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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:BTF3-CLN3 (FusionGDB2 ID:10513)

Fusion Gene Summary for BTF3-CLN3

check button Fusion gene summary
Fusion gene informationFusion gene name: BTF3-CLN3
Fusion gene ID: 10513
HgeneTgene
Gene symbol

BTF3

CLN3

Gene ID

10384

1201

Gene namebutyrophilin subfamily 3 member A3CLN3 lysosomal/endosomal transmembrane protein, battenin
SynonymsBTF3|BTN3.3BTN1|BTS|JNCL
Cytomap

6p22.2

16p12.1

Type of geneprotein-codingprotein-coding
Descriptionbutyrophilin subfamily 3 member A3butyrophilin 3butyrophilin subfamily 3 member A3 secreted isoformbatteninCLN3, batteninbatten disease proteinceroid-lipofuscinosis, neuronal 3
Modification date2020031320200328
UniProtAcc

P20290

Q13286

Ensembl transtripts involved in fusion geneENST00000514505, ENST00000335895, 
ENST00000380591, 		ENST00000333496, 
ENST00000354630, ENST00000355477, 
ENST00000357076, ENST00000357806, 
ENST00000357857, ENST00000359984, 
ENST00000360019, ENST00000395653, 
ENST00000535392, ENST00000565316, 
ENST00000567160, ENST00000567963, 
ENST00000568224, ENST00000569430, 
Fusion gene scores* DoF score7 X 5 X 2=708 X 8 X 3=192
# samples 78
** MAII scorelog2(7/70*10)=0log2(8/192*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BTF3 [Title/Abstract] AND CLN3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBTF3(72798334)-CLN3(28495052), # 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
TgeneCLN3

GO:0015809

arginine transport

16251196

TgeneCLN3

GO:0035752

lysosomal lumen pH elevation

10924275

TgeneCLN3

GO:0042987

amyloid precursor protein catabolic process

10924275


check buttonFusion gene breakpoints across BTF3 (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 CLN3 (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/AAV699275BTF3chr5

72798334

-CLN3chr16

28495052

+


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Fusion Gene ORF analysis for BTF3-CLN3

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-intronENST00000514505ENST00000333496BTF3chr5

72798334

-CLN3chr16

28495052

+
3UTR-intronENST00000514505ENST00000354630BTF3chr5

72798334

-CLN3chr16

28495052

+
3UTR-intronENST00000514505ENST00000355477BTF3chr5

72798334

-CLN3chr16

28495052

+
3UTR-intronENST00000514505ENST00000357076BTF3chr5

72798334

-CLN3chr16

28495052

+
3UTR-intronENST00000514505ENST00000357806BTF3chr5

72798334

-CLN3chr16

28495052

+
3UTR-intronENST00000514505ENST00000357857BTF3chr5

72798334

-CLN3chr16

28495052

+
3UTR-intronENST00000514505ENST00000359984BTF3chr5

72798334

-CLN3chr16

28495052

+
3UTR-intronENST00000514505ENST00000360019BTF3chr5

72798334

-CLN3chr16

28495052

+
3UTR-intronENST00000514505ENST00000395653BTF3chr5

72798334

-CLN3chr16

28495052

+
3UTR-intronENST00000514505ENST00000535392BTF3chr5

72798334

-CLN3chr16

28495052

+
3UTR-intronENST00000514505ENST00000565316BTF3chr5

72798334

-CLN3chr16

28495052

+
3UTR-intronENST00000514505ENST00000567160BTF3chr5

72798334

-CLN3chr16

28495052

+
3UTR-intronENST00000514505ENST00000567963BTF3chr5

72798334

-CLN3chr16

28495052

+
3UTR-intronENST00000514505ENST00000568224BTF3chr5

72798334

-CLN3chr16

28495052

+
3UTR-intronENST00000514505ENST00000569430BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000335895ENST00000333496BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000335895ENST00000354630BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000335895ENST00000355477BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000335895ENST00000357076BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000335895ENST00000357806BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000335895ENST00000357857BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000335895ENST00000359984BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000335895ENST00000360019BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000335895ENST00000395653BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000335895ENST00000535392BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000335895ENST00000565316BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000335895ENST00000567160BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000335895ENST00000567963BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000335895ENST00000568224BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000335895ENST00000569430BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000380591ENST00000333496BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000380591ENST00000354630BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000380591ENST00000355477BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000380591ENST00000357076BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000380591ENST00000357806BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000380591ENST00000357857BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000380591ENST00000359984BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000380591ENST00000360019BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000380591ENST00000395653BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000380591ENST00000535392BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000380591ENST00000565316BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000380591ENST00000567160BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000380591ENST00000567963BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000380591ENST00000568224BTF3chr5

72798334

-CLN3chr16

28495052

+
5CDS-intronENST00000380591ENST00000569430BTF3chr5

72798334

-CLN3chr16

28495052

+

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 BTF3-CLN3


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 BTF3-CLN3


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/:72798334/:28495052)
- 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
BTF3

P20290

CLN3

Q13286

FUNCTION: When associated with NACA, prevents inappropriate targeting of non-secretory polypeptides to the endoplasmic reticulum (ER). Binds to nascent polypeptide chains as they emerge from the ribosome and blocks their interaction with the signal recognition particle (SRP), which normally targets nascent secretory peptides to the ER. BTF3 is also a general transcription factor that can form a stable complex with RNA polymerase II. Required for the initiation of transcription. {ECO:0000269|PubMed:10982809}.FUNCTION: Mediates microtubule-dependent, anterograde transport connecting the Golgi network, endosomes, autophagosomes, lysosomes and plasma membrane, and participates in several cellular processes such as regulation of lysosomal pH, lysosome protein degradation, receptor-mediated endocytosis, autophagy, transport of proteins and lipids from the TGN, apoptosis and synaptic transmission (PubMed:10924275, PubMed:18817525, PubMed:18317235, PubMed:22261744, PubMed:15471887, PubMed:20850431). Facilitates the proteins transport from trans-Golgi network (TGN)-to other membrane compartments such as transport of microdomain-associated proteins to the plasma membrane, IGF2R transport to the lysosome where it regulates the CTSD release leading to regulation of CTSD maturation and thereby APP intracellular processing (PubMed:10924275, PubMed:18817525). Moreover regulates CTSD activity in response to osmotic stress (PubMed:23840424, PubMed:28390177). Also binds galactosylceramide and transports it from the trans Golgi to the rafts, which may have immediate and downstream effects on cell survival by modulating ceramide synthesis (PubMed:18317235). At the plasma membrane, regulates actin-dependent events including filopodia formation, cell migration, and pinocytosis through ARF1-CDC42 pathway and also the cytoskeleton organization through interaction with MYH10 and fodrin leading to the regulation of the plasma membrane association of Na+, K+ ATPase complex (PubMed:20850431). Regulates synaptic transmission in the amygdala, hippocampus, and cerebellum through regulation of synaptic vesicles density and their proximity to active zones leading to modulation of short-term plasticity and age-dependent anxious behavior, learning and memory (By similarity). Regulates autophagic vacuoles (AVs) maturation by modulating the trafficking between endocytic and autophagolysosomal/lysosomal compartments, which involves vesicle fusion leading to regulation of degradation process (By similarity). Participates also in cellular homeostasis of compounds such as, water, ions, amino acids, proteins and lipids in several tissue namely in brain and kidney through regulation of their transport and synthesis (PubMed:17482562). {ECO:0000250|UniProtKB:Q61124, ECO:0000269|PubMed:10924275, ECO:0000269|PubMed:15471887, ECO:0000269|PubMed:17482562, ECO:0000269|PubMed:18317235, ECO:0000269|PubMed:18817525, ECO:0000269|PubMed:20850431, ECO:0000269|PubMed:22261744, ECO:0000269|PubMed:23840424, ECO:0000269|PubMed:28390177}.

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 BTF3-CLN3


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 BTF3-CLN3


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 BTF3-CLN3


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 BTF3-CLN3


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