ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for SCARA3

Gene summary

Gene information	Gene symbol	SCARA3
	Gene ID	51435
	Gene name	scavenger receptor class A member 3
	Synonyms	APC7\|CSR\|CSR1\|MSLR1\|MSRL1
	Cytomap	8p21.1
	Type of gene	protein-coding
	Description	scavenger receptor class A member 3cellular stress response gene proteincellular stress response proteinmacrophage scavenger receptor-like 1
	Modification date	20200313
	UniProtAcc	Q6AZY7,
	Context

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

Gene

GO ID

GO term

PubMed ID

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Gene structures and expression levels for SCARA3

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.

ENSG00000168077

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
TC	UP	ENST00000337221.8	SCARA3-202:protein_coding:SCARA3	1.420269e+02	8.062974e-01	4.717089e-07	2.195074e-05

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 SCARA3

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_124905	chr8	27656782:27656880:27658496:27659539:27676569:27676776	27658496:27659539
exon_skip_141597	chr8	27651508:27651627:27656782:27656880:27658496:27659539	27656782:27656880
exon_skip_147826	chr8	27656782:27656880:27658496:27659539:27670900:27673018	27658496:27659539
exon_skip_165792	chr8	27633902:27634207:27649702:27649800:27651508:27651627	27649702:27649800
exon_skip_233863	chr8	27634044:27634207:27649702:27649800:27651508:27651627	27649702:27649800
exon_skip_74327	chr8	27656782:27656880:27658496:27659539:27670900:27671629	27658496:27659539
exon_skip_81854	chr8	27656782:27656880:27658496:27659539:27670900:27671569	27658496:27659539
exon_skip_8227	chr8	27649702:27649800:27651508:27651627:27656782:27656880	27651508:27651627

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 SCARA3

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
ENST00000301904	27649702	27649800	In-frame
ENST00000301904	27651508	27651627	In-frame
ENST00000301904	27658496	27659539	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
ENST00000301904	27651508	27651627	In-frame
ENST00000301904	27658496	27659539	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
ENST00000301904	27649702	27649800	In-frame
ENST00000301904	27651508	27651627	In-frame
ENST00000301904	27656782	27656880	In-frame
ENST00000301904	27658496	27659539	In-frame

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Infer the effects of exon skipping event on protein functional features for SCARA3

p-ENSG00000168077_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
ENST00000301904	3527	606	27649702	27649800	29	126	3	35
ENST00000301904	3527	606	27651508	27651627	128	246	36	75
ENST00000301904	3527	606	27658496	27659539	347	1389	109	456

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
ENST00000301904	3527	606	27651508	27651627	128	246	36	75
ENST00000301904	3527	606	27658496	27659539	347	1389	109	456

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
ENST00000301904	3527	606	27649702	27649800	29	126	3	35
ENST00000301904	3527	606	27651508	27651627	128	246	36	75
ENST00000301904	3527	606	27656782	27656880	248	345	76	108
ENST00000301904	3527	606	27658496	27659539	347	1389	109	456

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
Q6AZY7	3	35	1	606	Chain	ID=PRO_0000181633;Note=Scavenger receptor class A member 3
Q6AZY7	3	35	1	56	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	36	75	1	606	Chain	ID=PRO_0000181633;Note=Scavenger receptor class A member 3
Q6AZY7	36	75	1	56	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	36	75	57	77	Transmembrane	Note=Helical%3B Signal-anchor for type II membrane protein;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	1	606	Chain	ID=PRO_0000181633;Note=Scavenger receptor class A member 3
Q6AZY7	109	456	455	513	Domain	Note=Collagen-like 1
Q6AZY7	109	456	115	115	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	182	182	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	224	224	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	257	257	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	313	313	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	337	337	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	365	365	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	400	400	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	430	430	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	451	451	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	130	130	Natural variant	ID=VAR_025228;Note=R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|Ref.2;Dbxref=dbSNP:rs34791518
Q6AZY7	109	456	325	325	Natural variant	ID=VAR_025229;Note=M->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|Ref.2;Dbxref=dbSNP:rs33930667
Q6AZY7	109	456	423	423	Natural variant	ID=VAR_025230;Note=R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|Ref.2;Dbxref=dbSNP:rs3735754
Q6AZY7	109	456	428	428	Natural variant	ID=VAR_025231;Note=V->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|Ref.2;Dbxref=dbSNP:rs34086286
Q6AZY7	109	456	78	606	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
Q6AZY7	36	75	1	606	Chain	ID=PRO_0000181633;Note=Scavenger receptor class A member 3
Q6AZY7	36	75	1	56	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	36	75	57	77	Transmembrane	Note=Helical%3B Signal-anchor for type II membrane protein;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	1	606	Chain	ID=PRO_0000181633;Note=Scavenger receptor class A member 3
Q6AZY7	109	456	455	513	Domain	Note=Collagen-like 1
Q6AZY7	109	456	115	115	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	182	182	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	224	224	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	257	257	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	313	313	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	337	337	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	365	365	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	400	400	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	430	430	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	451	451	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	130	130	Natural variant	ID=VAR_025228;Note=R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|Ref.2;Dbxref=dbSNP:rs34791518
Q6AZY7	109	456	325	325	Natural variant	ID=VAR_025229;Note=M->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|Ref.2;Dbxref=dbSNP:rs33930667
Q6AZY7	109	456	423	423	Natural variant	ID=VAR_025230;Note=R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|Ref.2;Dbxref=dbSNP:rs3735754
Q6AZY7	109	456	428	428	Natural variant	ID=VAR_025231;Note=V->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|Ref.2;Dbxref=dbSNP:rs34086286
Q6AZY7	109	456	78	606	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

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
Q6AZY7	3	35	1	606	Chain	ID=PRO_0000181633;Note=Scavenger receptor class A member 3
Q6AZY7	3	35	1	56	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	36	75	1	606	Chain	ID=PRO_0000181633;Note=Scavenger receptor class A member 3
Q6AZY7	36	75	1	56	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	36	75	57	77	Transmembrane	Note=Helical%3B Signal-anchor for type II membrane protein;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	76	108	1	606	Chain	ID=PRO_0000181633;Note=Scavenger receptor class A member 3
Q6AZY7	76	108	78	606	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	76	108	57	77	Transmembrane	Note=Helical%3B Signal-anchor for type II membrane protein;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	1	606	Chain	ID=PRO_0000181633;Note=Scavenger receptor class A member 3
Q6AZY7	109	456	455	513	Domain	Note=Collagen-like 1
Q6AZY7	109	456	115	115	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	182	182	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	224	224	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	257	257	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	313	313	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	337	337	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	365	365	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	400	400	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	430	430	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	451	451	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q6AZY7	109	456	130	130	Natural variant	ID=VAR_025228;Note=R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|Ref.2;Dbxref=dbSNP:rs34791518
Q6AZY7	109	456	325	325	Natural variant	ID=VAR_025229;Note=M->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|Ref.2;Dbxref=dbSNP:rs33930667
Q6AZY7	109	456	423	423	Natural variant	ID=VAR_025230;Note=R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|Ref.2;Dbxref=dbSNP:rs3735754
Q6AZY7	109	456	428	428	Natural variant	ID=VAR_025231;Note=V->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|Ref.2;Dbxref=dbSNP:rs34086286
Q6AZY7	109	456	78	606	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 SCARA3

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 SCARA3

- 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 SCARA3

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 SCARA3

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
CB	exon_skip_8227	rs473024	chr8:27679399	1.662827e-04	2.582817e-02
CB	exon_skip_8227	rs568610	chr8:27670478	3.844605e-04	4.909269e-02
TC	exon_skip_8227	rs473024	chr8:27679399	1.356144e-05	3.201688e-03
TC	exon_skip_8227	rs2582369	chr8:27648239	1.780966e-05	3.987565e-03
TC	exon_skip_8227	rs568610	chr8:27670478	3.237848e-05	6.544390e-03
TC	exon_skip_8227	rs566398	chr8:27704694	3.546469e-05	7.074993e-03
TC	exon_skip_8227	rs492638	chr8:27621710	1.508159e-04	2.248644e-02
TC	exon_skip_8227	rs484458	chr8:27627435	2.910284e-04	3.812082e-02
TC	exon_skip_8227	rs538181	chr8:27619298	3.417105e-04	4.324432e-02
PCC	exon_skip_8227	rs549371	chr8:27647618	3.470852e-04	4.571476e-02
PCC	exon_skip_8227	rs478045	chr8:27650709	3.470852e-04	4.571476e-02

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Correlation with RNA binding proteins (RBPs) for SCARA3

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	RBM6	exon_skip_8227	-4.930612e-01	6.192229e-11

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RelatedDrugs for SCARA3

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 SCARA3

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 SCARA3

Gene structures and expression levels for SCARA3

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SCARA3

Open reading frame (ORF) annotation in the exon skipping event for SCARA3

Infer the effects of exon skipping event on protein functional features for SCARA3

3'-UTR located exon skipping events that lost miRNA binding sites in SCARA3

SNVs in the skipped exons for SCARA3

AD stage-associated exon skippint events for SCARA3

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SCARA3

Correlation with RNA binding proteins (RBPs) for SCARA3

RelatedDrugs for SCARA3

RelatedDiseases for SCARA3