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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 SNX3 |
Gene summary |
Gene information | Gene symbol | SNX3 | Gene ID | 8724 |
Gene name | sorting nexin 3 | |
Synonyms | Grd19|MCOPS8|SDP3 | |
Cytomap | 6q21 | |
Type of gene | protein-coding | |
Description | sorting nexin-3sorting nexin 3A | |
Modification date | 20200313 | |
UniProtAcc | O60493, | |
Context | - 29196797(Sorting Nexin 3 Mutation Impairs Development and Neuronal Function in Caenorhabditis Elegans) |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
SNX3 | GO:0009617 | response to bacterium | 20482551 |
SNX3 | GO:0010324 | membrane invagination | 18767904 |
SNX3 | GO:0022615 | protein to membrane docking | 24344282 |
SNX3 | GO:0042177 | negative regulation of protein catabolic process | 18767904 |
SNX3 | GO:0046597 | negative regulation of viral entry into host cell | 18767904 |
SNX3 | GO:0051224 | negative regulation of protein transport | 18767904 |
SNX3 | GO:2000642 | negative regulation of early endosome to late endosome transport | 18767904 |
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Gene structures and expression levels for SNX3 |
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 |
CB | UP | ENST00000368979.6 | SNX3-203:nonsense_mediated_decay:SNX3 | 8.746352e+01 | 1.035397e+00 | 2.153988e-05 | 2.016081e-04 |
TC | UP | ENST00000368979.6 | SNX3-203:nonsense_mediated_decay:SNX3 | 7.707275e+01 | 8.511016e-01 | 1.033204e-03 | 1.015022e-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 SNX3 |
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_117305 | chr6 | 108212164:108212254:108214498:108214622:108222950:108223045 | 108214498:108214622 |
exon_skip_146610 | chr6 | 108212005:108212254:108214498:108214622:108222950:108222986 | 108214498:108214622 |
exon_skip_177109 | chr6 | 108212005:108212254:108214498:108214622:108222234:108222320 | 108214498:108214622 |
exon_skip_199753 | chr6 | 108214498:108214622:108222950:108223045:108260826:108261244 | 108222950:108223045 |
exon_skip_200854 | chr6 | 108212005:108212254:108214498:108214622:108222950:108223045 | 108214498:108214622 |
exon_skip_241879 | chr6 | 108214578:108214622:108222950:108223045:108260826:108261244 | 108222950:108223045 |
exon_skip_91836 | chr6 | 108214498:108214622:108222234:108222320:108222950:108223045 | 108222234:108222320 |
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 SNX3 |
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 |
ENST00000230085 | 108214498 | 108214622 | 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 |
ENST00000230085 | 108214498 | 108214622 | 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 |
ENST00000230085 | 108214498 | 108214622 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for SNX3 |
p-ENSG00000112335_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 SNX3 |
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 SNX3 |
- 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 SNX3 |
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 SNX3 |
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 SNX3 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SNX3 |
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 SNX3 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |