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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 RPSMAP, MSBB, and Mayo

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

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SNVs in the skipped exons with depth of coverage

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AD stage-associated exon skipping events

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Correlation with RNA binding proteins (RBPs)

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Related drugs with this gene

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Related diseases with this gene

Gene summary for NCOA4

check button Gene summary
Gene informationGene symbol

NCOA4

Gene ID

8031

Gene namenuclear receptor coactivator 4
SynonymsARA70|ELE1|PTC3|RFG
Cytomap

10q11.22

Type of geneprotein-coding
Descriptionnuclear receptor coactivator 470 kDa AR-activator70 kDa androgen receptor coactivatorNCoA-4RET-activating gene ELE1androgen receptor-associated protein of 70 kDaret fused
Modification date20200313
UniProtAcc

A0A024QZI5,

B4DF87,

B4DZ85,

Q13772,

Context

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
NCOA4

GO:0006622

protein targeting to lysosome

25327288


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Gene structures and expression levels for NCOA4

check buttonSkipped 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.
all structure

ENSG00000266412
check button Differentially expressed gene analysis across multiple brain tissues between AD and control.
Tissue typeDEG directionBase mean exp.log2FC(AD/control)P-valueAdj. p-value

check button Differentially expressed isoform analysis across multiple brain tissues between AD and control.
gencode gene structure
Tissue typeDEG directionENSTTranscript info.Base mean exp.log2FC(AD/control)P-valueAdjc. p-value
CBUPENST00000585056.5NCOA4-206:protein_coding:NCOA45.860762e+011.069791e+009.368197e-069.982955e-05

check button Landscape of isoform expressions across multiple brain tissues between AD and control.
gencode gene structure

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for NCOA4

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

check button All exon skipping events in AD cohorts.
Exon skip IDchrExons involved in exon skippingSkipped exon
exon_skip_130917chr1046014444:46014552:46014854:46014942:46015126:4601526646014854:46014942
exon_skip_131259chr1046006412:46006597:46009124:46009212:46009411:4600954746009124:46009212
exon_skip_156688chr1046015207:46015266:46016540:46016694:46030526:4603059246016540:46016694
exon_skip_15671chr1046014444:46014552:46014854:46014942:46015126:4601513646014854:46014942
exon_skip_177058chr1046009411:46009551:46010223:46011206:46012883:4601302346010223:46011206
exon_skip_181330chr1046015170:46015266:46016540:46016694:46030526:4603059246016540:46016694
exon_skip_207442chr1046016540:46016694:46027432:46027528:46030526:4603060746027432:46027528
exon_skip_256397chr1046015126:46015266:46016540:46016694:46030526:4603059246016540:46016694
exon_skip_288414chr1046006412:46006597:46009124:46009212:46009411:4600952446009124:46009212
exon_skip_44155chr1046009411:46009551:46010223:46011206:46012883:4601302646010223:46011206
exon_skip_53952chr1046014444:46014552:46015126:46015266:46030526:4603059246015126:46015266
exon_skip_95233chr1046013550:46013639:46014444:46014552:46030526:4603059246014444:46014552
exon_skip_95444chr1046006427:46006597:46009411:46009551:46010223:4601120646009411:46009551
exon_skip_9954chr1046016540:46016694:46027432:46027528:46030526:4603059246027432:46027528

check button Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.
Exon skipping informationTissue typeAvg(PSIs) in ADAvg(PSIs) in controlDifference (PSI)Adj. p-value


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Open reading frame (ORF) annotation in the exon skipping event for NCOA4

check button Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST0000058148646016540460166943UTR-3CDS
ENST000005814864601485446014942Frame-shift
ENST000005835654601485446014942Frame-shift
ENST000005851324601485446014942Frame-shift
ENST000005814864600941146009551In-frame
ENST000005835654600941146009551In-frame
ENST000005851324600941146009551In-frame
ENST000005814864601022346011206In-frame
ENST000005835654601022346011206In-frame
ENST000005851324601022346011206In-frame

check button Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST0000058148646016540460166943UTR-3CDS
ENST000005814864601485446014942Frame-shift
ENST000005835654601485446014942Frame-shift
ENST000005851324601485446014942Frame-shift
ENST000005814864600941146009551In-frame
ENST000005835654600941146009551In-frame
ENST000005851324600941146009551In-frame
ENST000005814864601022346011206In-frame
ENST000005835654601022346011206In-frame
ENST000005851324601022346011206In-frame

check button Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST0000058148646016540460166943UTR-3CDS
ENST000005814864601485446014942Frame-shift
ENST000005835654601485446014942Frame-shift
ENST000005851324601485446014942Frame-shift
ENST000005814864600941146009551In-frame
ENST000005835654600941146009551In-frame
ENST000005851324600941146009551In-frame
ENST000005814864601022346011206In-frame
ENST000005835654601022346011206In-frame
ENST000005851324601022346011206In-frame

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Infer the effects of exon skipping event on protein functional features for NCOA4

p-ENSG00000266412_img4.png
boxplot

check button Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000581486356661446010223460112069181900238565
ENST00000583565238861446010223460112069441926238565
ENST00000585132350661446010223460112068551837238565
ENST000005814863566614460094114600955119022041566612
ENST000005835652388614460094114600955119282067566612
ENST000005851323506614460094114600955118391978566612

check button Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000581486356661446010223460112069181900238565
ENST00000583565238861446010223460112069441926238565
ENST00000585132350661446010223460112068551837238565
ENST000005814863566614460094114600955119022041566612
ENST000005835652388614460094114600955119282067566612
ENST000005851323506614460094114600955118391978566612

check button Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000581486356661446010223460112069181900238565
ENST00000583565238861446010223460112069441926238565
ENST00000585132350661446010223460112068551837238565
ENST000005814863566614460094114600955119022041566612
ENST000005835652388614460094114600955119282067566612
ENST000005851323506614460094114600955118391978566612

check button 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 featureDescription of feature
Q13772238565239565Alternative sequenceID=VSP_003409;Note=In isoform Beta. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565239565Alternative sequenceID=VSP_003409;Note=In isoform Beta. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565239565Alternative sequenceID=VSP_003409;Note=In isoform Beta. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9892017;Dbxref=PMID:9892017
Q137722385651614ChainID=PRO_0000094410;Note=Nuclear receptor coactivator 4
Q137722385651614ChainID=PRO_0000094410;Note=Nuclear receptor coactivator 4
Q137722385651614ChainID=PRO_0000094410;Note=Nuclear receptor coactivator 4
Q13772238565327333HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1T5Z
Q13772238565327333HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1T5Z
Q13772238565327333HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1T5Z
Q13772238565350350Natural variantID=VAR_009192;Note=C->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565350350Natural variantID=VAR_009192;Note=C->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565350350Natural variantID=VAR_009192;Note=C->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565474474Natural variantID=VAR_014928;Note=P->R;Dbxref=dbSNP:rs1132111
Q13772238565474474Natural variantID=VAR_014928;Note=P->R;Dbxref=dbSNP:rs1132111
Q13772238565474474Natural variantID=VAR_014928;Note=P->R;Dbxref=dbSNP:rs1132111
Q13772238565561561Natural variantID=VAR_009193;Note=L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565561561Natural variantID=VAR_009193;Note=L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565561561Natural variantID=VAR_009193;Note=L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565271271Sequence conflictNote=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13772238565271271Sequence conflictNote=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13772238565271271Sequence conflictNote=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13772238565238239SiteNote=Breakpoint for rearrangement to form RET/PTC3 oncogene
Q13772238565238239SiteNote=Breakpoint for rearrangement to form RET/PTC3 oncogene
Q13772238565238239SiteNote=Breakpoint for rearrangement to form RET/PTC3 oncogene
Q137725666121614ChainID=PRO_0000094410;Note=Nuclear receptor coactivator 4
Q137725666121614ChainID=PRO_0000094410;Note=Nuclear receptor coactivator 4
Q137725666121614ChainID=PRO_0000094410;Note=Nuclear receptor coactivator 4

check button 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 featureDescription of feature
Q13772238565239565Alternative sequenceID=VSP_003409;Note=In isoform Beta. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565239565Alternative sequenceID=VSP_003409;Note=In isoform Beta. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565239565Alternative sequenceID=VSP_003409;Note=In isoform Beta. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9892017;Dbxref=PMID:9892017
Q137722385651614ChainID=PRO_0000094410;Note=Nuclear receptor coactivator 4
Q137722385651614ChainID=PRO_0000094410;Note=Nuclear receptor coactivator 4
Q137722385651614ChainID=PRO_0000094410;Note=Nuclear receptor coactivator 4
Q13772238565327333HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1T5Z
Q13772238565327333HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1T5Z
Q13772238565327333HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1T5Z
Q13772238565350350Natural variantID=VAR_009192;Note=C->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565350350Natural variantID=VAR_009192;Note=C->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565350350Natural variantID=VAR_009192;Note=C->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565474474Natural variantID=VAR_014928;Note=P->R;Dbxref=dbSNP:rs1132111
Q13772238565474474Natural variantID=VAR_014928;Note=P->R;Dbxref=dbSNP:rs1132111
Q13772238565474474Natural variantID=VAR_014928;Note=P->R;Dbxref=dbSNP:rs1132111
Q13772238565561561Natural variantID=VAR_009193;Note=L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565561561Natural variantID=VAR_009193;Note=L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565561561Natural variantID=VAR_009193;Note=L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565271271Sequence conflictNote=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13772238565271271Sequence conflictNote=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13772238565271271Sequence conflictNote=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13772238565238239SiteNote=Breakpoint for rearrangement to form RET/PTC3 oncogene
Q13772238565238239SiteNote=Breakpoint for rearrangement to form RET/PTC3 oncogene
Q13772238565238239SiteNote=Breakpoint for rearrangement to form RET/PTC3 oncogene
Q137725666121614ChainID=PRO_0000094410;Note=Nuclear receptor coactivator 4
Q137725666121614ChainID=PRO_0000094410;Note=Nuclear receptor coactivator 4
Q137725666121614ChainID=PRO_0000094410;Note=Nuclear receptor coactivator 4

check button 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 featureDescription of feature
Q13772238565239565Alternative sequenceID=VSP_003409;Note=In isoform Beta. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565239565Alternative sequenceID=VSP_003409;Note=In isoform Beta. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565239565Alternative sequenceID=VSP_003409;Note=In isoform Beta. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9892017;Dbxref=PMID:9892017
Q137722385651614ChainID=PRO_0000094410;Note=Nuclear receptor coactivator 4
Q137722385651614ChainID=PRO_0000094410;Note=Nuclear receptor coactivator 4
Q137722385651614ChainID=PRO_0000094410;Note=Nuclear receptor coactivator 4
Q13772238565327333HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1T5Z
Q13772238565327333HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1T5Z
Q13772238565327333HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1T5Z
Q13772238565350350Natural variantID=VAR_009192;Note=C->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565350350Natural variantID=VAR_009192;Note=C->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565350350Natural variantID=VAR_009192;Note=C->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565474474Natural variantID=VAR_014928;Note=P->R;Dbxref=dbSNP:rs1132111
Q13772238565474474Natural variantID=VAR_014928;Note=P->R;Dbxref=dbSNP:rs1132111
Q13772238565474474Natural variantID=VAR_014928;Note=P->R;Dbxref=dbSNP:rs1132111
Q13772238565561561Natural variantID=VAR_009193;Note=L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565561561Natural variantID=VAR_009193;Note=L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565561561Natural variantID=VAR_009193;Note=L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9892017;Dbxref=PMID:9892017
Q13772238565271271Sequence conflictNote=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13772238565271271Sequence conflictNote=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13772238565271271Sequence conflictNote=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13772238565238239SiteNote=Breakpoint for rearrangement to form RET/PTC3 oncogene
Q13772238565238239SiteNote=Breakpoint for rearrangement to form RET/PTC3 oncogene
Q13772238565238239SiteNote=Breakpoint for rearrangement to form RET/PTC3 oncogene
Q137725666121614ChainID=PRO_0000094410;Note=Nuclear receptor coactivator 4
Q137725666121614ChainID=PRO_0000094410;Note=Nuclear receptor coactivator 4
Q137725666121614ChainID=PRO_0000094410;Note=Nuclear receptor coactivator 4


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3'-UTR located exon skipping events that lost miRNA binding sites in NCOA4

check button 3'-UTR exon skipping evnets lost miRNA binding.
Tissue typeENSTExon skip startExon skip endmicroRNABinding site by TargetScanBinding type by TargetScanBdinding site by miRandaScore of miRandaEnergy by miRanda

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SNVs in the skipped exons for NCOA4

check button - Differential PSIs between mutated versus non-mutated samples.

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

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

check button - Non-synonymous mutations located in the skipped exons.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange

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AD stage-associated exon skippint events for NCOA4

check button Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).
AD stage infoCohortTissueSE idCoefficient P-valueChromosomeStrandE1 startE1 endSkipped startSkipped endE2 startE2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NCOA4

check button sQTL information located at the skipped exons.
Tissue typeExon skip IDSNP idLocationP-valueFDR

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Correlation with RNA binding proteins (RBPs) for NCOA4

check button Correlated RBP and related information.
Tissue typeRBP nameExon skip IDCorrelation coeifficientP-value
CBTARDBPexon_skip_130917-4.819224e-014.268725e-10
CBRBM6exon_skip_130917-5.212169e-018.017256e-12
CBTARDBPexon_skip_256397-4.431591e-011.515671e-08
CBCNOT4exon_skip_256397-4.297941e-014.499631e-08
CBPCBP1exon_skip_256397-4.194701e-011.010424e-07
CBSRSF4exon_skip_256397-4.983197e-019.998414e-11

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RelatedDrugs for NCOA4

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
UniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for NCOA4

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource