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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:COLGALT1-COPE (FusionGDB2 ID:18492)

Fusion Gene Summary for COLGALT1-COPE

check button Fusion gene summary
Fusion gene informationFusion gene name: COLGALT1-COPE
Fusion gene ID: 18492
HgeneTgene
Gene symbol

COLGALT1

COPE

Gene ID

79709

11316

Gene namecollagen beta(1-O)galactosyltransferase 1COPI coat complex subunit epsilon
SynonymsBSVD3|ColGalT 1|GLT25D1epsilon-COP
Cytomap

19p13.11

19p13.11

Type of geneprotein-codingprotein-coding
Descriptionprocollagen galactosyltransferase 1glycosyltransferase 25 domain containing 1glycosyltransferase 25 family member 1hydroxylysine galactosyltransferase 1coatomer subunit epsiloncoatomer epsilon subunitcoatomer protein complex subunit epsilonepsilon coat protein
Modification date2020031320200313
UniProtAcc

Q8NBJ5

O14579

Ensembl transtripts involved in fusion geneENST00000252599, ENST00000601354, 
ENST00000351079, ENST00000598969, 
ENST00000262812, ENST00000349893, 
ENST00000600932, 
Fusion gene scores* DoF score7 X 6 X 4=1687 X 7 X 3=147
# samples 67
** MAII scorelog2(6/168*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/147*10)=-1.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: COLGALT1 [Title/Abstract] AND COPE [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCOLGALT1(17671274)-COPE(19021880), # 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

check buttonFusion gene breakpoints across COLGALT1 (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 COPE (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
ChimerDB4LGGTCGA-TM-A7CF-01ACOLGALT1chr19

17671274

+COPEchr19

19021880

-


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Fusion Gene ORF analysis for COLGALT1-COPE

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-5UTRENST00000252599ENST00000351079COLGALT1chr19

17671274

+COPEchr19

19021880

-
5CDS-5UTRENST00000252599ENST00000598969COLGALT1chr19

17671274

+COPEchr19

19021880

-
In-frameENST00000252599ENST00000262812COLGALT1chr19

17671274

+COPEchr19

19021880

-
In-frameENST00000252599ENST00000349893COLGALT1chr19

17671274

+COPEchr19

19021880

-
In-frameENST00000252599ENST00000600932COLGALT1chr19

17671274

+COPEchr19

19021880

-
intron-3CDSENST00000601354ENST00000262812COLGALT1chr19

17671274

+COPEchr19

19021880

-
intron-3CDSENST00000601354ENST00000349893COLGALT1chr19

17671274

+COPEchr19

19021880

-
intron-3CDSENST00000601354ENST00000600932COLGALT1chr19

17671274

+COPEchr19

19021880

-
intron-5UTRENST00000601354ENST00000351079COLGALT1chr19

17671274

+COPEchr19

19021880

-
intron-5UTRENST00000601354ENST00000598969COLGALT1chr19

17671274

+COPEchr19

19021880

-

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)
ENST00000252599COLGALT1chr1917671274+ENST00000262812COPEchr1919021880-15126091201346408
ENST00000252599COLGALT1chr1917671274+ENST00000349893COPEchr1919021880-13536091201190356
ENST00000252599COLGALT1chr1917671274+ENST00000600932COPEchr1919021880-15326091201415431

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
ENST00000252599ENST00000262812COLGALT1chr1917671274+COPEchr1919021880-0.0066779750.99332196
ENST00000252599ENST00000349893COLGALT1chr1917671274+COPEchr1919021880-0.0033671960.99663275
ENST00000252599ENST00000600932COLGALT1chr1917671274+COPEchr1919021880-0.0069841730.99301577

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Fusion Genomic Features for COLGALT1-COPE


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 COLGALT1-COPE


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/chr19:17671274/chr19:19021880)
- 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
COLGALT1

Q8NBJ5

COPE

O14579

FUNCTION: Beta-galactosyltransferase that transfers beta-galactose to hydroxylysine residues of type I collagen (PubMed:19075007, PubMed:22216269, PubMed:27402836). By acting on collagen glycosylation, facilitates the formation of collagen triple helix (PubMed:27402836). Also involved in the biosynthesis of collagen type IV (PubMed:30412317). {ECO:0000269|PubMed:19075007, ECO:0000269|PubMed:22216269, ECO:0000269|PubMed:27402836, ECO:0000269|PubMed:30412317}.FUNCTION: The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. The coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. In mammals, the coatomer can only be recruited by membranes associated with ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors (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
HgeneCOLGALT1chr19:17671274chr19:19021880ENST00000252599+312619_622163623.0MotifEndoplasmic reticulum retention motif


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Fusion Gene Sequence for COLGALT1-COPE


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.
>18492_18492_1_COLGALT1-COPE_COLGALT1_chr19_17671274_ENST00000252599_COPE_chr19_19021880_ENST00000262812_length(transcript)=1512nt_BP=609nt
TTCACGCCCGGCGCGCTCCTCCCCTTTAAGGCGCGCGGCCGGGCGGGGCCCCTATGACCCCTTTAAGGCGCGGCCAGAGTCCTCCCGCAG
AAAAACGACTTAAAGGAGACGCGTGGCGCGATGGCGGCGGCCCCACGCGCGGGCCGGCGGCGCGGGCAGCCGCTCCTGGCGCTGCTGCTT
CTGCTGCTGGCGCCACTGCCGCCGGGGGCCCCGCCGGGCGCCGACGCCTACTTCCCCGAGGAGCGCTGGAGCCCGGAGTCGCCCCTGCAG
GCGCCGCGCGTGCTCATCGCGCTGTTGGCGCGAAACGCGGCCCACGCGTTGCCCACCACGCTGGGCGCACTCGAGCGGCTGCGGCACCCG
CGGGAGCGCACGGCGCTATGGGTGGCTACGGACCACAACATGGATAACACGTCAACTGTGCTGCGGGAGTGGCTGGTGGCCGTGAAGAGT
TTGTACCATTCCGTGGAGTGGCGGCCAGCAGAGGAGCCCAGGTCCTACCCGGACGAGGAAGGCCCGAAACACTGGTCTGACTCACGCTAC
GAGCATGTCATGAAGTTGCGCCAGGCAGCCCTGAAATCAGCTCGAGACATGTGGGCTGATTACATCCTGAGGAAGTTCGGTGTGGTCCTG
GATGAGATCAAGCCCTCCTCGGCCCCTGAGCTCCAGGCCGTGCGCATGTTTGCTGACTACCTCGCCCACGAGAGTCGGAGGGACAGCATC
GTGGCCGAGCTGGACCGAGAGATGAGCAGGAGCGTGGACGTGACCAACACCACCTTCCTGCTCATGGCCGCCTCCATCTATCTCCACGAC
CAGAACCCGGATGCCGCCCTGCGTGCGCTGCACCAGGGGGACAGCCTGGAGTGCACAGCCATGACAGTGCAGATCCTGCTGAAGCTGGAC
CGCCTGGACCTCGCCCGGAAGGAGCTGAAGAGAATGCAGGACCTGGACGAGGATGCCACCCTCACCCAGCTCGCCACTGCCTGGGTCAGC
CTGGCCACGGGTGGTGAGAAGCTGCAGGATGCCTACTACATCTTCCAGGAGATGGCTGACAAGTGCTCGCCCACCCTGCTGCTGCTCAAT
GGGCAGGCGGCCTGCCACATGGCCCAGGGCCGCTGGGAGGCCGCTGAGGGCCTGCTGCAGGAGGCGCTAGACAAGGATAGTGGCTACCCA
GAGACGCTGGTCAACCTCATCGTCCTGTCCCAGCACCTGGGCAAGCCCCCTGAGGTGACAAACCGATACCTGTCCCAGCTGAAGGATGCC
CACAGGTCCCATCCCTTCATCAAGGAGTACCAGGCCAAGGAGAACGACTTTGACAGGCTGGTGCTACAGTACGCTCCCAGCGCCTGAGGC
TGGCCCAGAGCTGTCAGGACCATGAAGCCAGGACAGAGGCCAGGAGCCAGCCCTGCAGCCCTCCCCACCCGGCATCCACCTGCATCCCCT

>18492_18492_1_COLGALT1-COPE_COLGALT1_chr19_17671274_ENST00000252599_COPE_chr19_19021880_ENST00000262812_length(amino acids)=408AA_BP=163
MAAAPRAGRRRGQPLLALLLLLLAPLPPGAPPGADAYFPEERWSPESPLQAPRVLIALLARNAAHALPTTLGALERLRHPRERTALWVAT
DHNMDNTSTVLREWLVAVKSLYHSVEWRPAEEPRSYPDEEGPKHWSDSRYEHVMKLRQAALKSARDMWADYILRKFGVVLDEIKPSSAPE
LQAVRMFADYLAHESRRDSIVAELDREMSRSVDVTNTTFLLMAASIYLHDQNPDAALRALHQGDSLECTAMTVQILLKLDRLDLARKELK
RMQDLDEDATLTQLATAWVSLATGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQGRWEAAEGLLQEALDKDSGYPETLVNLIVLS

--------------------------------------------------------------
>18492_18492_2_COLGALT1-COPE_COLGALT1_chr19_17671274_ENST00000252599_COPE_chr19_19021880_ENST00000349893_length(transcript)=1353nt_BP=609nt
TTCACGCCCGGCGCGCTCCTCCCCTTTAAGGCGCGCGGCCGGGCGGGGCCCCTATGACCCCTTTAAGGCGCGGCCAGAGTCCTCCCGCAG
AAAAACGACTTAAAGGAGACGCGTGGCGCGATGGCGGCGGCCCCACGCGCGGGCCGGCGGCGCGGGCAGCCGCTCCTGGCGCTGCTGCTT
CTGCTGCTGGCGCCACTGCCGCCGGGGGCCCCGCCGGGCGCCGACGCCTACTTCCCCGAGGAGCGCTGGAGCCCGGAGTCGCCCCTGCAG
GCGCCGCGCGTGCTCATCGCGCTGTTGGCGCGAAACGCGGCCCACGCGTTGCCCACCACGCTGGGCGCACTCGAGCGGCTGCGGCACCCG
CGGGAGCGCACGGCGCTATGGGTGGCTACGGACCACAACATGGATAACACGTCAACTGTGCTGCGGGAGTGGCTGGTGGCCGTGAAGAGT
TTGTACCATTCCGTGGAGTGGCGGCCAGCAGAGGAGCCCAGGTCCTACCCGGACGAGGAAGGCCCGAAACACTGGTCTGACTCACGCTAC
GAGCATGTCATGAAGTTGCGCCAGGCAGCCCTGAAATCAGCTCGAGACATGTGGGCTGATTACATCCTGAGGAAGTTCGGTGTGGTCCTG
GATGAGATCAAGCCCTCCTCGGCCCCTGAGCTCCAGGCCGTGCGCATGTTTGCTGACTACCTCGCCCACGAGAGTCGGAGGGACAGCATC
GTGGCCGAGCTGGACCGAGAGATGAGCAGGAGCGTGGACGTGACCAACACCACCTTCCTGCTCATGGCCGCCTCCATCTATCTCCACGAC
CAGAACCCGGATGCCGCCCTGCGTGCGCTGCACCAGGGGGACAGCCTGGAGTGCACAGCCATGACAGTGCAGATCCTGCTGAAGCTGGAC
CGCCTGGACCTCGCCCGGAAGGAGCTGAAGAGAATGCAGGACCTGGACGAGGATGCCACCCTCACCCAGCTCGCCACTGCCTGGGTCAGC
CTGGCCACGGATAGTGGCTACCCAGAGACGCTGGTCAACCTCATCGTCCTGTCCCAGCACCTGGGCAAGCCCCCTGAGGTGACAAACCGA
TACCTGTCCCAGCTGAAGGATGCCCACAGGTCCCATCCCTTCATCAAGGAGTACCAGGCCAAGGAGAACGACTTTGACAGGCTGGTGCTA
CAGTACGCTCCCAGCGCCTGAGGCTGGCCCAGAGCTGTCAGGACCATGAAGCCAGGACAGAGGCCAGGAGCCAGCCCTGCAGCCCTCCCC
ACCCGGCATCCACCTGCATCCCCTCTGGGGGCAGGAGCCCACCCCCAGCACCCCCATCTGTTAATAAATATCTCAACTCCAGGGTGTTCC

>18492_18492_2_COLGALT1-COPE_COLGALT1_chr19_17671274_ENST00000252599_COPE_chr19_19021880_ENST00000349893_length(amino acids)=356AA_BP=163
MAAAPRAGRRRGQPLLALLLLLLAPLPPGAPPGADAYFPEERWSPESPLQAPRVLIALLARNAAHALPTTLGALERLRHPRERTALWVAT
DHNMDNTSTVLREWLVAVKSLYHSVEWRPAEEPRSYPDEEGPKHWSDSRYEHVMKLRQAALKSARDMWADYILRKFGVVLDEIKPSSAPE
LQAVRMFADYLAHESRRDSIVAELDREMSRSVDVTNTTFLLMAASIYLHDQNPDAALRALHQGDSLECTAMTVQILLKLDRLDLARKELK

--------------------------------------------------------------
>18492_18492_3_COLGALT1-COPE_COLGALT1_chr19_17671274_ENST00000252599_COPE_chr19_19021880_ENST00000600932_length(transcript)=1532nt_BP=609nt
TTCACGCCCGGCGCGCTCCTCCCCTTTAAGGCGCGCGGCCGGGCGGGGCCCCTATGACCCCTTTAAGGCGCGGCCAGAGTCCTCCCGCAG
AAAAACGACTTAAAGGAGACGCGTGGCGCGATGGCGGCGGCCCCACGCGCGGGCCGGCGGCGCGGGCAGCCGCTCCTGGCGCTGCTGCTT
CTGCTGCTGGCGCCACTGCCGCCGGGGGCCCCGCCGGGCGCCGACGCCTACTTCCCCGAGGAGCGCTGGAGCCCGGAGTCGCCCCTGCAG
GCGCCGCGCGTGCTCATCGCGCTGTTGGCGCGAAACGCGGCCCACGCGTTGCCCACCACGCTGGGCGCACTCGAGCGGCTGCGGCACCCG
CGGGAGCGCACGGCGCTATGGGTGGCTACGGACCACAACATGGATAACACGTCAACTGTGCTGCGGGAGTGGCTGGTGGCCGTGAAGAGT
TTGTACCATTCCGTGGAGTGGCGGCCAGCAGAGGAGCCCAGGTCCTACCCGGACGAGGAAGGCCCGAAACACTGGTCTGACTCACGCTAC
GAGCATGTCATGAAGTTGCGCCAGGCAGCCCTGAAATCAGCTCGAGACATGTGGGCTGATTACATCCTGAGGAAGTTCGGTGTGGTCCTG
GATGAGATCAAGCCCTCCTCGGCCCCTGAGCTCCAGGCCGTGCGCATGTTTGCTGACTACCTCGCCCACGAGAGTCGGAGGGACAGCATC
GTGGCCGAGCTGGACCGAGAGATGAGCAGGAGCGTGGACGTGACCAACACCACCTTCCTGCTCATGGCCGCCTCCATCTATCTCCACGAC
CAGAACCCGGATGCCGCCCTGCGTGCGCTGCACCAGGGGGACAGCCTGGAGTGGGTGTCGAGTCCGGGCAGGGCCCTCCATCTGGAAGCA
CAGCCCATGGAGGCTGCTTCTCCAGATGGGCGCACAGCCATGACAGTGCAGATCCTGCTGAAGCTGGACCGCCTGGACCTCGCCCGGAAG
GAGCTGAAGAGAATGCAGGACCTGGACGAGGATGCCACCCTCACCCAGCTCGCCACTGCCTGGGTCAGCCTGGCCACGGGTGGTGAGAAG
CTGCAGGATGCCTACTACATCTTCCAGGAGATGGCTGACAAGTGCTCGCCCACCCTGCTGCTGCTCAATGGGCAGGCGGCCTGCCACATG
GCCCAGGGCCGCTGGGAGGCCGCTGAGGGCCTGCTGCAGGAGGCGCTAGACAAGGATAGTGGCTACCCAGAGACGCTGGTCAACCTCATC
GTCCTGTCCCAGCACCTGGGCAAGCCCCCTGAGGTGACAAACCGATACCTGTCCCAGCTGAAGGATGCCCACAGGTCCCATCCCTTCATC
AAGGAGTACCAGGCCAAGGAGAACGACTTTGACAGGCTGGTGCTACAGTACGCTCCCAGCGCCTGAGGCTGGCCCAGAGCTGTCAGGACC
ATGAAGCCAGGACAGAGGCCAGGAGCCAGCCCTGCAGCCCTCCCCACCCGGCATCCACCTGCATCCCCTCTGGGGGCAGGAGCCCACCCC

>18492_18492_3_COLGALT1-COPE_COLGALT1_chr19_17671274_ENST00000252599_COPE_chr19_19021880_ENST00000600932_length(amino acids)=431AA_BP=163
MAAAPRAGRRRGQPLLALLLLLLAPLPPGAPPGADAYFPEERWSPESPLQAPRVLIALLARNAAHALPTTLGALERLRHPRERTALWVAT
DHNMDNTSTVLREWLVAVKSLYHSVEWRPAEEPRSYPDEEGPKHWSDSRYEHVMKLRQAALKSARDMWADYILRKFGVVLDEIKPSSAPE
LQAVRMFADYLAHESRRDSIVAELDREMSRSVDVTNTTFLLMAASIYLHDQNPDAALRALHQGDSLEWVSSPGRALHLEAQPMEAASPDG
RTAMTVQILLKLDRLDLARKELKRMQDLDEDATLTQLATAWVSLATGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQGRWEAAEG

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Fusion Gene PPI Analysis for COLGALT1-COPE


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 COLGALT1-COPE


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 COLGALT1-COPE


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