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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in TCGA

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Exon skipping events with PSIs in GTEx

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Open reading frame (ORF) annotation in the exon skipping event

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Exon skipping events in the canonical protein sequence

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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for NR1H3

check button Gene summary
Gene informationGene symbol

NR1H3

Gene ID

10062

Gene namenuclear receptor subfamily 1 group H member 3
SynonymsLXR-a|LXRA|RLD-1
Cytomap

11p11.2

Type of geneprotein-coding
Descriptionoxysterols receptor LXR-alphaliver X nuclear receptor alpha variant 1
Modification date20180524
UniProtAcc

Q13133

ContextPubMed: NR1H3 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
NR1H3

GO:0010870

positive regulation of receptor biosynthetic process

18511497

NR1H3

GO:0010875

positive regulation of cholesterol efflux

16141411|19481530

NR1H3

GO:0032376

positive regulation of cholesterol transport

16141411

NR1H3

GO:0032570

response to progesterone

16141411

NR1H3

GO:0034145

positive regulation of toll-like receptor 4 signaling pathway

18511497

NR1H3

GO:0042632

cholesterol homeostasis

18511497

NR1H3

GO:0045893

positive regulation of transcription, DNA-templated

25661920

NR1H3

GO:0045944

positive regulation of transcription by RNA polymerase II

16141411|18511497|19481530|20219900|20837115

NR1H3

GO:0071222

cellular response to lipopolysaccharide

18511497

NR1H3

GO:2000325

regulation of ligand-dependent nuclear receptor transcription coactivator activity

19481530


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Exon skipping events across known transcript of Ensembl for NR1H3 from UCSC genome browser

check buttonSkipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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Gene isoform structures and expression levels for NR1H3

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


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Exon skipping events with PSIs in TCGA for NR1H3

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_591051147270477:47270550:47272016:47272102:47280730:4728081047272016:47272102ENSG00000025434.14ENST00000436778.1
exon_skip_591121147270506:47270550:47280730:47280810:47281341:4728137447280730:47280810ENSG00000025434.14ENST00000407404.1
exon_skip_591161147270506:47270550:47281341:47281530:47282791:4728283147281341:47281530ENSG00000025434.14ENST00000531660.1
exon_skip_591231147279154:47279186:47279546:47279680:47280730:4728081047279546:47279680ENSG00000025434.14ENST00000444396.1
exon_skip_591321147279260:47279286:47279546:47279680:47280730:4728081047279546:47279680ENSG00000025434.14ENST00000449369.1
exon_skip_591351147279260:47279286:47279546:47279716:47280730:4728081047279546:47279716ENSG00000025434.14ENST00000419652.1,ENST00000457932.1
exon_skip_591521147279551:47279680:47280651:47280810:47281341:4728137447280651:47280810ENSG00000025434.14ENST00000436029.1,ENST00000461778.1
exon_skip_591531147279551:47279680:47280730:47280810:47281336:4728153047280730:47280810ENSG00000025434.14ENST00000420369.1
exon_skip_591541147279551:47279680:47280730:47280810:47281341:4728137447280730:47280810ENSG00000025434.14ENST00000405853.3,ENST00000449369.1,ENST00000441012.2,ENST00000525441.1,ENST00000444396.1
exon_skip_591621147279656:47279716:47280730:47280810:47281341:4728137447280730:47280810ENSG00000025434.14ENST00000457932.1
exon_skip_591641147279656:47279716:47280735:47280810:47281341:4728137447280735:47280810ENSG00000025434.14ENST00000437276.1
exon_skip_591661147280735:47280810:47280911:47281157:47281341:4728137447280911:47281157ENSG00000025434.14ENST00000419652.1
exon_skip_591671147281341:47281530:47281959:47282226:47282791:4728283147281959:47282226ENSG00000025434.14ENST00000529540.1,ENST00000412937.1,ENST00000420369.1,ENST00000405853.3,ENST00000449369.1,ENST00000436029.1,ENST00000436778.1,ENST00000467728.1,ENST00000527464.1,ENST00000395397.3,ENST00000441012.2,ENST00000481020.1,ENST00000481889.2,ENST00000405576.1,ENS
exon_skip_591691147281341:47281530:47282101:47282226:47282791:4728283147282101:47282226ENSG00000025434.14ENST00000461778.1
exon_skip_591711147281341:47281530:47282791:47283000:47283469:4728352547282791:47283000ENSG00000025434.14ENST00000531660.1
exon_skip_591791147282791:47283000:47283097:47283277:47283469:4728349547283097:47283277ENSG00000025434.14ENST00000529540.1,ENST00000467728.1,ENST00000527464.1,ENST00000395397.3,ENST00000441012.2
exon_skip_591821147282791:47283000:47283097:47283569:47289463:4728955947283097:47283569ENSG00000025434.14ENST00000481020.1,ENST00000481889.2
exon_skip_591851147282791:47283000:47283469:47283569:47289463:4728955947283469:47283569ENSG00000025434.14ENST00000531660.1,ENST00000405853.3,ENST00000405576.1,ENST00000527949.1,ENST00000407404.1
exon_skip_591861147283097:47283277:47283469:47283569:47289463:4728955947283469:47283569ENSG00000025434.14ENST00000529540.1,ENST00000467728.1,ENST00000395397.3,ENST00000441012.2
exon_skip_591911147283469:47283569:47289463:47289577:47289811:4728990647289463:47289577ENSG00000025434.14ENST00000529540.1,ENST00000405853.3,ENST00000467728.1,ENST00000395397.3,ENST00000441012.2,ENST00000481020.1,ENST00000481889.2,ENST00000405576.1,ENST00000527949.1,ENST00000407404.1
exon_skip_591981147289463:47289577:47289811:47289906:47290100:4729033247289811:47289906ENSG00000025434.14ENST00000529540.1,ENST00000532630.1,ENST00000405853.3,ENST00000467728.1,ENST00000395397.3,ENST00000441012.2,ENST00000481020.1,ENST00000481889.2,ENST00000405576.1,ENST00000527949.1,ENST00000407404.1

check button PSI values of skipped exons in TCGA.
psi tcga

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Exon skipping events with PSIs in GTEx for NR1H3

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_591051147270477:47270550:47272016:47272102:47280730:4728081047272016:47272102ENSG00000025434.14ENST00000436778.1
exon_skip_591121147270506:47270550:47280730:47280810:47281341:4728137447280730:47280810ENSG00000025434.14ENST00000407404.1
exon_skip_591161147270506:47270550:47281341:47281530:47282791:4728283147281341:47281530ENSG00000025434.14ENST00000531660.1
exon_skip_591231147279154:47279186:47279546:47279680:47280730:4728081047279546:47279680ENSG00000025434.14ENST00000444396.1
exon_skip_591321147279260:47279286:47279546:47279680:47280730:4728081047279546:47279680ENSG00000025434.14ENST00000449369.1
exon_skip_591351147279260:47279286:47279546:47279716:47280730:4728081047279546:47279716ENSG00000025434.14ENST00000457932.1,ENST00000419652.1
exon_skip_591521147279551:47279680:47280651:47280810:47281341:4728137447280651:47280810ENSG00000025434.14ENST00000461778.1,ENST00000436029.1
exon_skip_591531147279551:47279680:47280730:47280810:47281336:4728153047280730:47280810ENSG00000025434.14ENST00000420369.1
exon_skip_591541147279551:47279680:47280730:47280810:47281341:4728137447280730:47280810ENSG00000025434.14ENST00000444396.1,ENST00000449369.1,ENST00000441012.2,ENST00000525441.1,ENST00000405853.3
exon_skip_591621147279656:47279716:47280730:47280810:47281341:4728137447280730:47280810ENSG00000025434.14ENST00000457932.1
exon_skip_591641147279656:47279716:47280735:47280810:47281341:4728137447280735:47280810ENSG00000025434.14ENST00000437276.1
exon_skip_591661147280735:47280810:47280911:47281157:47281341:4728137447280911:47281157ENSG00000025434.14ENST00000419652.1
exon_skip_591671147281341:47281530:47281959:47282226:47282791:4728283147281959:47282226ENSG00000025434.14ENST00000527464.1,ENST00000529540.1,ENST00000395397.3,ENST00000405576.1,ENST00000481020.1,ENST00000481889.2,ENST00000436778.1,ENST00000407404.1,ENST00000444396.1,ENST00000412937.1,ENST00000449369.1,ENST00000441012.2,ENST00000436029.1,ENST00000467728.1,ENS
exon_skip_591691147281341:47281530:47282101:47282226:47282791:4728283147282101:47282226ENSG00000025434.14ENST00000461778.1
exon_skip_591711147281341:47281530:47282791:47283000:47283469:4728352547282791:47283000ENSG00000025434.14ENST00000531660.1
exon_skip_591791147282791:47283000:47283097:47283277:47283469:4728349547283097:47283277ENSG00000025434.14ENST00000527464.1,ENST00000529540.1,ENST00000395397.3,ENST00000441012.2,ENST00000467728.1
exon_skip_591821147282791:47283000:47283097:47283569:47289463:4728955947283097:47283569ENSG00000025434.14ENST00000481020.1,ENST00000481889.2
exon_skip_591851147282791:47283000:47283469:47283569:47289463:4728955947283469:47283569ENSG00000025434.14ENST00000405576.1,ENST00000531660.1,ENST00000407404.1,ENST00000405853.3,ENST00000527949.1
exon_skip_591861147283097:47283277:47283469:47283569:47289463:4728955947283469:47283569ENSG00000025434.14ENST00000529540.1,ENST00000395397.3,ENST00000441012.2,ENST00000467728.1
exon_skip_591911147283469:47283569:47289463:47289577:47289811:4728990647289463:47289577ENSG00000025434.14ENST00000529540.1,ENST00000395397.3,ENST00000405576.1,ENST00000481020.1,ENST00000481889.2,ENST00000407404.1,ENST00000441012.2,ENST00000467728.1,ENST00000405853.3,ENST00000527949.1
exon_skip_591981147289463:47289577:47289811:47289906:47290100:4729033247289811:47289906ENSG00000025434.14ENST00000529540.1,ENST00000395397.3,ENST00000405576.1,ENST00000481020.1,ENST00000481889.2,ENST00000532630.1,ENST00000407404.1,ENST00000441012.2,ENST00000467728.1,ENST00000405853.3,ENST00000527949.1

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for NR1H3

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST0000044101247280730472808105CDS-5UTR
ENST000004410124728346947283569Frame-shift
ENST000004677284728346947283569Frame-shift
ENST000004410124728981147289906Frame-shift
ENST000004677284728981147289906Frame-shift
ENST000004410124728195947282226In-frame
ENST000004677284728195947282226In-frame
ENST000004410124728309747283277In-frame
ENST000004677284728309747283277In-frame
ENST000004410124728946347289577In-frame
ENST000004677284728946347289577In-frame

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST0000044101247280730472808105CDS-5UTR
ENST000004410124728346947283569Frame-shift
ENST000004677284728346947283569Frame-shift
ENST000004410124728981147289906Frame-shift
ENST000004677284728981147289906Frame-shift
ENST000004410124728195947282226In-frame
ENST000004677284728195947282226In-frame
ENST000004410124728309747283277In-frame
ENST000004677284728309747283277In-frame
ENST000004410124728946347289577In-frame
ENST000004677284728946347289577In-frame

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Infer the effects of exon skipping event on protein functional features for NR1H3

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000004410121654447472819594728222643870477166
ENST00000467728274844747281959472822261471173777166
ENST00000441012165444747283097472832779141093236296
ENST000004677282748447472830974728327719472126236296
ENST000004410121654447472894634728957711941307329367
ENST000004677282748447472894634728957722272340329367

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000004410121654447472819594728222643870477166
ENST00000467728274844747281959472822261471173777166
ENST00000441012165444747283097472832779141093236296
ENST000004677282748447472830974728327719472126236296
ENST000004410121654447472894634728957711941307329367
ENST000004677282748447472894634728957722272340329367

check button Lost protein functional features of individual exon skipping events in TCGA.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q13133771661447ChainID=PRO_0000053535;Note=Oxysterols receptor LXR-alpha
Q13133771661447ChainID=PRO_0000053535;Note=Oxysterols receptor LXR-alpha
Q131337716695170DNA bindingNote=Nuclear receptor;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00407
Q131337716695170DNA bindingNote=Nuclear receptor;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00407
Q1313377166196RegionNote=Transactivation AF-1%3B required for ligand-independent transactivation function;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25661920;Dbxref=PMID:25661920
Q1313377166196RegionNote=Transactivation AF-1%3B required for ligand-independent transactivation function;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25661920;Dbxref=PMID:25661920
Q131337716698118Zinc fingerNote=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00407
Q131337716698118Zinc fingerNote=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00407
Q1313377166134158Zinc fingerNote=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00407
Q1313377166134158Zinc fingerNote=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00407
Q13133236296237296Alternative sequenceID=VSP_003664;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q13133236296237296Alternative sequenceID=VSP_003664;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q131332362961447ChainID=PRO_0000053535;Note=Oxysterols receptor LXR-alpha
Q131332362961447ChainID=PRO_0000053535;Note=Oxysterols receptor LXR-alpha
Q13133236296209447DomainNote=NR LBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01189
Q13133236296209447DomainNote=NR LBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01189
Q13133236296247272HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133236296247272HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133236296278280HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133236296278280HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133236296283304HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133236296283304HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133236296268273MutagenesisNote=Abolishes interaction with NCOA2 without affecting interaction with GPS2%3B when associated with 438-A-A-439. IVDFAK->EVDFAE;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19481530;Dbxref=PMID:19481530
Q13133236296268273MutagenesisNote=Abolishes interaction with NCOA2 without affecting interaction with GPS2%3B when associated with 438-A-A-439. IVDFAK->EVDFAE;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19481530;Dbxref=PMID:19481530
Q13133236296205447RegionNote=Transactivation AF-2%3B required for ligand-dependent transactivation function%3B mediates interaction with CCAR2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25661920;Dbxref=PMID:25661920
Q13133236296205447RegionNote=Transactivation AF-2%3B required for ligand-dependent transactivation function%3B mediates interaction with CCAR2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25661920;Dbxref=PMID:25661920
Q131333293671447ChainID=PRO_0000053535;Note=Oxysterols receptor LXR-alpha
Q131333293671447ChainID=PRO_0000053535;Note=Oxysterols receptor LXR-alpha
Q13133329367209447DomainNote=NR LBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01189
Q13133329367209447DomainNote=NR LBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01189
Q13133329367333349HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133329367333349HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133329367353364HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133329367353364HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133329367205447RegionNote=Transactivation AF-2%3B required for ligand-dependent transactivation function%3B mediates interaction with CCAR2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25661920;Dbxref=PMID:25661920
Q13133329367205447RegionNote=Transactivation AF-2%3B required for ligand-dependent transactivation function%3B mediates interaction with CCAR2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25661920;Dbxref=PMID:25661920


check button Lost protein functional features of individual exon skipping events in GTEx.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q13133771661447ChainID=PRO_0000053535;Note=Oxysterols receptor LXR-alpha
Q13133771661447ChainID=PRO_0000053535;Note=Oxysterols receptor LXR-alpha
Q131337716695170DNA bindingNote=Nuclear receptor;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00407
Q131337716695170DNA bindingNote=Nuclear receptor;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00407
Q1313377166196RegionNote=Transactivation AF-1%3B required for ligand-independent transactivation function;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25661920;Dbxref=PMID:25661920
Q1313377166196RegionNote=Transactivation AF-1%3B required for ligand-independent transactivation function;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25661920;Dbxref=PMID:25661920
Q131337716698118Zinc fingerNote=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00407
Q131337716698118Zinc fingerNote=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00407
Q1313377166134158Zinc fingerNote=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00407
Q1313377166134158Zinc fingerNote=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00407
Q13133236296237296Alternative sequenceID=VSP_003664;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q13133236296237296Alternative sequenceID=VSP_003664;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q131332362961447ChainID=PRO_0000053535;Note=Oxysterols receptor LXR-alpha
Q131332362961447ChainID=PRO_0000053535;Note=Oxysterols receptor LXR-alpha
Q13133236296209447DomainNote=NR LBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01189
Q13133236296209447DomainNote=NR LBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01189
Q13133236296247272HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133236296247272HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133236296278280HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133236296278280HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133236296283304HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133236296283304HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133236296268273MutagenesisNote=Abolishes interaction with NCOA2 without affecting interaction with GPS2%3B when associated with 438-A-A-439. IVDFAK->EVDFAE;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19481530;Dbxref=PMID:19481530
Q13133236296268273MutagenesisNote=Abolishes interaction with NCOA2 without affecting interaction with GPS2%3B when associated with 438-A-A-439. IVDFAK->EVDFAE;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19481530;Dbxref=PMID:19481530
Q13133236296205447RegionNote=Transactivation AF-2%3B required for ligand-dependent transactivation function%3B mediates interaction with CCAR2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25661920;Dbxref=PMID:25661920
Q13133236296205447RegionNote=Transactivation AF-2%3B required for ligand-dependent transactivation function%3B mediates interaction with CCAR2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25661920;Dbxref=PMID:25661920
Q131333293671447ChainID=PRO_0000053535;Note=Oxysterols receptor LXR-alpha
Q131333293671447ChainID=PRO_0000053535;Note=Oxysterols receptor LXR-alpha
Q13133329367209447DomainNote=NR LBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01189
Q13133329367209447DomainNote=NR LBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01189
Q13133329367333349HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133329367333349HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133329367353364HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133329367353364HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HJS
Q13133329367205447RegionNote=Transactivation AF-2%3B required for ligand-dependent transactivation function%3B mediates interaction with CCAR2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25661920;Dbxref=PMID:25661920
Q13133329367205447RegionNote=Transactivation AF-2%3B required for ligand-dependent transactivation function%3B mediates interaction with CCAR2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25661920;Dbxref=PMID:25661920


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SNVs in the skipped exons for NR1H3

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

check button - Differential PSIs between mutated versus non-mutated samples.
NR1H3_LIHC_exon_skip_59152_psi_boxplot.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
COADTCGA-CM-6674-01exon_skip_59167
47281960472822264728198047281980Frame_Shift_DelA-p.R84fs
LIHCTCGA-DD-A3A0-01exon_skip_59167
47281960472822264728204147282041Frame_Shift_DelC-p.A105fs
LIHCTCGA-DD-A1EG-01exon_skip_59171
47282792472830004728286447282864Frame_Shift_DelC-p.S191fs
COADTCGA-AM-5820-01exon_skip_59171
47282792472830004728288747282887Frame_Shift_DelC-p.S198fs
COADTCGA-CK-5916-01exon_skip_59171
47282792472830004728288747282887Frame_Shift_DelC-p.S198fs
STADTCGA-HU-A4GU-01exon_skip_59171
47282792472830004728288747282887Frame_Shift_DelC-p.P199fs
STADTCGA-HU-A4GU-01exon_skip_59171
47282792472830004728288747282887Frame_Shift_DelC-p.S204fs
UCECTCGA-D1-A0ZS-01exon_skip_59171
47282792472830004728288747282887Frame_Shift_DelC-p.P199fs
LIHCTCGA-DD-A3A0-01exon_skip_59182
47283098472835694728344047283440Frame_Shift_DelC-p.P306fs
LIHCTCGA-DD-A3A0-01exon_skip_59182
47283098472835694728356347283563Frame_Shift_DelA-p.A333fs
LIHCTCGA-DD-A3A0-01exon_skip_59182
47283098472835694728356347283563Frame_Shift_DelA-p.K328fs
LIHCTCGA-DD-A3A0-01exon_skip_59186
exon_skip_59185
47283470472835694728356347283563Frame_Shift_DelA-p.A333fs
LIHCTCGA-DD-A3A0-01exon_skip_59186
exon_skip_59185
47283470472835694728356347283563Frame_Shift_DelA-p.K328fs
LIHCTCGA-BC-A10T-01exon_skip_59152
47280652472808104728078147280782Frame_Shift_Ins-Gp.R5fs
LIHCTCGA-BC-A10T-01exon_skip_59112
exon_skip_59162
exon_skip_59164
exon_skip_59154
exon_skip_59153
47280731472808104728078147280782Frame_Shift_Ins-Gp.R5fs
LIHCTCGA-BC-A10T-01exon_skip_59112
exon_skip_59162
exon_skip_59164
exon_skip_59154
exon_skip_59153
47280736472808104728078147280782Frame_Shift_Ins-Gp.R5fs
COADTCGA-G4-6628-01exon_skip_59171
47282792472830004728286847282869Frame_Shift_Ins-Cp.L192fs
COADTCGA-G4-6309-01exon_skip_59171
47282792472830004728288647282887Frame_Shift_Ins-Cp.S198fs
HNSCTCGA-CV-A6K1-01exon_skip_59171
47282792472830004728288647282887Frame_Shift_Ins-Cp.SP198fs
KIRCTCGA-A3-3313-01exon_skip_59171
47282792472830004728288647282887Frame_Shift_Ins-Cp.SP198fs
KIRCTCGA-AK-3453-01exon_skip_59171
47282792472830004728288647282887Frame_Shift_Ins-Cp.SP198fs
LUADTCGA-17-Z031-01exon_skip_59171
47282792472830004728288647282887Frame_Shift_Ins-Cp.SP198fs
STADTCGA-HU-8602-01exon_skip_59171
47282792472830004728288747282888Frame_Shift_Ins-Cp.S198fs

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
NR1H3_47279551_47279680_47280651_47280810_47281341_47281374_TCGA-BC-A10T-01Sample: TCGA-BC-A10T-01
Cancer type: LIHC
ESID: exon_skip_59152
Skipped exon start: 47280652
Skipped exon end: 47280810
Mutation start: 47280781
Mutation end: 47280782
Mutation type: Frame_Shift_Ins
Reference seq: -
Mutation seq: G
AAchange: p.R5fs
NR1H3_47279551_47279680_47280651_47280810_47281341_47281374_TCGA-BC-A10T-01Sample: TCGA-BC-A10T-01
Cancer type: LIHC
ESID: exon_skip_59153
Skipped exon start: 47280731
Skipped exon end: 47280810
Mutation start: 47280781
Mutation end: 47280782
Mutation type: Frame_Shift_Ins
Reference seq: -
Mutation seq: G
AAchange: p.R5fs
NR1H3_47279551_47279680_47280651_47280810_47281341_47281374_TCGA-BC-A10T-01Sample: TCGA-BC-A10T-01
Cancer type: LIHC
ESID: exon_skip_59153
Skipped exon start: 47280736
Skipped exon end: 47280810
Mutation start: 47280781
Mutation end: 47280782
Mutation type: Frame_Shift_Ins
Reference seq: -
Mutation seq: G
AAchange: p.R5fs
exon_skip_478926_LIHC_TCGA-BC-A10T-01.png
boxplot
exon_skip_59152_LIHC_TCGA-BC-A10T-01.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
SNUC4_LARGE_INTESTINE47282792472830004728288747282887Frame_Shift_DelC-p.P200fs
CW2_LARGE_INTESTINE47282792472830004728288747282887Frame_Shift_DelC-p.P200fs
NCIH2342_LUNG47283098472832774728310447283104Frame_Shift_DelC-p.P239fs
NCIH2342_LUNG47283098472835694728310447283104Frame_Shift_DelC-p.P239fs
EN_ENDOMETRIUM47281342472815304728135747281357Missense_MutationTGp.L20R
HEC1_ENDOMETRIUM47281342472815304728136047281360Missense_MutationGTp.W21L
CW2_LARGE_INTESTINE47281342472815304728137147281371Missense_MutationGAp.A25T
LNCAPCLONEFGC_PROSTATE47281960472822264728200347282003Missense_MutationGAp.M92I
VMRCRCZ_KIDNEY47281960472822264728201647282016Missense_MutationCAp.L97I
RERFLCKJ_LUNG47281960472822264728204447282044Missense_MutationCTp.S106L
RH36_SOFT_TISSUE47281960472822264728209047282090Missense_MutationCAp.F121L
SKMEL1_SKIN47281960472822264728212547282125Missense_MutationTCp.I133T
SKMEL1_SKIN47282102472822264728212547282125Missense_MutationTCp.I133T
SNU175_LARGE_INTESTINE47281960472822264728216647282166Missense_MutationCTp.R147C
SNU175_LARGE_INTESTINE47282102472822264728216647282166Missense_MutationCTp.R147C
SNU1040_LARGE_INTESTINE47281960472822264728217047282170Missense_MutationGAp.R148H
SNU1040_LARGE_INTESTINE47282102472822264728217047282170Missense_MutationGAp.R148H
HEC108_ENDOMETRIUM47281960472822264728218547282185Missense_MutationGAp.C153Y
HEC108_ENDOMETRIUM47282102472822264728218547282185Missense_MutationGAp.C153Y
SNU1040_LARGE_INTESTINE47281960472822264728219447282194Missense_MutationGAp.R156H
SNU1040_LARGE_INTESTINE47282102472822264728219447282194Missense_MutationGAp.R156H
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE47281960472822264728221747282217Missense_MutationCTp.R164W
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE47282102472822264728221747282217Missense_MutationCTp.R164W
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE47282792472830004728281647282816Missense_MutationGAp.R175H
JIYOYEP2003_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE47282792472830004728282547282825Missense_MutationAGp.K178R
REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE47282792472830004728291247282912Missense_MutationGAp.S207N
NCIH211_LUNG47282792472830004728291547282915Missense_MutationCTp.P208L
RL952_ENDOMETRIUM47282792472830004728292047282920Missense_MutationCGp.Q210E
SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE47282792472830004728295147282951Missense_MutationCGp.A220G
NB69_AUTONOMIC_GANGLIA47283098472835694728349247283492Missense_MutationGAp.R304Q
NB69_AUTONOMIC_GANGLIA47283470472835694728349247283492Missense_MutationGAp.R304Q
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE47283098472835694728353147283531Missense_MutationACp.K317T
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE47283470472835694728353147283531Missense_MutationACp.K317T
KMRC1_KIDNEY47289464472895774728950147289501Missense_MutationCAp.F342L
JHUEM7_ENDOMETRIUM47289464472895774728951347289513Missense_MutationGTp.M346I
NTERA2CLD1_TESTIS47289812472899064728983447289834Missense_MutationGCp.Q375H
HEC50B_ENDOMETRIUM47289812472899064728984247289842Missense_MutationTGp.V378G
OVK18_OVARY47289812472899064728988947289889Missense_MutationTCp.S394P
P30OHK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE47289812472899064728989947289899Missense_MutationAGp.H397R
SNU1040_LARGE_INTESTINE47283098472832774728310347283103Nonsense_MutationGAp.W238*
SNU1040_LARGE_INTESTINE47283098472835694728310347283103Nonsense_MutationGAp.W238*
SN12C_KIDNEY47283098472835694728347047283470Splice_SiteGTp.V297L
SN12C_KIDNEY47283470472835694728347047283470Splice_SiteGTp.V297L

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NR1H3

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value
exon_skip_591521147279551:47279680:47280651:47280810:47281341:4728137447280651:47280810ENST00000436029.1,ENST00000461778.1KIRCrs11039155chr11:47280762G/A1.88e-10
exon_skip_591521147279551:47279680:47280651:47280810:47281341:4728137447280651:47280810ENST00000436029.1,ENST00000461778.1LIHCrs12221497chr11:47280653G/A2.90e-04
exon_skip_591521147279551:47279680:47280651:47280810:47281341:4728137447280651:47280810ENST00000436029.1,ENST00000461778.1OVrs11039155chr11:47280762G/A9.96e-06
exon_skip_591521147279551:47279680:47280651:47280810:47281341:4728137447280651:47280810ENST00000436029.1,ENST00000461778.1PRADrs11039155chr11:47280762G/A5.95e-05
exon_skip_591521147279551:47279680:47280651:47280810:47281341:4728137447280651:47280810ENST00000436029.1,ENST00000461778.1SARCrs11039155chr11:47280762G/A7.58e-04
exon_skip_591121147270506:47270550:47280730:47280810:47281341:4728137447280730:47280810ENST00000407404.1KIRCrs11039155chr11:47280762G/A1.88e-10
exon_skip_591121147270506:47270550:47280730:47280810:47281341:4728137447280730:47280810ENST00000407404.1OVrs11039155chr11:47280762G/A9.96e-06
exon_skip_591121147270506:47270550:47280730:47280810:47281341:4728137447280730:47280810ENST00000407404.1PRADrs11039155chr11:47280762G/A5.95e-05
exon_skip_591121147270506:47270550:47280730:47280810:47281341:4728137447280730:47280810ENST00000407404.1SARCrs11039155chr11:47280762G/A7.58e-04
exon_skip_591621147279656:47279716:47280730:47280810:47281341:4728137447280730:47280810ENST00000457932.1KIRCrs11039155chr11:47280762G/A1.88e-10
exon_skip_591621147279656:47279716:47280730:47280810:47281341:4728137447280730:47280810ENST00000457932.1OVrs11039155chr11:47280762G/A9.96e-06
exon_skip_591621147279656:47279716:47280730:47280810:47281341:4728137447280730:47280810ENST00000457932.1PRADrs11039155chr11:47280762G/A5.95e-05
exon_skip_591621147279656:47279716:47280730:47280810:47281341:4728137447280730:47280810ENST00000457932.1SARCrs11039155chr11:47280762G/A7.58e-04
exon_skip_591641147279656:47279716:47280735:47280810:47281341:4728137447280735:47280810ENST00000437276.1KIRCrs11039155chr11:47280762G/A1.88e-10
exon_skip_591641147279656:47279716:47280735:47280810:47281341:4728137447280735:47280810ENST00000437276.1OVrs11039155chr11:47280762G/A9.96e-06
exon_skip_591641147279656:47279716:47280735:47280810:47281341:4728137447280735:47280810ENST00000437276.1PRADrs11039155chr11:47280762G/A5.95e-05
exon_skip_591641147279656:47279716:47280735:47280810:47281341:4728137447280735:47280810ENST00000437276.1SARCrs11039155chr11:47280762G/A7.58e-04
exon_skip_591671147281341:47281530:47281959:47282226:47282791:4728283147281959:47282226ENST00000529540.1,ENST00000412937.1,ENST00000420369.1,ENST00000405853.3,ENST00000449369.1,ENST00000436029.1,ENST00000436778.1,ENST00000467728.1,ENST00000527464.1,ENST00000395397.3,ENST00000441012.2,ENST00000481020.1,ENST00000481889.2,ENST00000405576.1,ENSBRCArs2279238chr11:47282024C/T9.38e-12
exon_skip_591671147281341:47281530:47281959:47282226:47282791:4728283147281959:47282226ENST00000529540.1,ENST00000412937.1,ENST00000420369.1,ENST00000405853.3,ENST00000449369.1,ENST00000436029.1,ENST00000436778.1,ENST00000467728.1,ENST00000527464.1,ENST00000395397.3,ENST00000441012.2,ENST00000481020.1,ENST00000481889.2,ENST00000405576.1,ENSBRCArs2279238chr11:47282024C/T4.47e-04
exon_skip_591671147281341:47281530:47281959:47282226:47282791:4728283147281959:47282226ENST00000529540.1,ENST00000412937.1,ENST00000420369.1,ENST00000405853.3,ENST00000449369.1,ENST00000436029.1,ENST00000436778.1,ENST00000467728.1,ENST00000527464.1,ENST00000395397.3,ENST00000441012.2,ENST00000481020.1,ENST00000481889.2,ENST00000405576.1,ENSLGGrs2279238chr11:47282024C/T2.32e-16
exon_skip_591671147281341:47281530:47281959:47282226:47282791:4728283147281959:47282226ENST00000529540.1,ENST00000412937.1,ENST00000420369.1,ENST00000405853.3,ENST00000449369.1,ENST00000436029.1,ENST00000436778.1,ENST00000467728.1,ENST00000527464.1,ENST00000395397.3,ENST00000441012.2,ENST00000481020.1,ENST00000481889.2,ENST00000405576.1,ENSLGGrs2279238chr11:47282024C/T6.43e-04
exon_skip_591671147281341:47281530:47281959:47282226:47282791:4728283147281959:47282226ENST00000529540.1,ENST00000412937.1,ENST00000420369.1,ENST00000405853.3,ENST00000449369.1,ENST00000436029.1,ENST00000436778.1,ENST00000467728.1,ENST00000527464.1,ENST00000395397.3,ENST00000441012.2,ENST00000481020.1,ENST00000481889.2,ENST00000405576.1,ENSLGGrs2279238chr11:47282024C/T2.53e-03
exon_skip_591671147281341:47281530:47281959:47282226:47282791:4728283147281959:47282226ENST00000529540.1,ENST00000412937.1,ENST00000420369.1,ENST00000405853.3,ENST00000449369.1,ENST00000436029.1,ENST00000436778.1,ENST00000467728.1,ENST00000527464.1,ENST00000395397.3,ENST00000441012.2,ENST00000481020.1,ENST00000481889.2,ENST00000405576.1,ENSKIRCrs2279238chr11:47282024C/T1.13e-07
exon_skip_591671147281341:47281530:47281959:47282226:47282791:4728283147281959:47282226ENST00000529540.1,ENST00000412937.1,ENST00000420369.1,ENST00000405853.3,ENST00000449369.1,ENST00000436029.1,ENST00000436778.1,ENST00000467728.1,ENST00000527464.1,ENST00000395397.3,ENST00000441012.2,ENST00000481020.1,ENST00000481889.2,ENST00000405576.1,ENSLUADrs2279238chr11:47282024C/T5.13e-09
exon_skip_591671147281341:47281530:47281959:47282226:47282791:4728283147281959:47282226ENST00000529540.1,ENST00000412937.1,ENST00000420369.1,ENST00000405853.3,ENST00000449369.1,ENST00000436029.1,ENST00000436778.1,ENST00000467728.1,ENST00000527464.1,ENST00000395397.3,ENST00000441012.2,ENST00000481020.1,ENST00000481889.2,ENST00000405576.1,ENSLUSCrs2279238chr11:47282024C/T5.82e-10
exon_skip_591671147281341:47281530:47281959:47282226:47282791:4728283147281959:47282226ENST00000529540.1,ENST00000412937.1,ENST00000420369.1,ENST00000405853.3,ENST00000449369.1,ENST00000436029.1,ENST00000436778.1,ENST00000467728.1,ENST00000527464.1,ENST00000395397.3,ENST00000441012.2,ENST00000481020.1,ENST00000481889.2,ENST00000405576.1,ENSOVrs2279238chr11:47282024C/T5.47e-05
exon_skip_591671147281341:47281530:47281959:47282226:47282791:4728283147281959:47282226ENST00000529540.1,ENST00000412937.1,ENST00000420369.1,ENST00000405853.3,ENST00000449369.1,ENST00000436029.1,ENST00000436778.1,ENST00000467728.1,ENST00000527464.1,ENST00000395397.3,ENST00000441012.2,ENST00000481020.1,ENST00000481889.2,ENST00000405576.1,ENSPRADrs2279238chr11:47282024C/T1.95e-03
exon_skip_591671147281341:47281530:47281959:47282226:47282791:4728283147281959:47282226ENST00000529540.1,ENST00000412937.1,ENST00000420369.1,ENST00000405853.3,ENST00000449369.1,ENST00000436029.1,ENST00000436778.1,ENST00000467728.1,ENST00000527464.1,ENST00000395397.3,ENST00000441012.2,ENST00000481020.1,ENST00000481889.2,ENST00000405576.1,ENSTHYMrs2279238chr11:47282024C/T5.20e-04
exon_skip_591671147281341:47281530:47281959:47282226:47282791:4728283147281959:47282226ENST00000529540.1,ENST00000412937.1,ENST00000420369.1,ENST00000405853.3,ENST00000449369.1,ENST00000436029.1,ENST00000436778.1,ENST00000467728.1,ENST00000527464.1,ENST00000395397.3,ENST00000441012.2,ENST00000481020.1,ENST00000481889.2,ENST00000405576.1,ENSTHCArs2279238chr11:47282024C/T1.43e-06
exon_skip_591541147279551:47279680:47280730:47280810:47281341:4728137447280730:47280810ENST00000405853.3,ENST00000449369.1,ENST00000441012.2,ENST00000525441.1,ENST00000444396.1KIRCrs11039155chr11:47280762G/A1.88e-10
exon_skip_591541147279551:47279680:47280730:47280810:47281341:4728137447280730:47280810ENST00000405853.3,ENST00000449369.1,ENST00000441012.2,ENST00000525441.1,ENST00000444396.1OVrs11039155chr11:47280762G/A9.96e-06
exon_skip_591541147279551:47279680:47280730:47280810:47281341:4728137447280730:47280810ENST00000405853.3,ENST00000449369.1,ENST00000441012.2,ENST00000525441.1,ENST00000444396.1PRADrs11039155chr11:47280762G/A5.95e-05
exon_skip_591541147279551:47279680:47280730:47280810:47281341:4728137447280730:47280810ENST00000405853.3,ENST00000449369.1,ENST00000441012.2,ENST00000525441.1,ENST00000444396.1SARCrs11039155chr11:47280762G/A7.58e-04
exon_skip_591531147279551:47279680:47280730:47280810:47281336:4728153047280730:47280810ENST00000420369.1KIRCrs11039155chr11:47280762G/A1.88e-10
exon_skip_591531147279551:47279680:47280730:47280810:47281336:4728153047280730:47280810ENST00000420369.1OVrs11039155chr11:47280762G/A9.96e-06
exon_skip_591531147279551:47279680:47280730:47280810:47281336:4728153047280730:47280810ENST00000420369.1PRADrs11039155chr11:47280762G/A5.95e-05
exon_skip_591531147279551:47279680:47280730:47280810:47281336:4728153047280730:47280810ENST00000420369.1SARCrs11039155chr11:47280762G/A7.58e-04

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NR1H3


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NR1H3


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RelatedDrugs for NR1H3

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
Q13133DB11994DiacereinOxysterols receptor LXR-alphasmall moleculeapproved|investigational

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RelatedDiseases for NR1H3

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
NR1H3C0008370Cholestasis1CTD_human
NR1H3C0015695Fatty Liver1CTD_human
NR1H3C4277682Chemical and Drug Induced Liver Injury1CTD_human