ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for SCN8A

Gene summary

Gene information	Gene symbol	SCN8A
	Gene ID	6334
	Gene name	sodium voltage-gated channel alpha subunit 8
	Synonyms	BFIS5\|CERIII\|CIAT\|EIEE13\|MED\|MYOCL2\|NaCh6\|Nav1.6\|PN4
	Cytomap	12q13.13
	Type of gene	protein-coding
	Description	sodium channel protein type 8 subunit alphahNa6/Scn8a voltage-gated sodium channelsodium channel, voltage gated, type VIII, alpha subunitvoltage-gated sodium channel subunit alpha Nav1.6voltage-gated sodium channel type VIII alpha protein
	Modification date	20200313
	UniProtAcc	A0A1B0GVD4, A0A1B0GVM8, A0A1W2PQI5, A0A590UJP2, A0A590UK43, A0A590UK68, F8W0Q0, Q6B4S2, Q6B4S3, Q6B4S4, Q8WWN3, Q9GZR0, Q9P2Q6, Q9UQD0,
	Context	- 28522250(PPARgamma Agonists Rescue Increased Phosphorylation of FGF14 at S226 in the Tg2576 Mouse Model of 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

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Gene structures and expression levels for SCN8A

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.

ENSG00000196876

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	DOWN	ENST00000662684.1	SCN8A-216:protein_coding:SCN8A	2.452199e+02	-1.072035e+00	3.324972e-03	3.427803e-02
PG	DOWN	ENST00000627665.1	SCN8A-210:retained_intron:SCN8A	1.466521e+01	-8.919837e-01	3.931100e-03	3.860931e-02
CB	UP	ENST00000637709.2	SCN8A-214:nonsense_mediated_decay:SCN8A	7.159333e+01	9.653507e-01	7.253593e-12	7.502054e-10
CB	UP	ENST00000548086.3	SCN8A-205:nonsense_mediated_decay:SCN8A	3.129277e+01	1.347444e+00	2.255040e-11	1.883869e-09

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 SCN8A

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_135077	chr12	51769957:51769985:51770529:51770683:51774189:51774362	51770529:51770683
exon_skip_148978	chr12	51745903:51746035:51751355:51751593:51762503:51762676	51751355:51751593
exon_skip_160182	chr12	51689005:51689096:51699570:51699791:51701144:51701207	51699570:51699791
exon_skip_23474	chr12	51706422:51706715:51721546:51721908:51745903:51745948	51721546:51721908
exon_skip_236074	chr12	51774189:51774362:51780649:51780771:51786542:51786826	51780649:51780771
exon_skip_267985	chr12	51745903:51746035:51751355:51751593:51762503:51762578	51751355:51751593
exon_skip_271601	chr12	51770529:51770683:51774189:51774362:51780649:51780771	51774189:51774362
exon_skip_288125	chr12	51770529:51770683:51774189:51774362:51780202:51780271	51774189:51774362
exon_skip_293570	chr12	51770529:51770683:51774189:51774362:51786542:51786826	51774189:51774362
exon_skip_34552	chr12	51701144:51701207:51702773:51702914:51705417:51705623	51702773:51702914
exon_skip_35946	chr12	51765671:51766027:51768113:51768172:51768865:51769335	51768113:51768172
exon_skip_61871	chr12	51774189:51774362:51780202:51780271:51786542:51786826	51780202:51780271
exon_skip_72564	chr12	51706422:51706715:51721546:51721941:51745903:51745948	51721546:51721941
exon_skip_81864	chr12	51591236:51591359:51662764:51663093:51684174:51684292	51662764:51663093

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 SCN8A

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
ENST00000354534	51662764	51663093	5CDS-5UTR
ENST00000354534	51702773	51702914	Frame-shift
ENST00000354534	51751355	51751593	Frame-shift
ENST00000354534	51774189	51774362	In-frame
ENST00000354534	51780649	51780771	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
ENST00000354534	51662764	51663093	5CDS-5UTR
ENST00000354534	51702773	51702914	Frame-shift
ENST00000354534	51751355	51751593	Frame-shift
ENST00000354534	51721546	51721908	In-frame
ENST00000354534	51780649	51780771	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
ENST00000354534	51662764	51663093	5CDS-5UTR
ENST00000354534	51702773	51702914	Frame-shift
ENST00000354534	51751355	51751593	Frame-shift
ENST00000354534	51770529	51770683	Frame-shift
ENST00000354534	51774189	51774362	In-frame
ENST00000354534	51780649	51780771	In-frame

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Infer the effects of exon skipping event on protein functional features for SCN8A

p-ENSG00000196876_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
ENST00000354534	11573	1980	51774189	51774362	3825	3997	1215	1273
ENST00000354534	11573	1980	51780649	51780771	3999	4120	1273	1314

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
ENST00000354534	11573	1980	51721546	51721908	1815	2176	545	666
ENST00000354534	11573	1980	51780649	51780771	3999	4120	1273	1314

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
ENST00000354534	11573	1980	51774189	51774362	3825	3997	1215	1273
ENST00000354534	11573	1980	51780649	51780771	3999	4120	1273	1314

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
Q9UQD0	1215	1273	1	1980	Chain	ID=PRO_0000048500;Note=Sodium channel protein type 8 subunit alpha
Q9UQD0	1215	1273	1180	1495	Repeat	Note=III;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UQD0	1215	1273	1218	1230	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UQD0	1215	1273	1250	1263	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UQD0	1215	1273	1200	1217	Transmembrane	Note=Helical%3B Name%3DS1 of repeat III;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2
Q9UQD0	1215	1273	1231	1249	Transmembrane	Note=Helical%3B Name%3DS2 of repeat III;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2
Q9UQD0	1215	1273	1264	1282	Transmembrane	Note=Helical%3B Name%3DS3 of repeat III;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2
Q9UQD0	1273	1314	1275	1315	Alternative sequence	ID=VSP_038651;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:19136557;Dbxref=PMID:19136557
Q9UQD0	1273	1314	1275	1283	Alternative sequence	ID=VSP_050592;Note=In isoform 4. SLVSLIANA->PLNLSGLI;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:9295353;Dbxref=PMID:9295353
Q9UQD0	1273	1314	1284	1980	Alternative sequence	ID=VSP_050593;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:9295353;Dbxref=PMID:9295353
Q9UQD0	1273	1314	1	1980	Chain	ID=PRO_0000048500;Note=Sodium channel protein type 8 subunit alpha
Q9UQD0	1273	1314	1279	1279	Natural variant	ID=VAR_078613;Note=In EIEE13. L->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q9UQD0	1273	1314	1180	1495	Repeat	Note=III;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UQD0	1273	1314	1283	1290	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UQD0	1273	1314	1310	1326	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UQD0	1273	1314	1264	1282	Transmembrane	Note=Helical%3B Name%3DS3 of repeat III;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2
Q9UQD0	1273	1314	1291	1309	Transmembrane	Note=Helical%3B Name%3DS4 of repeat III;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2

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
Q9UQD0	545	666	666	666	Alternative sequence	ID=VSP_050591;Note=In isoform 3. E->EVKIDKAATDDS;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:9828131;Dbxref=PMID:9828131
Q9UQD0	545	666	1	1980	Chain	ID=PRO_0000048500;Note=Sodium channel protein type 8 subunit alpha
Q9UQD0	545	666	662	662	Natural variant	ID=VAR_078612;Note=In EIEE13%3B unknown pathological significance. R->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=dbSNP:rs76222829,PMID:23708187
Q9UQD0	545	666	547	548	Sequence conflict	Note=LL->MF;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UQD0	545	666	409	753	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UQD0	1273	1314	1275	1315	Alternative sequence	ID=VSP_038651;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:19136557;Dbxref=PMID:19136557
Q9UQD0	1273	1314	1275	1283	Alternative sequence	ID=VSP_050592;Note=In isoform 4. SLVSLIANA->PLNLSGLI;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:9295353;Dbxref=PMID:9295353
Q9UQD0	1273	1314	1284	1980	Alternative sequence	ID=VSP_050593;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:9295353;Dbxref=PMID:9295353
Q9UQD0	1273	1314	1	1980	Chain	ID=PRO_0000048500;Note=Sodium channel protein type 8 subunit alpha
Q9UQD0	1273	1314	1279	1279	Natural variant	ID=VAR_078613;Note=In EIEE13. L->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q9UQD0	1273	1314	1180	1495	Repeat	Note=III;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UQD0	1273	1314	1283	1290	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UQD0	1273	1314	1310	1326	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UQD0	1273	1314	1264	1282	Transmembrane	Note=Helical%3B Name%3DS3 of repeat III;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2
Q9UQD0	1273	1314	1291	1309	Transmembrane	Note=Helical%3B Name%3DS4 of repeat III;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2

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
Q9UQD0	1215	1273	1	1980	Chain	ID=PRO_0000048500;Note=Sodium channel protein type 8 subunit alpha
Q9UQD0	1215	1273	1180	1495	Repeat	Note=III;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UQD0	1215	1273	1218	1230	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UQD0	1215	1273	1250	1263	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UQD0	1215	1273	1200	1217	Transmembrane	Note=Helical%3B Name%3DS1 of repeat III;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2
Q9UQD0	1215	1273	1231	1249	Transmembrane	Note=Helical%3B Name%3DS2 of repeat III;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2
Q9UQD0	1215	1273	1264	1282	Transmembrane	Note=Helical%3B Name%3DS3 of repeat III;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2
Q9UQD0	1273	1314	1275	1315	Alternative sequence	ID=VSP_038651;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:19136557;Dbxref=PMID:19136557
Q9UQD0	1273	1314	1275	1283	Alternative sequence	ID=VSP_050592;Note=In isoform 4. SLVSLIANA->PLNLSGLI;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:9295353;Dbxref=PMID:9295353
Q9UQD0	1273	1314	1284	1980	Alternative sequence	ID=VSP_050593;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:9295353;Dbxref=PMID:9295353
Q9UQD0	1273	1314	1	1980	Chain	ID=PRO_0000048500;Note=Sodium channel protein type 8 subunit alpha
Q9UQD0	1273	1314	1279	1279	Natural variant	ID=VAR_078613;Note=In EIEE13. L->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q9UQD0	1273	1314	1180	1495	Repeat	Note=III;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UQD0	1273	1314	1283	1290	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UQD0	1273	1314	1310	1326	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UQD0	1273	1314	1264	1282	Transmembrane	Note=Helical%3B Name%3DS3 of repeat III;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2
Q9UQD0	1273	1314	1291	1309	Transmembrane	Note=Helical%3B Name%3DS4 of repeat III;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2

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3'-UTR located exon skipping events that lost miRNA binding sites in SCN8A

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 SCN8A

- 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 SCN8A

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 SCN8A

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 SCN8A

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for SCN8A

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 SCN8A

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 SCN8A

Gene structures and expression levels for SCN8A

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SCN8A

Open reading frame (ORF) annotation in the exon skipping event for SCN8A

Infer the effects of exon skipping event on protein functional features for SCN8A

3'-UTR located exon skipping events that lost miRNA binding sites in SCN8A

SNVs in the skipped exons for SCN8A

AD stage-associated exon skippint events for SCN8A

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SCN8A

Correlation with RNA binding proteins (RBPs) for SCN8A

RelatedDrugs for SCN8A

RelatedDiseases for SCN8A