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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:HADH-HADH (FusionGDB2 ID:35581)

Fusion Gene Summary for HADH-HADH

check button Fusion gene summary
Fusion gene informationFusion gene name: HADH-HADH
Fusion gene ID: 35581
HgeneTgene
Gene symbol

HADH

HADH

Gene ID

3033

3033

Gene namehydroxyacyl-CoA dehydrogenasehydroxyacyl-CoA dehydrogenase
SynonymsHAD|HADH1|HADHSC|HCDH|HHF4|MSCHAD|SCHADHAD|HADH1|HADHSC|HCDH|HHF4|MSCHAD|SCHAD
Cytomap

4q25

4q25

Type of geneprotein-codingprotein-coding
Descriptionhydroxyacyl-coenzyme A dehydrogenase, mitochondrialL-3-hydroxyacyl-Coenzyme A dehydrogenase, short chainmedium and short-chain L-3-hydroxyacyl-coenzyme A dehydrogenaseshort-chain 3-hydroxyacyl-CoA dehydrogenasetestis secretory sperm-binding protein Lihydroxyacyl-coenzyme A dehydrogenase, mitochondrialL-3-hydroxyacyl-Coenzyme A dehydrogenase, short chainmedium and short-chain L-3-hydroxyacyl-coenzyme A dehydrogenaseshort-chain 3-hydroxyacyl-CoA dehydrogenasetestis secretory sperm-binding protein Li
Modification date2020032020200320
UniProtAcc

Q16836

P55084

Ensembl transtripts involved in fusion geneENST00000403312, ENST00000309522, 
ENST00000603302, ENST00000454409, 
ENST00000505878, ENST00000510728, 
ENST00000510728, ENST00000309522, 
ENST00000403312, ENST00000454409, 
ENST00000505878, ENST00000603302, 
Fusion gene scores* DoF score7 X 6 X 3=1265 X 7 X 3=105
# samples 75
** MAII scorelog2(7/126*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/105*10)=-1.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HADH [Title/Abstract] AND HADH [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHADH(108911008)-HADH(108935650), # 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

check buttonFusion gene breakpoints across HADH (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 HADH (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 from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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
ChiTaRS5.0N/ACB164018HADHchr4

108911008

-HADHchr4

108935650

+


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Fusion Gene ORF analysis for HADH-HADH

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-intronENST00000403312ENST00000510728HADHchr4

108911008

-HADHchr4

108935650

+
5UTR-3CDSENST00000309522ENST00000309522HADHchr4

108911008

-HADHchr4

108935650

+
5UTR-3CDSENST00000309522ENST00000403312HADHchr4

108911008

-HADHchr4

108935650

+
5UTR-3CDSENST00000309522ENST00000454409HADHchr4

108911008

-HADHchr4

108935650

+
5UTR-3CDSENST00000309522ENST00000505878HADHchr4

108911008

-HADHchr4

108935650

+
5UTR-3CDSENST00000309522ENST00000603302HADHchr4

108911008

-HADHchr4

108935650

+
5UTR-3CDSENST00000603302ENST00000309522HADHchr4

108911008

-HADHchr4

108935650

+
5UTR-3CDSENST00000603302ENST00000403312HADHchr4

108911008

-HADHchr4

108935650

+
5UTR-3CDSENST00000603302ENST00000454409HADHchr4

108911008

-HADHchr4

108935650

+
5UTR-3CDSENST00000603302ENST00000505878HADHchr4

108911008

-HADHchr4

108935650

+
5UTR-3CDSENST00000603302ENST00000603302HADHchr4

108911008

-HADHchr4

108935650

+
5UTR-intronENST00000309522ENST00000510728HADHchr4

108911008

-HADHchr4

108935650

+
5UTR-intronENST00000603302ENST00000510728HADHchr4

108911008

-HADHchr4

108935650

+
In-frameENST00000403312ENST00000309522HADHchr4

108911008

-HADHchr4

108935650

+
In-frameENST00000403312ENST00000403312HADHchr4

108911008

-HADHchr4

108935650

+
In-frameENST00000403312ENST00000454409HADHchr4

108911008

-HADHchr4

108935650

+
In-frameENST00000403312ENST00000505878HADHchr4

108911008

-HADHchr4

108935650

+
In-frameENST00000403312ENST00000603302HADHchr4

108911008

-HADHchr4

108935650

+
intron-3CDSENST00000454409ENST00000309522HADHchr4

108911008

-HADHchr4

108935650

+
intron-3CDSENST00000454409ENST00000403312HADHchr4

108911008

-HADHchr4

108935650

+
intron-3CDSENST00000454409ENST00000454409HADHchr4

108911008

-HADHchr4

108935650

+
intron-3CDSENST00000454409ENST00000505878HADHchr4

108911008

-HADHchr4

108935650

+
intron-3CDSENST00000454409ENST00000603302HADHchr4

108911008

-HADHchr4

108935650

+
intron-3CDSENST00000505878ENST00000309522HADHchr4

108911008

-HADHchr4

108935650

+
intron-3CDSENST00000505878ENST00000403312HADHchr4

108911008

-HADHchr4

108935650

+
intron-3CDSENST00000505878ENST00000454409HADHchr4

108911008

-HADHchr4

108935650

+
intron-3CDSENST00000505878ENST00000505878HADHchr4

108911008

-HADHchr4

108935650

+
intron-3CDSENST00000505878ENST00000603302HADHchr4

108911008

-HADHchr4

108935650

+
intron-3CDSENST00000510728ENST00000309522HADHchr4

108911008

-HADHchr4

108935650

+
intron-3CDSENST00000510728ENST00000403312HADHchr4

108911008

-HADHchr4

108935650

+
intron-3CDSENST00000510728ENST00000454409HADHchr4

108911008

-HADHchr4

108935650

+
intron-3CDSENST00000510728ENST00000505878HADHchr4

108911008

-HADHchr4

108935650

+
intron-3CDSENST00000510728ENST00000603302HADHchr4

108911008

-HADHchr4

108935650

+
intron-intronENST00000454409ENST00000510728HADHchr4

108911008

-HADHchr4

108935650

+
intron-intronENST00000505878ENST00000510728HADHchr4

108911008

-HADHchr4

108935650

+
intron-intronENST00000510728ENST00000510728HADHchr4

108911008

-HADHchr4

108935650

+

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 HADH-HADH


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

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.

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Fusion Protein Features for HADH-HADH


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/chr4:108911008/chr4:108935650)
- 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
HADH

Q16836

HADH

P55084

FUNCTION: Mitochondrial fatty acid beta-oxidation enzyme that catalyzes the third step of the beta-oxidation cycle for medium and short-chain 3-hydroxy fatty acyl-CoAs (C4 to C10) (PubMed:10231530, PubMed:11489939, PubMed:16725361). Plays a role in the control of insulin secretion by inhibiting the activation of glutamate dehydrogenase 1 (GLUD1), an enzyme that has an important role in regulating amino acid-induced insulin secretion (By similarity). {ECO:0000250|UniProtKB:Q61425, ECO:0000269|PubMed:10231530, ECO:0000269|PubMed:11489939, ECO:0000269|PubMed:16725361}.FUNCTION: Mitochondrial trifunctional enzyme catalyzes the last three of the four reactions of the mitochondrial beta-oxidation pathway (PubMed:8135828, PubMed:29915090, PubMed:30850536). The mitochondrial beta-oxidation pathway is the major energy-producing process in tissues and is performed through four consecutive reactions breaking down fatty acids into acetyl-CoA (PubMed:29915090). Among the enzymes involved in this pathway, the trifunctional enzyme exhibits specificity for long-chain fatty acids (PubMed:30850536). Mitochondrial trifunctional enzyme is a heterotetrameric complex composed of two proteins, the trifunctional enzyme subunit alpha/HADHA carries the 2,3-enoyl-CoA hydratase and the 3-hydroxyacyl-CoA dehydrogenase activities, while the trifunctional enzyme subunit beta/HADHB described here bears the 3-ketoacyl-CoA thiolase activity (PubMed:8135828, PubMed:29915090, PubMed:30850536). {ECO:0000269|PubMed:29915090, ECO:0000269|PubMed:30850536, ECO:0000269|PubMed:8135828, ECO:0000303|PubMed:29915090, ECO:0000303|PubMed:30850536}.

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
TgeneHADHchr4:108911008chr4:108935650ENST000003095220834_390315.0Nucleotide bindingNAD
TgeneHADHchr4:108911008chr4:108935650ENST000006033020934_390332.0Nucleotide bindingNAD

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneHADHchr4:108911008chr4:108935650ENST00000309522-1834_390315.0Nucleotide bindingNAD
HgeneHADHchr4:108911008chr4:108935650ENST00000603302-1934_390332.0Nucleotide bindingNAD


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Fusion Gene Sequence for HADH-HADH


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 HADH-HADH


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 HADH-HADH


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 HADH-HADH


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource