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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:COL12A1-COL12A1 (FusionGDB2 ID:18058)

Fusion Gene Summary for COL12A1-COL12A1

check button Fusion gene summary
Fusion gene informationFusion gene name: COL12A1-COL12A1
Fusion gene ID: 18058
HgeneTgene
Gene symbol

COL12A1

COL12A1

Gene ID

1303

1303

Gene namecollagen type XII alpha 1 chaincollagen type XII alpha 1 chain
SynonymsBA209D8.1|BTHLM2|COL12A1L|DJ234P15.1|EDSMYP|UCMD2BA209D8.1|BTHLM2|COL12A1L|DJ234P15.1|EDSMYP|UCMD2
Cytomap

6q13-q14.1

6q13-q14.1

Type of geneprotein-codingprotein-coding
Descriptioncollagen alpha-1(XII) chaincollagen type XII proteoglycancollagen, type XII, alpha 1collagen alpha-1(XII) chaincollagen type XII proteoglycancollagen, type XII, alpha 1
Modification date2020031320200313
UniProtAcc

Q99715

Q99715

Ensembl transtripts involved in fusion geneENST00000322507, ENST00000345356, 
ENST00000416123, ENST00000483888, 
ENST00000511023, 		ENST00000322507, 
ENST00000345356, ENST00000416123, 
ENST00000483888, ENST00000511023, 
Fusion gene scores* DoF score6 X 9 X 4=2168 X 11 X 3=264
# samples 911
** MAII scorelog2(9/216*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/264*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: COL12A1 [Title/Abstract] AND COL12A1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCOL12A1(75794208)-COL12A1(75794136), # samples:2
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

check buttonFusion gene breakpoints across COL12A1 (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 COL12A1 (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
ChiTaRS5.0N/AAA541569COL12A1chr6

75794078

-COL12A1chr6

75794202

+
ChiTaRS5.0N/AAL359627COL12A1chr6

75794622

+COL12A1chr6

75794572

-
ChiTaRS5.0N/AAW019988COL12A1chr6

75794208

+COL12A1chr6

75794136

-
ChiTaRS5.0N/AAW023072COL12A1chr6

75794208

+COL12A1chr6

75794136

-
ChiTaRS5.0N/ABF154542COL12A1chr6

75795888

+COL12A1chr6

75795958

-


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Fusion Gene ORF analysis for COL12A1-COL12A1

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
intron-3UTRENST00000322507ENST00000322507COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-3UTRENST00000322507ENST00000322507COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-3UTRENST00000322507ENST00000322507COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-3UTRENST00000322507ENST00000322507COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-3UTRENST00000345356ENST00000322507COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-3UTRENST00000345356ENST00000322507COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-3UTRENST00000345356ENST00000322507COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-3UTRENST00000345356ENST00000322507COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-3UTRENST00000416123ENST00000322507COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-3UTRENST00000416123ENST00000322507COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-3UTRENST00000416123ENST00000322507COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-3UTRENST00000416123ENST00000322507COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-3UTRENST00000483888ENST00000322507COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-3UTRENST00000483888ENST00000322507COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-3UTRENST00000483888ENST00000322507COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-3UTRENST00000483888ENST00000322507COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-3UTRENST00000511023ENST00000322507COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-3UTRENST00000511023ENST00000322507COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-3UTRENST00000511023ENST00000322507COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-3UTRENST00000511023ENST00000322507COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000322507ENST00000345356COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000322507ENST00000345356COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000322507ENST00000345356COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000322507ENST00000345356COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000322507ENST00000416123COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000322507ENST00000416123COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000322507ENST00000416123COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000322507ENST00000416123COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000322507ENST00000483888COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000322507ENST00000483888COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000322507ENST00000483888COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000322507ENST00000483888COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000322507ENST00000511023COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000322507ENST00000511023COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000322507ENST00000511023COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000322507ENST00000511023COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000345356ENST00000345356COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000345356ENST00000345356COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000345356ENST00000345356COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000345356ENST00000345356COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000345356ENST00000416123COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000345356ENST00000416123COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000345356ENST00000416123COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000345356ENST00000416123COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000345356ENST00000483888COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000345356ENST00000483888COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000345356ENST00000483888COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000345356ENST00000483888COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000345356ENST00000511023COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000345356ENST00000511023COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000345356ENST00000511023COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000345356ENST00000511023COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000416123ENST00000345356COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000416123ENST00000345356COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000416123ENST00000345356COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000416123ENST00000345356COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000416123ENST00000416123COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000416123ENST00000416123COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000416123ENST00000416123COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000416123ENST00000416123COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000416123ENST00000483888COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000416123ENST00000483888COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000416123ENST00000483888COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000416123ENST00000483888COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000416123ENST00000511023COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000416123ENST00000511023COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000416123ENST00000511023COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000416123ENST00000511023COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000483888ENST00000345356COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000483888ENST00000345356COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000483888ENST00000345356COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000483888ENST00000345356COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000483888ENST00000416123COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000483888ENST00000416123COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000483888ENST00000416123COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000483888ENST00000416123COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000483888ENST00000483888COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000483888ENST00000483888COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000483888ENST00000483888COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000483888ENST00000483888COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000483888ENST00000511023COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000483888ENST00000511023COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000483888ENST00000511023COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000483888ENST00000511023COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000511023ENST00000345356COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000511023ENST00000345356COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000511023ENST00000345356COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000511023ENST00000345356COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000511023ENST00000416123COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000511023ENST00000416123COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000511023ENST00000416123COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000511023ENST00000416123COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000511023ENST00000483888COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000511023ENST00000483888COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000511023ENST00000483888COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000511023ENST00000483888COL12A1chr6

75795888

+COL12A1chr6

75795958

-
intron-intronENST00000511023ENST00000511023COL12A1chr6

75794078

-COL12A1chr6

75794202

+
intron-intronENST00000511023ENST00000511023COL12A1chr6

75794622

+COL12A1chr6

75794572

-
intron-intronENST00000511023ENST00000511023COL12A1chr6

75794208

+COL12A1chr6

75794136

-
intron-intronENST00000511023ENST00000511023COL12A1chr6

75795888

+COL12A1chr6

75795958

-

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 COL12A1-COL12A1


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.

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 COL12A1-COL12A1


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/:75794208/:75794136)
- 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
COL12A1

Q99715

COL12A1

Q99715

FUNCTION: Type XII collagen interacts with type I collagen-containing fibrils, the COL1 domain could be associated with the surface of the fibrils, and the COL2 and NC3 domains may be localized in the perifibrillar matrix. {ECO:0000250}.FUNCTION: Type XII collagen interacts with type I collagen-containing fibrils, the COL1 domain could be associated with the surface of the fibrils, and the COL2 and NC3 domains may be localized in the perifibrillar matrix. {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 COL12A1-COL12A1


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 COL12A1-COL12A1


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 COL12A1-COL12A1


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 COL12A1-COL12A1


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