ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for SBDS

Gene summary

Gene information	Gene symbol	SBDS
	Gene ID	51119
	Gene name	SBDS ribosome maturation factor
	Synonyms	CGI-97\|SDS\|SWDS
	Cytomap	7q11.21
	Type of gene	protein-coding
	Description	ribosome maturation protein SBDSSBDS, ribosome assembly guanine nucleotide exchange factor
	Modification date	20200313
	UniProtAcc	A0A087X020, A0A0S2Z5F7, A0A0S2Z5I7, F8WE72, Q9Y3A5,
	Context

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

Gene	GO ID	GO term	PubMed ID
SBDS	GO:0007052	mitotic spindle organization	18324336
SBDS	GO:0030595	leukocyte chemotaxis	14743349
SBDS	GO:0042256	mature ribosome assembly	21536732

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Gene structures and expression levels for SBDS

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.

ENSG00000126524

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 SBDS

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_13586	chr7	66993217:66993417:66994212:66994342:66995290:66995293	66994212:66994342
exon_skip_141831	chr7	66988341:66988499:66991137:66991301:66993217:66993417	66991137:66991301
exon_skip_164211	chr7	66991214:66991301:66993217:66993417:66994212:66994282	66993217:66993417
exon_skip_172807	chr7	66993385:66993417:66994220:66994341:66995290:66995293	66994220:66994341
exon_skip_237144	chr7	66993385:66993417:66994212:66994342:66995290:66995293	66994212:66994342
exon_skip_272839	chr7	66991137:66991301:66993217:66993417:66994212:66994341	66993217:66993417
exon_skip_277971	chr7	66993217:66993417:66994220:66994341:66995290:66995293	66994220:66994341
exon_skip_289222	chr7	66991176:66991301:66993217:66993417:66994212:66994341	66993217:66993417
exon_skip_46533	chr7	66991137:66991301:66993217:66993417:66994212:66994282	66993217:66993417

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 SBDS

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
ENST00000246868	66991137	66991301	In-frame
ENST00000246868	66993217	66993417	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
ENST00000246868	66991137	66991301	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
ENST00000246868	66991137	66991301	In-frame
ENST00000246868	66993217	66993417	In-frame

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

p-ENSG00000126524_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
ENST00000246868	1648	250	66993217	66993417	443	642	86	152
ENST00000246868	1648	250	66991137	66991301	644	807	153	207

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
ENST00000246868	1648	250	66991137	66991301	644	807	153	207

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
ENST00000246868	1648	250	66993217	66993417	443	642	86	152
ENST00000246868	1648	250	66991137	66991301	644	807	153	207

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
Q9Y3A5	86	152	91	94	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	86	152	116	118	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	86	152	122	124	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	86	152	146	148	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	86	152	2	250	Chain	ID=PRO_0000123762;Note=Ribosome maturation protein SBDS
Q9Y3A5	86	152	80	90	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	86	152	97	115	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	86	152	130	140	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	86	152	150	164	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	86	152	151	151	Mutagenesis	Note=Strongly reduced release of EIF6 from pre-60S ribosome subunits. K->N;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21536732;Dbxref=PMID:21536732
Q9Y3A5	86	152	87	87	Natural variant	ID=VAR_015393;Note=In SDS1%3B unknown pathological significance. I->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12496757;Dbxref=PMID:12496757
Q9Y3A5	86	152	126	126	Natural variant	ID=VAR_015394;Note=In SDS1%3B strongly reduced release of EIF6 from pre-60S ribosome subunits. R->T;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12496757,ECO:0000269\|PubMed:21536732;Dbxref=dbSNP:rs113993995,PMID:12496757,PMID:21536732
Q9Y3A5	86	152	89	89	Sequence conflict	Note=T->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9Y3A5	86	152	105	105	Sequence conflict	Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9Y3A5	86	152	114	114	Sequence conflict	Note=I->F;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9Y3A5	86	152	126	126	Sequence conflict	Note=R->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9Y3A5	86	152	143	143	Sequence conflict	Note=S->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9Y3A5	86	152	146	146	Sequence conflict	Note=T->P;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9Y3A5	153	207	170	178	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	153	207	194	200	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	153	207	203	205	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	153	207	207	214	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	153	207	2	250	Chain	ID=PRO_0000123762;Note=Ribosome maturation protein SBDS
Q9Y3A5	153	207	150	164	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	153	207	183	193	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	153	207	169	169	Natural variant	ID=VAR_015395;Note=In SDS1%3B unknown pathological significance. R->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12496757;Dbxref=dbSNP:rs113993996,PMID:12496757
Q9Y3A5	153	207	180	182	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9

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
Q9Y3A5	153	207	170	178	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	153	207	194	200	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	153	207	203	205	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	153	207	207	214	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	153	207	2	250	Chain	ID=PRO_0000123762;Note=Ribosome maturation protein SBDS
Q9Y3A5	153	207	150	164	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	153	207	183	193	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	153	207	169	169	Natural variant	ID=VAR_015395;Note=In SDS1%3B unknown pathological significance. R->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12496757;Dbxref=dbSNP:rs113993996,PMID:12496757
Q9Y3A5	153	207	180	182	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9

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
Q9Y3A5	86	152	91	94	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	86	152	116	118	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	86	152	122	124	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	86	152	146	148	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	86	152	2	250	Chain	ID=PRO_0000123762;Note=Ribosome maturation protein SBDS
Q9Y3A5	86	152	80	90	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	86	152	97	115	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	86	152	130	140	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	86	152	150	164	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	86	152	151	151	Mutagenesis	Note=Strongly reduced release of EIF6 from pre-60S ribosome subunits. K->N;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21536732;Dbxref=PMID:21536732
Q9Y3A5	86	152	87	87	Natural variant	ID=VAR_015393;Note=In SDS1%3B unknown pathological significance. I->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12496757;Dbxref=PMID:12496757
Q9Y3A5	86	152	126	126	Natural variant	ID=VAR_015394;Note=In SDS1%3B strongly reduced release of EIF6 from pre-60S ribosome subunits. R->T;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12496757,ECO:0000269\|PubMed:21536732;Dbxref=dbSNP:rs113993995,PMID:12496757,PMID:21536732
Q9Y3A5	86	152	89	89	Sequence conflict	Note=T->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9Y3A5	86	152	105	105	Sequence conflict	Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9Y3A5	86	152	114	114	Sequence conflict	Note=I->F;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9Y3A5	86	152	126	126	Sequence conflict	Note=R->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9Y3A5	86	152	143	143	Sequence conflict	Note=S->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9Y3A5	86	152	146	146	Sequence conflict	Note=T->P;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9Y3A5	153	207	170	178	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	153	207	194	200	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	153	207	203	205	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	153	207	207	214	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	153	207	2	250	Chain	ID=PRO_0000123762;Note=Ribosome maturation protein SBDS
Q9Y3A5	153	207	150	164	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	153	207	183	193	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9
Q9Y3A5	153	207	169	169	Natural variant	ID=VAR_015395;Note=In SDS1%3B unknown pathological significance. R->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12496757;Dbxref=dbSNP:rs113993996,PMID:12496757
Q9Y3A5	153	207	180	182	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AN9

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

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 SBDS

- Differential PSIs between mutated versus non-mutated samples.

ENSG00000126524.exon_skip_200848.ROSMAP_DLPFC.WGS.boxplot.svg
boxplot

ENSG00000126524.exon_skip_200848.ROSMAP_PCC.WGS.boxplot.svg
boxplot

- 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 SBDS

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 SBDS

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 SBDS

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for SBDS

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 SBDS

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 SBDS

Gene structures and expression levels for SBDS

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

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

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

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

SNVs in the skipped exons for SBDS

AD stage-associated exon skippint events for SBDS

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

Correlation with RNA binding proteins (RBPs) for SBDS

RelatedDrugs for SBDS

RelatedDiseases for SBDS