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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:COL3A1-COL6A3 (FusionGDB2 ID:HG1281TG1293)

Fusion Gene Summary for COL3A1-COL6A3

check button Fusion gene summary
Fusion gene informationFusion gene name: COL3A1-COL6A3
Fusion gene ID: hg1281tg1293
HgeneTgene
Gene symbol

COL3A1

COL6A3

Gene ID

1281

1293

Gene namecollagen type III alpha 1 chaincollagen type VI alpha 3 chain
SynonymsEDS4A|EDSVASC|PMGEDSVBTHLM1|DYT27|UCMD1
Cytomap('COL3A1')('COL6A3')

2q32.2

2q37.3

Type of geneprotein-codingprotein-coding
Descriptioncollagen alpha-1(III) chainEhlers-Danlos syndrome type IV, autosomal dominantalpha-1 type III collagenalpha1 (III) collagencollagen, fetalcollagen, type III, alpha 1collagen alpha-3(VI) chaincollagen VI, alpha-3 polypeptidecollagen, type VI, alpha 3epididymis secretory sperm binding protein
Modification date2020031320200328
UniProtAcc

P02461

P12111

Ensembl transtripts involved in fusion geneENST00000304636, ENST00000317840, 
Fusion gene scores* DoF score46 X 40 X 15=2760013 X 13 X 4=676
# samples 5613
** MAII scorelog2(56/27600*10)=-5.62309762960793
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/676*10)=-2.37851162325373
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: COL3A1 [Title/Abstract] AND COL6A3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCOL3A1(189876582)-COL6A3(238245123), # 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
HgeneCOL3A1

GO:0007160

cell-matrix adhesion

16912226

HgeneCOL3A1

GO:0007179

transforming growth factor beta receptor signaling pathway

16360482

HgeneCOL3A1

GO:0009314

response to radiation

14736764

HgeneCOL3A1

GO:0018149

peptide cross-linking

16754721

HgeneCOL3A1

GO:0034097

response to cytokine

9076960|16360482

HgeneCOL3A1

GO:0042060

wound healing

1466622



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
ChiTaRS5.0N/AAA055353COL3A1chr2

189876582

-COL6A3chr2

238245123

+


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Fusion Gene ORF analysis for COL3A1-COL6A3

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-3CDSENST00000304636ENST00000295550COL3A1chr2

189876582

-COL6A3chr2

238245123

+
3UTR-3CDSENST00000304636ENST00000346358COL3A1chr2

189876582

-COL6A3chr2

238245123

+
3UTR-3CDSENST00000304636ENST00000347401COL3A1chr2

189876582

-COL6A3chr2

238245123

+
3UTR-3CDSENST00000304636ENST00000353578COL3A1chr2

189876582

-COL6A3chr2

238245123

+
3UTR-3CDSENST00000304636ENST00000409809COL3A1chr2

189876582

-COL6A3chr2

238245123

+
3UTR-3CDSENST00000304636ENST00000472056COL3A1chr2

189876582

-COL6A3chr2

238245123

+
3UTR-3CDSENST00000317840ENST00000295550COL3A1chr2

189876582

-COL6A3chr2

238245123

+
3UTR-3CDSENST00000317840ENST00000346358COL3A1chr2

189876582

-COL6A3chr2

238245123

+
3UTR-3CDSENST00000317840ENST00000347401COL3A1chr2

189876582

-COL6A3chr2

238245123

+
3UTR-3CDSENST00000317840ENST00000353578COL3A1chr2

189876582

-COL6A3chr2

238245123

+
3UTR-3CDSENST00000317840ENST00000409809COL3A1chr2

189876582

-COL6A3chr2

238245123

+
3UTR-3CDSENST00000317840ENST00000472056COL3A1chr2

189876582

-COL6A3chr2

238245123

+
3UTR-intronENST00000304636ENST00000392003COL3A1chr2

189876582

-COL6A3chr2

238245123

+
3UTR-intronENST00000304636ENST00000392004COL3A1chr2

189876582

-COL6A3chr2

238245123

+
3UTR-intronENST00000304636ENST00000473258COL3A1chr2

189876582

-COL6A3chr2

238245123

+
3UTR-intronENST00000317840ENST00000392003COL3A1chr2

189876582

-COL6A3chr2

238245123

+
3UTR-intronENST00000317840ENST00000392004COL3A1chr2

189876582

-COL6A3chr2

238245123

+
3UTR-intronENST00000317840ENST00000473258COL3A1chr2

189876582

-COL6A3chr2

238245123

+

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 COL3A1-COL6A3


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 COL3A1-COL6A3


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/:189876582/:238245123)
- 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
COL3A1

P02461

COL6A3

P12111

FUNCTION: Collagen type III occurs in most soft connective tissues along with type I collagen. Involved in regulation of cortical development. Is the major ligand of ADGRG1 in the developing brain and binding to ADGRG1 inhibits neuronal migration and activates the RhoA pathway by coupling ADGRG1 to GNA13 and possibly GNA12.FUNCTION: Collagen VI acts as a cell-binding protein.

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 COL3A1-COL6A3


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 COL3A1-COL6A3


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 COL3A1-COL6A3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneCOL3A1P02461DB00048Collagenase clostridium histolyticumBinderBiotechApproved|Investigational

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Related Diseases for COL3A1-COL6A3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCOL3A1C0268338Ehlers-Danlos Syndrome, Type IV43CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCOL3A1C4707243Familial thoracic aortic aneurysm and aortic dissection10CLINGEN;GENOMICS_ENGLAND
HgeneCOL3A1C0023890Liver Cirrhosis5CTD_human
HgeneCOL3A1C0239946Fibrosis, Liver5CTD_human
HgeneCOL3A1C0023893Liver Cirrhosis, Experimental2CTD_human
HgeneCOL3A1C0162871Aortic Aneurysm, Abdominal2ORPHANET
HgeneCOL3A1C1853365AORTIC ANEURYSM, FAMILIAL ABDOMINAL 12ORPHANET
HgeneCOL3A1C2697932Loeys-Dietz Syndrome2GENOMICS_ENGLAND
HgeneCOL3A1C0003504Aortic Valve Insufficiency1CTD_human
HgeneCOL3A1C0005398Cholestasis, Extrahepatic1CTD_human
HgeneCOL3A1C0015695Fatty Liver1CTD_human
HgeneCOL3A1C0016059Fibrosis1CTD_human
HgeneCOL3A1C0019193Hepatitis, Toxic1CTD_human
HgeneCOL3A1C0020443Hypercholesterolemia1CTD_human
HgeneCOL3A1C0020456Hyperglycemia1CTD_human
HgeneCOL3A1C0020459Hyperinsulinism1CTD_human
HgeneCOL3A1C0020538Hypertensive disease1CTD_human
HgeneCOL3A1C0022548Keloid1CTD_human
HgeneCOL3A1C0023891Liver Cirrhosis, Alcoholic1CTD_human
HgeneCOL3A1C0023895Liver diseases1CTD_human
HgeneCOL3A1C0027719Nephrosclerosis1CTD_human
HgeneCOL3A1C0034069Pulmonary Fibrosis1CTD_human
HgeneCOL3A1C0036341Schizophrenia1CTD_human
HgeneCOL3A1C0038454Cerebrovascular accident1GENOMICS_ENGLAND
HgeneCOL3A1C0041956Ureteral obstruction1CTD_human
HgeneCOL3A1C0086565Liver Dysfunction1CTD_human
HgeneCOL3A1C0149721Left Ventricular Hypertrophy1CTD_human
HgeneCOL3A1C0238288Muscular Dystrophy, Facioscapulohumeral1CTD_human
HgeneCOL3A1C0238590Acrogeria1ORPHANET
HgeneCOL3A1C0338586Vertebral Artery Dissection1GENOMICS_ENGLAND
HgeneCOL3A1C0406584Acrogeria, gottron type1ORPHANET
HgeneCOL3A1C0553692Brain hemorrhage1GENOMICS_ENGLAND
HgeneCOL3A1C0553980Endomyocardial Fibrosis1CTD_human
HgeneCOL3A1C0860207Drug-Induced Liver Disease1CTD_human
HgeneCOL3A1C0948008Ischemic stroke1GENOMICS_ENGLAND
HgeneCOL3A1C1257963Endogenous Hyperinsulinism1CTD_human
HgeneCOL3A1C1257964Exogenous Hyperinsulinism1CTD_human
HgeneCOL3A1C1257965Compensatory Hyperinsulinemia1CTD_human
HgeneCOL3A1C1262760Hepatitis, Drug-Induced1CTD_human
HgeneCOL3A1C1623038Cirrhosis1CTD_human
HgeneCOL3A1C1855520Hyperglycemia, Postprandial1CTD_human
HgeneCOL3A1C1862932ANEURYSM, INTRACRANIAL BERRY, 1 (disorder)1ORPHANET
HgeneCOL3A1C2711227Steatohepatitis1CTD_human
HgeneCOL3A1C3658290Drug-Induced Acute Liver Injury1CTD_human
HgeneCOL3A1C4277682Chemical and Drug Induced Liver Injury1CTD_human
HgeneCOL3A1C4279912Chemically-Induced Liver Toxicity1CTD_human
HgeneCOL3A1C4721507Alveolitis, Fibrosing1CTD_human
TgeneC1834674BETHLEM MYOPATHY 15CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0410179Ullrich congenital muscular dystrophy 14CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC4225336DYSTONIA 272GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0000786Spontaneous abortion1CTD_human
TgeneC0000822Abortion, Tubal1CTD_human
TgeneC0027708Nephroblastoma1CTD_human
TgeneC2930471Bilateral Wilms Tumor1CTD_human
TgeneC3830362Early Pregnancy Loss1CTD_human
TgeneC4552766Miscarriage1CTD_human