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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:CPT1A-GAL3ST3 (FusionGDB2 ID:HG1374TG89792)

Fusion Gene Summary for CPT1A-GAL3ST3

check button Fusion gene summary
Fusion gene informationFusion gene name: CPT1A-GAL3ST3
Fusion gene ID: hg1374tg89792
HgeneTgene
Gene symbol

CPT1A

GAL3ST3

Gene ID

1374

89792

Gene namecarnitine palmitoyltransferase 1Agalactose-3-O-sulfotransferase 3
SynonymsCPT1|CPT1-L|L-CPT1GAL3ST-3|GAL3ST2
Cytomap('CPT1A')('GAL3ST3')

11q13.3

11q13.1

Type of geneprotein-codingprotein-coding
Descriptioncarnitine O-palmitoyltransferase 1, liver isoformCPT ICPTI-Lcarnitine O-palmitoyltransferase I, liver isoformcarnitine palmitoyltransferase 1A (liver)carnitine palmitoyltransferase I, livergalactose-3-O-sulfotransferase 3beta-galactose-3-O-sulfotransferase 3gal-beta-1, 3-GalNAc 3'-sulfotransferase 3galactose 3'-sulfotransferasegalbeta1-3GalNAc 3'-sulfotransferase 3
Modification date2020031520200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000265641, ENST00000376618, 
ENST00000537756, ENST00000538994, 
ENST00000539743, ENST00000540367, 
Fusion gene scores* DoF score25 X 23 X 12=69001 X 1 X 1=1
# samples 321
** MAII scorelog2(32/6900*10)=-4.43045255166553
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Context

PubMed: CPT1A [Title/Abstract] AND GAL3ST3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCPT1A(68609243)-GAL3ST3(65816620), # 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
HgeneCPT1A

GO:0001676

long-chain fatty acid metabolic process

11350182

HgeneCPT1A

GO:0009437

carnitine metabolic process

11350182



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
ChimerDB4BLCATCGA-XF-A9T4-01ACPT1Achr11

68609243

-GAL3ST3chr11

65816620

-
ChimerDB4BLCATCGA-XF-A9T4CPT1Achr11

68609243

-GAL3ST3chr11

65816620

-


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Fusion Gene ORF analysis for CPT1A-GAL3ST3

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
5UTR-5UTRENST00000265641ENST00000312006CPT1Achr11

68609243

-GAL3ST3chr11

65816620

-
5UTR-5UTRENST00000376618ENST00000312006CPT1Achr11

68609243

-GAL3ST3chr11

65816620

-
5UTR-intronENST00000265641ENST00000527878CPT1Achr11

68609243

-GAL3ST3chr11

65816620

-
5UTR-intronENST00000376618ENST00000527878CPT1Achr11

68609243

-GAL3ST3chr11

65816620

-
intron-5UTRENST00000537756ENST00000312006CPT1Achr11

68609243

-GAL3ST3chr11

65816620

-
intron-5UTRENST00000538994ENST00000312006CPT1Achr11

68609243

-GAL3ST3chr11

65816620

-
intron-5UTRENST00000539743ENST00000312006CPT1Achr11

68609243

-GAL3ST3chr11

65816620

-
intron-5UTRENST00000540367ENST00000312006CPT1Achr11

68609243

-GAL3ST3chr11

65816620

-
intron-intronENST00000537756ENST00000527878CPT1Achr11

68609243

-GAL3ST3chr11

65816620

-
intron-intronENST00000538994ENST00000527878CPT1Achr11

68609243

-GAL3ST3chr11

65816620

-
intron-intronENST00000539743ENST00000527878CPT1Achr11

68609243

-GAL3ST3chr11

65816620

-
intron-intronENST00000540367ENST00000527878CPT1Achr11

68609243

-GAL3ST3chr11

65816620

-

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 CPT1A-GAL3ST3


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 CPT1A-GAL3ST3


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/:68609243/:65816620)
- 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
..
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}.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

- 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 CPT1A-GAL3ST3


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 CPT1A-GAL3ST3


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 CPT1A-GAL3ST3


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 CPT1A-GAL3ST3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCPT1AC1829703Carnitine palmitoyl transferase 1A deficiency13CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCPT1AC0002152Alloxan Diabetes1CTD_human
HgeneCPT1AC0006142Malignant neoplasm of breast1CTD_human
HgeneCPT1AC0011849Diabetes Mellitus1CTD_human
HgeneCPT1AC0011853Diabetes Mellitus, Experimental1CTD_human
HgeneCPT1AC0011860Diabetes Mellitus, Non-Insulin-Dependent1CTD_human
HgeneCPT1AC0022661Kidney Failure, Chronic1CTD_human
HgeneCPT1AC0038433Streptozotocin Diabetes1CTD_human
HgeneCPT1AC0400966Non-alcoholic Fatty Liver Disease1CTD_human
HgeneCPT1AC0678222Breast Carcinoma1CTD_human
HgeneCPT1AC1257931Mammary Neoplasms, Human1CTD_human
HgeneCPT1AC1458155Mammary Neoplasms1CTD_human
HgeneCPT1AC3241937Nonalcoholic Steatohepatitis1CTD_human
HgeneCPT1AC4704874Mammary Carcinoma, Human1CTD_human