ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for NR1H2

Gene summary

Gene information	Gene symbol	NR1H2
	Gene ID	7376
	Gene name	nuclear receptor subfamily 1 group H member 2
	Synonyms	LXR-b\|LXRB\|NER\|NER-I\|RIP15\|UNR
	Cytomap	19q13.33
	Type of gene	protein-coding
	Description	oxysterols receptor LXR-betaLX receptor betaliver X nuclear receptor betanuclear orphan receptor LXR-betanuclear receptor NERsteroid hormone-nuclear receptor NERubiquitously-expressed nuclear receptor
	Modification date	20200313
	UniProtAcc	B6ZGS7, F1D8P7, M0QYE6, M0QZF5, M0R0K3, M0R1V8, M0R229, M0R2F9, M0R3A7, P55055, Q6IBU6,
	Context	- 28099631(Associations of Cerebrovascular Metabolism Genotypes With Neuropsychiatric Symptoms and Age at Onset of Alzheimer's Disease Dementia)

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene	GO ID	GO term	PubMed ID
NR1H2	GO:0032376	positive regulation of cholesterol transport	16141411
NR1H2	GO:0045892	negative regulation of transcription, DNA-templated	12393874
NR1H2	GO:0045893	positive regulation of transcription, DNA-templated	25661920
NR1H2	GO:0045944	positive regulation of transcription by RNA polymerase II	9013544\|16141411\|20219900

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Gene structures and expression levels for NR1H2

Skipped exons in the ROSMAP, MSBB, and Mayo 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.

ENSG00000131408

Differentially expressed gene analysis across multiple brain tissues between AD and control.

Tissue type

DEG direction

Base mean exp.

log2FC(AD/control)

P-value

Adj. p-value

Differentially expressed isoform analysis across multiple brain tissues between AD and control.

Tissue type

DEG direction

ENST

Transcript info.

Base mean exp.

log2FC(AD/control)

P-value

Adjc. p-value

Landscape of isoform expressions across multiple brain tissues between AD and control.

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for NR1H2

Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).

All exon skipping events in AD cohorts.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon
exon_skip_102456	chr19	50372871:50372985:50376235:50376576:50376719:50376826	50376235:50376576
exon_skip_146422	chr19	50377733:50377870:50378149:50378439:50378522:50378664	50378149:50378439
exon_skip_149195	chr19	50377783:50377870:50378149:50378439:50378522:50378678	50378149:50378439
exon_skip_205835	chr19	50377733:50377870:50378149:50378439:50378522:50378678	50378149:50378439
exon_skip_245010	chr19	50377783:50377870:50378149:50378312:50378522:50378678	50378149:50378312
exon_skip_265390	chr19	50338002:50338076:50352491:50352606:50372871:50372985	50352491:50352606
exon_skip_43262	chr19	50377733:50377870:50378149:50378312:50378522:50378796	50378149:50378312
exon_skip_44639	chr19	50377733:50377870:50378149:50378312:50378522:50378678	50378149:50378312
exon_skip_58480	chr19	50377733:50377870:50378149:50378312:50378522:50378664	50378149:50378312
exon_skip_84143	chr19	50372888:50372985:50376235:50376576:50376719:50376826	50376235:50376576
exon_skip_88050	chr19	50376473:50376576:50376719:50376826:50377587:50377648	50376719:50376826
exon_skip_91431	chr19	50377733:50377870:50378149:50378439:50378522:50378796	50378149:50378439

Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.

Exon skipping information

Tissue type

Avg(PSIs) in AD

Avg(PSIs) in control

Difference (PSI)

Adj. p-value

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Open reading frame (ORF) annotation in the exon skipping event for NR1H2

Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000253727	50376719	50376826	5UTR-5UTR
ENST00000253727	50378149	50378439	In-frame
ENST00000593926	50378149	50378439	In-frame

Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000253727	50378149	50378439	In-frame
ENST00000593926	50378149	50378439	In-frame

Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000253727	50376719	50376826	5UTR-5UTR
ENST00000253727	50378149	50378439	In-frame
ENST00000593926	50378149	50378439	In-frame

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Infer the effects of exon skipping event on protein functional features for NR1H2

p-ENSG00000131408_img4.png
boxplot

Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000253727	2015	460	50378149	50378439	418	707	61	157
ENST00000593926	1845	460	50378149	50378439	286	575	61	157

Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000253727	2015	460	50378149	50378439	418	707	61	157
ENST00000593926	1845	460	50378149	50378439	286	575	61	157

Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000253727	2015	460	50378149	50378439	418	707	61	157
ENST00000593926	1845	460	50378149	50378439	286	575	61	157

Lost protein functional features of individual exon skipping events in ROSMAP.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
P55055	61	157	61	158	Alternative sequence	ID=VSP_053789;Note=In isoform 2. VIPDPEEEPERKRKKGPAPKMLGHELCRVCGDKASGFHYNVLSCEGCKGFFRRSVVRGGARRYACRGGGTCQMDAFMRRKCQQCRLRKCKEAGMREQC->G;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P55055	61	157	61	158	Alternative sequence	ID=VSP_053789;Note=In isoform 2. VIPDPEEEPERKRKKGPAPKMLGHELCRVCGDKASGFHYNVLSCEGCKGFFRRSVVRGGARRYACRGGGTCQMDAFMRRKCQQCRLRKCKEAGMREQC->G;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P55055	61	157	88	90	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	88	90	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	99	103	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	99	103	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	1	460	Chain	ID=PRO_0000053532;Note=Oxysterols receptor LXR-beta
P55055	61	157	1	460	Chain	ID=PRO_0000053532;Note=Oxysterols receptor LXR-beta
P55055	61	157	84	161	DNA binding	Note=Nuclear receptor;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00407
P55055	61	157	84	161	DNA binding	Note=Nuclear receptor;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00407
P55055	61	157	105	116	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	105	116	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	137	139	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	137	139	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	142	151	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	142	151	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	1	85	Region	Note=Transactivation AF-1%3B required for ligand-independent transactivation function;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25661920;Dbxref=PMID:25661920
P55055	61	157	1	85	Region	Note=Transactivation AF-1%3B required for ligand-independent transactivation function;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25661920;Dbxref=PMID:25661920
P55055	61	157	87	107	Zinc finger	Note=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00407
P55055	61	157	87	107	Zinc finger	Note=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00407
P55055	61	157	125	149	Zinc finger	Note=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00407
P55055	61	157	125	149	Zinc finger	Note=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00407

Lost protein functional features of individual exon skipping events in MSBB.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
P55055	61	157	61	158	Alternative sequence	ID=VSP_053789;Note=In isoform 2. VIPDPEEEPERKRKKGPAPKMLGHELCRVCGDKASGFHYNVLSCEGCKGFFRRSVVRGGARRYACRGGGTCQMDAFMRRKCQQCRLRKCKEAGMREQC->G;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P55055	61	157	61	158	Alternative sequence	ID=VSP_053789;Note=In isoform 2. VIPDPEEEPERKRKKGPAPKMLGHELCRVCGDKASGFHYNVLSCEGCKGFFRRSVVRGGARRYACRGGGTCQMDAFMRRKCQQCRLRKCKEAGMREQC->G;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P55055	61	157	88	90	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	88	90	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	99	103	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	99	103	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	1	460	Chain	ID=PRO_0000053532;Note=Oxysterols receptor LXR-beta
P55055	61	157	1	460	Chain	ID=PRO_0000053532;Note=Oxysterols receptor LXR-beta
P55055	61	157	84	161	DNA binding	Note=Nuclear receptor;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00407
P55055	61	157	84	161	DNA binding	Note=Nuclear receptor;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00407
P55055	61	157	105	116	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	105	116	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	137	139	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	137	139	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	142	151	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	142	151	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	1	85	Region	Note=Transactivation AF-1%3B required for ligand-independent transactivation function;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25661920;Dbxref=PMID:25661920
P55055	61	157	1	85	Region	Note=Transactivation AF-1%3B required for ligand-independent transactivation function;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25661920;Dbxref=PMID:25661920
P55055	61	157	87	107	Zinc finger	Note=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00407
P55055	61	157	87	107	Zinc finger	Note=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00407
P55055	61	157	125	149	Zinc finger	Note=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00407
P55055	61	157	125	149	Zinc finger	Note=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00407

Lost protein functional features of individual exon skipping events in Mayo.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
P55055	61	157	61	158	Alternative sequence	ID=VSP_053789;Note=In isoform 2. VIPDPEEEPERKRKKGPAPKMLGHELCRVCGDKASGFHYNVLSCEGCKGFFRRSVVRGGARRYACRGGGTCQMDAFMRRKCQQCRLRKCKEAGMREQC->G;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P55055	61	157	61	158	Alternative sequence	ID=VSP_053789;Note=In isoform 2. VIPDPEEEPERKRKKGPAPKMLGHELCRVCGDKASGFHYNVLSCEGCKGFFRRSVVRGGARRYACRGGGTCQMDAFMRRKCQQCRLRKCKEAGMREQC->G;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P55055	61	157	88	90	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	88	90	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	99	103	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	99	103	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	1	460	Chain	ID=PRO_0000053532;Note=Oxysterols receptor LXR-beta
P55055	61	157	1	460	Chain	ID=PRO_0000053532;Note=Oxysterols receptor LXR-beta
P55055	61	157	84	161	DNA binding	Note=Nuclear receptor;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00407
P55055	61	157	84	161	DNA binding	Note=Nuclear receptor;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00407
P55055	61	157	105	116	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	105	116	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	137	139	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	137	139	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	142	151	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	142	151	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NQA
P55055	61	157	1	85	Region	Note=Transactivation AF-1%3B required for ligand-independent transactivation function;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25661920;Dbxref=PMID:25661920
P55055	61	157	1	85	Region	Note=Transactivation AF-1%3B required for ligand-independent transactivation function;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25661920;Dbxref=PMID:25661920
P55055	61	157	87	107	Zinc finger	Note=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00407
P55055	61	157	87	107	Zinc finger	Note=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00407
P55055	61	157	125	149	Zinc finger	Note=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00407
P55055	61	157	125	149	Zinc finger	Note=NR C4-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00407

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3'-UTR located exon skipping events that lost miRNA binding sites in NR1H2

3'-UTR exon skipping evnets lost miRNA binding.

Tissue type

ENST

Exon skip start

Exon skip end

microRNA

Binding site by TargetScan

Binding type by TargetScan

Bdinding site by miRanda

Score of miRanda

Energy by miRanda

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SNVs in the skipped exons for NR1H2

- Differential PSIs between mutated versus non-mutated samples.

- Depth of Coverage in the skipped exon of the mutated samples.

- Sashimi plot in the skipped exon of the mutated samples.

- Non-synonymous mutations located in the skipped exons.

Cancer type

Sample

ESID

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

- Non-synonymous mutations located in the skipped exons in CCLE.

Sample

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

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AD stage-associated exon skippint events for NR1H2

Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).

AD stage info

Cohort

Tissue

SE id

Coefficient

P-value

Chromosome

Strand

E1 start

E1 end

Skipped start

Skipped end

E2 start

E2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NR1H2

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

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Correlation with RNA binding proteins (RBPs) for NR1H2

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for NR1H2

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
P55055	approved\|investigational	DB11994	Diacerein	small molecule	P55055

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RelatedDiseases for NR1H2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in RPSMAP, MSBB, and Mayo
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	3'-UTR located exon skipping events lost miRNA binding sites
	SNVs in the skipped exons with depth of coverage
	AD stage-associated exon skipping events
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Correlation with RNA binding proteins (RBPs)
	Related drugs with this gene
	Related diseases with this gene

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Gene summary for NR1H2

Gene structures and expression levels for NR1H2

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for NR1H2

Open reading frame (ORF) annotation in the exon skipping event for NR1H2

Infer the effects of exon skipping event on protein functional features for NR1H2

3'-UTR located exon skipping events that lost miRNA binding sites in NR1H2

SNVs in the skipped exons for NR1H2

AD stage-associated exon skippint events for NR1H2

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NR1H2

Correlation with RNA binding proteins (RBPs) for NR1H2

RelatedDrugs for NR1H2

RelatedDiseases for NR1H2