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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 SLC4A4 |
 Gene summary |
| Gene information | Gene symbol | SLC4A4 | Gene ID | 8671 |
| Gene name | solute carrier family 4 member 4 | |
| Synonyms | HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC | |
| Cytomap | 4q13.3 | |
| Type of gene | protein-coding | |
| Description | electrogenic sodium bicarbonate cotransporter 1Na(+)/HCO3(-) cotransportersodium bicarbonate cotransporter 1 (sodium bicarbonate cotransporter, kidney; sodium bicarbonate cotransporter, pancreas)solute carrier family 4 (sodium bicarbonate cotransporter | |
| 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 |
| SLC4A4 | GO:0006814 | sodium ion transport | 16769890 |
| SLC4A4 | GO:0015701 | bicarbonate transport | 10069984 |
| SLC4A4 | GO:0035725 | sodium ion transmembrane transport | 10069984 |
| SLC4A4 | GO:0042391 | regulation of membrane potential | 10069984|15273250 |
| SLC4A4 | GO:0051453 | regulation of intracellular pH | 10069984 |
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Gene structures and expression levels for SLC4A4 |
| 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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ENSG00000080493
| 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 | DOWN | ENST00000340595.3 | SLC4A4-202:protein_coding:SLC4A4 | 9.697282e+02 | -1.132326e+00 | 1.253064e-07 | 2.573485e-06 |
| CB | DOWN | ENST00000425175.5 | SLC4A4-204:protein_coding:SLC4A4 | 1.095565e+03 | -1.576411e+00 | 3.814816e-04 | 2.293231e-03 |
| TC | UP | ENST00000638464.1 | SLC4A4-207:protein_coding:SLC4A4 | 1.708731e+00 | 1.053693e+00 | 2.641749e-04 | 3.483736e-03 |
| TC | UP | ENST00000351898.10 | SLC4A4-203:protein_coding:SLC4A4 | 1.809794e+00 | 1.550825e+00 | 1.429496e-03 | 1.297326e-02 |
| 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 SLC4A4 |
| 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_205965 | chr4 | 71255220:71255399:71339370:71339505:71349912:71349930 | 71339370:71339505 |
| exon_skip_217361 | chr4 | 71472699:71472970:71486948:71487018:71497501:71497692 | 71486948:71487018 |
| exon_skip_280117 | chr4 | 71560093:71560254:71563793:71563889:71567004:71567024 | 71563793:71563889 |
| exon_skip_35373 | chr4 | 71450389:71450543:71451188:71451301:71453495:71453669 | 71451188:71451301 |
| exon_skip_78416 | chr4 | 71187327:71187401:71236576:71236649:71255220:71255399 | 71236576:71236649 |
| exon_skip_80722 | chr4 | 71560093:71560254:71563793:71563889:71567004:71567073 | 71563793:71563889 |
| exon_skip_82454 | chr4 | 71546350:71546528:71547648:71547720:71555140:71555208 | 71547648:71547720 |
| 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 SLC4A4 |
| 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 |
| ENST00000264485 | 71236576 | 71236649 | 5CDS-5UTR |
| ENST00000264485 | 71339370 | 71339505 | Frame-shift |
| ENST00000264485 | 71486948 | 71487018 | Frame-shift |
| ENST00000264485 | 71547648 | 71547720 | Frame-shift |
| ENST00000264485 | 71563793 | 71563889 | Frame-shift |
| ENST00000264485 | 71451188 | 71451301 | 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 |
| ENST00000264485 | 71339370 | 71339505 | Frame-shift |
| ENST00000264485 | 71563793 | 71563889 | 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 |
| ENST00000264485 | 71236576 | 71236649 | 5CDS-5UTR |
| ENST00000264485 | 71339370 | 71339505 | Frame-shift |
| ENST00000264485 | 71486948 | 71487018 | Frame-shift |
| ENST00000264485 | 71547648 | 71547720 | Frame-shift |
| ENST00000264485 | 71563793 | 71563889 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for SLC4A4 |
p-ENSG00000080493_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 |
| ENST00000264485 | 5869 | 1079 | 71451188 | 71451301 | 1856 | 1968 | 403 | 440 |
| 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 |
| Q9Y6R1 | 403 | 440 | 1 | 1079 | Chain | ID=PRO_0000079227;Note=Electrogenic sodium bicarbonate cotransporter 1 |
| Q9Y6R1 | 403 | 440 | 1 | 466 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000269,ECO:0000305;evidence=ECO:0000269|PubMed:12534288,ECO:0000305|PubMed:29500354;Dbxref=PMID:12534288,PMID:29500354 |
| 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 SLC4A4 |
| 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 SLC4A4 |
| - 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 SLC4A4 |
| 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 SLC4A4 |
| 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 SLC4A4 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SLC4A4 |
| 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 SLC4A4 |
| 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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