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Open reading frame (ORF) annotation in the exon skipping event | |
3'-UTR located exon skipping events lost miRNA binding sites | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Gene summary for SCN9A |
Gene summary |
Gene information | Gene symbol | SCN9A | Gene ID | 6335 |
Gene name | sodium voltage-gated channel alpha subunit 9 | |
Synonyms | ETHA|FEB3B|GEFSP7|HSAN2D|NE-NA|NENA|Nav1.7|PN1|SFNP | |
Cytomap | 2q24.3 | |
Type of gene | protein-coding | |
Description | sodium channel protein type 9 subunit alphahNE-Naneuroendocrine sodium channelperipheral sodium channel 1sodium channel protein type IX subunit alphasodium channel, voltage-gated, type IX, alpha polypeptidesodium channel, voltage-gated, type IX, alp | |
Modification date | 20200313 | |
UniProtAcc | ||
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
SCN9A | GO:0035725 | sodium ion transmembrane transport | 17145499 |
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Gene structures and expression levels for SCN9A |
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. |
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 SCN9A |
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_135654 | chr2 | 166251765:166251885:166259206:166259287:166272399:166272498 | 166259206:166259287 |
exon_skip_199076 | chr2 | 166303090:166303302:166304031:166304122:166305792:166305920 | 166304031:166304122 |
exon_skip_208791 | chr2 | 166303090:166303302:166304238:166304329:166305792:166305920 | 166304238:166304329 |
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 SCN9A |
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 |
ENST00000303354 | 166304238 | 166304329 | Frame-shift |
ENST00000642356 | 166304238 | 166304329 | Frame-shift |
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 |
ENST00000303354 | 166304238 | 166304329 | Frame-shift |
ENST00000642356 | 166304238 | 166304329 | Frame-shift |
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 |
ENST00000303354 | 166304238 | 166304329 | Frame-shift |
ENST00000642356 | 166304238 | 166304329 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for SCN9A |
p-ENSG00000169432_img4.png |
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 |
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 |
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 |
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 |
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 |
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 |
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3'-UTR located exon skipping events that lost miRNA binding sites in SCN9A |
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 SCN9A |
- 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 SCN9A |
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 SCN9A |
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 SCN9A |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SCN9A |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Q15858 | approved|vet_approved | DB00281 | Lidocaine | small molecule | Q15858 |
Q15858 | approved|investigational | DB00909 | Zonisamide | small molecule | Q15858 |
Q15858 | approved | DB06201 | Rufinamide | small molecule | Q15858 |
Q15858 | approved | DB06218 | Lacosamide | small molecule | Q15858 |
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RelatedDiseases for SCN9A |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |