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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 AP3D1 |
 Gene summary |
| Gene information | Gene symbol | AP3D1 | Gene ID | 8943 |
| Gene name | adaptor related protein complex 3 subunit delta 1 | |
| Synonyms | ADTD|HPS10|hBLVR | |
| Cytomap | 19p13.3 | |
| Type of gene | protein-coding | |
| Description | AP-3 complex subunit delta-1AP-3 complex delta subunit, partial CDSadapter-related protein complex 3 subunit delta-1adaptor related protein complex 3 delta 1 subunitdelta adaptinsubunit of putative vesicle coat adaptor complex AP-3 | |
| Modification date | 20200313 | |
| UniProtAcc | A0A087WYN6, | |
| 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 AP3D1 |
| 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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ENSG00000065000
| 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 |
| STG | UP | ENST00000585652.5 | AP3D1-202:retained_intron:AP3D1 | 3.778727e+01 | 8.966804e-01 | 2.551133e-06 | 1.025268e-03 |
| STG | UP | ENST00000592488.2 | AP3D1-211:retained_intron:AP3D1 | 6.333368e+00 | 8.027668e-01 | 9.726752e-04 | 3.793757e-02 |
| PG | UP | ENST00000590683.2 | AP3D1-207:nonsense_mediated_decay:AP3D1 | 4.553369e+00 | 3.075743e+00 | 5.224802e-07 | 5.390503e-05 |
| CB | DOWN | ENST00000586370.6 | AP3D1-204:protein_coding:AP3D1 | 4.963903e+02 | -1.321409e+00 | 2.340046e-10 | 1.293932e-08 |
| CB | UP | ENST00000590683.2 | AP3D1-207:nonsense_mediated_decay:AP3D1 | 3.778496e+01 | 8.654136e-01 | 1.658805e-08 | 4.636825e-07 |
| 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 AP3D1 |
| 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_105323 | chr19 | 2109086:2109207:2109873:2109958:2110136:2110224 | 2109873:2109958 |
| exon_skip_110380 | chr19 | 2129090:2129163:2129318:2129457:2130408:2130478 | 2129318:2129457 |
| exon_skip_132274 | chr19 | 2111792:2111828:2112860:2112931:2113336:2113413 | 2112860:2112931 |
| exon_skip_133808 | chr19 | 2111792:2111828:2112860:2113413:2114125:2114239 | 2112860:2113413 |
| exon_skip_136101 | chr19 | 2102237:2102268:2108687:2108876:2109086:2109125 | 2108687:2108876 |
| exon_skip_154469 | chr19 | 2130522:2130537:2132471:2132578:2137011:2137091 | 2132471:2132578 |
| exon_skip_167109 | chr19 | 2123830:2123879:2127152:2127201:2129090:2129163 | 2127152:2127201 |
| exon_skip_200195 | chr19 | 2115538:2115613:2116207:2116278:2116605:2116746 | 2116207:2116278 |
| exon_skip_20654 | chr19 | 2111791:2111828:2112860:2113413:2114125:2114239 | 2112860:2113413 |
| exon_skip_227169 | chr19 | 2102237:2102268:2108687:2108766:2109086:2109125 | 2108687:2108766 |
| exon_skip_230691 | chr19 | 2132471:2132578:2137011:2137091:2137727:2137807 | 2137011:2137091 |
| exon_skip_23440 | chr19 | 2111730:2111828:2112860:2113413:2114125:2114302 | 2112860:2113413 |
| exon_skip_240186 | chr19 | 2111791:2111828:2112860:2112967:2113336:2113413 | 2112860:2112967 |
| exon_skip_259194 | chr19 | 2111791:2111828:2112860:2112931:2113336:2113413 | 2112860:2112931 |
| exon_skip_286229 | chr19 | 2111679:2111828:2112860:2113413:2114125:2114302 | 2112860:2113413 |
| exon_skip_287417 | chr19 | 2132471:2132578:2133397:2133484:2137011:2137091 | 2133397:2133484 |
| exon_skip_32176 | chr19 | 2114125:2114302:2114748:2114821:2115219:2115418 | 2114748:2114821 |
| exon_skip_40677 | chr19 | 2137011:2137091:2137727:2137807:2138619:2138714 | 2137727:2137807 |
| exon_skip_44696 | chr19 | 2132471:2132578:2133397:2133484:2137011:2137064 | 2133397:2133484 |
| exon_skip_49669 | chr19 | 2123830:2123879:2127152:2127201:2129090:2129121 | 2127152:2127201 |
| exon_skip_63532 | chr19 | 2112860:2112967:2113336:2113413:2114125:2114239 | 2113336:2113413 |
| exon_skip_73032 | chr19 | 2111792:2111828:2112860:2112967:2113336:2113413 | 2112860:2112967 |
| exon_skip_81695 | chr19 | 2110707:2110896:2111285:2111332:2111679:2111828 | 2111285:2111332 |
| 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 AP3D1 |
| 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 |
| ENST00000345016 | 2108687 | 2108766 | Frame-shift |
| ENST00000345016 | 2127152 | 2127201 | Frame-shift |
| ENST00000345016 | 2111285 | 2111332 | 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 |
| ENST00000345016 | 2127152 | 2127201 | 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 |
| ENST00000345016 | 2108687 | 2108766 | Frame-shift |
| ENST00000345016 | 2109873 | 2109958 | Frame-shift |
| ENST00000345016 | 2114748 | 2114821 | Frame-shift |
| ENST00000345016 | 2127152 | 2127201 | Frame-shift |
| ENST00000345016 | 2129318 | 2129457 | Frame-shift |
| ENST00000345016 | 2111285 | 2111332 | In-frame |
| ENST00000345016 | 2116207 | 2116278 | In-frame |
| ENST00000345016 | 2132471 | 2132578 | In-frame |
| ENST00000345016 | 2137011 | 2137091 | In-frame |
| ENST00000345016 | 2137727 | 2137807 | In-frame |
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Infer the effects of exon skipping event on protein functional features for AP3D1 |
p-ENSG00000065000_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 |
| ENST00000345016 | 4887 | 1153 | 2111285 | 2111332 | 2975 | 3021 | 917 | 932 |
| 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 |
| ENST00000345016 | 4887 | 1153 | 2137727 | 2137807 | 416 | 495 | 64 | 90 |
| ENST00000345016 | 4887 | 1153 | 2137011 | 2137091 | 497 | 576 | 91 | 117 |
| ENST00000345016 | 4887 | 1153 | 2132471 | 2132578 | 578 | 684 | 118 | 153 |
| ENST00000345016 | 4887 | 1153 | 2116207 | 2116278 | 2225 | 2295 | 667 | 690 |
| ENST00000345016 | 4887 | 1153 | 2111285 | 2111332 | 2975 | 3021 | 917 | 932 |
| 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 |
| O14617 | 917 | 932 | 2 | 1153 | Chain | ID=PRO_0000193766;Note=AP-3 complex subunit delta-1 |
| 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 |
| O14617 | 64 | 90 | 2 | 1153 | Chain | ID=PRO_0000193766;Note=AP-3 complex subunit delta-1 |
| O14617 | 64 | 90 | 34 | 71 | Repeat | Note=HEAT 1 |
| O14617 | 64 | 90 | 77 | 114 | Repeat | Note=HEAT 2 |
| O14617 | 91 | 117 | 117 | 285 | Alternative sequence | ID=VSP_000167;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9303295;Dbxref=PMID:9303295 |
| O14617 | 91 | 117 | 2 | 1153 | Chain | ID=PRO_0000193766;Note=AP-3 complex subunit delta-1 |
| O14617 | 91 | 117 | 77 | 114 | Repeat | Note=HEAT 2 |
| O14617 | 118 | 153 | 117 | 285 | Alternative sequence | ID=VSP_000167;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9303295;Dbxref=PMID:9303295 |
| O14617 | 118 | 153 | 2 | 1153 | Chain | ID=PRO_0000193766;Note=AP-3 complex subunit delta-1 |
| O14617 | 118 | 153 | 142 | 179 | Repeat | Note=HEAT 3 |
| O14617 | 667 | 690 | 2 | 1153 | Chain | ID=PRO_0000193766;Note=AP-3 complex subunit delta-1 |
| O14617 | 667 | 690 | 659 | 679 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O14617 | 667 | 690 | 688 | 688 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
| O14617 | 917 | 932 | 2 | 1153 | Chain | ID=PRO_0000193766;Note=AP-3 complex subunit delta-1 |
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3'-UTR located exon skipping events that lost miRNA binding sites in AP3D1 |
| 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 AP3D1 |
| - 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 AP3D1 |
| 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 |
| CDR | MSBB | IFG | exon_skip_49669 | -4.459545e-01 | 1.738117e-02 | chr19 | - | 2123830 | 2123879 | 2127152 | 2127201 | 2129090 | 2129121 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for AP3D1 |
| 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 AP3D1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for AP3D1 |
| 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 AP3D1 |
| 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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