|
||||||
|
 | |
| |
| |
| 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 SLC23A2 |
 Gene summary |
| Gene information | Gene symbol | SLC23A2 | Gene ID | 9962 |
| Gene name | solute carrier family 23 member 2 | |
| Synonyms | NBTL1|SLC23A1|SVCT2|YSPL2 | |
| Cytomap | 20p13 | |
| Type of gene | protein-coding | |
| Description | solute carrier family 23 member 2Na(+)/L-ascorbic acid transporter 2nucleobase transporter-like 1 proteinsodium-dependent vitamin C transporter-2solute carrier family 23 (ascorbic acid transporter), member 2solute carrier family 23 (nucleobase transp | |
| 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 |
| SLC23A2 | GO:0015882 | L-ascorbic acid transmembrane transport | 10471399|10631088|18247577|18417304|19216494 |
| SLC23A2 | GO:0070904 | transepithelial L-ascorbic acid transport | 18417304 |
Top |
Gene structures and expression levels for SLC23A2 |
| 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. |
 |
ENSG00000089057
| 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 |
| CB | UP | ENST00000468355.5 | SLC23A2-204:lncRNA:SLC23A2 | 1.779758e+01 | 8.165049e-01 | 5.782929e-09 | 1.900009e-07 |
| CB | DOWN | ENST00000379333.5 | SLC23A2-202:protein_coding:SLC23A2 | 1.896777e+02 | -1.943946e+00 | 5.177458e-03 | 2.025094e-02 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SLC23A2 |
| 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_103580 | chr20 | 4902442:4902558:4912880:4912978:4932455:4932529 | 4912880:4912978 |
| exon_skip_11006 | chr20 | 4884753:4884823:4885821:4885909:4899555:4899647 | 4885821:4885909 |
| exon_skip_120669 | chr20 | 4874576:4874696:4883642:4883823:4884753:4884823 | 4883642:4883823 |
| exon_skip_16403 | chr20 | 4899555:4899712:4902442:4902558:4912880:4912978 | 4902442:4902558 |
| exon_skip_16911 | chr20 | 4912880:4912978:4932455:4932716:4970793:4970915 | 4932455:4932716 |
| exon_skip_23189 | chr20 | 4932580:4932716:4970793:4970919:5001406:5001510 | 4970793:4970919 |
| exon_skip_264271 | chr20 | 4885821:4885909:4899555:4899712:4902442:4902558 | 4899555:4899712 |
| exon_skip_270479 | chr20 | 4902442:4902558:4912880:4912978:4932455:4932716 | 4912880:4912978 |
| exon_skip_52398 | chr20 | 4867770:4867875:4869906:4870053:4873936:4874092 | 4869906:4870053 |
| exon_skip_92920 | chr20 | 4932455:4932716:4970793:4970919:5001406:5001510 | 4970793:4970919 |
| 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 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for SLC23A2 |
| 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 |
| ENST00000338244 | 4932455 | 4932716 | 3UTR-3CDS |
| ENST00000379333 | 4932455 | 4932716 | 3UTR-3CDS |
| ENST00000338244 | 4970793 | 4970919 | 3UTR-3UTR |
| ENST00000338244 | 4885821 | 4885909 | Frame-shift |
| ENST00000379333 | 4885821 | 4885909 | Frame-shift |
| ENST00000338244 | 4899555 | 4899712 | Frame-shift |
| ENST00000379333 | 4899555 | 4899712 | Frame-shift |
| ENST00000338244 | 4902442 | 4902558 | In-frame |
| ENST00000379333 | 4902442 | 4902558 | In-frame |
| ENST00000338244 | 4912880 | 4912978 | In-frame |
| ENST00000379333 | 4912880 | 4912978 | 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 |
| ENST00000338244 | 4970793 | 4970919 | 3UTR-3UTR |
| ENST00000338244 | 4885821 | 4885909 | Frame-shift |
| ENST00000379333 | 4885821 | 4885909 | Frame-shift |
| ENST00000338244 | 4912880 | 4912978 | In-frame |
| ENST00000379333 | 4912880 | 4912978 | 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 |
| ENST00000338244 | 4932455 | 4932716 | 3UTR-3CDS |
| ENST00000379333 | 4932455 | 4932716 | 3UTR-3CDS |
| ENST00000338244 | 4970793 | 4970919 | 3UTR-3UTR |
| ENST00000338244 | 4869906 | 4870053 | Frame-shift |
| ENST00000379333 | 4869906 | 4870053 | Frame-shift |
| ENST00000338244 | 4883642 | 4883823 | Frame-shift |
| ENST00000379333 | 4883642 | 4883823 | Frame-shift |
| ENST00000338244 | 4885821 | 4885909 | Frame-shift |
| ENST00000379333 | 4885821 | 4885909 | Frame-shift |
| ENST00000338244 | 4902442 | 4902558 | In-frame |
| ENST00000379333 | 4902442 | 4902558 | In-frame |
| ENST00000338244 | 4912880 | 4912978 | In-frame |
| ENST00000379333 | 4912880 | 4912978 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for SLC23A2 |
p-ENSG00000089057_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 |
| ENST00000338244 | 6961 | 650 | 4912880 | 4912978 | 484 | 581 | 36 | 68 |
| ENST00000379333 | 6979 | 650 | 4912880 | 4912978 | 502 | 599 | 36 | 68 |
| ENST00000338244 | 6961 | 650 | 4902442 | 4902558 | 583 | 698 | 69 | 107 |
| ENST00000379333 | 6979 | 650 | 4902442 | 4902558 | 601 | 716 | 69 | 107 |
| 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 |
| ENST00000338244 | 6961 | 650 | 4912880 | 4912978 | 484 | 581 | 36 | 68 |
| ENST00000379333 | 6979 | 650 | 4912880 | 4912978 | 502 | 599 | 36 | 68 |
| 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 |
| ENST00000338244 | 6961 | 650 | 4912880 | 4912978 | 484 | 581 | 36 | 68 |
| ENST00000379333 | 6979 | 650 | 4912880 | 4912978 | 502 | 599 | 36 | 68 |
| ENST00000338244 | 6961 | 650 | 4902442 | 4902558 | 583 | 698 | 69 | 107 |
| ENST00000379333 | 6979 | 650 | 4902442 | 4902558 | 601 | 716 | 69 | 107 |
| 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 |
| Q9UGH3 | 36 | 68 | 1 | 650 | Chain | ID=PRO_0000165978;Note=Solute carrier family 23 member 2 |
| Q9UGH3 | 36 | 68 | 1 | 650 | Chain | ID=PRO_0000165978;Note=Solute carrier family 23 member 2 |
| Q9UGH3 | 36 | 68 | 9 | 110 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UGH3 | 36 | 68 | 9 | 110 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UGH3 | 69 | 107 | 1 | 650 | Chain | ID=PRO_0000165978;Note=Solute carrier family 23 member 2 |
| Q9UGH3 | 69 | 107 | 1 | 650 | Chain | ID=PRO_0000165978;Note=Solute carrier family 23 member 2 |
| Q9UGH3 | 69 | 107 | 70 | 70 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9EPR4 |
| Q9UGH3 | 69 | 107 | 70 | 70 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9EPR4 |
| Q9UGH3 | 69 | 107 | 75 | 75 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9WTW8 |
| Q9UGH3 | 69 | 107 | 75 | 75 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9WTW8 |
| Q9UGH3 | 69 | 107 | 78 | 78 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9EPR4 |
| Q9UGH3 | 69 | 107 | 78 | 78 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9EPR4 |
| Q9UGH3 | 69 | 107 | 79 | 79 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9EPR4 |
| Q9UGH3 | 69 | 107 | 79 | 79 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9EPR4 |
| Q9UGH3 | 69 | 107 | 81 | 81 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:23186163;Dbxref=PMID:19690332,PMID:23186163 |
| Q9UGH3 | 69 | 107 | 81 | 81 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:23186163;Dbxref=PMID:19690332,PMID:23186163 |
| Q9UGH3 | 69 | 107 | 9 | 110 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UGH3 | 69 | 107 | 9 | 110 | Topological domain | Note=Cytoplasmic;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 |
| Q9UGH3 | 36 | 68 | 1 | 650 | Chain | ID=PRO_0000165978;Note=Solute carrier family 23 member 2 |
| Q9UGH3 | 36 | 68 | 1 | 650 | Chain | ID=PRO_0000165978;Note=Solute carrier family 23 member 2 |
| Q9UGH3 | 36 | 68 | 9 | 110 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UGH3 | 36 | 68 | 9 | 110 | Topological domain | Note=Cytoplasmic;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 |
| Q9UGH3 | 36 | 68 | 1 | 650 | Chain | ID=PRO_0000165978;Note=Solute carrier family 23 member 2 |
| Q9UGH3 | 36 | 68 | 1 | 650 | Chain | ID=PRO_0000165978;Note=Solute carrier family 23 member 2 |
| Q9UGH3 | 36 | 68 | 9 | 110 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UGH3 | 36 | 68 | 9 | 110 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UGH3 | 69 | 107 | 1 | 650 | Chain | ID=PRO_0000165978;Note=Solute carrier family 23 member 2 |
| Q9UGH3 | 69 | 107 | 1 | 650 | Chain | ID=PRO_0000165978;Note=Solute carrier family 23 member 2 |
| Q9UGH3 | 69 | 107 | 70 | 70 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9EPR4 |
| Q9UGH3 | 69 | 107 | 70 | 70 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9EPR4 |
| Q9UGH3 | 69 | 107 | 75 | 75 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9WTW8 |
| Q9UGH3 | 69 | 107 | 75 | 75 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9WTW8 |
| Q9UGH3 | 69 | 107 | 78 | 78 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9EPR4 |
| Q9UGH3 | 69 | 107 | 78 | 78 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9EPR4 |
| Q9UGH3 | 69 | 107 | 79 | 79 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9EPR4 |
| Q9UGH3 | 69 | 107 | 79 | 79 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9EPR4 |
| Q9UGH3 | 69 | 107 | 81 | 81 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:23186163;Dbxref=PMID:19690332,PMID:23186163 |
| Q9UGH3 | 69 | 107 | 81 | 81 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:23186163;Dbxref=PMID:19690332,PMID:23186163 |
| Q9UGH3 | 69 | 107 | 9 | 110 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UGH3 | 69 | 107 | 9 | 110 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in SLC23A2 |
| 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 | ENST00000338244 | 4970793 | 4970919 | hsa-miR-10527-5p | chr20:4970851-4970858 | 8mer-1a | chr20:4970833-4970858 | 162.00 | -18.72 |
| Mayo | ENST00000338244 | 4970793 | 4970919 | hsa-miR-659-5p | chr20:4970865-4970872 | 8mer-1a | chr20:4970857-4970873 | 149.00 | -16.95 |
| Mayo | ENST00000338244 | 4970793 | 4970919 | hsa-miR-4535 | chr20:4970866-4970873 | 8mer-1a | chr20:4970857-4970873 | 149.00 | -16.95 |
| MSBB | ENST00000338244 | 4970793 | 4970919 | hsa-miR-10527-5p | chr20:4970851-4970858 | 8mer-1a | chr20:4970833-4970858 | 162.00 | -18.72 |
| MSBB | ENST00000338244 | 4970793 | 4970919 | hsa-miR-659-5p | chr20:4970865-4970872 | 8mer-1a | chr20:4970857-4970873 | 149.00 | -16.95 |
| MSBB | ENST00000338244 | 4970793 | 4970919 | hsa-miR-4535 | chr20:4970866-4970873 | 8mer-1a | chr20:4970857-4970873 | 149.00 | -16.95 |
| ROSMAP | ENST00000338244 | 4970793 | 4970919 | hsa-miR-10527-5p | chr20:4970851-4970858 | 8mer-1a | chr20:4970833-4970858 | 162.00 | -18.72 |
| ROSMAP | ENST00000338244 | 4970793 | 4970919 | hsa-miR-659-5p | chr20:4970865-4970872 | 8mer-1a | chr20:4970857-4970873 | 149.00 | -16.95 |
| ROSMAP | ENST00000338244 | 4970793 | 4970919 | hsa-miR-4535 | chr20:4970866-4970873 | 8mer-1a | chr20:4970857-4970873 | 149.00 | -16.95 |
Top |
SNVs in the skipped exons for SLC23A2 |
| - 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 |
Top |
AD stage-associated exon skippint events for SLC23A2 |
| 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 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SLC23A2 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| TC | exon_skip_11006 | rs13042717 | chr20:4846688 | 1.032365e-06 | 3.508530e-04 |
Top |
Correlation with RNA binding proteins (RBPs) for SLC23A2 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
Top |
RelatedDrugs for SLC23A2 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for SLC23A2 |
| 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)
|