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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:NR1H3-DDB2 (FusionGDB2 ID:60083)

Fusion Gene Summary for NR1H3-DDB2

check button Fusion gene summary
Fusion gene informationFusion gene name: NR1H3-DDB2
Fusion gene ID: 60083
HgeneTgene
Gene symbol

NR1H3

DDB2

Gene ID

10062

1643

Gene namenuclear receptor subfamily 1 group H member 3damage specific DNA binding protein 2
SynonymsLXR-a|LXRA|RLD-1DDBB|UV-DDB2|XPE
Cytomap

11p11.2

11p11.2

Type of geneprotein-codingprotein-coding
Descriptionoxysterols receptor LXR-alphaliver X nuclear receptor alpha variant 1DNA damage-binding protein 2DDB p48 subunitUV-DDB 2UV-damaged DNA-binding protein 2damage-specific DNA binding protein 2, 48kDaxeroderma pigmentosum group E protein
Modification date2020032020200327
UniProtAcc

Q13133

Q92466

Ensembl transtripts involved in fusion geneENST00000395397, ENST00000405576, 
ENST00000407404, ENST00000481889, 
ENST00000405853, ENST00000441012, 
ENST00000467728, ENST00000527949, 
ENST00000529540, 		ENST00000256996, 
ENST00000378600, ENST00000378603, 
ENST00000378601, 
Fusion gene scores* DoF score1 X 1 X 1=112 X 6 X 7=504
# samples 111
** MAII scorelog2(1/1*10)=3.32192809488736log2(11/504*10)=-2.19592020997526
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NR1H3 [Title/Abstract] AND DDB2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNR1H3(47270550)-DDB2(47259387), # 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
HgeneNR1H3

GO:0010870

positive regulation of receptor biosynthetic process

18511497

HgeneNR1H3

GO:0010875

positive regulation of cholesterol efflux

16141411|19481530

HgeneNR1H3

GO:0032376

positive regulation of cholesterol transport

16141411

HgeneNR1H3

GO:0032570

response to progesterone

16141411

HgeneNR1H3

GO:0034145

positive regulation of toll-like receptor 4 signaling pathway

18511497

HgeneNR1H3

GO:0042632

cholesterol homeostasis

18511497

HgeneNR1H3

GO:0045893

positive regulation of transcription, DNA-templated

25661920

HgeneNR1H3

GO:0045944

positive regulation of transcription by RNA polymerase II

16141411|18511497|19481530|20219900|20837115

HgeneNR1H3

GO:0071222

cellular response to lipopolysaccharide

18511497

HgeneNR1H3

GO:2000325

regulation of nuclear receptor transcription coactivator activity

19481530

TgeneDDB2

GO:0000209

protein polyubiquitination

12732143

TgeneDDB2

GO:0009411

response to UV

12732143

TgeneDDB2

GO:0035518

histone H2A monoubiquitination

22334663

TgeneDDB2

GO:0051865

protein autoubiquitination

12732143

TgeneDDB2

GO:0070914

UV-damage excision repair

22334663


check buttonFusion gene breakpoints across NR1H3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across DDB2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4UCECTCGA-AP-A0L9NR1H3chr11

47270550

+DDB2chr11

47259387

+


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Fusion Gene ORF analysis for NR1H3-DDB2

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-3CDSENST00000395397ENST00000256996NR1H3chr11

47270550

+DDB2chr11

47259387

+
5UTR-3CDSENST00000395397ENST00000378600NR1H3chr11

47270550

+DDB2chr11

47259387

+
5UTR-3CDSENST00000395397ENST00000378603NR1H3chr11

47270550

+DDB2chr11

47259387

+
5UTR-3CDSENST00000405576ENST00000256996NR1H3chr11

47270550

+DDB2chr11

47259387

+
5UTR-3CDSENST00000405576ENST00000378600NR1H3chr11

47270550

+DDB2chr11

47259387

+
5UTR-3CDSENST00000405576ENST00000378603NR1H3chr11

47270550

+DDB2chr11

47259387

+
5UTR-3CDSENST00000407404ENST00000256996NR1H3chr11

47270550

+DDB2chr11

47259387

+
5UTR-3CDSENST00000407404ENST00000378600NR1H3chr11

47270550

+DDB2chr11

47259387

+
5UTR-3CDSENST00000407404ENST00000378603NR1H3chr11

47270550

+DDB2chr11

47259387

+
5UTR-3CDSENST00000481889ENST00000256996NR1H3chr11

47270550

+DDB2chr11

47259387

+
5UTR-3CDSENST00000481889ENST00000378600NR1H3chr11

47270550

+DDB2chr11

47259387

+
5UTR-3CDSENST00000481889ENST00000378603NR1H3chr11

47270550

+DDB2chr11

47259387

+
5UTR-3UTRENST00000395397ENST00000378601NR1H3chr11

47270550

+DDB2chr11

47259387

+
5UTR-3UTRENST00000405576ENST00000378601NR1H3chr11

47270550

+DDB2chr11

47259387

+
5UTR-3UTRENST00000407404ENST00000378601NR1H3chr11

47270550

+DDB2chr11

47259387

+
5UTR-3UTRENST00000481889ENST00000378601NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3CDSENST00000405853ENST00000256996NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3CDSENST00000405853ENST00000378600NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3CDSENST00000405853ENST00000378603NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3CDSENST00000441012ENST00000256996NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3CDSENST00000441012ENST00000378600NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3CDSENST00000441012ENST00000378603NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3CDSENST00000467728ENST00000256996NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3CDSENST00000467728ENST00000378600NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3CDSENST00000467728ENST00000378603NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3CDSENST00000527949ENST00000256996NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3CDSENST00000527949ENST00000378600NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3CDSENST00000527949ENST00000378603NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3CDSENST00000529540ENST00000256996NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3CDSENST00000529540ENST00000378600NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3CDSENST00000529540ENST00000378603NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3UTRENST00000405853ENST00000378601NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3UTRENST00000441012ENST00000378601NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3UTRENST00000467728ENST00000378601NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3UTRENST00000527949ENST00000378601NR1H3chr11

47270550

+DDB2chr11

47259387

+
intron-3UTRENST00000529540ENST00000378601NR1H3chr11

47270550

+DDB2chr11

47259387

+

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 NR1H3-DDB2


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)
NR1H3chr1147270550+DDB2chr1147259387+0.0002368750.9997631
NR1H3chr1147270550+DDB2chr1147259387+0.0002368750.9997631

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.

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 NR1H3-DDB2


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/:47270550/:47259387)
- 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
NR1H3

Q13133

DDB2

Q92466

FUNCTION: Nuclear receptor that exhibits a ligand-dependent transcriptional activation activity (PubMed:19481530, PubMed:25661920). Interaction with retinoic acid receptor (RXR) shifts RXR from its role as a silent DNA-binding partner to an active ligand-binding subunit in mediating retinoid responses through target genes defined by LXRES (By similarity). LXRES are DR4-type response elements characterized by direct repeats of two similar hexanuclotide half-sites spaced by four nucleotides (By similarity). Plays an important role in the regulation of cholesterol homeostasis, regulating cholesterol uptake through MYLIP-dependent ubiquitination of LDLR, VLDLR and LRP8 (PubMed:19481530). Interplays functionally with RORA for the regulation of genes involved in liver metabolism (By similarity). Induces LPCAT3-dependent phospholipid remodeling in endoplasmic reticulum (ER) membranes of hepatocytes, driving SREBF1 processing and lipogenesis (By similarity). Via LPCAT3, triggers the incorporation of arachidonate into phosphatidylcholines of ER membranes, increasing membrane dynamics and enabling triacylglycerols transfer to nascent very low-density lipoprotein (VLDL) particles. Via LPCAT3 also counteracts lipid-induced ER stress response and inflammation, likely by modulating SRC kinase membrane compartmentalization and limiting the synthesis of lipid inflammatory mediators (By similarity). {ECO:0000250|UniProtKB:Q9Z0Y9, ECO:0000269|PubMed:19481530, ECO:0000269|PubMed:25661920}.FUNCTION: Protein, which is both involved in DNA repair and protein ubiquitination, as part of the UV-DDB complex and DCX (DDB1-CUL4-X-box) complexes, respectively (PubMed:10882109, PubMed:11278856, PubMed:11705987, PubMed:9892649, PubMed:12732143, PubMed:15882621, PubMed:16473935, PubMed:18593899). Core component of the UV-DDB complex (UV-damaged DNA-binding protein complex), a complex that recognizes UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair (PubMed:10882109, PubMed:11278856, PubMed:11705987, PubMed:16260596, PubMed:12944386, PubMed:14751237). The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches (PubMed:10882109, PubMed:11278856, PubMed:11705987, PubMed:16260596, PubMed:12944386). Also functions as the substrate recognition module for the DCX (DDB2-CUL4-X-box) E3 ubiquitin-protein ligase complex DDB2-CUL4-ROC1 (also known as CUL4-DDB-ROC1 and CUL4-DDB-RBX1) (PubMed:12732143, PubMed:15882621, PubMed:16473935, PubMed:18593899, PubMed:26572825). The DDB2-CUL4-ROC1 complex may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage (PubMed:16678110, PubMed:16473935). The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair (PubMed:16678110, PubMed:16473935). The DDB2-CUL4-ROC1 complex also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER (PubMed:15882621). The DDB2-CUL4-ROC1 complex also ubiquitinates KAT7/HBO1 in response to DNA damage, leading to its degradation: recognizes KAT7/HBO1 following phosphorylation by ATR (PubMed:26572825). {ECO:0000269|PubMed:10882109, ECO:0000269|PubMed:11278856, ECO:0000269|PubMed:11705987, ECO:0000269|PubMed:12732143, ECO:0000269|PubMed:12944386, ECO:0000269|PubMed:14751237, ECO:0000269|PubMed:15882621, ECO:0000269|PubMed:16260596, ECO:0000269|PubMed:16473935, ECO:0000269|PubMed:16678110, ECO:0000269|PubMed:18593899, ECO:0000269|PubMed:26572825, ECO:0000269|PubMed:9892649}.; FUNCTION: [Isoform D1]: Inhibits UV-damaged DNA repair. {ECO:0000269|PubMed:14751237}.; FUNCTION: [Isoform D2]: Inhibits UV-damaged DNA repair. {ECO:0000269|PubMed:14751237}.

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 NR1H3-DDB2


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 NR1H3-DDB2


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 NR1H3-DDB2


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 NR1H3-DDB2


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