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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-LY6G5B (FusionGDB2 ID:18494)

Fusion Gene Summary for COLGALT1-LY6G5B

check button Fusion gene summary
Fusion gene informationFusion gene name: COLGALT1-LY6G5B
Fusion gene ID: 18494
HgeneTgene
Gene symbol

COLGALT1

LY6G5B

Gene ID

79709

58496

Gene namecollagen beta(1-O)galactosyltransferase 1lymphocyte antigen 6 family member G5B
SynonymsBSVD3|ColGalT 1|GLT25D1C6orf19|G5b
Cytomap

19p13.11

6p21.33

Type of geneprotein-codingprotein-coding
Descriptionprocollagen galactosyltransferase 1glycosyltransferase 25 domain containing 1glycosyltransferase 25 family member 1hydroxylysine galactosyltransferase 1lymphocyte antigen 6 complex locus protein G5blymphocyte antigen 6 complex, locus G5Blymphocyte antigen-6 G5B splicing isoform 288lymphocyte antigen-6 G5B splicing isoform 452lymphocyte antigen-6 G5B splicing isoform 690lymphocyte antigen-6 G5B splic
Modification date2020031320200313
UniProtAcc

Q8NBJ5

Q8NDX9

Ensembl transtripts involved in fusion geneENST00000601354, ENST00000252599, 
ENST00000375864, ENST00000409525, 
ENST00000383429, ENST00000437674, 
ENST00000456439, ENST00000471088, 
ENST00000480515, ENST00000480530, 
ENST00000484964, ENST00000556456, 
Fusion gene scores* DoF score7 X 6 X 4=1684 X 4 X 3=48
# samples 64
** MAII scorelog2(6/168*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: COLGALT1 [Title/Abstract] AND LY6G5B [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCOLGALT1(17679522)-LY6G5B(31638933), # 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 LY6G5B (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

17679522

+LY6G5Bchr6

31638933

+


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Fusion Gene ORF analysis for COLGALT1-LY6G5B

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-3CDSENST00000601354ENST00000375864COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+
3UTR-5UTRENST00000601354ENST00000409525COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+
3UTR-intronENST00000601354ENST00000383429COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+
3UTR-intronENST00000601354ENST00000437674COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+
3UTR-intronENST00000601354ENST00000456439COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+
3UTR-intronENST00000601354ENST00000471088COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+
3UTR-intronENST00000601354ENST00000480515COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+
3UTR-intronENST00000601354ENST00000480530COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+
3UTR-intronENST00000601354ENST00000484964COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+
3UTR-intronENST00000601354ENST00000556456COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+
5CDS-5UTRENST00000252599ENST00000409525COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+
5CDS-intronENST00000252599ENST00000383429COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+
5CDS-intronENST00000252599ENST00000437674COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+
5CDS-intronENST00000252599ENST00000456439COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+
5CDS-intronENST00000252599ENST00000471088COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+
5CDS-intronENST00000252599ENST00000480515COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+
5CDS-intronENST00000252599ENST00000480530COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+
5CDS-intronENST00000252599ENST00000484964COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+
5CDS-intronENST00000252599ENST00000556456COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+
In-frameENST00000252599ENST00000375864COLGALT1chr19

17679522

+LY6G5Bchr6

31638933

+

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)
ENST00000252599COLGALT1chr1917679522+ENST00000375864LY6G5Bchr631638933+27619491201496458

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
ENST00000252599ENST00000375864COLGALT1chr1917679522+LY6G5Bchr631638933+0.0145414750.9854585

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Fusion Genomic Features for COLGALT1-LY6G5B


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)
COLGALT1chr1917679522+LY6G5Bchr631638932+7.09E-060.99999297
COLGALT1chr1917679522+LY6G5Bchr631638932+7.09E-060.99999297

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.
genomic feature of top 1%

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Fusion Protein Features for COLGALT1-LY6G5B


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/chr19:17679522/chr6:31638933)
- 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

LY6G5B

Q8NDX9

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}.

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
TgeneLY6G5Bchr19:17679522chr6:31638933ENST000003758640350_5319202.0Compositional biasNote=Poly-Ser
TgeneLY6G5Bchr19:17679522chr6:31638933ENST000004095250250_530147.0Compositional biasNote=Poly-Ser
TgeneLY6G5Bchr19:17679522chr6:31638933ENST000004805150350_530202.0Compositional biasNote=Poly-Ser
TgeneLY6G5Bchr19:17679522chr6:31638933ENST000004805300350_530202.0Compositional biasNote=Poly-Ser
TgeneLY6G5Bchr19:17679522chr6:31638933ENST000004849640350_530202.0Compositional biasNote=Poly-Ser
TgeneLY6G5Bchr19:17679522chr6:31638933ENST000003758640326_11819202.0DomainNote=UPAR/Ly6
TgeneLY6G5Bchr19:17679522chr6:31638933ENST000004095250226_1180147.0DomainNote=UPAR/Ly6
TgeneLY6G5Bchr19:17679522chr6:31638933ENST000004805150326_1180202.0DomainNote=UPAR/Ly6
TgeneLY6G5Bchr19:17679522chr6:31638933ENST000004805300326_1180202.0DomainNote=UPAR/Ly6
TgeneLY6G5Bchr19:17679522chr6:31638933ENST000004849640326_1180202.0DomainNote=UPAR/Ly6

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCOLGALT1chr19:17679522chr6:31638933ENST00000252599+512619_622276623.0MotifEndoplasmic reticulum retention motif


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Fusion Gene Sequence for COLGALT1-LY6G5B


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.
>18494_18494_1_COLGALT1-LY6G5B_COLGALT1_chr19_17679522_ENST00000252599_LY6G5B_chr6_31638933_ENST00000375864_length(transcript)=2761nt_BP=949nt
TTCACGCCCGGCGCGCTCCTCCCCTTTAAGGCGCGCGGCCGGGCGGGGCCCCTATGACCCCTTTAAGGCGCGGCCAGAGTCCTCCCGCAG
AAAAACGACTTAAAGGAGACGCGTGGCGCGATGGCGGCGGCCCCACGCGCGGGCCGGCGGCGCGGGCAGCCGCTCCTGGCGCTGCTGCTT
CTGCTGCTGGCGCCACTGCCGCCGGGGGCCCCGCCGGGCGCCGACGCCTACTTCCCCGAGGAGCGCTGGAGCCCGGAGTCGCCCCTGCAG
GCGCCGCGCGTGCTCATCGCGCTGTTGGCGCGAAACGCGGCCCACGCGTTGCCCACCACGCTGGGCGCACTCGAGCGGCTGCGGCACCCG
CGGGAGCGCACGGCGCTATGGGTGGCTACGGACCACAACATGGATAACACGTCAACTGTGCTGCGGGAGTGGCTGGTGGCCGTGAAGAGT
TTGTACCATTCCGTGGAGTGGCGGCCAGCAGAGGAGCCCAGGTCCTACCCGGACGAGGAAGGCCCGAAACACTGGTCTGACTCACGCTAC
GAGCATGTCATGAAGTTGCGCCAGGCAGCCCTGAAATCAGCTCGAGACATGTGGGCTGATTACATCCTGTTTGTAGATGCGGACAACCTG
ATCCTCAACCCTGACACACTGAGCCTGCTCATCGCTGAGAACAAGACGGTGGTCGCCCCCATGCTGGATTCCCGGGCTGCGTACTCCAAC
TTCTGGTGTGGAATGACTTCCCAGGGCTACTACAAGCGCACACCTGCCTACATCCCTATCCGCAAGCGAGACCGCCGGGGCTGCTTTGCA
GTTCCCATGGTGCACTCGACCTTCCTGATCGACCTGCGGAAGGCGGCGTCCAGGAACCTGGCCTTCTACCCACCTCACCCTGACTACACC
TGGTCCTTTGACGACATCATCGTCTTTGCCTTCTCCTGCAAGCAGGCAGTTCCTGTTCCCGACATCCGGACGTGCCACTTCTGCCTCGTA
GAAGACCCTTCTGTAGGATGCATTTCAGGCTCAGAGAAGTGTACCATCAGCAGCTCATCCCTGTGCATGGTGATCACCATCTATTATGAT
GTCAAGGTTCGCTTCATCGTTCGAGGCTGTGGACAGTACATTTCCTACCGCTGCCAAGAAAAACGCAACACCTACTTTGCAGAGTACTGG
TATCAGGCCCAGTGCTGTCAGTACGATTATTGCAACTCCTGGTCAAGCCCCCAACTCCAGAGCTCTCTGCCGGAGCCCCATGACAGGCCC
CTGGCCCTGCCTCTGTCTGACTCCCAGATTCAGTGGTTCTACCAGGCCCTGAACCTCTCCCTGCCCCTCCCCAATTTCCATGCTGGGACG
GAGCCTGATGGCCTGGACCCCATGGTCACACTGTCCCTGAACCTGGGCTTGTCTTTTGCTGAGCTGCGCCGCATGTACTTGTTCCTCAAT
AGTTCAGGACTTTTGGTTCTTCCCCAGGCTGGACTCTTGACACCTCACCCTTCCTGAATTCCACAGTGCAAATATCTTTCTGTAACACCC
TCAGCATCCTGCACTGCCCTCTCTGAAAACACCCACATTCTTTGGTCACTGTGATTTCTTAGGCCTCCGTCTGTTGTACCACTAGCATCT
ATATGACTTTTGTGTAATTTTCTCTCTTGAACTCTGGTGCTGTTTTTTTGTTTGTTTGAGACAAAGTCTCGCTCTGTCACCCAGGGTGGA
GTGCAGTGGCATGATCTCTGCTCACTACAACCTCCACCTCCCGGGTTCCAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTAC
AGGCGTGCACCACCACGCCTGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGTCAGGCTGGTCTCGAACTCCTGA
CCTCGTAATCTGCCCTCCTCGACCTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACTGTGCCTGTCTGAGCTCTGGTGCTGTTCTTCCC
CCTAGAAAAGAATCTCTAGTGTGGATTCTGCCCAGACAGGCTGACCTGAGAAAGGCACAGTGGTTCCTCCATTCCTTCCCCATCATCTGA
GTGTTCCAGTATCCCCCATCCCTCTCAATCCAGTCACCTGCCTATTGACATCTAGCTCTGTTTCCCCTGTCTTGTCCATGTCTCTAAGAC
CCAGTACCAGACTGAACTAGCAGCAAGAAGGACGAGGAGGCCGGGCATGGTGGCTCACGCCGGTAATCCCAGCACTTTGGGAGGCCGAGG
TGGGCGGATCACTTGAGATTGGGAGTTTGAGACCAGCCTGGCCAACATGGTAAAACCCGCTCTCTATTAAAAATAGAAAAATCAGCTGGG
TGTGGTGGCACACCTCTGTAATCCCAGCTACTCAGGAGGCTGAGACAGGAGAATCACTTGAACCCGGGAGGCAGAGGTTGCAGTGAGCCG
AGATCGCGCCACTGCACTCCAGCCTGGGTGACACAGTGAGACTCCGTCTCCAAAAAAAAGGATGAGGAATAGAATTCTGTGCAGATGTCC
TGACTTGGCAATTTTGTGTCCCTGCCTCACTGTCTCCACCAACCCCCGCCTGTCCTAGTGTTGTTCTGCCTCCTGTCCTCTCTTGCTCTC
TTGTCAGTCTCTGGCTTCCTCGGCCCCATTTCACTTCACTGAGTCCTGACACCCATCTCCCTAGGGGCCTGTGAGAGGAGAGGGAAGGGT

>18494_18494_1_COLGALT1-LY6G5B_COLGALT1_chr19_17679522_ENST00000252599_LY6G5B_chr6_31638933_ENST00000375864_length(amino acids)=458AA_BP=276
MAAAPRAGRRRGQPLLALLLLLLAPLPPGAPPGADAYFPEERWSPESPLQAPRVLIALLARNAAHALPTTLGALERLRHPRERTALWVAT
DHNMDNTSTVLREWLVAVKSLYHSVEWRPAEEPRSYPDEEGPKHWSDSRYEHVMKLRQAALKSARDMWADYILFVDADNLILNPDTLSLL
IAENKTVVAPMLDSRAAYSNFWCGMTSQGYYKRTPAYIPIRKRDRRGCFAVPMVHSTFLIDLRKAASRNLAFYPPHPDYTWSFDDIIVFA
FSCKQAVPVPDIRTCHFCLVEDPSVGCISGSEKCTISSSSLCMVITIYYDVKVRFIVRGCGQYISYRCQEKRNTYFAEYWYQAQCCQYDY
CNSWSSPQLQSSLPEPHDRPLALPLSDSQIQWFYQALNLSLPLPNFHAGTEPDGLDPMVTLSLNLGLSFAELRRMYLFLNSSGLLVLPQA

--------------------------------------------------------------

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Fusion Gene PPI Analysis for COLGALT1-LY6G5B


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-LY6G5B


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-LY6G5B


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