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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for SLC5A6 |
 Gene summary |
| Gene information | Gene symbol | SLC5A6 | Gene ID | 8884 |
| Gene name | solute carrier family 5 member 6 | |
| Synonyms | SMVT | |
| Cytomap | 2p23.3 | |
| Type of gene | protein-coding | |
| Description | sodium-dependent multivitamin transporterNa(+)-dependent multivitamin transporterNa+-dependent multivitamin transportersolute carrier family 5 (sodium-dependent vitamin transporter), member 6solute carrier family 5 (sodium/multivitamin and iodide cotr | |
| 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 |
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Gene structures and expression levels for SLC5A6 |
| 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. |
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ENSG00000138074
| 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. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | UP | ENST00000445802.5 | SLC5A6-211:nonsense_mediated_decay:SLC5A6 | 6.651311e+00 | 1.120912e+00 | 1.133722e-04 | 8.233342e-04 |
| 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 SLC5A6 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_106173 | chr2 | 27202813:27202880:27203233:27203345:27203779:27203867 | 27203233:27203345 |
| exon_skip_123553 | chr2 | 27207415:27207790:27208394:27208448:27211467:27211533 | 27208394:27208448 |
| exon_skip_164754 | chr2 | 27206026:27206093:27206483:27206534:27206877:27206942 | 27206483:27206534 |
| exon_skip_207361 | chr2 | 27211467:27211533:27212020:27212146:27212629:27212777 | 27212020:27212146 |
| exon_skip_207791 | chr2 | 27204461:27204590:27204791:27204931:27205350:27205504 | 27204791:27204931 |
| exon_skip_269931 | chr2 | 27201988:27202074:27202813:27202880:27203233:27203345 | 27202813:27202880 |
| exon_skip_291467 | chr2 | 27201102:27201113:27201350:27201453:27201666:27201847 | 27201350:27201453 |
| exon_skip_292546 | chr2 | 27207639:27207790:27208614:27208686:27211467:27211533 | 27208614:27208686 |
| exon_skip_295450 | chr2 | 27201988:27202074:27202813:27203345:27203779:27203867 | 27202813:27203345 |
| exon_skip_50623 | chr2 | 27211467:27211533:27212020:27212146:27212832:27212950 | 27212020:27212146 |
| exon_skip_76329 | chr2 | 27207570:27207790:27208614:27208686:27211467:27211533 | 27208614:27208686 |
| 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 SLC5A6 |
| 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 |
| ENST00000408041 | 27208614 | 27208686 | 3UTR-3UTR |
| ENST00000310574 | 27201350 | 27201453 | Frame-shift |
| ENST00000408041 | 27201350 | 27201453 | Frame-shift |
| ENST00000310574 | 27202813 | 27202880 | Frame-shift |
| ENST00000408041 | 27202813 | 27202880 | Frame-shift |
| ENST00000310574 | 27203233 | 27203345 | Frame-shift |
| ENST00000408041 | 27203233 | 27203345 | Frame-shift |
| ENST00000310574 | 27206483 | 27206534 | Frame-shift |
| ENST00000408041 | 27206483 | 27206534 | 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 |
| ENST00000310574 | 27206483 | 27206534 | Frame-shift |
| ENST00000408041 | 27206483 | 27206534 | 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 |
| ENST00000408041 | 27208614 | 27208686 | 3UTR-3UTR |
| ENST00000310574 | 27201350 | 27201453 | Frame-shift |
| ENST00000408041 | 27201350 | 27201453 | Frame-shift |
| ENST00000310574 | 27202813 | 27202880 | Frame-shift |
| ENST00000408041 | 27202813 | 27202880 | Frame-shift |
| ENST00000310574 | 27203233 | 27203345 | Frame-shift |
| ENST00000408041 | 27203233 | 27203345 | Frame-shift |
| ENST00000310574 | 27206483 | 27206534 | Frame-shift |
| ENST00000408041 | 27206483 | 27206534 | Frame-shift |
| ENST00000310574 | 27204791 | 27204931 | In-frame |
| ENST00000408041 | 27204791 | 27204931 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SLC5A6 |
p-ENSG00000138074_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 |
| ENST00000310574 | 3248 | 635 | 27204791 | 27204931 | 1209 | 1348 | 245 | 291 |
| ENST00000408041 | 2247 | 635 | 27204791 | 27204931 | 1057 | 1196 | 245 | 291 |
| 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 |
| Q9Y289 | 245 | 291 | 1 | 635 | Chain | ID=PRO_0000105386;Note=Sodium-dependent multivitamin transporter |
| Q9Y289 | 245 | 291 | 1 | 635 | Chain | ID=PRO_0000105386;Note=Sodium-dependent multivitamin transporter |
| Q9Y289 | 245 | 291 | 256 | 276 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9Y289 | 245 | 291 | 256 | 276 | 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 SLC5A6 |
| 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 |
| Mayo | ENST00000408041 | 27208614 | 27208686 | hsa-miR-4645-5p | chr2:27208646-27208653 | 8mer-1a | chr2:27208644-27208664 | 170.00 | -31.45 |
| Mayo | ENST00000408041 | 27208614 | 27208686 | hsa-miR-589-3p | chr2:27208630-27208637 | 8mer-1a | chr2:27208623-27208644 | 161.00 | -24.54 |
| Mayo | ENST00000408041 | 27208614 | 27208686 | hsa-miR-4660 | chr2:27208652-27208659 | 8mer-1a | chr2:27208644-27208664 | 170.00 | -31.45 |
| Mayo | ENST00000408041 | 27208614 | 27208686 | hsa-miR-4673 | chr2:27208646-27208653 | 8mer-1a | chr2:27208644-27208664 | 170.00 | -31.45 |
| Mayo | ENST00000408041 | 27208614 | 27208686 | hsa-miR-1184 | chr2:27208654-27208661 | 8mer-1a | chr2:27208644-27208664 | 170.00 | -31.45 |
| ROSMAP | ENST00000408041 | 27208614 | 27208686 | hsa-miR-4645-5p | chr2:27208646-27208653 | 8mer-1a | chr2:27208644-27208664 | 170.00 | -31.45 |
| ROSMAP | ENST00000408041 | 27208614 | 27208686 | hsa-miR-589-3p | chr2:27208630-27208637 | 8mer-1a | chr2:27208623-27208644 | 161.00 | -24.54 |
| ROSMAP | ENST00000408041 | 27208614 | 27208686 | hsa-miR-4660 | chr2:27208652-27208659 | 8mer-1a | chr2:27208644-27208664 | 170.00 | -31.45 |
| ROSMAP | ENST00000408041 | 27208614 | 27208686 | hsa-miR-4673 | chr2:27208646-27208653 | 8mer-1a | chr2:27208644-27208664 | 170.00 | -31.45 |
| ROSMAP | ENST00000408041 | 27208614 | 27208686 | hsa-miR-1184 | chr2:27208654-27208661 | 8mer-1a | chr2:27208644-27208664 | 170.00 | -31.45 |
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SNVs in the skipped exons for SLC5A6 |
| - 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 SLC5A6 |
| 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 SLC5A6 |
| 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 SLC5A6 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SLC5A6 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Q9Y289 | approved|investigational|nutraceutical | DB00121 | Biotin | small molecule | Q9Y289 |
| Q9Y289 | approved|investigational|nutraceutical | DB00166 | Lipoic Acid | small molecule | Q9Y289 |
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RelatedDiseases for SLC5A6 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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