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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 SNX1 |
 Gene summary |
| Gene information | Gene symbol | SNX1 | Gene ID | 6642 |
| Gene name | sorting nexin 1 | |
| Synonyms | HsT17379|VPS5 | |
| Cytomap | 15q22.31 | |
| Type of gene | protein-coding | |
| Description | sorting nexin-1sorting nexin 1A | |
| Modification date | 20200313 | |
| UniProtAcc | ||
| Context | - 17646382(Sorting by the cytoplasmic domain of the amyloid precursor protein binding receptor SorLA) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| SNX1 | GO:0072673 | lamellipodium morphogenesis | 20604901 |
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Gene structures and expression levels for SNX1 |
| 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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ENSG00000028528
| 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 | UP | ENST00000560260.5 | SNX1-210:nonsense_mediated_decay:SNX1 | 1.996269e+01 | 1.087207e+00 | 1.626588e-11 | 1.449559e-09 |
| CB | UP | ENST00000560829.5 | SNX1-211:protein_coding:SNX1 | 7.680148e+01 | 8.980393e-01 | 1.195970e-03 | 6.004132e-03 |
| CB | UP | ENST00000559389.1 | SNX1-206:nonsense_mediated_decay:SNX1 | 9.504487e+00 | 1.016731e+00 | 3.094070e-03 | 1.323535e-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 SNX1 |
| 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_100818 | chr15 | 64131829:64131892:64134664:64134807:64136330:64136409 | 64134664:64134807 |
| exon_skip_111376 | chr15 | 64096031:64096172:64112573:64112684:64126079:64126099 | 64112573:64112684 |
| exon_skip_159164 | chr15 | 64112573:64112684:64123503:64123546:64126079:64126099 | 64123503:64123546 |
| exon_skip_170980 | chr15 | 64123503:64123546:64126079:64126220:64127174:64127252 | 64126079:64126220 |
| exon_skip_176711 | chr15 | 64118788:64118854:64123503:64123546:64126079:64126099 | 64123503:64123546 |
| exon_skip_192457 | chr15 | 64118788:64118854:64123503:64123546:64127174:64127252 | 64123503:64123546 |
| exon_skip_193614 | chr15 | 64112634:64112684:64115589:64115706:64118117:64118166 | 64115589:64115706 |
| exon_skip_221064 | chr15 | 64118792:64118854:64123503:64123546:64126079:64126099 | 64123503:64123546 |
| exon_skip_225639 | chr15 | 64112634:64112684:64123503:64123546:64126079:64126099 | 64123503:64123546 |
| exon_skip_242151 | chr15 | 64129916:64130029:64130228:64130321:64131687:64131892 | 64130228:64130321 |
| exon_skip_262848 | chr15 | 64112573:64112684:64123503:64123546:64126079:64126131 | 64123503:64123546 |
| exon_skip_294519 | chr15 | 64118203:64118244:64118788:64118854:64123503:64123546 | 64118788:64118854 |
| exon_skip_29594 | chr15 | 64096031:64096172:64112573:64112684:64123503:64123546 | 64112573:64112684 |
| exon_skip_4303 | chr15 | 64112573:64112684:64115589:64115706:64118117:64118166 | 64115589:64115706 |
| exon_skip_95984 | chr15 | 64112573:64112684:64126079:64126220:64127174:64127252 | 64126079:64126220 |
| exon_skip_9938 | chr15 | 64096031:64096172:64112573:64112684:64118117:64118166 | 64112573:64112684 |
| 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 SNX1 |
| 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 |
| ENST00000559844 | 64118788 | 64118854 | Frame-shift |
| ENST00000559844 | 64123503 | 64123546 | Frame-shift |
| ENST00000559844 | 64126079 | 64126220 | Frame-shift |
| ENST00000559844 | 64134664 | 64134807 | 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 |
| ENST00000559844 | 64123503 | 64123546 | Frame-shift |
| ENST00000559844 | 64126079 | 64126220 | Frame-shift |
| ENST00000559844 | 64134664 | 64134807 | 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 |
| ENST00000559844 | 64112573 | 64112684 | Frame-shift |
| ENST00000559844 | 64118788 | 64118854 | Frame-shift |
| ENST00000559844 | 64123503 | 64123546 | Frame-shift |
| ENST00000559844 | 64126079 | 64126220 | Frame-shift |
| ENST00000559844 | 64130228 | 64130321 | Frame-shift |
| ENST00000559844 | 64134664 | 64134807 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SNX1 |
p-ENSG00000028528_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 |
| ENST00000559844 | 1988 | 522 | 64134664 | 64134807 | 1237 | 1379 | 407 | 455 |
| 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 |
| ENST00000559844 | 1988 | 522 | 64134664 | 64134807 | 1237 | 1379 | 407 | 455 |
| 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 |
| ENST00000559844 | 1988 | 522 | 64134664 | 64134807 | 1237 | 1379 | 407 | 455 |
| 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 |
| Q13596 | 407 | 455 | 1 | 522 | Chain | ID=PRO_0000213835;Note=Sorting nexin-1 |
| Q13596 | 407 | 455 | 302 | 522 | Domain | Note=BAR |
| Q13596 | 407 | 455 | 388 | 440 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4FZS |
| Q13596 | 407 | 455 | 443 | 483 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4FZS |
| Q13596 | 407 | 455 | 429 | 431 | Mutagenesis | Note=Loss of endosomal location. KKR->EEE;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15498486;Dbxref=PMID:15498486 |
| Q13596 | 407 | 455 | 442 | 442 | Mutagenesis | Note=No effect on membrane remodeling and membrane binding%3B when associated with A-445. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23085988;Dbxref=PMID:23085988 |
| Q13596 | 407 | 455 | 445 | 445 | Mutagenesis | Note=No effect on membrane remodeling and membrane binding%3B when associated with A-442. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23085988;Dbxref=PMID:23085988 |
| 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 |
| Q13596 | 407 | 455 | 1 | 522 | Chain | ID=PRO_0000213835;Note=Sorting nexin-1 |
| Q13596 | 407 | 455 | 302 | 522 | Domain | Note=BAR |
| Q13596 | 407 | 455 | 388 | 440 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4FZS |
| Q13596 | 407 | 455 | 443 | 483 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4FZS |
| Q13596 | 407 | 455 | 429 | 431 | Mutagenesis | Note=Loss of endosomal location. KKR->EEE;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15498486;Dbxref=PMID:15498486 |
| Q13596 | 407 | 455 | 442 | 442 | Mutagenesis | Note=No effect on membrane remodeling and membrane binding%3B when associated with A-445. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23085988;Dbxref=PMID:23085988 |
| Q13596 | 407 | 455 | 445 | 445 | Mutagenesis | Note=No effect on membrane remodeling and membrane binding%3B when associated with A-442. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23085988;Dbxref=PMID:23085988 |
| 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 |
| Q13596 | 407 | 455 | 1 | 522 | Chain | ID=PRO_0000213835;Note=Sorting nexin-1 |
| Q13596 | 407 | 455 | 302 | 522 | Domain | Note=BAR |
| Q13596 | 407 | 455 | 388 | 440 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4FZS |
| Q13596 | 407 | 455 | 443 | 483 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4FZS |
| Q13596 | 407 | 455 | 429 | 431 | Mutagenesis | Note=Loss of endosomal location. KKR->EEE;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15498486;Dbxref=PMID:15498486 |
| Q13596 | 407 | 455 | 442 | 442 | Mutagenesis | Note=No effect on membrane remodeling and membrane binding%3B when associated with A-445. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23085988;Dbxref=PMID:23085988 |
| Q13596 | 407 | 455 | 445 | 445 | Mutagenesis | Note=No effect on membrane remodeling and membrane binding%3B when associated with A-442. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23085988;Dbxref=PMID:23085988 |
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3'-UTR located exon skipping events that lost miRNA binding sites in SNX1 |
| 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 SNX1 |
| - 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 SNX1 |
| 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 SNX1 |
| 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 SNX1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SNX1 |
| 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 SNX1 |
| 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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