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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 RDH13 |
Gene summary |
Gene information | Gene symbol | RDH13 | Gene ID | 112724 |
Gene name | retinol dehydrogenase 13 | |
Synonyms | SDR7C3 | |
Cytomap | 19q13.42 | |
Type of gene | protein-coding | |
Description | retinol dehydrogenase 13retinol dehydrogenase 13 (all-trans and 9-cis)retinol dehydrogenase 13 (all-trans/9-cis)short chain dehydrogenase/reductase family 7C member 3 | |
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 |
RDH13 | GO:0042574 | retinal metabolic process | 18039331 |
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Gene structures and expression levels for RDH13 |
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 RDH13 |
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_171123 | chr19 | 55047387:55047488:55048046:55048257:55048329:55048541 | 55048046:55048257 |
exon_skip_225917 | chr19 | 55063271:55063371:55063864:55063999:55064296:55064412 | 55063864:55063999 |
exon_skip_250989 | chr19 | 55056676:55056808:55059157:55059275:55062968:55063076 | 55059157:55059275 |
exon_skip_66365 | chr19 | 55059157:55059275:55062968:55063217:55068413:55068530 | 55062968:55063217 |
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 RDH13 |
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 |
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 |
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 |
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Infer the effects of exon skipping event on protein functional features for RDH13 |
p-ENSG00000160439_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 RDH13 |
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 RDH13 |
- 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 RDH13 |
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 RDH13 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
CB | exon_skip_250989 | rs2569513 | chr19:55040776 | 8.186802e-09 | 5.282717e-06 |
CB | exon_skip_250989 | rs1654416 | chr19:55018667 | 1.568817e-07 | 7.143346e-05 |
CB | exon_skip_250989 | rs11671922 | chr19:55023921 | 2.521141e-06 | 7.893547e-04 |
CB | exon_skip_250989 | rs1654452 | chr19:55060916 | 2.573880e-06 | 8.014229e-04 |
DLPFC | exon_skip_171123 | rs2569513 | chr19:55040776 | 5.642859e-04 | 3.556982e-02 |
DLPFC | exon_skip_171123 | rs1654444 | chr19:55055086 | 6.786785e-04 | 4.115622e-02 |
DLPFC | exon_skip_171123 | rs1654416 | chr19:55018667 | 6.987279e-04 | 4.207556e-02 |
DLPFC | exon_skip_171123 | rs11668169 | chr19:55024114 | 7.209898e-04 | 4.307450e-02 |
DLPFC | exon_skip_171123 | rs1654419 | chr19:55024513 | 7.209898e-04 | 4.307450e-02 |
DLPFC | exon_skip_171123 | rs1654420 | chr19:55024838 | 7.209898e-04 | 4.307450e-02 |
DLPFC | exon_skip_171123 | rs1654421 | chr19:55026094 | 7.296872e-04 | 4.348525e-02 |
DLPFC | exon_skip_171123 | rs11671922 | chr19:55023921 | 7.324794e-04 | 4.360497e-02 |
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Correlation with RNA binding proteins (RBPs) for RDH13 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | RBM45 | exon_skip_171123 | 4.178058e-01 | 6.337367e-08 |
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RelatedDrugs for RDH13 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Q8NBN7 | approved|nutraceutical|vet_approved | DB00162 | Vitamin A | small molecule | Q8NBN7 |
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RelatedDiseases for RDH13 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |