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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 PHF6 |
 Gene summary |
| Gene information | Gene symbol | PHF6 | Gene ID | 84295 |
| Gene name | PHD finger protein 6 | |
| Synonyms | BFLS|BORJ|CENP-31 | |
| Cytomap | Xq26.2 | |
| Type of gene | protein-coding | |
| Description | PHD finger protein 6PHD-like zinc finger proteincentromere protein 31 | |
| 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 |
| PHF6 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 24554700 |
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Gene structures and expression levels for PHF6 |
| 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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ENSG00000156531
| 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 | ENST00000370800.4 | PHF6-203:protein_coding:PHF6 | 2.251704e+00 | 9.938172e-01 | 1.652342e-03 | 7.863063e-03 |
| 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 PHF6 |
| 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_122216 | chrX | 134378005:134378106:134393501:134393634:134393909:134393952 | 134393501:134393634 |
| exon_skip_26780 | chrX | 134377572:134377755:134378005:134378106:134393501:134393634 | 134378005:134378106 |
| 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 PHF6 |
| 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 |
| ENST00000332070 | 134378005 | 134378106 | In-frame |
| ENST00000370803 | 134378005 | 134378106 | 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 |
| ENST00000332070 | 134378005 | 134378106 | In-frame |
| ENST00000370803 | 134378005 | 134378106 | 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 |
| ENST00000332070 | 134393501 | 134393634 | Frame-shift |
| ENST00000370803 | 134393501 | 134393634 | Frame-shift |
| ENST00000332070 | 134378005 | 134378106 | In-frame |
| ENST00000370803 | 134378005 | 134378106 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PHF6 |
p-ENSG00000156531_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 |
| ENST00000332070 | 4776 | 365 | 134378005 | 134378106 | 342 | 442 | 46 | 80 |
| ENST00000370803 | 4506 | 365 | 134378005 | 134378106 | 401 | 501 | 46 | 80 |
| 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 |
| ENST00000332070 | 4776 | 365 | 134378005 | 134378106 | 342 | 442 | 46 | 80 |
| ENST00000370803 | 4506 | 365 | 134378005 | 134378106 | 401 | 501 | 46 | 80 |
| 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 |
| ENST00000332070 | 4776 | 365 | 134378005 | 134378106 | 342 | 442 | 46 | 80 |
| ENST00000370803 | 4506 | 365 | 134378005 | 134378106 | 401 | 501 | 46 | 80 |
| 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 |
| Q8IWS0 | 46 | 80 | 47 | 80 | Alternative sequence | ID=VSP_054937;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q8IWS0 | 46 | 80 | 47 | 80 | Alternative sequence | ID=VSP_054937;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q8IWS0 | 46 | 80 | 2 | 365 | Chain | ID=PRO_0000059293;Note=PHD finger protein 6 |
| Q8IWS0 | 46 | 80 | 2 | 365 | Chain | ID=PRO_0000059293;Note=PHD finger protein 6 |
| Q8IWS0 | 46 | 80 | 14 | 132 | Region | Note=Extended PHD1 domain (ePHD1);Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01146 |
| Q8IWS0 | 46 | 80 | 14 | 132 | Region | Note=Extended PHD1 domain (ePHD1);Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01146 |
| Q8IWS0 | 46 | 80 | 14 | 52 | Zinc finger | Note=C2HC pre-PHD-type 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01146 |
| Q8IWS0 | 46 | 80 | 14 | 52 | Zinc finger | Note=C2HC pre-PHD-type 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01146 |
| Q8IWS0 | 46 | 80 | 80 | 132 | Zinc finger | Note=PHD-type 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01146 |
| Q8IWS0 | 46 | 80 | 80 | 132 | Zinc finger | Note=PHD-type 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01146 |
| 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 |
| Q8IWS0 | 46 | 80 | 47 | 80 | Alternative sequence | ID=VSP_054937;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q8IWS0 | 46 | 80 | 47 | 80 | Alternative sequence | ID=VSP_054937;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q8IWS0 | 46 | 80 | 2 | 365 | Chain | ID=PRO_0000059293;Note=PHD finger protein 6 |
| Q8IWS0 | 46 | 80 | 2 | 365 | Chain | ID=PRO_0000059293;Note=PHD finger protein 6 |
| Q8IWS0 | 46 | 80 | 14 | 132 | Region | Note=Extended PHD1 domain (ePHD1);Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01146 |
| Q8IWS0 | 46 | 80 | 14 | 132 | Region | Note=Extended PHD1 domain (ePHD1);Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01146 |
| Q8IWS0 | 46 | 80 | 14 | 52 | Zinc finger | Note=C2HC pre-PHD-type 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01146 |
| Q8IWS0 | 46 | 80 | 14 | 52 | Zinc finger | Note=C2HC pre-PHD-type 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01146 |
| Q8IWS0 | 46 | 80 | 80 | 132 | Zinc finger | Note=PHD-type 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01146 |
| Q8IWS0 | 46 | 80 | 80 | 132 | Zinc finger | Note=PHD-type 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01146 |
| 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 |
| Q8IWS0 | 46 | 80 | 47 | 80 | Alternative sequence | ID=VSP_054937;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q8IWS0 | 46 | 80 | 47 | 80 | Alternative sequence | ID=VSP_054937;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q8IWS0 | 46 | 80 | 2 | 365 | Chain | ID=PRO_0000059293;Note=PHD finger protein 6 |
| Q8IWS0 | 46 | 80 | 2 | 365 | Chain | ID=PRO_0000059293;Note=PHD finger protein 6 |
| Q8IWS0 | 46 | 80 | 14 | 132 | Region | Note=Extended PHD1 domain (ePHD1);Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01146 |
| Q8IWS0 | 46 | 80 | 14 | 132 | Region | Note=Extended PHD1 domain (ePHD1);Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01146 |
| Q8IWS0 | 46 | 80 | 14 | 52 | Zinc finger | Note=C2HC pre-PHD-type 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01146 |
| Q8IWS0 | 46 | 80 | 14 | 52 | Zinc finger | Note=C2HC pre-PHD-type 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01146 |
| Q8IWS0 | 46 | 80 | 80 | 132 | Zinc finger | Note=PHD-type 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01146 |
| Q8IWS0 | 46 | 80 | 80 | 132 | Zinc finger | Note=PHD-type 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01146 |
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3'-UTR located exon skipping events that lost miRNA binding sites in PHF6 |
| 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 PHF6 |
| - 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 PHF6 |
| 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 PHF6 |
| 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 PHF6 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| IFG | PUF60 | exon_skip_26780 | 4.112724e-01 | 3.685799e-02 |
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RelatedDrugs for PHF6 |
| 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 PHF6 |
| 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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