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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:ALMS1-TNC (FusionGDB2 ID:HG7840TG3371)

Fusion Gene Summary for ALMS1-TNC

check button Fusion gene summary
Fusion gene informationFusion gene name: ALMS1-TNC
Fusion gene ID: hg7840tg3371
HgeneTgene
Gene symbol

ALMS1

TNC

Gene ID

7840

3371

Gene nameALMS1 centrosome and basal body associated proteintenascin C
SynonymsALSS150-225|DFNA56|GMEM|GP|HXB|JI|TN|TN-C
Cytomap('ALMS1')('TNC')

2p13.1

9q33.1

Type of geneprotein-codingprotein-coding
DescriptionAlstrom syndrome protein 1Alstrom syndrome 1tenascinGP 150-225cytotactindeafness, autosomal dominant 56glioma-associated-extracellular matrix antigenhexabrachion (tenascin)myotendinous antigenneuronectintenascin-C additional domain 1tenascin-C isoform 14/AD1/16
Modification date2020032920200315
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000264448, ENST00000409009, 
ENST00000377715, ENST00000464408, 
Fusion gene scores* DoF score3 X 3 X 3=278 X 8 X 4=256
# samples 311
** MAII scorelog2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(11/256*10)=-1.21864028647534
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ALMS1 [Title/Abstract] AND TNC [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointALMS1(73800551)-TNC(117804620), # samples:1
Anticipated loss of major functional domain due to fusion event.ALMS1-TNC seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted 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


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
ChimerDB4OVTCGA-25-2391ALMS1chr2

73800551

+TNCchr9

117804620

-


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Fusion Gene ORF analysis for ALMS1-TNC

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-intronENST00000264448ENST00000481475ALMS1chr2

73800551

+TNCchr9

117804620

-
5CDS-intronENST00000409009ENST00000481475ALMS1chr2

73800551

+TNCchr9

117804620

-
Frame-shiftENST00000264448ENST00000340094ALMS1chr2

73800551

+TNCchr9

117804620

-
Frame-shiftENST00000264448ENST00000341037ALMS1chr2

73800551

+TNCchr9

117804620

-
Frame-shiftENST00000264448ENST00000345230ALMS1chr2

73800551

+TNCchr9

117804620

-
Frame-shiftENST00000264448ENST00000346706ALMS1chr2

73800551

+TNCchr9

117804620

-
Frame-shiftENST00000264448ENST00000350763ALMS1chr2

73800551

+TNCchr9

117804620

-
Frame-shiftENST00000264448ENST00000423613ALMS1chr2

73800551

+TNCchr9

117804620

-
Frame-shiftENST00000264448ENST00000535648ALMS1chr2

73800551

+TNCchr9

117804620

-
Frame-shiftENST00000264448ENST00000537320ALMS1chr2

73800551

+TNCchr9

117804620

-
Frame-shiftENST00000264448ENST00000542877ALMS1chr2

73800551

+TNCchr9

117804620

-
Frame-shiftENST00000409009ENST00000340094ALMS1chr2

73800551

+TNCchr9

117804620

-
Frame-shiftENST00000409009ENST00000341037ALMS1chr2

73800551

+TNCchr9

117804620

-
Frame-shiftENST00000409009ENST00000345230ALMS1chr2

73800551

+TNCchr9

117804620

-
Frame-shiftENST00000409009ENST00000346706ALMS1chr2

73800551

+TNCchr9

117804620

-
Frame-shiftENST00000409009ENST00000350763ALMS1chr2

73800551

+TNCchr9

117804620

-
Frame-shiftENST00000409009ENST00000423613ALMS1chr2

73800551

+TNCchr9

117804620

-
Frame-shiftENST00000409009ENST00000535648ALMS1chr2

73800551

+TNCchr9

117804620

-
Frame-shiftENST00000409009ENST00000537320ALMS1chr2

73800551

+TNCchr9

117804620

-
Frame-shiftENST00000409009ENST00000542877ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-3CDSENST00000377715ENST00000340094ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-3CDSENST00000377715ENST00000341037ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-3CDSENST00000377715ENST00000345230ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-3CDSENST00000377715ENST00000346706ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-3CDSENST00000377715ENST00000350763ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-3CDSENST00000377715ENST00000423613ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-3CDSENST00000377715ENST00000535648ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-3CDSENST00000377715ENST00000537320ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-3CDSENST00000377715ENST00000542877ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-3CDSENST00000464408ENST00000340094ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-3CDSENST00000464408ENST00000341037ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-3CDSENST00000464408ENST00000345230ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-3CDSENST00000464408ENST00000346706ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-3CDSENST00000464408ENST00000350763ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-3CDSENST00000464408ENST00000423613ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-3CDSENST00000464408ENST00000535648ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-3CDSENST00000464408ENST00000537320ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-3CDSENST00000464408ENST00000542877ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-intronENST00000377715ENST00000481475ALMS1chr2

73800551

+TNCchr9

117804620

-
intron-intronENST00000464408ENST00000481475ALMS1chr2

73800551

+TNCchr9

117804620

-

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 ALMS1-TNC


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)


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Fusion Protein Features for ALMS1-TNC


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/:73800551/:117804620)
- 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 ALMS1-TNC


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 ALMS1-TNC


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 ALMS1-TNC


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 ALMS1-TNC


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneALMS1C0268425Alstrom Syndrome11CLINGEN;CTD_human;GENOMICS_ENGLAND
HgeneALMS1C0007193Cardiomyopathy, Dilated1CTD_human
HgeneALMS1C0152427Polydactyly1GENOMICS_ENGLAND
HgeneALMS1C0752166Bardet-Biedl Syndrome1GENOMICS_ENGLAND
HgeneALMS1C1449563Cardiomyopathy, Familial Idiopathic1CTD_human
TgeneC3711374Nonsyndromic Deafness3CLINGEN
TgeneC0004096Asthma1CTD_human
TgeneC0014175Endometriosis1CTD_human
TgeneC0025202melanoma1CTD_human
TgeneC0029410Osteoarthritis of hip1CTD_human
TgeneC0032226Pleural Diseases1CTD_human
TgeneC0042345Varicosity1CTD_human
TgeneC0269102Endometrioma1CTD_human
TgeneC0273115Lung Injury1CTD_human
TgeneC2350344Chronic Lung Injury1CTD_human
TgeneC3810170DEAFNESS, AUTOSOMAL DOMINANT 561CTD_human;GENOMICS_ENGLAND;UNIPROT