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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:COL6A2-ELK3 (FusionGDB2 ID:HG1292TG2004)

Fusion Gene Summary for COL6A2-ELK3

check button Fusion gene summary
Fusion gene informationFusion gene name: COL6A2-ELK3
Fusion gene ID: hg1292tg2004
HgeneTgene
Gene symbol

COL6A2

ELK3

Gene ID

1292

2004

Gene namecollagen type VI alpha 2 chainETS transcription factor ELK3
SynonymsBTHLM1|PP3610|UCMD1ERP|NET|SAP-2|SAP2
Cytomap('COL6A2')('ELK3')

21q22.3

12q23.1

Type of geneprotein-codingprotein-coding
Descriptioncollagen alpha-2(VI) chaincollagen VI, alpha-2 polypeptidecollagen, type VI, alpha 2epididymis secretory sperm binding proteinhuman mRNA for collagen VI alpha-2 C-terminal globular domainETS domain-containing protein Elk-3ELK3, ETS transcription factorELK3, ETS-domain protein (SRF accessory protein 2)ETS-related protein ERPETS-related protein NETSRF accessory protein 2serum response factor accessory protein 2
Modification date2020032820200313
UniProtAcc

P12110

.
Ensembl transtripts involved in fusion geneENST00000300527, ENST00000310645, 
ENST00000357838, ENST00000397763, 
ENST00000409416, ENST00000460886, 
Fusion gene scores* DoF score13 X 9 X 8=93624 X 8 X 11=2112
# samples 1322
** MAII scorelog2(13/936*10)=-2.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(22/2112*10)=-3.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: COL6A2 [Title/Abstract] AND ELK3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCOL6A2(47552763)-ELK3(96588323), # 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
TgeneELK3

GO:0045892

negative regulation of transcription, DNA-templated

12933792

TgeneELK3

GO:0045944

positive regulation of transcription by RNA polymerase II

12788937



check button Fusion gene information
* 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-CR-7382-01ACOL6A2chr21

47552763

-ELK3chr12

96588323

+


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Fusion Gene ORF analysis for COL6A2-ELK3

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-5UTRENST00000300527ENST00000228741COL6A2chr21

47552763

-ELK3chr12

96588323

+
5CDS-5UTRENST00000300527ENST00000552142COL6A2chr21

47552763

-ELK3chr12

96588323

+
5CDS-intronENST00000300527ENST00000549529COL6A2chr21

47552763

-ELK3chr12

96588323

+
intron-5UTRENST00000310645ENST00000228741COL6A2chr21

47552763

-ELK3chr12

96588323

+
intron-5UTRENST00000310645ENST00000552142COL6A2chr21

47552763

-ELK3chr12

96588323

+
intron-5UTRENST00000357838ENST00000228741COL6A2chr21

47552763

-ELK3chr12

96588323

+
intron-5UTRENST00000357838ENST00000552142COL6A2chr21

47552763

-ELK3chr12

96588323

+
intron-5UTRENST00000397763ENST00000228741COL6A2chr21

47552763

-ELK3chr12

96588323

+
intron-5UTRENST00000397763ENST00000552142COL6A2chr21

47552763

-ELK3chr12

96588323

+
intron-5UTRENST00000409416ENST00000228741COL6A2chr21

47552763

-ELK3chr12

96588323

+
intron-5UTRENST00000409416ENST00000552142COL6A2chr21

47552763

-ELK3chr12

96588323

+
intron-5UTRENST00000460886ENST00000228741COL6A2chr21

47552763

-ELK3chr12

96588323

+
intron-5UTRENST00000460886ENST00000552142COL6A2chr21

47552763

-ELK3chr12

96588323

+
intron-intronENST00000310645ENST00000549529COL6A2chr21

47552763

-ELK3chr12

96588323

+
intron-intronENST00000357838ENST00000549529COL6A2chr21

47552763

-ELK3chr12

96588323

+
intron-intronENST00000397763ENST00000549529COL6A2chr21

47552763

-ELK3chr12

96588323

+
intron-intronENST00000409416ENST00000549529COL6A2chr21

47552763

-ELK3chr12

96588323

+
intron-intronENST00000460886ENST00000549529COL6A2chr21

47552763

-ELK3chr12

96588323

+

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 COL6A2-ELK3


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)


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Fusion Protein Features for COL6A2-ELK3


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/:47552763/:96588323)
- 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
COL6A2

P12110

.
FUNCTION: Collagen VI acts as a cell-binding protein.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}.

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 COL6A2-ELK3


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 COL6A2-ELK3


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 COL6A2-ELK3


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 COL6A2-ELK3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCOL6A2C0410179Ullrich congenital muscular dystrophy 15CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCOL6A2C1834674BETHLEM MYOPATHY 15CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCOL6A2C0023893Liver Cirrhosis, Experimental1CTD_human
HgeneCOL6A2C0029408Degenerative polyarthritis1CTD_human
HgeneCOL6A2C0086743Osteoarthrosis Deformans1CTD_human
HgeneCOL6A2C1611706Myosclerosis1ORPHANET
HgeneCOL6A2C1850671Myosclerosis, Autosomal Recessive1CTD_human;GENOMICS_ENGLAND
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC1135196Heart Failure, Diastolic1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC4704874Mammary Carcinoma, Human1CTD_human