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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for PACS1 |
 Gene summary |
| Gene information | Gene symbol | PACS1 | Gene ID | 55690 |
| Gene name | phosphofurin acidic cluster sorting protein 1 | |
| Synonyms | MRD17|SHMS | |
| Cytomap | 11q13.1-q13.2 | |
| Type of gene | protein-coding | |
| Description | phosphofurin acidic cluster sorting protein 1PACS-1cytosolic sorting protein PACS-1 | |
| Modification date | 20180523 | |
| UniProtAcc | Q6VY07 | |
| Context | PubMed: PACS1 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| 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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Exon skipping events across known transcript of Ensembl for PACS1 from UCSC genome browser |
| Skipped exons in TCGA and GTEx 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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Gene isoform structures and expression levels for PACS1 |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for PACS1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_61365 | 11 | 65851443:65851701:65888491:65888538:65960956:65961044 | 65888491:65888538 | ENSG00000175115.7 | ENST00000533756.1 |
| exon_skip_61367 | 11 | 65984165:65984246:65984976:65985088:65987216:65987276 | 65984976:65985088 | ENSG00000175115.7 | ENST00000524784.1 |
| exon_skip_61371 | 11 | 65988140:65988262:65988624:65988718:65994974:65995055 | 65988624:65988718 | ENSG00000175115.7 | ENST00000320580.4 |
| exon_skip_61372 | 11 | 66000430:66000537:66001255:66001410:66001602:66001703 | 66001255:66001410 | ENSG00000175115.7 | ENST00000528935.1,ENST00000529757.1,ENST00000320580.4 |
| exon_skip_61374 | 11 | 66002771:66002874:66003368:66003411:66006274:66006317 | 66003368:66003411 | ENSG00000175115.7 | ENST00000529757.1,ENST00000320580.4 |
| exon_skip_61375 | 11 | 66009039:66009124:66010382:66010502:66010635:66010705 | 66010382:66010502 | ENSG00000175115.7 | ENST00000524815.1,ENST00000529757.1,ENST00000320580.4,ENST00000531597.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PACS1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_61364 | 11 | 65837924:65838313:65960956:65961044:65977832:65977922 | 65960956:65961044 | ENSG00000175115.7 | ENST00000320580.4 |
| exon_skip_61365 | 11 | 65851443:65851701:65888491:65888538:65960956:65961044 | 65888491:65888538 | ENSG00000175115.7 | ENST00000533756.1 |
| exon_skip_61367 | 11 | 65984165:65984246:65984976:65985088:65987216:65987276 | 65984976:65985088 | ENSG00000175115.7 | ENST00000524784.1 |
| exon_skip_61371 | 11 | 65988140:65988262:65988624:65988718:65994974:65995055 | 65988624:65988718 | ENSG00000175115.7 | ENST00000320580.4 |
| exon_skip_61372 | 11 | 66000430:66000537:66001255:66001410:66001602:66001703 | 66001255:66001410 | ENSG00000175115.7 | ENST00000320580.4,ENST00000529757.1,ENST00000528935.1 |
| exon_skip_61374 | 11 | 66002771:66002874:66003368:66003411:66006274:66006317 | 66003368:66003411 | ENSG00000175115.7 | ENST00000320580.4,ENST00000529757.1 |
| exon_skip_61375 | 11 | 66009039:66009124:66010382:66010502:66010635:66010705 | 66010382:66010502 | ENSG00000175115.7 | ENST00000320580.4,ENST00000529757.1,ENST00000524815.1,ENST00000531597.1 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for PACS1 |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000320580 | 65988624 | 65988718 | Frame-shift |
| ENST00000320580 | 66001255 | 66001410 | Frame-shift |
| ENST00000320580 | 66003368 | 66003411 | Frame-shift |
| ENST00000320580 | 66010382 | 66010502 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000320580 | 65960956 | 65961044 | Frame-shift |
| ENST00000320580 | 65988624 | 65988718 | Frame-shift |
| ENST00000320580 | 66001255 | 66001410 | Frame-shift |
| ENST00000320580 | 66003368 | 66003411 | Frame-shift |
| ENST00000320580 | 66010382 | 66010502 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PACS1 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| Loci of skipped exons in TCGA 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 |
| ENST00000320580 | 4409 | 963 | 66010382 | 66010502 | 2690 | 2809 | 885 | 925 |
| Loci of skipped exons in GTEx 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 |
| ENST00000320580 | 4409 | 963 | 66010382 | 66010502 | 2690 | 2809 | 885 | 925 |
| Lost protein functional features of individual exon skipping events in TCGA. |
| 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 GTEx. |
| 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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SNVs in the skipped exons for PACS1 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| HNSC | TCGA-CR-7402-01 | exon_skip_61374 | 66003369 | 66003411 | 66003368 | 66003368 | Splice_Site | G | A | p.F736_splice |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - 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 |
| SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 65988625 | 65988718 | 65988684 | 65988684 | Missense_Mutation | G | A | p.S420N |
| SNU175_LARGE_INTESTINE | 66001256 | 66001410 | 66001356 | 66001356 | Missense_Mutation | G | A | p.A647T |
| SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 66001256 | 66001410 | 66001387 | 66001387 | Missense_Mutation | T | A | p.M657K |
| SISO_CERVIX | 66001256 | 66001410 | 66001389 | 66001389 | Missense_Mutation | C | T | p.R658C |
| GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 66001256 | 66001410 | 66001389 | 66001389 | Missense_Mutation | C | T | p.R658C |
| SKOV3_OVARY | 66010383 | 66010502 | 66010478 | 66010478 | Missense_Mutation | A | G | p.K918E |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PACS1 |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PACS1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PACS1 |
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RelatedDrugs for PACS1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for PACS1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| PACS1 | C0028754 | Obesity | 1 | CTD_human |
| PACS1 | C0236969 | Substance-Related Disorders | 1 | CTD_human |
| PACS1 | C3554343 | MENTAL RETARDATION, AUTOSOMAL DOMINANT 17 | 1 | ORPHANET;UNIPROT |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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