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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:CHST11-TRAC (FusionGDB2 ID:HG50515TG28755)

Fusion Gene Summary for CHST11-TRAC

check button Fusion gene summary
Fusion gene informationFusion gene name: CHST11-TRAC
Fusion gene ID: hg50515tg28755
HgeneTgene
Gene symbol

CHST11

TRAC

Gene ID

50515

28755

Gene namecarbohydrate sulfotransferase 11
SynonymsC4ST|C4ST-1|C4ST1|HSA269537|OCBMD
Cytomap('CHST11')('TRAC')

12q23.3

Type of geneprotein-coding
Descriptioncarbohydrate sulfotransferase 11C4S-1IgH/CHST11 fusioncarbohydrate (chondroitin 4) sulfotransferase 11chondroitin 4-O-sulfotransferase 1
Modification date20200313
UniProtAcc

Q9NPF2

.
Ensembl transtripts involved in fusion geneENST00000303694, ENST00000547956, 
ENST00000546689, ENST00000549260, 
ENST00000550711, 
Fusion gene scores* DoF score13 X 8 X 6=6248 X 3 X 3=72
# samples 158
** MAII scorelog2(15/624*10)=-2.05658352836637
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/72*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CHST11 [Title/Abstract] AND TRAC [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCHST11(104851307)-TRAC(23016447), # 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
HgeneCHST11

GO:0030206

chondroitin sulfate biosynthetic process

11056388


check buttonFusion gene breakpoints across CHST11 (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 TRAC (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
* 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
ChimerDB4STADTCGA-BR-A4IY-01ACHST11chr12

104851307

+TRACchr14

23016447

+


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Fusion Gene ORF analysis for CHST11-TRAC

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
In-frameENST00000303694ENST00000478163CHST11chr12

104851307

+TRACchr14

23016447

+
In-frameENST00000547956ENST00000478163CHST11chr12

104851307

+TRACchr14

23016447

+
intron-3CDSENST00000546689ENST00000478163CHST11chr12

104851307

+TRACchr14

23016447

+
intron-3CDSENST00000549260ENST00000478163CHST11chr12

104851307

+TRACchr14

23016447

+
intron-3CDSENST00000550711ENST00000478163CHST11chr12

104851307

+TRACchr14

23016447

+

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)
ENST00000547956CHST11chr12104851307+ENST00000478163TRACchr1423016447+153656215986323
ENST00000303694CHST11chr12104851307+ENST00000478163TRACchr1423016447+153155710981323

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
ENST00000547956ENST00000478163CHST11chr12104851307+TRACchr1423016447+0.0135705540.98642945
ENST00000303694ENST00000478163CHST11chr12104851307+TRACchr1423016447+0.0140224760.98597753

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Fusion Genomic Features for CHST11-TRAC


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)
CHST11chr12104851307+TRACchr1423016446+0.0021707330.99782926
CHST11chr12104851307+TRACchr1423016446+0.0021707330.99782926

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 CHST11-TRAC


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/chr12:104851307/chr14:23016447)
- 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
CHST11

Q9NPF2

.
FUNCTION: Catalyzes the transfer of sulfate to position 4 of the N-acetylgalactosamine (GalNAc) residue of chondroitin. Chondroitin sulfate constitutes the predominant proteoglycan present in cartilage and is distributed on the surfaces of many cells and extracellular matrices. Can also sulfate Gal residues in desulfated dermatan sulfate. Preferentially sulfates in GlcA->GalNAc unit than in IdoA->GalNAc unit. Does not form 4, 6-di-O-sulfated GalNAc when chondroitin sulfate C is used as an acceptor.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
HgeneCHST11chr12:104851307chr14:23016447ENST00000303694+131_1639353.0Topological domainCytoplasmic
HgeneCHST11chr12:104851307chr14:23016447ENST00000303694+1317_3739353.0TransmembraneHelical%3B Signal-anchor for type II membrane protein

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCHST11chr12:104851307chr14:23016447ENST00000303694+13124_13039353.0Nucleotide bindingPAPS
HgeneCHST11chr12:104851307chr14:23016447ENST00000303694+13186_19439353.0Nucleotide bindingPAPS
HgeneCHST11chr12:104851307chr14:23016447ENST00000549260+13124_1300348.0Nucleotide bindingPAPS
HgeneCHST11chr12:104851307chr14:23016447ENST00000549260+13186_1940348.0Nucleotide bindingPAPS
HgeneCHST11chr12:104851307chr14:23016447ENST00000303694+1338_35239353.0Topological domainLumenal
HgeneCHST11chr12:104851307chr14:23016447ENST00000549260+131_160348.0Topological domainCytoplasmic
HgeneCHST11chr12:104851307chr14:23016447ENST00000549260+1338_3520348.0Topological domainLumenal
HgeneCHST11chr12:104851307chr14:23016447ENST00000549260+1317_370348.0TransmembraneHelical%3B Signal-anchor for type II membrane protein


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Fusion Gene Sequence for CHST11-TRAC


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.
>16691_16691_1_CHST11-TRAC_CHST11_chr12_104851307_ENST00000303694_TRAC_chr14_23016447_ENST00000478163_length(transcript)=1531nt_BP=557nt
ATATAGATCGTTGGAGCGCAATGAAGTAGCCTTTGGAGAGAAGGGAGAGGGCCCGTCGGACAGCCACAGCGGCCAGCGCAGCGGCAGCGG
CGGCGGCACCACCATCACCGCTCGCACCCCAGCCGCCCGGCCCGCGACCAGGCAGCGGCGGCCGCCGGCGGGATCGGAGGAGGCGGCGGA
GCGGCGAGGAGGAGGAGCAGGAGCGCGCAGCCAGCGGGTCCACGCATCTCAGCACTTCCAGACCAACTCCGGCACCTTCCACACCCCTGC
CCGGGCTGGGGGCTCCGAGAGCGGCCGCGAAGCGACTCCGATCCTCCCTCTGAGCCTTGCTCAGCTCTGCCCCGCGCCTCCCGGGCTCCG
GTCCGCGCGGCGGGGTCCCTGCTCCTGCGCCCCGGGCGCGCTTCCCGGACACCCCGGTCCCCGCAGCCAGGACAAAGCCATGAAGCCAGC
GCTGCTGGAAGTGATGAGGATGAACAGAATCTGCCGGATGGTGCTGGCCACTTGCTTGGGATCCTTTATCCTGGTCATCTTCTATTTCCA
AAGTATGTTGCACCCAGATATCCAGAACCCTGACCCTGCCGTGTACCAGCTGAGAGACTCTAAATCCAGTGACAAGTCTGTCTGCCTATT
CACCGATTTTGATTCTCAAACAAATGTGTCACAAAGTAAGGATTCTGATGTGTATATCACAGACAAAACTGTGCTAGACATGAGGTCTAT
GGACTTCAAGAGCAACAGTGCTGTGGCCTGGAGCAACAAATCTGACTTTGCATGTGCAAACGCCTTCAACAACAGCATTATTCCAGAAGA
CACCTTCTTCCCCAGCCCAGAAAGTTCCTGTGATGTCAAGCTGGTCGAGAAAAGCTTTGAAACAGATACGAACCTAAACTTTCAAAACCT
GTCAGTGATTGGGTTCCGAATCCTCCTCCTGAAAGTGGCCGGGTTTAATCTGCTCATGACGCTGCGGCTGTGGTCCAGCTGAGATCTGCA
AGATTGTAAGACAGCCTGTGCTCCCTCGCTCCTTCCTCTGCATTGCCCCTCTTCTCCCTCTCCAAACAGAGGGAACTCTCCTACCCCCAA
GGAGGTGAAAGCTGCTACCACCTCTGTGCCCCCCCGGCAATGCACCAACTGGATCCTACCCGAATTTATGATTAAGATTGCTGAAGAGCT
GCCAAACACTGCTGCCACCCCCTCTGTTCCCTTATTGCTGCTTGTCACTGCCTGACATTCACGGCAGAGGCAAGGCTGCTGCAGCTCCGC
TGGCTGTGCACATTCCCTCCTGCTCCCCAGAGACTGCCTCCGCCATCCCACAGATGATGGATCTTCAGTGGGTTCTCTTGGGCTCTAGGT
CCCGGAGAATGTTGTGAGGGGTTTATTTTTTTTTAATAGTGTTCATAAAGAAAGACATAGTATTCTTCTTCTCAAGACGTGGGGGGAAAT
TATCTCATTATCGAGGCCCTGCTATGCTGTGTGTCTGGGCGTGTTGTATGTCCTGCTGCCGATGCCTTCATTAAAATGATTTGGAAGAGC

>16691_16691_1_CHST11-TRAC_CHST11_chr12_104851307_ENST00000303694_TRAC_chr14_23016447_ENST00000478163_length(amino acids)=323AA_BP=182
MERNEVAFGEKGEGPSDSHSGQRSGSGGGTTITARTPAARPATRQRRPPAGSEEAAERRGGGAGARSQRVHASQHFQTNSGTFHTPARAG
GSESGREATPILPLSLAQLCPAPPGLRSARRGPCSCAPGALPGHPGPRSQDKAMKPALLEVMRMNRICRMVLATCLGSFILVIFYFQSML
HPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFF

--------------------------------------------------------------
>16691_16691_2_CHST11-TRAC_CHST11_chr12_104851307_ENST00000547956_TRAC_chr14_23016447_ENST00000478163_length(transcript)=1536nt_BP=562nt
GGAATATATAGATCGTTGGAGCGCAATGAAGTAGCCTTTGGAGAGAAGGGAGAGGGCCCGTCGGACAGCCACAGCGGCCAGCGCAGCGGC
AGCGGCGGCGGCACCACCATCACCGCTCGCACCCCAGCCGCCCGGCCCGCGACCAGGCAGCGGCGGCCGCCGGCGGGATCGGAGGAGGCG
GCGGAGCGGCGAGGAGGAGGAGCAGGAGCGCGCAGCCAGCGGGTCCACGCATCTCAGCACTTCCAGACCAACTCCGGCACCTTCCACACC
CCTGCCCGGGCTGGGGGCTCCGAGAGCGGCCGCGAAGCGACTCCGATCCTCCCTCTGAGCCTTGCTCAGCTCTGCCCCGCGCCTCCCGGG
CTCCGGTCCGCGCGGCGGGGTCCCTGCTCCTGCGCCCCGGGCGCGCTTCCCGGACACCCCGGTCCCCGCAGCCAGGACAAAGCCATGAAG
CCAGCGCTGCTGGAAGTGATGAGGATGAACAGAATCTGCCGGATGGTGCTGGCCACTTGCTTGGGATCCTTTATCCTGGTCATCTTCTAT
TTCCAAAGTATGTTGCACCCAGATATCCAGAACCCTGACCCTGCCGTGTACCAGCTGAGAGACTCTAAATCCAGTGACAAGTCTGTCTGC
CTATTCACCGATTTTGATTCTCAAACAAATGTGTCACAAAGTAAGGATTCTGATGTGTATATCACAGACAAAACTGTGCTAGACATGAGG
TCTATGGACTTCAAGAGCAACAGTGCTGTGGCCTGGAGCAACAAATCTGACTTTGCATGTGCAAACGCCTTCAACAACAGCATTATTCCA
GAAGACACCTTCTTCCCCAGCCCAGAAAGTTCCTGTGATGTCAAGCTGGTCGAGAAAAGCTTTGAAACAGATACGAACCTAAACTTTCAA
AACCTGTCAGTGATTGGGTTCCGAATCCTCCTCCTGAAAGTGGCCGGGTTTAATCTGCTCATGACGCTGCGGCTGTGGTCCAGCTGAGAT
CTGCAAGATTGTAAGACAGCCTGTGCTCCCTCGCTCCTTCCTCTGCATTGCCCCTCTTCTCCCTCTCCAAACAGAGGGAACTCTCCTACC
CCCAAGGAGGTGAAAGCTGCTACCACCTCTGTGCCCCCCCGGCAATGCACCAACTGGATCCTACCCGAATTTATGATTAAGATTGCTGAA
GAGCTGCCAAACACTGCTGCCACCCCCTCTGTTCCCTTATTGCTGCTTGTCACTGCCTGACATTCACGGCAGAGGCAAGGCTGCTGCAGC
TCCGCTGGCTGTGCACATTCCCTCCTGCTCCCCAGAGACTGCCTCCGCCATCCCACAGATGATGGATCTTCAGTGGGTTCTCTTGGGCTC
TAGGTCCCGGAGAATGTTGTGAGGGGTTTATTTTTTTTTAATAGTGTTCATAAAGAAAGACATAGTATTCTTCTTCTCAAGACGTGGGGG
GAAATTATCTCATTATCGAGGCCCTGCTATGCTGTGTGTCTGGGCGTGTTGTATGTCCTGCTGCCGATGCCTTCATTAAAATGATTTGGA

>16691_16691_2_CHST11-TRAC_CHST11_chr12_104851307_ENST00000547956_TRAC_chr14_23016447_ENST00000478163_length(amino acids)=323AA_BP=182
MERNEVAFGEKGEGPSDSHSGQRSGSGGGTTITARTPAARPATRQRRPPAGSEEAAERRGGGAGARSQRVHASQHFQTNSGTFHTPARAG
GSESGREATPILPLSLAQLCPAPPGLRSARRGPCSCAPGALPGHPGPRSQDKAMKPALLEVMRMNRICRMVLATCLGSFILVIFYFQSML
HPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFF

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

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Fusion Gene PPI Analysis for CHST11-TRAC


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 CHST11-TRAC


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 CHST11-TRAC


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC3809332T-CELL RECEPTOR-ALPHA/BETA DEFICIENCY2CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC0494261Combined immunodeficiency1GENOMICS_ENGLAND