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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 SNX29 |
 Gene summary |
| Gene information | Gene symbol | SNX29 | Gene ID | 92017 |
| Gene name | sorting nexin 29 | |
| Synonyms | A-388D4.1|RUNDC2A | |
| Cytomap | 16p13.13-p13.12 | |
| Type of gene | protein-coding | |
| Description | sorting nexin-29RUN domain containing 2ARUN domain-containing protein 2A | |
| 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 SNX29 |
| 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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ENSG00000048471
| 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 SNX29 |
| 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_144799 | chr16 | 11999297:11999358:12002991:12003043:12027320:12027444 | 12002991:12003043 |
| exon_skip_150811 | chr16 | 12027320:12027444:12042897:12043077:12046384:12046454 | 12042897:12043077 |
| exon_skip_153345 | chr16 | 12052198:12052222:12061528:12061646:12069057:12069126 | 12061528:12061646 |
| exon_skip_189687 | chr16 | 12052198:12052222:12061528:12061646:12069057:12069132 | 12061528:12061646 |
| exon_skip_214471 | chr16 | 12129697:12129758:12199601:12199683:12277933:12278036 | 12199601:12199683 |
| exon_skip_273151 | chr16 | 12027320:12027444:12029613:12029734:12042897:12042997 | 12029613:12029734 |
| exon_skip_72756 | chr16 | 11976745:11976813:11999297:11999358:12002991:12003043 | 11999297:11999358 |
| 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 SNX29 |
| 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 |
| ENST00000566228 | 12002991 | 12003043 | Frame-shift |
| ENST00000566228 | 12042897 | 12043077 | Frame-shift |
| ENST00000566228 | 12061528 | 12061646 | Frame-shift |
| ENST00000566228 | 12199601 | 12199683 | 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 |
| ENST00000566228 | 12002991 | 12003043 | Frame-shift |
| ENST00000566228 | 12042897 | 12043077 | Frame-shift |
| ENST00000566228 | 12061528 | 12061646 | Frame-shift |
| ENST00000566228 | 12199601 | 12199683 | 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 |
| ENST00000566228 | 12002991 | 12003043 | Frame-shift |
| ENST00000566228 | 12042897 | 12043077 | Frame-shift |
| ENST00000566228 | 12061528 | 12061646 | Frame-shift |
| ENST00000566228 | 12199601 | 12199683 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for SNX29 |
p-ENSG00000048471_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 SNX29 |
| 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 SNX29 |
| - 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 SNX29 |
| 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 SNX29 |
| 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 SNX29 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SNX29 |
| 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 SNX29 |
| 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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