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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:ALDH9A1-TMCO1 (FusionGDB2 ID:HG223TG54499)

Fusion Gene Summary for ALDH9A1-TMCO1

check button Fusion gene summary
Fusion gene informationFusion gene name: ALDH9A1-TMCO1
Fusion gene ID: hg223tg54499
HgeneTgene
Gene symbol

ALDH9A1

TMCO1

Gene ID

223

54499

Gene namealdehyde dehydrogenase 9 family member A1transmembrane and coiled-coil domains 1
SynonymsALDH4|ALDH7|ALDH9|E3|TMABA-DH|TMABADH|TMABALDHHP10122|PCIA3|PNAS-136|TMCC4
Cytomap('ALDH9A1')('TMCO1')

1q24.1

1q24.1

Type of geneprotein-codingprotein-coding
Description4-trimethylaminobutyraldehyde dehydrogenaseR-aminobutyraldehyde dehydrogenasealdehyde dehydrogenase (NAD+)aldehyde dehydrogenase E3 isozymealdehyde dehydrogenase family 9 member A1gamma-aminobutyraldehyde dehydrogenasecalcium load-activated calcium channelCLAC channelCa(2+) load-activated Ca(2+) channelputative membrane proteintransmembrane and coiled-coil domain-containing protein 1transmembrane and coiled-coil domains 4xenogeneic cross-immune protein PCIA3
Modification date2020031320200327
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000461664, ENST00000538148, 
ENST00000354775, 
Fusion gene scores* DoF score5 X 7 X 4=14013 X 9 X 6=702
# samples 614
** MAII scorelog2(6/140*10)=-1.22239242133645
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(14/702*10)=-2.32604420335959
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ALDH9A1 [Title/Abstract] AND TMCO1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointALDH9A1(165667487)-TMCO1(165697358), # samples:2
Anticipated loss of major functional domain due to fusion event.ALDH9A1-TMCO1 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.
ALDH9A1-TMCO1 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.
ALDH9A1-TMCO1 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
ALDH9A1-TMCO1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
ALDH9A1-TMCO1 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
HgeneALDH9A1

GO:0006081

cellular aldehyde metabolic process

8645224|30914451

HgeneALDH9A1

GO:0042136

neurotransmitter biosynthetic process

2925663

HgeneALDH9A1

GO:0051289

protein homotetramerization

30914451

HgeneALDH9A1

GO:0055114

oxidation-reduction process

2925663

TgeneTMCO1

GO:0006983

ER overload response

27212239

TgeneTMCO1

GO:0032469

endoplasmic reticulum calcium ion homeostasis

27212239

TgeneTMCO1

GO:0070588

calcium ion transmembrane transport

27212239


check buttonFusion gene breakpoints across ALDH9A1 (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 TMCO1 (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
ChimerDB4OVTCGA-24-1558-01AALDH9A1chr1

165667487

-TMCO1chr1

165697358

-
ChimerDB4OVTCGA-24-1558-01AALDH9A1chr1

165667615

-TMCO1chr1

165697358

-
ChimerDB4OVTCGA-24-1558ALDH9A1chr1

165667614

-TMCO1chr1

165697358

-


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Fusion Gene ORF analysis for ALDH9A1-TMCO1

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
5UTR-3CDSENST00000461664ENST00000367881ALDH9A1chr1

165667487

-TMCO1chr1

165697358

-
5UTR-3CDSENST00000461664ENST00000392129ALDH9A1chr1

165667487

-TMCO1chr1

165697358

-
5UTR-3CDSENST00000461664ENST00000464650ALDH9A1chr1

165667487

-TMCO1chr1

165697358

-
5UTR-3CDSENST00000461664ENST00000580248ALDH9A1chr1

165667487

-TMCO1chr1

165697358

-
5UTR-3CDSENST00000538148ENST00000367881ALDH9A1chr1

165667487

-TMCO1chr1

165697358

-
5UTR-3CDSENST00000538148ENST00000392129ALDH9A1chr1

165667487

-TMCO1chr1

165697358

-
5UTR-3CDSENST00000538148ENST00000464650ALDH9A1chr1

165667487

-TMCO1chr1

165697358

-
5UTR-3CDSENST00000538148ENST00000580248ALDH9A1chr1

165667487

-TMCO1chr1

165697358

-
Frame-shiftENST00000354775ENST00000367881ALDH9A1chr1

165667615

-TMCO1chr1

165697358

-
Frame-shiftENST00000354775ENST00000367881ALDH9A1chr1

165667614

-TMCO1chr1

165697358

-
Frame-shiftENST00000354775ENST00000392129ALDH9A1chr1

165667615

-TMCO1chr1

165697358

-
Frame-shiftENST00000354775ENST00000392129ALDH9A1chr1

165667614

-TMCO1chr1

165697358

-
Frame-shiftENST00000354775ENST00000580248ALDH9A1chr1

165667615

-TMCO1chr1

165697358

-
Frame-shiftENST00000354775ENST00000580248ALDH9A1chr1

165667614

-TMCO1chr1

165697358

-
In-frameENST00000354775ENST00000464650ALDH9A1chr1

165667615

-TMCO1chr1

165697358

-
In-frameENST00000354775ENST00000464650ALDH9A1chr1

165667614

-TMCO1chr1

165697358

-
intron-3CDSENST00000354775ENST00000367881ALDH9A1chr1

165667487

-TMCO1chr1

165697358

-
intron-3CDSENST00000354775ENST00000392129ALDH9A1chr1

165667487

-TMCO1chr1

165697358

-
intron-3CDSENST00000354775ENST00000464650ALDH9A1chr1

165667487

-TMCO1chr1

165697358

-
intron-3CDSENST00000354775ENST00000580248ALDH9A1chr1

165667487

-TMCO1chr1

165697358

-
intron-3CDSENST00000461664ENST00000367881ALDH9A1chr1

165667615

-TMCO1chr1

165697358

-
intron-3CDSENST00000461664ENST00000367881ALDH9A1chr1

165667614

-TMCO1chr1

165697358

-
intron-3CDSENST00000461664ENST00000392129ALDH9A1chr1

165667615

-TMCO1chr1

165697358

-
intron-3CDSENST00000461664ENST00000392129ALDH9A1chr1

165667614

-TMCO1chr1

165697358

-
intron-3CDSENST00000461664ENST00000464650ALDH9A1chr1

165667615

-TMCO1chr1

165697358

-
intron-3CDSENST00000461664ENST00000464650ALDH9A1chr1

165667614

-TMCO1chr1

165697358

-
intron-3CDSENST00000461664ENST00000580248ALDH9A1chr1

165667615

-TMCO1chr1

165697358

-
intron-3CDSENST00000461664ENST00000580248ALDH9A1chr1

165667614

-TMCO1chr1

165697358

-
intron-3CDSENST00000538148ENST00000367881ALDH9A1chr1

165667615

-TMCO1chr1

165697358

-
intron-3CDSENST00000538148ENST00000367881ALDH9A1chr1

165667614

-TMCO1chr1

165697358

-
intron-3CDSENST00000538148ENST00000392129ALDH9A1chr1

165667615

-TMCO1chr1

165697358

-
intron-3CDSENST00000538148ENST00000392129ALDH9A1chr1

165667614

-TMCO1chr1

165697358

-
intron-3CDSENST00000538148ENST00000464650ALDH9A1chr1

165667615

-TMCO1chr1

165697358

-
intron-3CDSENST00000538148ENST00000464650ALDH9A1chr1

165667614

-TMCO1chr1

165697358

-
intron-3CDSENST00000538148ENST00000580248ALDH9A1chr1

165667615

-TMCO1chr1

165697358

-
intron-3CDSENST00000538148ENST00000580248ALDH9A1chr1

165667614

-TMCO1chr1

165697358

-

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 ALDH9A1-TMCO1


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.
genomic feature

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Fusion Protein Features for ALDH9A1-TMCO1


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/chr1:165667487/chr1:165697358)
- 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
TgeneTMCO1chr1:165667614chr1:165697358ENST0000039212957231_234156189.0Compositional biasNote=Poly-Pro
TgeneTMCO1chr1:165667615chr1:165697358ENST0000039212957231_234156189.0Compositional biasNote=Poly-Pro
TgeneTMCO1chr1:165667614chr1:165697358ENST0000039212957189_205156189.0IntramembranePore-forming
TgeneTMCO1chr1:165667615chr1:165697358ENST0000039212957189_205156189.0IntramembranePore-forming
TgeneTMCO1chr1:165667614chr1:165697358ENST0000039212957163_188156189.0Topological domainCytoplasmic
TgeneTMCO1chr1:165667614chr1:165697358ENST0000039212957206_239156189.0Topological domainCytoplasmic
TgeneTMCO1chr1:165667615chr1:165697358ENST0000039212957163_188156189.0Topological domainCytoplasmic
TgeneTMCO1chr1:165667615chr1:165697358ENST0000039212957206_239156189.0Topological domainCytoplasmic

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneALDH9A1chr1:165667614chr1:165697358ENST00000354775-111232_23660519.0Nucleotide bindingNAD
HgeneALDH9A1chr1:165667615chr1:165697358ENST00000354775-111232_23660519.0Nucleotide bindingNAD
TgeneTMCO1chr1:165667614chr1:165697358ENST000003921295783_140156189.0Coiled coilOntology_term=ECO:0000255
TgeneTMCO1chr1:165667615chr1:165697358ENST000003921295783_140156189.0Coiled coilOntology_term=ECO:0000255
TgeneTMCO1chr1:165667614chr1:165697358ENST00000392129571_60156189.0Topological domainCytoplasmic
TgeneTMCO1chr1:165667614chr1:165697358ENST000003921295782_141156189.0Topological domainLumenal
TgeneTMCO1chr1:165667615chr1:165697358ENST00000392129571_60156189.0Topological domainCytoplasmic
TgeneTMCO1chr1:165667615chr1:165697358ENST000003921295782_141156189.0Topological domainLumenal
TgeneTMCO1chr1:165667614chr1:165697358ENST0000039212957142_162156189.0TransmembraneHelical
TgeneTMCO1chr1:165667614chr1:165697358ENST000003921295761_81156189.0TransmembraneHelical
TgeneTMCO1chr1:165667615chr1:165697358ENST0000039212957142_162156189.0TransmembraneHelical
TgeneTMCO1chr1:165667615chr1:165697358ENST000003921295761_81156189.0TransmembraneHelical


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Fusion Gene Sequence for ALDH9A1-TMCO1


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 ALDH9A1-TMCO1


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 ALDH9A1-TMCO1


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 ALDH9A1-TMCO1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneALDH9A1C0019193Hepatitis, Toxic1CTD_human
HgeneALDH9A1C0860207Drug-Induced Liver Disease1CTD_human
HgeneALDH9A1C1262760Hepatitis, Drug-Induced1CTD_human
HgeneALDH9A1C3658290Drug-Induced Acute Liver Injury1CTD_human
HgeneALDH9A1C4277682Chemical and Drug Induced Liver Injury1CTD_human
HgeneALDH9A1C4279912Chemically-Induced Liver Toxicity1CTD_human
TgeneC1859252Cerebrofaciothoracic Dysplasia3GENOMICS_ENGLAND;ORPHANET
TgeneC0005941Bone Diseases, Developmental1CTD_human
TgeneC0017612Glaucoma, Open-Angle1CTD_human
TgeneC0020796Profound Mental Retardation1CTD_human
TgeneC0025363Mental Retardation, Psychosocial1CTD_human
TgeneC0040427Tooth Abnormalities1CTD_human
TgeneC0151491Congenital musculoskeletal anomalies1CTD_human
TgeneC0271148Secondary Open Angle Glaucoma1CTD_human
TgeneC0339573Glaucoma, Primary Open Angle1CTD_human
TgeneC0376634Craniofacial Abnormalities1CTD_human
TgeneC0524730Odontome1CTD_human
TgeneC0917816Mental deficiency1CTD_human
TgeneC3714756Intellectual Disability1CTD_human
TgeneC4021790Abnormality of the skeletal system1GENOMICS_ENGLAND