.0Compositional biasNote=Poly-Arg
HgeneSMG5chr1:156228795chr1:156288808ENST00000361813-1622529_5328141017.0Compositional biasNote=Poly-Glu
HgeneSMG5chr1:156228796chr1:156288808ENST00000361813-1622460_4638141017.0Compositional biasNote=Poly-Arg
HgeneSMG5chr1:156228796chr1:156288808ENST00000361813-1622529_5328141017.0Compositional biasNote=Poly-Glu

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSMG5chr1:156228795chr1:156288808ENST00000361813-1622798_8418141017.0Coiled coilOntology_term=ECO:0000255
HgeneSMG5chr1:156228796chr1:156288808ENST00000361813-1622798_8418141017.0Coiled coilOntology_term=ECO:0000255
HgeneSMG5chr1:156228795chr1:156288808ENST00000361813-1622872_9958141017.0DomainNote=PINc
HgeneSMG5chr1:156228796chr1:156288808ENST00000361813-1622872_9958141017.0DomainNote=PINc


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Fusion Gene Sequence for SMG5-CCT3


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 SMG5-CCT3


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 SMG5-CCT3


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 SMG5-CCT3


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