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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 SLC24A4 |
Gene summary |
Gene information | Gene symbol | SLC24A4 | Gene ID | 123041 |
Gene name | solute carrier family 24 member 4 | |
Synonyms | AI2A5|NCKX4|SHEP6|SLC24A2 | |
Cytomap | 14q32.12 | |
Type of gene | protein-coding | |
Description | sodium/potassium/calcium exchanger 4Na(+)/K(+)/Ca(2+)-exchange protein 4solute carrier family 24 (sodium/potassium/calcium exchanger), member 4 | |
Modification date | 20200327 | |
UniProtAcc | ||
Context | - 27215332(Lack of Association Between SLC24A4 Polymorphism and Late-onset Alzheimer's Disease in Han Chinese) |
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 SLC24A4 |
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 SLC24A4 |
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_11578 | chr14 | 92445317:92445342:92447371:92447424:92449074:92449129 | 92447371:92447424 |
exon_skip_139325 | chr14 | 92445317:92445342:92447371:92447424:92449074:92449159 | 92447371:92447424 |
exon_skip_183141 | chr14 | 92456404:92456608:92482680:92482846:92486666:92486780 | 92482680:92482846 |
exon_skip_248928 | chr14 | 92482680:92482846:92486666:92486780:92491665:92491777 | 92486666:92486780 |
exon_skip_250278 | chr14 | 92325868:92325978:92433912:92433988:92439335:92439409 | 92433912:92433988 |
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 SLC24A4 |
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 |
ENST00000532405 | 92482680 | 92482846 | Frame-shift |
ENST00000532405 | 92447371 | 92447424 | 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 |
ENST00000532405 | 92433912 | 92433988 | Frame-shift |
ENST00000532405 | 92447371 | 92447424 | 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 |
ENST00000532405 | 92486666 | 92486780 | Frame-shift |
ENST00000532405 | 92447371 | 92447424 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SLC24A4 |
p-ENSG00000140090_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 |
ENST00000532405 | 9967 | 622 | 92447371 | 92447424 | 911 | 963 | 228 | 245 |
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 |
ENST00000532405 | 9967 | 622 | 92447371 | 92447424 | 911 | 963 | 228 | 245 |
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 |
ENST00000532405 | 9967 | 622 | 92447371 | 92447424 | 911 | 963 | 228 | 245 |
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 |
Q8NFF2 | 228 | 245 | 39 | 622 | Chain | ID=PRO_0000019373;Note=Sodium/potassium/calcium exchanger 4 |
Q8NFF2 | 228 | 245 | 225 | 245 | 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 |
Q8NFF2 | 228 | 245 | 39 | 622 | Chain | ID=PRO_0000019373;Note=Sodium/potassium/calcium exchanger 4 |
Q8NFF2 | 228 | 245 | 225 | 245 | 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 |
Q8NFF2 | 228 | 245 | 39 | 622 | Chain | ID=PRO_0000019373;Note=Sodium/potassium/calcium exchanger 4 |
Q8NFF2 | 228 | 245 | 225 | 245 | 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 SLC24A4 |
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 SLC24A4 |
- 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 SLC24A4 |
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 SLC24A4 |
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 SLC24A4 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SLC24A4 |
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 SLC24A4 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |