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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:CHD6-CHD6 (FusionGDB2 ID:16341)

Fusion Gene Summary for CHD6-CHD6

check button Fusion gene summary
Fusion gene informationFusion gene name: CHD6-CHD6
Fusion gene ID: 16341
HgeneTgene
Gene symbol

CHD6

CHD6

Gene ID

84181

84181

Gene namechromodomain helicase DNA binding protein 6chromodomain helicase DNA binding protein 6
SynonymsCHD-6|CHD5|RIGBCHD-6|CHD5|RIGB
Cytomap

20q12

20q12

Type of geneprotein-codingprotein-coding
Descriptionchromodomain-helicase-DNA-binding protein 6ATP-dependent helicase CHD6helicase C-terminal domain- and SNF2 N-terminal domain-containing proteinradiation-induced gene B proteinchromodomain-helicase-DNA-binding protein 6ATP-dependent helicase CHD6helicase C-terminal domain- and SNF2 N-terminal domain-containing proteinradiation-induced gene B protein
Modification date2020031320200313
UniProtAcc

Q8TD26

Q8TD26

Ensembl transtripts involved in fusion geneENST00000309279, ENST00000373222, 
ENST00000373233, ENST00000480022, 
ENST00000480022, ENST00000309279, 
ENST00000373222, ENST00000373233, 
Fusion gene scores* DoF score30 X 18 X 11=594013 X 15 X 6=1170
# samples 3516
** MAII scorelog2(35/5940*10)=-4.0850361038558
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/1170*10)=-2.8703647195834
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CHD6 [Title/Abstract] AND CHD6 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCHD6(40141485)-CHD6(40143593), # samples:1
CHD6(40141485)-CHD6(40162211), # samples:1
CHD6(40050694)-CHD6(40247063), # samples:1
Anticipated loss of major functional domain due to fusion event.CHD6-CHD6 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
CHD6-CHD6 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CHD6-CHD6 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
CHD6-CHD6 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

check buttonFusion gene breakpoints across CHD6 (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 CHD6 (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/AAI312497CHD6chr20

40141485

-CHD6chr20

40143593

-
ChiTaRS5.0N/AAK026022CHD6chr20

40050694

-CHD6chr20

40247063

-
ChiTaRS5.0N/ADA120241CHD6chr20

40141485

-CHD6chr20

40162211

-


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Fusion Gene ORF analysis for CHD6-CHD6

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-intronENST00000309279ENST00000480022CHD6chr20

40141485

-CHD6chr20

40143593

-
5CDS-intronENST00000309279ENST00000480022CHD6chr20

40141485

-CHD6chr20

40162211

-
5CDS-intronENST00000373222ENST00000480022CHD6chr20

40141485

-CHD6chr20

40143593

-
5CDS-intronENST00000373222ENST00000480022CHD6chr20

40141485

-CHD6chr20

40162211

-
5CDS-intronENST00000373233ENST00000480022CHD6chr20

40141485

-CHD6chr20

40143593

-
5CDS-intronENST00000373233ENST00000480022CHD6chr20

40141485

-CHD6chr20

40162211

-
Frame-shiftENST00000309279ENST00000309279CHD6chr20

40141485

-CHD6chr20

40162211

-
Frame-shiftENST00000309279ENST00000373222CHD6chr20

40141485

-CHD6chr20

40162211

-
Frame-shiftENST00000309279ENST00000373233CHD6chr20

40141485

-CHD6chr20

40162211

-
Frame-shiftENST00000373222ENST00000309279CHD6chr20

40141485

-CHD6chr20

40143593

-
Frame-shiftENST00000373222ENST00000309279CHD6chr20

40141485

-CHD6chr20

40162211

-
Frame-shiftENST00000373222ENST00000373222CHD6chr20

40141485

-CHD6chr20

40143593

-
Frame-shiftENST00000373222ENST00000373222CHD6chr20

40141485

-CHD6chr20

40162211

-
Frame-shiftENST00000373222ENST00000373233CHD6chr20

40141485

-CHD6chr20

40143593

-
Frame-shiftENST00000373222ENST00000373233CHD6chr20

40141485

-CHD6chr20

40162211

-
Frame-shiftENST00000373233ENST00000309279CHD6chr20

40141485

-CHD6chr20

40162211

-
Frame-shiftENST00000373233ENST00000373222CHD6chr20

40141485

-CHD6chr20

40162211

-
Frame-shiftENST00000373233ENST00000373233CHD6chr20

40141485

-CHD6chr20

40162211

-
In-frameENST00000309279ENST00000309279CHD6chr20

40141485

-CHD6chr20

40143593

-
In-frameENST00000309279ENST00000373222CHD6chr20

40141485

-CHD6chr20

40143593

-
In-frameENST00000309279ENST00000373233CHD6chr20

40141485

-CHD6chr20

40143593

-
In-frameENST00000373233ENST00000309279CHD6chr20

40141485

-CHD6chr20

40143593

-
In-frameENST00000373233ENST00000373222CHD6chr20

40141485

-CHD6chr20

40143593

-
In-frameENST00000373233ENST00000373233CHD6chr20

40141485

-CHD6chr20

40143593

-
intron-3CDSENST00000480022ENST00000309279CHD6chr20

40141485

-CHD6chr20

40143593

-
intron-3CDSENST00000480022ENST00000309279CHD6chr20

40141485

-CHD6chr20

40162211

-
intron-3CDSENST00000480022ENST00000373222CHD6chr20

40141485

-CHD6chr20

40143593

-
intron-3CDSENST00000480022ENST00000373222CHD6chr20

40141485

-CHD6chr20

40162211

-
intron-3CDSENST00000480022ENST00000373233CHD6chr20

40141485

-CHD6chr20

40143593

-
intron-3CDSENST00000480022ENST00000373233CHD6chr20

40141485

-CHD6chr20

40162211

-
intron-5UTRENST00000309279ENST00000309279CHD6chr20

40050694

-CHD6chr20

40247063

-
intron-5UTRENST00000309279ENST00000373233CHD6chr20

40050694

-CHD6chr20

40247063

-
intron-5UTRENST00000373222ENST00000309279CHD6chr20

40050694

-CHD6chr20

40247063

-
intron-5UTRENST00000373222ENST00000373233CHD6chr20

40050694

-CHD6chr20

40247063

-
intron-5UTRENST00000373233ENST00000309279CHD6chr20

40050694

-CHD6chr20

40247063

-
intron-5UTRENST00000373233ENST00000373233CHD6chr20

40050694

-CHD6chr20

40247063

-
intron-5UTRENST00000480022ENST00000309279CHD6chr20

40050694

-CHD6chr20

40247063

-
intron-5UTRENST00000480022ENST00000373233CHD6chr20

40050694

-CHD6chr20

40247063

-
intron-intronENST00000309279ENST00000373222CHD6chr20

40050694

-CHD6chr20

40247063

-
intron-intronENST00000309279ENST00000480022CHD6chr20

40050694

-CHD6chr20

40247063

-
intron-intronENST00000373222ENST00000373222CHD6chr20

40050694

-CHD6chr20

40247063

-
intron-intronENST00000373222ENST00000480022CHD6chr20

40050694

-CHD6chr20

40247063

-
intron-intronENST00000373233ENST00000373222CHD6chr20

40050694

-CHD6chr20

40247063

-
intron-intronENST00000373233ENST00000480022CHD6chr20

40050694

-CHD6chr20

40247063

-
intron-intronENST00000480022ENST00000373222CHD6chr20

40050694

-CHD6chr20

40247063

-
intron-intronENST00000480022ENST00000480022CHD6chr20

40141485

-CHD6chr20

40143593

-
intron-intronENST00000480022ENST00000480022CHD6chr20

40050694

-CHD6chr20

40247063

-
intron-intronENST00000480022ENST00000480022CHD6chr20

40141485

-CHD6chr20

40162211

-

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 CHD6-CHD6


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 CHD6-CHD6


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/chr20:40141485/chr20:40143593)
- 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
CHD6

Q8TD26

CHD6

Q8TD26

FUNCTION: DNA-dependent ATPase that plays a role in chromatin remodeling. Regulates transcription by disrupting nucleosomes in a largely non-sliding manner which strongly increases the accessibility of chromatin (PubMed:28533432). Activates transcription of specific genes in response to oxidative stress through interaction with NFE2L2. {ECO:0000269|PubMed:16314513, ECO:0000269|PubMed:28533432}.; FUNCTION: (Microbial infection) Acts as a transcriptional repressor of different viruses including influenza virus or papillomavirus. During influenza virus infection, the viral polymerase complex localizes CHD6 to inactive chromatin where it gets degraded in a proteasome independent-manner. {ECO:0000269|PubMed:20631145, ECO:0000269|PubMed:21899694, ECO:0000269|PubMed:23408615}.FUNCTION: DNA-dependent ATPase that plays a role in chromatin remodeling. Regulates transcription by disrupting nucleosomes in a largely non-sliding manner which strongly increases the accessibility of chromatin (PubMed:28533432). Activates transcription of specific genes in response to oxidative stress through interaction with NFE2L2. {ECO:0000269|PubMed:16314513, ECO:0000269|PubMed:28533432}.; FUNCTION: (Microbial infection) Acts as a transcriptional repressor of different viruses including influenza virus or papillomavirus. During influenza virus infection, the viral polymerase complex localizes CHD6 to inactive chromatin where it gets degraded in a proteasome independent-manner. {ECO:0000269|PubMed:20631145, ECO:0000269|PubMed:21899694, ECO:0000269|PubMed:23408615}.

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
HgeneCHD6chr20:40141485chr20:40143593ENST00000373222-5793_202319374.0Compositional biasNote=Lys-rich
HgeneCHD6chr20:40141485chr20:40143593ENST00000373233-53793_2022842716.0Compositional biasNote=Lys-rich
TgeneCHD6chr20:40141485chr20:40143593ENST00000373222271449_1503219374.0DomainNote=Myb-like
TgeneCHD6chr20:40141485chr20:40143593ENST0000037322227292_343219374.0DomainChromo 1
TgeneCHD6chr20:40141485chr20:40143593ENST0000037322227375_439219374.0DomainChromo 2
TgeneCHD6chr20:40141485chr20:40143593ENST0000037322227473_647219374.0DomainHelicase ATP-binding
TgeneCHD6chr20:40141485chr20:40143593ENST0000037322227787_956219374.0DomainHelicase C-terminal
TgeneCHD6chr20:40141485chr20:40143593ENST000003732332371449_15031842716.0DomainNote=Myb-like
TgeneCHD6chr20:40141485chr20:40143593ENST00000373233237292_3431842716.0DomainChromo 1
TgeneCHD6chr20:40141485chr20:40143593ENST00000373233237375_4391842716.0DomainChromo 2
TgeneCHD6chr20:40141485chr20:40143593ENST00000373233237473_6471842716.0DomainHelicase ATP-binding
TgeneCHD6chr20:40141485chr20:40143593ENST00000373233237787_9561842716.0DomainHelicase C-terminal
TgeneCHD6chr20:40141485chr20:40143593ENST0000037322227598_601219374.0MotifNote=DEAH box
TgeneCHD6chr20:40141485chr20:40143593ENST00000373233237598_6011842716.0MotifNote=DEAH box
TgeneCHD6chr20:40141485chr20:40143593ENST0000037322227486_493219374.0Nucleotide bindingATP
TgeneCHD6chr20:40141485chr20:40143593ENST00000373233237486_4931842716.0Nucleotide bindingATP

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCHD6chr20:40141485chr20:40143593ENST00000373222-571449_1503319374.0DomainNote=Myb-like
HgeneCHD6chr20:40141485chr20:40143593ENST00000373222-57292_343319374.0DomainChromo 1
HgeneCHD6chr20:40141485chr20:40143593ENST00000373222-57375_439319374.0DomainChromo 2
HgeneCHD6chr20:40141485chr20:40143593ENST00000373222-57473_647319374.0DomainHelicase ATP-binding
HgeneCHD6chr20:40141485chr20:40143593ENST00000373222-57787_956319374.0DomainHelicase C-terminal
HgeneCHD6chr20:40141485chr20:40143593ENST00000373233-5371449_15032842716.0DomainNote=Myb-like
HgeneCHD6chr20:40141485chr20:40143593ENST00000373233-537292_3432842716.0DomainChromo 1
HgeneCHD6chr20:40141485chr20:40143593ENST00000373233-537375_4392842716.0DomainChromo 2
HgeneCHD6chr20:40141485chr20:40143593ENST00000373233-537473_6472842716.0DomainHelicase ATP-binding
HgeneCHD6chr20:40141485chr20:40143593ENST00000373233-537787_9562842716.0DomainHelicase C-terminal
HgeneCHD6chr20:40141485chr20:40143593ENST00000373222-57598_601319374.0MotifNote=DEAH box
HgeneCHD6chr20:40141485chr20:40143593ENST00000373233-537598_6012842716.0MotifNote=DEAH box
HgeneCHD6chr20:40141485chr20:40143593ENST00000373222-57486_493319374.0Nucleotide bindingATP
HgeneCHD6chr20:40141485chr20:40143593ENST00000373233-537486_4932842716.0Nucleotide bindingATP
HgeneCHD6chr20:40141485chr20:40143593ENST00000373222-571_747319374.0RegionNote=Required for DNA-dependent ATPase activity
HgeneCHD6chr20:40141485chr20:40143593ENST00000373233-5371_7472842716.0RegionNote=Required for DNA-dependent ATPase activity
TgeneCHD6chr20:40141485chr20:40143593ENST000003732222793_202219374.0Compositional biasNote=Lys-rich
TgeneCHD6chr20:40141485chr20:40143593ENST0000037323323793_2021842716.0Compositional biasNote=Lys-rich
TgeneCHD6chr20:40141485chr20:40143593ENST00000373222271_747219374.0RegionNote=Required for DNA-dependent ATPase activity
TgeneCHD6chr20:40141485chr20:40143593ENST000003732332371_7471842716.0RegionNote=Required for DNA-dependent ATPase activity


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Fusion Gene Sequence for CHD6-CHD6


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 CHD6-CHD6


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 CHD6-CHD6


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 CHD6-CHD6


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