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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:TSEN2-SYN2 (FusionGDB2 ID:HG80746TG6854)

Fusion Gene Summary for TSEN2-SYN2

check button Fusion gene summary
Fusion gene informationFusion gene name: TSEN2-SYN2
Fusion gene ID: hg80746tg6854
HgeneTgene
Gene symbol

TSEN2

SYN2

Gene ID

80746

6854

Gene nametRNA splicing endonuclease subunit 2synapsin II
SynonymsPCH2B|SEN2|SEN2LSYNII
Cytomap('TSEN2')('SYN2')

3p25.2

3p25.2

Type of geneprotein-codingprotein-coding
DescriptiontRNA-splicing endonuclease subunit Sen2TSEN2 tRNA splicing endonuclease subunithsSen2tRNA-intron endonuclease Sen2synapsin-2
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000284995, ENST00000314571, 
ENST00000383797, ENST00000402228, 
ENST00000415684, ENST00000444864, 
ENST00000454502, ENST00000475595, 
Fusion gene scores* DoF score7 X 12 X 4=3365 X 11 X 3=165
# samples 1310
** MAII scorelog2(13/336*10)=-1.36994960975031
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/165*10)=-0.722466024471091
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TSEN2 [Title/Abstract] AND SYN2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTSEN2(12538053)-SYN2(12224812), # samples:3
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
HgeneTSEN2

GO:0006388

tRNA splicing, via endonucleolytic cleavage and ligation

17495927



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-DK-AA75-01ATSEN2chr3

12546730

+SYN2chr3

12182151

+
ChimerDB4BLCATCGA-XF-AAMY-01ATSEN2chr3

12538053

-SYN2chr3

12224812

+
ChimerDB4BLCATCGA-XF-AAMY-01ATSEN2chr3

12538053

+SYN2chr3

12224812

+
ChimerDB4BLCATCGA-XF-AAMYTSEN2chr3

12538053

+SYN2chr3

12224812

+


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Fusion Gene ORF analysis for TSEN2-SYN2

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-3UTRENST00000284995ENST00000432424TSEN2chr3

12546730

+SYN2chr3

12182151

+
5CDS-3UTRENST00000284995ENST00000432424TSEN2chr3

12538053

+SYN2chr3

12224812

+
5CDS-3UTRENST00000314571ENST00000432424TSEN2chr3

12538053

+SYN2chr3

12224812

+
5CDS-3UTRENST00000383797ENST00000432424TSEN2chr3

12546730

+SYN2chr3

12182151

+
5CDS-3UTRENST00000383797ENST00000432424TSEN2chr3

12538053

+SYN2chr3

12224812

+
5CDS-3UTRENST00000402228ENST00000432424TSEN2chr3

12546730

+SYN2chr3

12182151

+
5CDS-3UTRENST00000402228ENST00000432424TSEN2chr3

12538053

+SYN2chr3

12224812

+
5CDS-3UTRENST00000415684ENST00000432424TSEN2chr3

12538053

+SYN2chr3

12224812

+
5CDS-3UTRENST00000444864ENST00000432424TSEN2chr3

12538053

+SYN2chr3

12224812

+
5CDS-3UTRENST00000454502ENST00000432424TSEN2chr3

12546730

+SYN2chr3

12182151

+
5CDS-3UTRENST00000454502ENST00000432424TSEN2chr3

12538053

+SYN2chr3

12224812

+
intron-3UTRENST00000314571ENST00000432424TSEN2chr3

12546730

+SYN2chr3

12182151

+
intron-3UTRENST00000415684ENST00000432424TSEN2chr3

12546730

+SYN2chr3

12182151

+
intron-3UTRENST00000444864ENST00000432424TSEN2chr3

12546730

+SYN2chr3

12182151

+
intron-3UTRENST00000475595ENST00000432424TSEN2chr3

12546730

+SYN2chr3

12182151

+
intron-3UTRENST00000475595ENST00000432424TSEN2chr3

12538053

+SYN2chr3

12224812

+

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 TSEN2-SYN2


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)
TSEN2chr312546730+SYN2chr312182150+0.074572920.9254271
TSEN2chr312538053+SYN2chr312224811+0.0057087330.9942913
TSEN2chr312538053+SYN2chr312224811+0.0057087330.9942913
TSEN2chr312546730+SYN2chr312182150+0.074572920.9254271
TSEN2chr312538053+SYN2chr312224811+0.0057087330.9942913
TSEN2chr312538053+SYN2chr312224811+0.0057087330.9942913


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 TSEN2-SYN2


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/:12538053/:12224812)
- 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 TSEN2-SYN2


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 TSEN2-SYN2


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 TSEN2-SYN2


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 TSEN2-SYN2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTSEN2C2676466Pontocerebellar Hypoplasia Type 2B2CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneTSEN2C0011168Deglutition Disorders1CTD_human
HgeneTSEN2C0018975Hemeralopia1CTD_human
HgeneTSEN2C0020796Profound Mental Retardation1CTD_human
HgeneTSEN2C0025363Mental Retardation, Psychosocial1CTD_human
HgeneTSEN2C0025958Microcephaly1CTD_human
HgeneTSEN2C0026650Movement Disorders1CTD_human
HgeneTSEN2C0042790Vision Disorders1CTD_human
HgeneTSEN2C0043094Weight Gain1CTD_human
HgeneTSEN2C0233769Micropsia1CTD_human
HgeneTSEN2C0233771Macropsia1CTD_human
HgeneTSEN2C0266468Congenital pontocerebellar hypoplasia1GENOMICS_ENGLAND
HgeneTSEN2C0266487Etat Marbre1CTD_human
HgeneTSEN2C0267071Oropharyngeal Dysphagia1CTD_human
HgeneTSEN2C0267072Esophageal Dysphagia1CTD_human
HgeneTSEN2C0271185Metamorphopsia1CTD_human
HgeneTSEN2C0917816Mental deficiency1CTD_human
HgeneTSEN2C1956147Microlissencephaly1CTD_human
HgeneTSEN2C2932714Pontocerebellar Hypoplasia Type 21ORPHANET
HgeneTSEN2C3489704Vision Disability1CTD_human
HgeneTSEN2C3665347Visual Impairment1CTD_human
HgeneTSEN2C3714756Intellectual Disability1CTD_human
HgeneTSEN2C3853041Severe Congenital Microcephaly1CTD_human
TgeneC0020429Hyperalgesia1CTD_human
TgeneC0022333Jacksonian Seizure1CTD_human
TgeneC0036572Seizures1CTD_human
TgeneC0149958Complex partial seizures1CTD_human
TgeneC0234533Generalized seizures1CTD_human
TgeneC0234535Clonic Seizures1CTD_human
TgeneC0270824Visual seizure1CTD_human
TgeneC0270844Tonic Seizures1CTD_human
TgeneC0270846Epileptic drop attack1CTD_human
TgeneC0422850Seizures, Somatosensory1CTD_human
TgeneC0422852Seizures, Auditory1CTD_human
TgeneC0422853Olfactory seizure1CTD_human
TgeneC0422854Gustatory seizure1CTD_human
TgeneC0422855Vertiginous seizure1CTD_human
TgeneC0458247Allodynia1CTD_human
TgeneC0494475Tonic - clonic seizures1CTD_human
TgeneC0751056Non-epileptic convulsion1CTD_human
TgeneC0751110Single Seizure1CTD_human
TgeneC0751123Atonic Absence Seizures1CTD_human
TgeneC0751211Hyperalgesia, Primary1CTD_human
TgeneC0751212Hyperalgesia, Secondary1CTD_human
TgeneC0751213Tactile Allodynia1CTD_human
TgeneC0751214Hyperalgesia, Thermal1CTD_human
TgeneC0751494Convulsive Seizures1CTD_human
TgeneC0751495Seizures, Focal1CTD_human
TgeneC0751496Seizures, Sensory1CTD_human
TgeneC2936719Mechanical Allodynia1CTD_human
TgeneC3495874Nonepileptic Seizures1CTD_human
TgeneC4048158Convulsions1CTD_human
TgeneC4316903Absence Seizures1CTD_human
TgeneC4317109Epileptic Seizures1CTD_human
TgeneC4317123Myoclonic Seizures1CTD_human
TgeneC4505436Generalized Absence Seizures1CTD_human