ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for CD33

Gene summary

Gene information	Gene symbol	CD33
	Gene ID	945
	Gene name	CD33 molecule
	Synonyms	SIGLEC-3\|SIGLEC3\|p67
	Cytomap	19q13.41
	Type of gene	protein-coding
	Description	myeloid cell surface antigen CD33CD33 antigen (gp67)CD33 molecule transcriptgp67sialic acid-binding Ig-like lectin 3
	Modification date	20200320
	UniProtAcc	A0A173G4N9, B4DF51, P20138, Q546G0,
	Context	- 31301936(TREM2 Acts Downstream of CD33 in Modulating Microglial Pathology in Alzheimer's Disease)

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

Gene	GO ID	GO term	PubMed ID
CD33	GO:0002765	immune response-inhibiting signal transduction	10887109

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Gene structures and expression levels for CD33

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.

ENSG00000105383

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
PG	UP	ENST00000600557.1	CD33-206:lncRNA:CD33	2.293481e+00	8.248525e-01	3.071998e-03	3.235716e-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 CD33

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_102626	chr19	51235157:51235253:51235518:51235676:51239518:51239942	51235518:51235676
exon_skip_144845	chr19	51225098:51225155:51225218:51225598:51225803:51226081	51225218:51225598
exon_skip_35293	chr19	51225966:51226081:51226309:51226356:51235157:51235253	51226309:51226356
exon_skip_59858	chr19	51235157:51235253:51235595:51235676:51239518:51239942	51235595:51235676

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 CD33

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
ENST00000262262	51225218	51225598	In-frame
ENST00000262262	51226309	51226356	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
ENST00000262262	51225218	51225598	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
ENST00000262262	51235595	51235676	Frame-shift
ENST00000262262	51225218	51225598	In-frame
ENST00000262262	51226309	51226356	In-frame

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Infer the effects of exon skipping event on protein functional features for CD33

p-ENSG00000105383_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
ENST00000262262	1461	364	51225218	51225598	60	439	13	139
ENST00000262262	1461	364	51226309	51226356	720	766	233	248

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
ENST00000262262	1461	364	51225218	51225598	60	439	13	139

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
ENST00000262262	1461	364	51225218	51225598	60	439	13	139
ENST00000262262	1461	364	51226309	51226356	720	766	233	248

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
P20138	13	139	13	139	Alternative sequence	ID=VSP_046172;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:16380601;Dbxref=PMID:16380601
P20138	13	139	22	25	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	27	32	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	37	39	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	41	44	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	56	62	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	73	76	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	90	92	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	103	105	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	114	122	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	125	128	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	134	139	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	119	119	Binding site	Note=Sialic acid;Ontology_term=ECO:0000250;evidence=ECO:0000250
P20138	13	139	18	364	Chain	ID=PRO_0000014878;Note=Myeloid cell surface antigen CD33
P20138	13	139	36	169	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00114
P20138	13	139	41	101	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00114
P20138	13	139	19	135	Domain	Note=Ig-like V-type
P20138	13	139	100	100	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P20138	13	139	113	113	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P20138	13	139	49	51	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	65	68	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	96	98	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	110	112	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	14	14	Natural variant	ID=VAR_049904;Note=A->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14702039;Dbxref=dbSNP:rs12459419,PMID:14702039
P20138	13	139	22	22	Natural variant	ID=VAR_049905;Note=W->R;Dbxref=dbSNP:rs35814802
P20138	13	139	69	69	Natural variant	ID=VAR_028260;Note=R->G;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15489334,ECO:0000269\|PubMed:3139766;Dbxref=dbSNP:rs2455069,PMID:15489334,PMID:3139766
P20138	13	139	128	128	Natural variant	ID=VAR_049906;Note=S->N;Dbxref=dbSNP:rs34919259
P20138	13	139	1	17	Signal peptide	Ontology_term=ECO:0000255;evidence=ECO:0000255
P20138	13	139	18	259	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
P20138	13	139	84	89	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	233	248	18	364	Chain	ID=PRO_0000014878;Note=Myeloid cell surface antigen CD33
P20138	233	248	242	242	Natural variant	ID=VAR_028262;Note=I->L;Dbxref=dbSNP:rs988337
P20138	233	248	243	243	Natural variant	ID=VAR_028263;Note=F->L;Dbxref=dbSNP:rs11882250
P20138	233	248	18	259	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

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
P20138	13	139	13	139	Alternative sequence	ID=VSP_046172;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:16380601;Dbxref=PMID:16380601
P20138	13	139	22	25	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	27	32	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	37	39	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	41	44	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	56	62	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	73	76	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	90	92	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	103	105	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	114	122	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	125	128	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	134	139	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	119	119	Binding site	Note=Sialic acid;Ontology_term=ECO:0000250;evidence=ECO:0000250
P20138	13	139	18	364	Chain	ID=PRO_0000014878;Note=Myeloid cell surface antigen CD33
P20138	13	139	36	169	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00114
P20138	13	139	41	101	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00114
P20138	13	139	19	135	Domain	Note=Ig-like V-type
P20138	13	139	100	100	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P20138	13	139	113	113	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P20138	13	139	49	51	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	65	68	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	96	98	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	110	112	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	14	14	Natural variant	ID=VAR_049904;Note=A->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14702039;Dbxref=dbSNP:rs12459419,PMID:14702039
P20138	13	139	22	22	Natural variant	ID=VAR_049905;Note=W->R;Dbxref=dbSNP:rs35814802
P20138	13	139	69	69	Natural variant	ID=VAR_028260;Note=R->G;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15489334,ECO:0000269\|PubMed:3139766;Dbxref=dbSNP:rs2455069,PMID:15489334,PMID:3139766
P20138	13	139	128	128	Natural variant	ID=VAR_049906;Note=S->N;Dbxref=dbSNP:rs34919259
P20138	13	139	1	17	Signal peptide	Ontology_term=ECO:0000255;evidence=ECO:0000255
P20138	13	139	18	259	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
P20138	13	139	84	89	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB

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
P20138	13	139	13	139	Alternative sequence	ID=VSP_046172;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:16380601;Dbxref=PMID:16380601
P20138	13	139	22	25	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	27	32	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	37	39	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	41	44	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	56	62	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	73	76	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	90	92	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	103	105	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	114	122	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	125	128	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	134	139	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	119	119	Binding site	Note=Sialic acid;Ontology_term=ECO:0000250;evidence=ECO:0000250
P20138	13	139	18	364	Chain	ID=PRO_0000014878;Note=Myeloid cell surface antigen CD33
P20138	13	139	36	169	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00114
P20138	13	139	41	101	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00114
P20138	13	139	19	135	Domain	Note=Ig-like V-type
P20138	13	139	100	100	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P20138	13	139	113	113	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P20138	13	139	49	51	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	65	68	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	96	98	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	110	112	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	13	139	14	14	Natural variant	ID=VAR_049904;Note=A->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14702039;Dbxref=dbSNP:rs12459419,PMID:14702039
P20138	13	139	22	22	Natural variant	ID=VAR_049905;Note=W->R;Dbxref=dbSNP:rs35814802
P20138	13	139	69	69	Natural variant	ID=VAR_028260;Note=R->G;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15489334,ECO:0000269\|PubMed:3139766;Dbxref=dbSNP:rs2455069,PMID:15489334,PMID:3139766
P20138	13	139	128	128	Natural variant	ID=VAR_049906;Note=S->N;Dbxref=dbSNP:rs34919259
P20138	13	139	1	17	Signal peptide	Ontology_term=ECO:0000255;evidence=ECO:0000255
P20138	13	139	18	259	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
P20138	13	139	84	89	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IHB
P20138	233	248	18	364	Chain	ID=PRO_0000014878;Note=Myeloid cell surface antigen CD33
P20138	233	248	242	242	Natural variant	ID=VAR_028262;Note=I->L;Dbxref=dbSNP:rs988337
P20138	233	248	243	243	Natural variant	ID=VAR_028263;Note=F->L;Dbxref=dbSNP:rs11882250
P20138	233	248	18	259	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

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3'-UTR located exon skipping events that lost miRNA binding sites in CD33

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 CD33

- 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 CD33

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 CD33

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 CD33

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for CD33

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

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
P20138	approved\|investigational	DB00056	Gemtuzumab ozogamicin	biotech	P20138

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RelatedDiseases for CD33

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 CD33

Gene structures and expression levels for CD33

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for CD33

Open reading frame (ORF) annotation in the exon skipping event for CD33

Infer the effects of exon skipping event on protein functional features for CD33

3'-UTR located exon skipping events that lost miRNA binding sites in CD33

SNVs in the skipped exons for CD33

AD stage-associated exon skippint events for CD33

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CD33

Correlation with RNA binding proteins (RBPs) for CD33

RelatedDrugs for CD33

RelatedDiseases for CD33