ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for CUL3

Gene summary

Gene information	Gene symbol	CUL3
	Gene ID	8452
	Gene name	cullin 3
	Synonyms	CUL-3\|PHA2E
	Cytomap	2q36.2
	Type of gene	protein-coding
	Description	cullin-3
	Modification date	20200327
	UniProtAcc	A0A024R475, A0A087WTG3, A0A087X1R9, H7C1J0, H7C1L6, H7C399, Q13618, Q53RD1, Q53S54,
	Context

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

Gene	GO ID	GO term	PubMed ID
CUL3	GO:0000209	protein polyubiquitination	19261606
CUL3	GO:0006511	ubiquitin-dependent protein catabolic process	25401743\|27561354
CUL3	GO:0006513	protein monoubiquitination	22358839
CUL3	GO:0006888	ER to Golgi vesicle-mediated transport	22358839
CUL3	GO:0016567	protein ubiquitination	17543862\|19782033\|19995937\|20389280\|23213400
CUL3	GO:0031145	anaphase-promoting complex-dependent catabolic process	10500095
CUL3	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	19261606\|19782033\|20389280
CUL3	GO:0071630	nuclear protein quality control by the ubiquitin-proteasome system	27561354

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Gene structures and expression levels for CUL3

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.

ENSG00000036257

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
CB	DOWN	ENST00000454323.1	CUL3-208:nonsense_mediated_decay:CUL3	1.716996e+02	-8.938612e-01	1.760601e-03	8.290120e-03
CB	UP	ENST00000409096.5	CUL3-203:protein_coding:CUL3	1.047025e+03	8.707682e-01	3.237778e-03	1.373878e-02

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 CUL3

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_111451	chr2	224514636:224514772:224535528:224535641:224557659:224557820	224535528:224535641
exon_skip_12408	chr2	224535607:224535641:224556295:224556389:224557659:224557856	224556295:224556389
exon_skip_137749	chr2	224474033:224474376:224478200:224478345:224495832:224495966	224478200:224478345
exon_skip_138654	chr2	224474199:224474376:224478200:224478345:224495832:224495966	224478200:224478345
exon_skip_158394	chr2	224502992:224503072:224503652:224503822:224505956:224505971	224503652:224503822
exon_skip_186808	chr2	224506858:224507003:224511354:224511582:224513524:224513638	224511354:224511582
exon_skip_189566	chr2	224478331:224478345:224481892:224482078:224495832:224495906	224481892:224482078
exon_skip_245384	chr2	224481892:224482078:224495832:224495966:224497753:224497819	224495832:224495966
exon_skip_266811	chr2	224514636:224514772:224535528:224535641:224584944:224585363	224535528:224535641
exon_skip_274868	chr2	224478303:224478345:224481892:224482078:224495832:224495906	224481892:224482078
exon_skip_276074	chr2	224535607:224535641:224556295:224556420:224557659:224557820	224556295:224556420
exon_skip_31247	chr2	224505956:224506132:224506858:224507003:224511354:224511411	224506858:224507003
exon_skip_35663	chr2	224535607:224535641:224556295:224556389:224557659:224557820	224556295:224556389

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 CUL3

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
ENST00000264414	224481892	224482078	Frame-shift
ENST00000264414	224535528	224535641	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
ENST00000264414	224481892	224482078	Frame-shift
ENST00000264414	224535528	224535641	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
ENST00000264414	224481892	224482078	Frame-shift
ENST00000264414	224506858	224507003	Frame-shift
ENST00000264414	224511354	224511582	Frame-shift
ENST00000264414	224495832	224495966	In-frame
ENST00000264414	224503652	224503822	In-frame
ENST00000264414	224535528	224535641	In-frame

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Infer the effects of exon skipping event on protein functional features for CUL3

p-ENSG00000036257_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
ENST00000264414	6758	768	224535528	224535641	604	716	88	125

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
ENST00000264414	6758	768	224535528	224535641	604	716	88	125

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
ENST00000264414	6758	768	224535528	224535641	604	716	88	125
ENST00000264414	6758	768	224503652	224503822	1546	1715	402	458
ENST00000264414	6758	768	224495832	224495966	2047	2180	569	613

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
Q13618	88	125	23	88	Alternative sequence	ID=VSP_008825;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13618	88	125	2	768	Chain	ID=PRO_0000119793;Note=Cullin-3
Q13618	88	125	89	94	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4EOZ
Q13618	88	125	101	122	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4EOZ
Q13618	88	125	124	129	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4EOZ
Q13618	88	125	95	98	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4EOZ

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
Q13618	88	125	23	88	Alternative sequence	ID=VSP_008825;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13618	88	125	2	768	Chain	ID=PRO_0000119793;Note=Cullin-3
Q13618	88	125	89	94	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4EOZ
Q13618	88	125	101	122	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4EOZ
Q13618	88	125	124	129	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4EOZ
Q13618	88	125	95	98	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4EOZ

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
Q13618	88	125	23	88	Alternative sequence	ID=VSP_008825;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13618	88	125	2	768	Chain	ID=PRO_0000119793;Note=Cullin-3
Q13618	88	125	89	94	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4EOZ
Q13618	88	125	101	122	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4EOZ
Q13618	88	125	124	129	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4EOZ
Q13618	88	125	95	98	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4EOZ
Q13618	402	458	2	768	Chain	ID=PRO_0000119793;Note=Cullin-3
Q13618	402	458	413	413	Natural variant	ID=VAR_067532;Note=In PHA2E. D->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22266938;Dbxref=dbSNP:rs199469656,PMID:22266938
Q13618	569	613	2	768	Chain	ID=PRO_0000119793;Note=Cullin-3
Q13618	569	613	585	585	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q13618	569	613	609	609	Sequence conflict	Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305

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3'-UTR located exon skipping events that lost miRNA binding sites in CUL3

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 CUL3

- 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 CUL3

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

ADstage

MSBB

IFG

exon_skip_250481

4.678760e-01

1.204769e-02

chr2

224535607

224535641

224556295

224556444

224557659

224557820

ADstage

MSBB

IFG

exon_skip_276074

3.855476e-01

4.274296e-02

chr2

224535607

224535641

224556295

224556420

224557659

224557820

CDR

MSBB

IFG

exon_skip_276074

4.322327e-01

2.161610e-02

chr2

224535607

224535641

224556295

224556420

224557659

224557820

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CUL3

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 CUL3

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for CUL3

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

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for CUL3

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 CUL3

Gene structures and expression levels for CUL3

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for CUL3

Open reading frame (ORF) annotation in the exon skipping event for CUL3

Infer the effects of exon skipping event on protein functional features for CUL3

3'-UTR located exon skipping events that lost miRNA binding sites in CUL3

SNVs in the skipped exons for CUL3

AD stage-associated exon skippint events for CUL3

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CUL3

Correlation with RNA binding proteins (RBPs) for CUL3

RelatedDrugs for CUL3

RelatedDiseases for CUL3