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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 PSD |
 Gene summary |
| Gene information | Gene symbol | PSD | Gene ID | 5662 |
| Gene name | pleckstrin and Sec7 domain containing | |
| Synonyms | EFA6|EFA6A|PSD1|TYL | |
| Cytomap | 10q24.32 | |
| Type of gene | protein-coding | |
| Description | PH and SEC7 domain-containing protein 1exchange factor for ADP-ribosylation factor guanine nucleotide factor 6exchange factor for ARF6exchange factor for ARF6 Apleckstrin homology and SEC7 domain-containing protein 1pleckstrin-Sec7 domains-containing | |
| 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 PSD |
| 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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ENSG00000059915
| 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 | ENST00000611678.4 | PSD-209:protein_coding:PSD | 1.262473e+03 | -8.365392e-01 | 6.129673e-10 | 2.918596e-08 |
| 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 PSD |
| 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_10032 | chr10 | 102405348:102405536:102407223:102407266:102410858:102410947 | 102407223:102407266 |
| exon_skip_126701 | chr10 | 102412147:102412227:102412381:102412575:102413769:102414197 | 102412381:102412575 |
| exon_skip_152523 | chr10 | 102416710:102417121:102418701:102418759:102420081:102420288 | 102418701:102418759 |
| exon_skip_168826 | chr10 | 102405183:102405253:102405346:102405536:102407223:102407255 | 102405346:102405536 |
| exon_skip_190949 | chr10 | 102407223:102407266:102410858:102410947:102411058:102411116 | 102410858:102410947 |
| exon_skip_205529 | chr10 | 102404583:102404727:102404898:102405055:102405183:102405253 | 102404898:102405055 |
| exon_skip_221787 | chr10 | 102405348:102405536:102407223:102407266:102408895:102409290 | 102407223:102407266 |
| exon_skip_257286 | chr10 | 102410858:102410947:102411058:102411116:102411707:102411756 | 102411058:102411116 |
| exon_skip_267318 | chr10 | 102405348:102405536:102407223:102407266:102408895:102409095 | 102407223:102407266 |
| exon_skip_51349 | chr10 | 102405183:102405253:102405346:102405536:102407223:102407266 | 102405346:102405536 |
| exon_skip_55383 | chr10 | 102416710:102417121:102418701:102418759:102419656:102419718 | 102418701:102418759 |
| exon_skip_87445 | chr10 | 102416710:102417121:102418701:102418759:102419874:102419934 | 102418701:102418759 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_269135 | Mayo_TC | 7.772603e-01 | 8.796667e-01 | -1.024064e-01 | 7.761609e-03 |
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Open reading frame (ORF) annotation in the exon skipping event for PSD |
| 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 |
| ENST00000020673 | 102404898 | 102405055 | Frame-shift |
| ENST00000406432 | 102404898 | 102405055 | Frame-shift |
| ENST00000020673 | 102405346 | 102405536 | Frame-shift |
| ENST00000406432 | 102405346 | 102405536 | Frame-shift |
| ENST00000020673 | 102407223 | 102407266 | Frame-shift |
| ENST00000406432 | 102407223 | 102407266 | Frame-shift |
| ENST00000020673 | 102410858 | 102410947 | In-frame |
| ENST00000406432 | 102410858 | 102410947 | In-frame |
| ENST00000020673 | 102412381 | 102412575 | In-frame |
| ENST00000406432 | 102412381 | 102412575 | 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 |
| ENST00000020673 | 102405346 | 102405536 | Frame-shift |
| ENST00000406432 | 102405346 | 102405536 | 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 |
| ENST00000406432 | 102418701 | 102418759 | 3UTR-3UTR |
| ENST00000020673 | 102404898 | 102405055 | Frame-shift |
| ENST00000406432 | 102404898 | 102405055 | Frame-shift |
| ENST00000020673 | 102405346 | 102405536 | Frame-shift |
| ENST00000406432 | 102405346 | 102405536 | Frame-shift |
| ENST00000020673 | 102407223 | 102407266 | Frame-shift |
| ENST00000406432 | 102407223 | 102407266 | Frame-shift |
| ENST00000020673 | 102411058 | 102411116 | Frame-shift |
| ENST00000406432 | 102411058 | 102411116 | Frame-shift |
| ENST00000020673 | 102410858 | 102410947 | In-frame |
| ENST00000406432 | 102410858 | 102410947 | In-frame |
| ENST00000020673 | 102412381 | 102412575 | In-frame |
| ENST00000406432 | 102412381 | 102412575 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PSD |
p-ENSG00000059915_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 |
| ENST00000020673 | 4200 | 1024 | 102412381 | 102412575 | 2081 | 2274 | 518 | 582 |
| ENST00000406432 | 3878 | 1024 | 102412381 | 102412575 | 1757 | 1950 | 518 | 582 |
| ENST00000020673 | 4200 | 1024 | 102410858 | 102410947 | 2529 | 2617 | 667 | 696 |
| ENST00000406432 | 3878 | 1024 | 102410858 | 102410947 | 2205 | 2293 | 667 | 696 |
| 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 |
| ENST00000020673 | 4200 | 1024 | 102412381 | 102412575 | 2081 | 2274 | 518 | 582 |
| ENST00000406432 | 3878 | 1024 | 102412381 | 102412575 | 1757 | 1950 | 518 | 582 |
| ENST00000020673 | 4200 | 1024 | 102410858 | 102410947 | 2529 | 2617 | 667 | 696 |
| ENST00000406432 | 3878 | 1024 | 102410858 | 102410947 | 2205 | 2293 | 667 | 696 |
| 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 |
| A5PKW4 | 518 | 582 | 1 | 1024 | Chain | ID=PRO_0000318298;Note=PH and SEC7 domain-containing protein 1 |
| A5PKW4 | 518 | 582 | 1 | 1024 | Chain | ID=PRO_0000318298;Note=PH and SEC7 domain-containing protein 1 |
| A5PKW4 | 518 | 582 | 512 | 706 | Domain | Note=SEC7;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00189 |
| A5PKW4 | 518 | 582 | 512 | 706 | Domain | Note=SEC7;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00189 |
| A5PKW4 | 518 | 582 | 537 | 537 | Sequence conflict | Note=E->D;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| A5PKW4 | 518 | 582 | 537 | 537 | Sequence conflict | Note=E->D;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| A5PKW4 | 667 | 696 | 1 | 1024 | Chain | ID=PRO_0000318298;Note=PH and SEC7 domain-containing protein 1 |
| A5PKW4 | 667 | 696 | 1 | 1024 | Chain | ID=PRO_0000318298;Note=PH and SEC7 domain-containing protein 1 |
| A5PKW4 | 667 | 696 | 512 | 706 | Domain | Note=SEC7;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00189 |
| A5PKW4 | 667 | 696 | 512 | 706 | Domain | Note=SEC7;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00189 |
| 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 |
| A5PKW4 | 518 | 582 | 1 | 1024 | Chain | ID=PRO_0000318298;Note=PH and SEC7 domain-containing protein 1 |
| A5PKW4 | 518 | 582 | 1 | 1024 | Chain | ID=PRO_0000318298;Note=PH and SEC7 domain-containing protein 1 |
| A5PKW4 | 518 | 582 | 512 | 706 | Domain | Note=SEC7;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00189 |
| A5PKW4 | 518 | 582 | 512 | 706 | Domain | Note=SEC7;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00189 |
| A5PKW4 | 518 | 582 | 537 | 537 | Sequence conflict | Note=E->D;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| A5PKW4 | 518 | 582 | 537 | 537 | Sequence conflict | Note=E->D;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| A5PKW4 | 667 | 696 | 1 | 1024 | Chain | ID=PRO_0000318298;Note=PH and SEC7 domain-containing protein 1 |
| A5PKW4 | 667 | 696 | 1 | 1024 | Chain | ID=PRO_0000318298;Note=PH and SEC7 domain-containing protein 1 |
| A5PKW4 | 667 | 696 | 512 | 706 | Domain | Note=SEC7;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00189 |
| A5PKW4 | 667 | 696 | 512 | 706 | Domain | Note=SEC7;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00189 |
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3'-UTR located exon skipping events that lost miRNA binding sites in PSD |
| 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 |
| Mayo | ENST00000406432 | 102418701 | 102418759 | hsa-miR-1207-3p | chr10:102418751-102418758 | 8mer-1a | chr10:102418736-102418759 | 167.00 | -28.71 |
| Mayo | ENST00000406432 | 102418701 | 102418759 | hsa-miR-6895-3p | chr10:102418728-102418735 | 8mer-1a | chr10:102418721-102418741 | 161.00 | -27.02 |
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SNVs in the skipped exons for PSD |
| - 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 PSD |
| 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 PSD |
| 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 PSD |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for PSD |
| 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 PSD |
| 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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