ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for SLC8A2

Gene summary

Gene information	Gene symbol	SLC8A2
	Gene ID	6543
	Gene name	solute carrier family 8 member A2
	Synonyms	NCX2
	Cytomap	19q13.32
	Type of gene	protein-coding
	Description	sodium/calcium exchanger 2Na(+)/Ca(2+)-exchange protein 2Na+/Ca2+-exchanging protein Nac2solute carrier family 8 (sodium/calcium exchanger), member 2solute carrier family 8 member 2
	Modification date	20200313
	UniProtAcc	F5H6L7, M0R1Z4, M0R211, Q9UPR5,
	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 SLC8A2

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.

ENSG00000118160

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
PCC	DOWN	ENST00000597014.1	SLC8A2-205:protein_coding:SLC8A2	4.189468e+00	-8.348014e-01	5.213927e-04	1.696278e-02
STG	DOWN	ENST00000542837.2	SLC8A2-203:protein_coding:SLC8A2	3.376982e+02	-8.212951e-01	5.238365e-04	2.767187e-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 SLC8A2

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_103874	chr19	47447809:47448231:47456930:47457594:47465729:47466147	47456930:47457594
exon_skip_109625	chr19	47432407:47432445:47437462:47437561:47437849:47437973	47437462:47437561
exon_skip_149743	chr19	47437462:47437561:47437849:47437973:47441169:47441186	47437849:47437973
exon_skip_152450	chr19	47437849:47437973:47441169:47441186:47441337:47441440	47441169:47441186
exon_skip_167797	chr19	47430447:47430465:47432167:47432445:47437462:47437561	47432167:47432445
exon_skip_176199	chr19	47430235:47430465:47432167:47432445:47437462:47437561	47432167:47432445
exon_skip_183724	chr19	47457513:47457594:47465729:47466147:47471789:47471868	47465729:47466147
exon_skip_197667	chr19	47441337:47441440:47447809:47448231:47456930:47457594	47447809:47448231
exon_skip_207843	chr19	47457513:47457594:47465729:47466147:47471789:47471863	47465729:47466147
exon_skip_274138	chr19	47447809:47448231:47456930:47457594:47471789:47471863	47456930:47457594
exon_skip_280446	chr19	47437948:47437973:47441169:47441186:47441337:47441440	47441169:47441186

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
exon_skip_212581	Mayo_CB	8.149231e-01	9.213559e-01	-1.064329e-01	2.879118e-03

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Open reading frame (ORF) annotation in the exon skipping event for SLC8A2

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
ENST00000236877	47432167	47432445	In-frame
ENST00000236877	47441169	47441186	In-frame
ENST00000236877	47447809	47448231	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
ENST00000236877	47432167	47432445	In-frame
ENST00000236877	47441169	47441186	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
ENST00000236877	47437462	47437561	Frame-shift
ENST00000236877	47437849	47437973	Frame-shift
ENST00000236877	47456930	47457594	Frame-shift
ENST00000236877	47432167	47432445	In-frame
ENST00000236877	47441169	47441186	In-frame
ENST00000236877	47447809	47448231	In-frame

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Infer the effects of exon skipping event on protein functional features for SLC8A2

p-ENSG00000118160_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
ENST00000236877	5251	921	47447809	47448231	1737	2158	447	587
ENST00000236877	5251	921	47432167	47432445	2507	2784	703	796

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
ENST00000236877	5251	921	47432167	47432445	2507	2784	703	796

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
ENST00000236877	5251	921	47447809	47448231	1737	2158	447	587
ENST00000236877	5251	921	47432167	47432445	2507	2784	703	796

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
Q9UPR5	447	587	21	921	Chain	ID=PRO_0000019382;Note=Sodium/calcium exchanger 2
Q9UPR5	447	587	384	483	Domain	Note=Calx-beta 1
Q9UPR5	447	587	512	612	Domain	Note=Calx-beta 2
Q9UPR5	447	587	468	468	Metal binding	Note=Calcium 2;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	469	469	Metal binding	Note=Calcium 1;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	469	469	Metal binding	Note=Calcium 2%3B via carbonyl oxygen;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	469	469	Metal binding	Note=Calcium 3;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	469	469	Metal binding	Note=Calcium 4;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	471	471	Metal binding	Note=Calcium 3%3B via carbonyl oxygen;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	473	473	Metal binding	Note=Calcium 1;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	473	473	Metal binding	Note=Calcium 3;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	473	473	Metal binding	Note=Calcium 4;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	476	476	Metal binding	Note=Calcium 4;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	518	518	Metal binding	Note=Calcium 3;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	519	519	Metal binding	Note=Calcium 2;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	520	520	Metal binding	Note=Calcium 2;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	520	520	Metal binding	Note=Calcium 3;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	536	536	Metal binding	Note=Calcium 5;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	247	720	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	21	921	Chain	ID=PRO_0000019382;Note=Sodium/calcium exchanger 2
Q9UPR5	703	796	790	826	Repeat	Note=Alpha-2
Q9UPR5	703	796	247	720	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	741	747	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	771	772	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	792	822	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	721	740	Transmembrane	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	748	770	Transmembrane	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	773	791	Transmembrane	Note=Helical;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
Q9UPR5	703	796	21	921	Chain	ID=PRO_0000019382;Note=Sodium/calcium exchanger 2
Q9UPR5	703	796	790	826	Repeat	Note=Alpha-2
Q9UPR5	703	796	247	720	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	741	747	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	771	772	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	792	822	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	721	740	Transmembrane	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	748	770	Transmembrane	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	773	791	Transmembrane	Note=Helical;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
Q9UPR5	447	587	21	921	Chain	ID=PRO_0000019382;Note=Sodium/calcium exchanger 2
Q9UPR5	447	587	384	483	Domain	Note=Calx-beta 1
Q9UPR5	447	587	512	612	Domain	Note=Calx-beta 2
Q9UPR5	447	587	468	468	Metal binding	Note=Calcium 2;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	469	469	Metal binding	Note=Calcium 1;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	469	469	Metal binding	Note=Calcium 2%3B via carbonyl oxygen;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	469	469	Metal binding	Note=Calcium 3;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	469	469	Metal binding	Note=Calcium 4;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	471	471	Metal binding	Note=Calcium 3%3B via carbonyl oxygen;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	473	473	Metal binding	Note=Calcium 1;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	473	473	Metal binding	Note=Calcium 3;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	473	473	Metal binding	Note=Calcium 4;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	476	476	Metal binding	Note=Calcium 4;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	518	518	Metal binding	Note=Calcium 3;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	519	519	Metal binding	Note=Calcium 2;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	520	520	Metal binding	Note=Calcium 2;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	520	520	Metal binding	Note=Calcium 3;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	536	536	Metal binding	Note=Calcium 5;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P23685
Q9UPR5	447	587	247	720	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	21	921	Chain	ID=PRO_0000019382;Note=Sodium/calcium exchanger 2
Q9UPR5	703	796	790	826	Repeat	Note=Alpha-2
Q9UPR5	703	796	247	720	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	741	747	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	771	772	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	792	822	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	721	740	Transmembrane	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	748	770	Transmembrane	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPR5	703	796	773	791	Transmembrane	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255

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3'-UTR located exon skipping events that lost miRNA binding sites in SLC8A2

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 SLC8A2

- 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 SLC8A2

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 SLC8A2

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 SLC8A2

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for SLC8A2

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 SLC8A2

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 SLC8A2

Gene structures and expression levels for SLC8A2

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SLC8A2

Open reading frame (ORF) annotation in the exon skipping event for SLC8A2

Infer the effects of exon skipping event on protein functional features for SLC8A2

3'-UTR located exon skipping events that lost miRNA binding sites in SLC8A2

SNVs in the skipped exons for SLC8A2

AD stage-associated exon skippint events for SLC8A2

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SLC8A2

Correlation with RNA binding proteins (RBPs) for SLC8A2

RelatedDrugs for SLC8A2

RelatedDiseases for SLC8A2