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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 PACS2 |
 Gene summary |
| Gene information | Gene symbol | PACS2 | Gene ID | 23241 |
| Gene name | phosphofurin acidic cluster sorting protein 2 | |
| Synonyms | EIEE66|PACS-2|PACS1L | |
| Cytomap | 14q32.33 | |
| Type of gene | protein-coding | |
| Description | phosphofurin acidic cluster sorting protein 2PACS1-like protein | |
| 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 |
| PACS2 | GO:0000045 | autophagosome assembly | 23455425 |
| PACS2 | GO:0034497 | protein localization to phagophore assembly site | 23455425 |
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Gene structures and expression levels for PACS2 |
| 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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ENSG00000179364
| 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 |
| PCC | UP | ENST00000551743.5 | PACS2-212:retained_intron:PACS2 | 1.164375e+02 | 8.208524e-01 | 5.051481e-04 | 1.666777e-02 |
| TC | DOWN | ENST00000551743.5 | PACS2-212:retained_intron:PACS2 | 7.113166e+02 | -8.520426e-01 | 5.516102e-08 | 3.761889e-06 |
| 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 PACS2 |
| 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_117886 | chr14 | 105392761:105392845:105393222:105393335:105394554:105394672 | 105393222:105393335 |
| exon_skip_156284 | chr14 | 105381914:105382046:105382477:105382581:105382807:105382913 | 105382477:105382581 |
| exon_skip_173191 | chr14 | 105376768:105376925:105379739:105379829:105380080:105380154 | 105379739:105379829 |
| exon_skip_184355 | chr14 | 105381986:105382046:105382477:105382581:105382807:105382913 | 105382477:105382581 |
| exon_skip_193144 | chr14 | 105389961:105390003:105391207:105391249:105391631:105391766 | 105391207:105391249 |
| exon_skip_212056 | chr14 | 105314890:105315037:105348493:105348580:105352378:105352467 | 105348493:105348580 |
| exon_skip_227199 | chr14 | 105384884:105384987:105389961:105390003:105391207:105391249 | 105389961:105390003 |
| exon_skip_259499 | chr14 | 105348493:105348580:105352378:105352467:105355052:105355177 | 105352378:105352467 |
| exon_skip_264685 | chr14 | 105384884:105384987:105385685:105385717:105389961:105390003 | 105385685:105385717 |
| exon_skip_278691 | chr14 | 105380080:105380154:105380957:105381099:105381914:105382046 | 105380957:105381099 |
| exon_skip_30895 | chr14 | 105348493:105348580:105355052:105355177:105367213:105367250 | 105355052:105355177 |
| exon_skip_40334 | chr14 | 105352378:105352467:105355052:105355177:105367213:105367250 | 105355052:105355177 |
| exon_skip_43927 | chr14 | 105391207:105391249:105391631:105391766:105392619:105392845 | 105391631:105391766 |
| exon_skip_45245 | chr14 | 105384879:105384987:105389961:105390003:105391207:105391249 | 105389961:105390003 |
| exon_skip_55379 | chr14 | 105391207:105391249:105391500:105391766:105392619:105392845 | 105391500:105391766 |
| exon_skip_66998 | chr14 | 105385685:105385717:105389961:105390003:105391207:105391249 | 105389961:105390003 |
| exon_skip_7186 | chr14 | 105382477:105382581:105382807:105382913:105383359:105383513 | 105382807:105382913 |
| 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_264685 | MSBB_PG | 3.687611e-01 | 5.440476e-01 | -1.752866e-01 | 8.929822e-04 |
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Open reading frame (ORF) annotation in the exon skipping event for PACS2 |
| 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 |
| ENST00000325438 | 105348493 | 105348580 | Frame-shift |
| ENST00000325438 | 105382807 | 105382913 | Frame-shift |
| ENST00000325438 | 105389961 | 105390003 | Frame-shift |
| ENST00000325438 | 105391207 | 105391249 | Frame-shift |
| ENST00000325438 | 105391631 | 105391766 | Frame-shift |
| ENST00000325438 | 105352378 | 105352467 | In-frame |
| ENST00000325438 | 105393222 | 105393335 | 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 |
| ENST00000325438 | 105352378 | 105352467 | 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 |
| ENST00000325438 | 105348493 | 105348580 | Frame-shift |
| ENST00000325438 | 105379739 | 105379829 | Frame-shift |
| ENST00000325438 | 105380957 | 105381099 | Frame-shift |
| ENST00000325438 | 105382807 | 105382913 | Frame-shift |
| ENST00000325438 | 105389961 | 105390003 | Frame-shift |
| ENST00000325438 | 105391631 | 105391766 | Frame-shift |
| ENST00000325438 | 105352378 | 105352467 | In-frame |
| ENST00000325438 | 105355052 | 105355177 | In-frame |
| ENST00000325438 | 105382477 | 105382581 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PACS2 |
p-ENSG00000179364_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 |
| ENST00000325438 | 3725 | 889 | 105352378 | 105352467 | 713 | 801 | 69 | 99 |
| ENST00000325438 | 3725 | 889 | 105393222 | 105393335 | 2943 | 3055 | 813 | 850 |
| 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 |
| ENST00000325438 | 3725 | 889 | 105352378 | 105352467 | 713 | 801 | 69 | 99 |
| 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 |
| ENST00000325438 | 3725 | 889 | 105352378 | 105352467 | 713 | 801 | 69 | 99 |
| ENST00000325438 | 3725 | 889 | 105355052 | 105355177 | 803 | 927 | 99 | 141 |
| ENST00000325438 | 3725 | 889 | 105382477 | 105382581 | 1907 | 2010 | 467 | 502 |
| 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 |
| Q86VP3 | 69 | 99 | 1 | 889 | Chain | ID=PRO_0000259511;Note=Phosphofurin acidic cluster sorting protein 2 |
| Q86VP3 | 813 | 850 | 1 | 889 | Chain | ID=PRO_0000259511;Note=Phosphofurin acidic cluster sorting protein 2 |
| 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 |
| Q86VP3 | 69 | 99 | 1 | 889 | Chain | ID=PRO_0000259511;Note=Phosphofurin acidic cluster sorting protein 2 |
| 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 |
| Q86VP3 | 69 | 99 | 1 | 889 | Chain | ID=PRO_0000259511;Note=Phosphofurin acidic cluster sorting protein 2 |
| Q86VP3 | 99 | 141 | 1 | 889 | Chain | ID=PRO_0000259511;Note=Phosphofurin acidic cluster sorting protein 2 |
| Q86VP3 | 467 | 502 | 467 | 467 | Alternative sequence | ID=VSP_021409;Note=In isoform 2. Q->QVQLQ;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9628581;Dbxref=PMID:9628581 |
| Q86VP3 | 467 | 502 | 1 | 889 | Chain | ID=PRO_0000259511;Note=Phosphofurin acidic cluster sorting protein 2 |
| Q86VP3 | 467 | 502 | 493 | 493 | Natural variant | ID=VAR_053798;Note=L->S;Dbxref=dbSNP:rs4076933 |
| Q86VP3 | 467 | 502 | 469 | 469 | Sequence conflict | Note=P->H;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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3'-UTR located exon skipping events that lost miRNA binding sites in PACS2 |
| 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 PACS2 |
| - 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 PACS2 |
| 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 |
| ADstage | MSBB | IFG | exon_skip_184002 | -3.768205e-01 | 4.808838e-02 | chr14 | + | 105384879 | 105384987 | 105385685 | 105388036 | 105389961 | 105390003 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PACS2 |
| 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 PACS2 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | PCBP1 | exon_skip_264685 | 4.004506e-01 | 1.693326e-07 |
| CB | RALYL | exon_skip_264685 | 5.484710e-01 | 7.214803e-14 |
| CB | SRSF9 | exon_skip_264685 | 4.477596e-01 | 3.263606e-09 |
| DLPFC | ELAVL4 | exon_skip_264685 | 4.204807e-01 | 4.384936e-16 |
| HCC | TRNAU1AP | exon_skip_264685 | -5.438386e-01 | 2.051128e-22 |
| IFG | ELAVL4 | exon_skip_264685 | 5.454546e-01 | 2.682175e-03 |
| IFG | RALYL | exon_skip_264685 | 5.900877e-01 | 9.491160e-04 |
| PCC | ELAVL4 | exon_skip_264685 | 5.719883e-01 | 4.442949e-20 |
| PG | ELAVL4 | exon_skip_264685 | 6.038702e-01 | 8.978451e-17 |
| PG | PCBP1 | exon_skip_264685 | 4.419476e-01 | 8.568730e-09 |
| PG | RALYL | exon_skip_264685 | 5.492120e-01 | 1.365355e-13 |
| STG | ELAVL4 | exon_skip_264685 | 4.335634e-01 | 3.398470e-05 |
| STG | RALYL | exon_skip_264685 | 4.750214e-01 | 4.358270e-06 |
| TC | ELAVL4 | exon_skip_264685 | 7.304404e-01 | 5.917048e-28 |
| TC | NUP42 | exon_skip_264685 | 4.954120e-01 | 2.735887e-11 |
| TC | RALYL | exon_skip_264685 | 7.455060e-01 | 1.223596e-29 |
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RelatedDrugs for PACS2 |
| 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 PACS2 |
| 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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