FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:CLN3-SIVA1 (FusionGDB2 ID:17234)

Fusion Gene Summary for CLN3-SIVA1

check button Fusion gene summary
Fusion gene informationFusion gene name: CLN3-SIVA1
Fusion gene ID: 17234
HgeneTgene
Gene symbol

CLN3

SIVA1

Gene ID

1201

10572

Gene nameCLN3 lysosomal/endosomal transmembrane protein, batteninSIVA1 apoptosis inducing factor
SynonymsBTN1|BTS|JNCLCD27BP|SIVA|Siva-1|Siva-2
Cytomap

16p12.1

14q32.33

Type of geneprotein-codingprotein-coding
DescriptionbatteninCLN3, batteninbatten disease proteinceroid-lipofuscinosis, neuronal 3apoptosis regulatory protein SivaCD27-binding (Siva) protein
Modification date2020032820200313
UniProtAcc

Q13286

.
Ensembl transtripts involved in fusion geneENST00000333496, ENST00000354630, 
ENST00000357857, ENST00000359984, 
ENST00000360019, ENST00000395653, 
ENST00000535392, ENST00000565316, 
ENST00000567963, ENST00000568224, 
ENST00000569430, ENST00000355477, 
ENST00000357076, ENST00000357806, 
ENST00000567160, 		ENST00000329967, 
ENST00000347067, 
Fusion gene scores* DoF score5 X 4 X 3=605 X 4 X 5=100
# samples 55
** MAII scorelog2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/100*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CLN3 [Title/Abstract] AND SIVA1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLN3(28497668)-SIVA1(105225556), # 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
HgeneCLN3

GO:0015809

arginine transport

16251196

HgeneCLN3

GO:0035752

lysosomal lumen pH elevation

10924275

HgeneCLN3

GO:0042987

amyloid precursor protein catabolic process

10924275

TgeneSIVA1

GO:0097191

extrinsic apoptotic signaling pathway

9177220


check buttonFusion gene breakpoints across CLN3 (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 SIVA1 (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
ChimerDB4OVTCGA-29-A5NZ-01ACLN3chr16

28497668

-SIVA1chr14

105225218

+
ChimerDB4OVTCGA-29-A5NZ-01ACLN3chr16

28497668

-SIVA1chr14

105225556

+


Top

Fusion Gene ORF analysis for CLN3-SIVA1

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-intronENST00000333496ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000333496ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000333496ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000333496ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000354630ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000354630ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000354630ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000354630ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000357857ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000357857ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000357857ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000357857ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000359984ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000359984ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000359984ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000359984ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000360019ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000360019ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000360019ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000360019ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000395653ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000395653ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000395653ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000395653ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000535392ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000535392ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000535392ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000535392ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000565316ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000565316ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000565316ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000565316ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000567963ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000567963ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000567963ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000567963ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000568224ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000568224ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000568224ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000568224ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000569430ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000569430ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000569430ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225218

+
5CDS-intronENST00000569430ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
intron-intronENST00000355477ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225218

+
intron-intronENST00000355477ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
intron-intronENST00000355477ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225218

+
intron-intronENST00000355477ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
intron-intronENST00000357076ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225218

+
intron-intronENST00000357076ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
intron-intronENST00000357076ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225218

+
intron-intronENST00000357076ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
intron-intronENST00000357806ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225218

+
intron-intronENST00000357806ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
intron-intronENST00000357806ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225218

+
intron-intronENST00000357806ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
intron-intronENST00000567160ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225218

+
intron-intronENST00000567160ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
intron-intronENST00000567160ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225218

+
intron-intronENST00000567160ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+

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

Top

Fusion Genomic Features for CLN3-SIVA1


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.

Top

Fusion Protein Features for CLN3-SIVA1


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/:28497668/:105225556)
- 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
CLN3

Q13286

.
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}.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


Top

Fusion Gene Sequence for CLN3-SIVA1


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.

Top

Fusion Gene PPI Analysis for CLN3-SIVA1


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


Top

Related Drugs for CLN3-SIVA1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for CLN3-SIVA1


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