Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
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:CARS2-SMN2 (FusionGDB2 ID:HG79587TG6607)

Fusion Gene Summary for CARS2-SMN2

check button Fusion gene summary
Fusion gene informationFusion gene name: CARS2-SMN2
Fusion gene ID: hg79587tg6607
HgeneTgene
Gene symbol

CARS2

SMN2

Gene ID

79587

6607

Gene namecysteinyl-tRNA synthetase 2, mitochondrialsurvival of motor neuron 2, centromeric
SynonymsCOXPD27|cysRSBCD541|C-BCD541|GEMIN1|SMNC|TDRD16B
Cytomap('CARS2')('SMN2')

13q34

5q13.2

Type of geneprotein-codingprotein-coding
Descriptionprobable cysteine--tRNA ligase, mitochondrialcysteine tRNA ligase 2, mitochondrial (putative)cysteinyl-tRNA synthetase 2, mitochondrial (putative)survival motor neuron proteincomponent of gems 1gemin-1survival of motor neuron 2 isoform D2A2B345survival of motor neuron 2 isoform D2A2B3457survival of motor neuron 2 isoform D2A3457survival of motor neuron 2 isoform D2B3457survival of motor neur
Modification date2020031320200329
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000257347, ENST00000535398, 
Fusion gene scores* DoF score4 X 3 X 3=366 X 6 X 5=180
# samples 36
** MAII scorelog2(3/36*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(6/180*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CARS2 [Title/Abstract] AND SMN2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCARS2(111340068)-SMN2(70247768), # 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
TgeneSMN2

GO:0000387

spliceosomal snRNP assembly

18984161



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
ChimerDB4BRCATCGA-BH-A0E2-01ACARS2chr13

111340068

-SMN2chr5

70247768

+


Top

Fusion Gene ORF analysis for CARS2-SMN2

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-intronENST00000257347ENST00000380741CARS2chr13

111340068

-SMN2chr5

70247768

+
5CDS-intronENST00000257347ENST00000380742CARS2chr13

111340068

-SMN2chr5

70247768

+
5CDS-intronENST00000257347ENST00000380743CARS2chr13

111340068

-SMN2chr5

70247768

+
5CDS-intronENST00000257347ENST00000511812CARS2chr13

111340068

-SMN2chr5

70247768

+
5UTR-intronENST00000535398ENST00000380741CARS2chr13

111340068

-SMN2chr5

70247768

+
5UTR-intronENST00000535398ENST00000380742CARS2chr13

111340068

-SMN2chr5

70247768

+
5UTR-intronENST00000535398ENST00000380743CARS2chr13

111340068

-SMN2chr5

70247768

+
5UTR-intronENST00000535398ENST00000511812CARS2chr13

111340068

-SMN2chr5

70247768

+

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 CARS2-SMN2


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)


Top

Fusion Protein Features for CARS2-SMN2


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/:111340068/:70247768)
- 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


Top

Fusion Gene Sequence for CARS2-SMN2


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 CARS2-SMN2


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 CARS2-SMN2


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 CARS2-SMN2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCARS2C4225251COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 273CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0026847Spinal Muscular Atrophy1CTD_human;GENOMICS_ENGLAND
TgeneC0270765Myelopathic Muscular Atrophy1CTD_human
TgeneC0393541Distal Spinal Muscular Atrophy1CTD_human
TgeneC0393546Oculopharyngeal Spinal Muscular Atrophy1CTD_human
TgeneC0393547Bulbospinal Neuronopathy1CTD_human
TgeneC0751334Progressive Proximal Myelopathic Muscular Atrophy1CTD_human
TgeneC0751335Scapuloperoneal Form of Spinal Muscular Atrophy1CTD_human
TgeneC0917981Progressive Muscular Atrophy1CTD_human
TgeneC3661519Hereditary Motor Neuronopathy1CTD_human