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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:AVIL-TSFM (FusionGDB2 ID:HG10677TG10102)

Fusion Gene Summary for AVIL-TSFM

check button Fusion gene summary
Fusion gene informationFusion gene name: AVIL-TSFM
Fusion gene ID: hg10677tg10102
HgeneTgene
Gene symbol

AVIL

TSFM

Gene ID

10677

10102

Gene nameadvillinTs translation elongation factor, mitochondrial
SynonymsADVIL|DOC6|NPHS21|p92EFTS|EFTSMT
Cytomap('AVIL')('TSFM')

12q14.1

12q14.1

Type of geneprotein-codingprotein-coding
Descriptionadvillinelongation factor Ts, mitochondrialEF-TsEF-TsMtmitochondrial elongation factor Ts
Modification date2020031320200313
UniProtAcc

O75366

.
Ensembl transtripts involved in fusion geneENST00000257861, ENST00000537081, 
ENST00000550083, 
ENST00000257861, 
ENST00000537081, ENST00000550083, 
Fusion gene scores* DoF score4 X 5 X 4=806 X 5 X 4=120
# samples 59
** MAII scorelog2(5/80*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(9/120*10)=-0.415037499278844
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: AVIL [Title/Abstract] AND TSFM [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAVIL(58197029)-TSFM(58186768), # samples:1
Anticipated loss of major functional domain due to fusion event.AVIL-TSFM seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
AVIL-TSFM seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
AVIL-TSFM seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
AVIL-TSFM seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
TSFM-AVIL seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
TSFM-AVIL seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
* 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
TgeneTSFM

GO:0070129

regulation of mitochondrial translation

27677415


check buttonFusion gene breakpoints across AVIL (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure
check buttonFusion gene breakpoints across TSFM (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4LUSCTCGA-43-2581AVILchr12

58197029

-TSFMchr12

58186768

+


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Fusion Gene ORF analysis for AVIL-TSFM

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-3UTRENST00000257861ENST00000497617AVILchr12

58197029

-TSFMchr12

58186768

+
5CDS-3UTRENST00000537081ENST00000497617AVILchr12

58197029

-TSFMchr12

58186768

+
5CDS-intronENST00000257861ENST00000323833AVILchr12

58197029

-TSFMchr12

58186768

+
5CDS-intronENST00000257861ENST00000350762AVILchr12

58197029

-TSFMchr12

58186768

+
5CDS-intronENST00000257861ENST00000540550AVILchr12

58197029

-TSFMchr12

58186768

+
5CDS-intronENST00000537081ENST00000323833AVILchr12

58197029

-TSFMchr12

58186768

+
5CDS-intronENST00000537081ENST00000350762AVILchr12

58197029

-TSFMchr12

58186768

+
5CDS-intronENST00000537081ENST00000540550AVILchr12

58197029

-TSFMchr12

58186768

+
In-frameENST00000257861ENST00000454289AVILchr12

58197029

-TSFMchr12

58186768

+
In-frameENST00000257861ENST00000543727AVILchr12

58197029

-TSFMchr12

58186768

+
In-frameENST00000257861ENST00000548851AVILchr12

58197029

-TSFMchr12

58186768

+
In-frameENST00000257861ENST00000550559AVILchr12

58197029

-TSFMchr12

58186768

+
In-frameENST00000537081ENST00000454289AVILchr12

58197029

-TSFMchr12

58186768

+
In-frameENST00000537081ENST00000543727AVILchr12

58197029

-TSFMchr12

58186768

+
In-frameENST00000537081ENST00000548851AVILchr12

58197029

-TSFMchr12

58186768

+
In-frameENST00000537081ENST00000550559AVILchr12

58197029

-TSFMchr12

58186768

+
intron-3CDSENST00000550083ENST00000454289AVILchr12

58197029

-TSFMchr12

58186768

+
intron-3CDSENST00000550083ENST00000543727AVILchr12

58197029

-TSFMchr12

58186768

+
intron-3CDSENST00000550083ENST00000548851AVILchr12

58197029

-TSFMchr12

58186768

+
intron-3CDSENST00000550083ENST00000550559AVILchr12

58197029

-TSFMchr12

58186768

+
intron-3UTRENST00000550083ENST00000497617AVILchr12

58197029

-TSFMchr12

58186768

+
intron-intronENST00000550083ENST00000323833AVILchr12

58197029

-TSFMchr12

58186768

+
intron-intronENST00000550083ENST00000350762AVILchr12

58197029

-TSFMchr12

58186768

+
intron-intronENST00000550083ENST00000540550AVILchr12

58197029

-TSFMchr12

58186768

+

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 AVIL-TSFM


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)
AVILchr1258197029-TSFMchr1258186768+2.35E-060.9999976
AVILchr1258197029-TSFMchr1258186768+2.35E-060.9999976

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.
genomic feature

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 AVIL-TSFM


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/chr12:58197029/chr12:58186768)
- 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
AVIL

O75366

.
FUNCTION: Ca(2+)-regulated actin-binding protein which plays an important role in actin bundling (PubMed:29058690). May have a unique function in the morphogenesis of neuronal cells which form ganglia. Required for SREC1-mediated regulation of neurite-like outgrowth. Plays a role in regenerative sensory axon outgrowth and remodeling processes after peripheral injury in neonates. Involved in the formation of long fine actin-containing filopodia-like structures in fibroblast. Plays a role in ciliogenesis. In podocytes, controls lamellipodia formation through the regulation of EGF-induced diacylglycerol generation by PLCE1 and ARP2/3 complex assembly (PubMed:29058690). {ECO:0000269|PubMed:20393563, ECO:0000269|PubMed:29058690}.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
HgeneAVILchr12:58197029chr12:58186768ENST00000257861-1519109_116654820.0RegionPolyphosphoinositide binding
HgeneAVILchr12:58197029chr12:58186768ENST00000257861-1519135_143654820.0RegionPolyphosphoinositide binding
HgeneAVILchr12:58197029chr12:58186768ENST00000537081-1519109_116647813.0RegionPolyphosphoinositide binding
HgeneAVILchr12:58197029chr12:58186768ENST00000537081-1519135_143647813.0RegionPolyphosphoinositide binding
HgeneAVILchr12:58197029chr12:58186768ENST00000257861-1519145_185654820.0RepeatNote=Gelsolin-like 2
HgeneAVILchr12:58197029chr12:58186768ENST00000257861-151924_73654820.0RepeatNote=Gelsolin-like 1
HgeneAVILchr12:58197029chr12:58186768ENST00000257861-1519262_306654820.0RepeatNote=Gelsolin-like 3
HgeneAVILchr12:58197029chr12:58186768ENST00000257861-1519403_454654820.0RepeatNote=Gelsolin-like 4
HgeneAVILchr12:58197029chr12:58186768ENST00000257861-1519525_565654820.0RepeatNote=Gelsolin-like 5
HgeneAVILchr12:58197029chr12:58186768ENST00000537081-1519145_185647813.0RepeatNote=Gelsolin-like 2
HgeneAVILchr12:58197029chr12:58186768ENST00000537081-151924_73647813.0RepeatNote=Gelsolin-like 1
HgeneAVILchr12:58197029chr12:58186768ENST00000537081-1519262_306647813.0RepeatNote=Gelsolin-like 3
HgeneAVILchr12:58197029chr12:58186768ENST00000537081-1519403_454647813.0RepeatNote=Gelsolin-like 4
HgeneAVILchr12:58197029chr12:58186768ENST00000537081-1519525_565647813.0RepeatNote=Gelsolin-like 5

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneAVILchr12:58197029chr12:58186768ENST00000257861-1519753_819654820.0DomainHP
HgeneAVILchr12:58197029chr12:58186768ENST00000537081-1519753_819647813.0DomainHP
HgeneAVILchr12:58197029chr12:58186768ENST00000257861-15191_731654820.0RegionCore
HgeneAVILchr12:58197029chr12:58186768ENST00000257861-1519731_819654820.0RegionHeadpiece
HgeneAVILchr12:58197029chr12:58186768ENST00000537081-15191_731647813.0RegionCore
HgeneAVILchr12:58197029chr12:58186768ENST00000537081-1519731_819647813.0RegionHeadpiece
HgeneAVILchr12:58197029chr12:58186768ENST00000257861-1519628_669654820.0RepeatNote=Gelsolin-like 6
HgeneAVILchr12:58197029chr12:58186768ENST00000537081-1519628_669647813.0RepeatNote=Gelsolin-like 6


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Fusion Gene Sequence for AVIL-TSFM


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 AVIL-TSFM


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 AVIL-TSFM


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 AVIL-TSFM


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC1864840Combined Oxidative Phosphorylation Deficiency 36CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0036572Seizures1GENOMICS_ENGLAND