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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 PHF2 |
 Gene summary |
| Gene information | Gene symbol | PHF2 | Gene ID | 5253 |
| Gene name | PHD finger protein 2 | |
| Synonyms | CENP-35|GRC5|JHDM1E|KDM7C | |
| Cytomap | 9q22.31 | |
| Type of gene | protein-coding | |
| Description | lysine-specific demethylase PHF2centromere protein 35jumonji C domain-containing histone demethylase 1E | |
| 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 |
| PHF2 | GO:0006482 | protein demethylation | 21532585 |
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Gene structures and expression levels for PHF2 |
| 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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ENSG00000197724
| 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. |
| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| 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 PHF2 |
| 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_173981 | chr9 | 93658145:93658236:93659511:93659600:93660192:93660560 | 93659511:93659600 |
| exon_skip_180706 | chr9 | 93673790:93673862:93674927:93675022:93675680:93675789 | 93674927:93675022 |
| exon_skip_23027 | chr9 | 93675680:93675789:93676594:93676963:93677588:93679583 | 93676594:93676963 |
| exon_skip_26166 | chr9 | 93654518:93654575:93655934:93656021:93656489:93656595 | 93655934:93656021 |
| 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 PHF2 |
| 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 |
| ENST00000359246 | 93659511 | 93659600 | 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 |
| ENST00000359246 | 93659511 | 93659600 | 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 |
| ENST00000359246 | 93655934 | 93656021 | Frame-shift |
| ENST00000359246 | 93676594 | 93676963 | Frame-shift |
| ENST00000359246 | 93659511 | 93659600 | In-frame |
| ENST00000359246 | 93674927 | 93675022 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PHF2 |
p-ENSG00000197724_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 |
| ENST00000359246 | 5586 | 1096 | 93659511 | 93659600 | 1608 | 1696 | 413 | 443 |
| 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 |
| ENST00000359246 | 5586 | 1096 | 93659511 | 93659600 | 1608 | 1696 | 413 | 443 |
| 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 |
| ENST00000359246 | 5586 | 1096 | 93659511 | 93659600 | 1608 | 1696 | 413 | 443 |
| ENST00000359246 | 5586 | 1096 | 93674927 | 93675022 | 2995 | 3089 | 876 | 907 |
| 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 |
| O75151 | 413 | 443 | 1 | 1096 | Chain | ID=PRO_0000059290;Note=Lysine-specific demethylase PHF2 |
| O75151 | 413 | 443 | 415 | 418 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3PU8 |
| O75151 | 413 | 443 | 419 | 421 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3PUA |
| O75151 | 413 | 443 | 428 | 443 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3PUA |
| O75151 | 413 | 443 | 412 | 414 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3PU8 |
| 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 |
| O75151 | 413 | 443 | 1 | 1096 | Chain | ID=PRO_0000059290;Note=Lysine-specific demethylase PHF2 |
| O75151 | 413 | 443 | 415 | 418 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3PU8 |
| O75151 | 413 | 443 | 419 | 421 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3PUA |
| O75151 | 413 | 443 | 428 | 443 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3PUA |
| O75151 | 413 | 443 | 412 | 414 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3PU8 |
| 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 |
| O75151 | 413 | 443 | 1 | 1096 | Chain | ID=PRO_0000059290;Note=Lysine-specific demethylase PHF2 |
| O75151 | 413 | 443 | 415 | 418 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3PU8 |
| O75151 | 413 | 443 | 419 | 421 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3PUA |
| O75151 | 413 | 443 | 428 | 443 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3PUA |
| O75151 | 413 | 443 | 412 | 414 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3PU8 |
| O75151 | 876 | 907 | 1 | 1096 | Chain | ID=PRO_0000059290;Note=Lysine-specific demethylase PHF2 |
| O75151 | 876 | 907 | 879 | 879 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9WTU0 |
| O75151 | 876 | 907 | 882 | 882 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:23186163,ECO:0000244|PubMed:24275569;Dbxref=PMID:1 |
| O75151 | 876 | 907 | 899 | 899 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569 |
| O75151 | 876 | 907 | 899 | 899 | Mutagenesis | Note=Abolishes phosphorylation by PKA and activation of demethylase activity%3B when associated with A-757%3B A-954 and A-1056. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21532585;Dbxref=PMID:21532585 |
| O75151 | 876 | 907 | 888 | 888 | Sequence conflict | Note=I->V;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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3'-UTR located exon skipping events that lost miRNA binding sites in PHF2 |
| 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 PHF2 |
| - 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 PHF2 |
| 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 PHF2 |
| 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 PHF2 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | CNOT4 | exon_skip_173981 | -4.234015e-01 | 2.689049e-08 |
| CB | NUP42 | exon_skip_173981 | 4.958839e-01 | 3.006374e-11 |
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RelatedDrugs for PHF2 |
| 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 PHF2 |
| 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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