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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 PHF21A |
 Gene summary |
| Gene information | Gene symbol | PHF21A | Gene ID | 51317 |
| Gene name | PHD finger protein 21A | |
| Synonyms | BHC80|BM-006|IDDBCS|NEDMS | |
| Cytomap | 11p11.2 | |
| Type of gene | protein-coding | |
| Description | PHD finger protein 21ABHC80aBRAF35-HDAC complex protein BHC80BRAF35/HDAC2 complex (80 kDa) | |
| Modification date | 20200327 | |
| 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 |
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Gene structures and expression levels for PHF21A |
| 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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ENSG00000135365
| 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 | ENST00000531959.5 | PHF21A-215:protein_coding:PHF21A | 4.315702e+00 | 1.501235e+00 | 3.581299e-06 | 4.426950e-05 |
| CB | UP | ENST00000532010.5 | PHF21A-216:protein_coding:PHF21A | 4.200501e+00 | 8.550611e-01 | 2.393330e-03 | 1.069249e-02 |
| 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 PHF21A |
| 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_106801 | chr11 | 45938219:45938312:45945840:45946098:45948886:45948946 | 45945840:45946098 |
| exon_skip_122412 | chr11 | 45938157:45938312:45946076:45946098:45948886:45948946 | 45946076:45946098 |
| exon_skip_125559 | chr11 | 45969815:45969904:45971116:45971367:45979760:45979966 | 45971116:45971367 |
| exon_skip_126507 | chr11 | 46079141:46079166:46084166:46084302:46090455:46090581 | 46084166:46084302 |
| exon_skip_147668 | chr11 | 45935694:45935739:45936494:45936569:45938157:45938264 | 45936494:45936569 |
| exon_skip_153497 | chr11 | 46079134:46079166:46083555:46083611:46084166:46084267 | 46083555:46083611 |
| exon_skip_160081 | chr11 | 45936494:45936569:45938157:45938312:45945840:45945869 | 45938157:45938312 |
| exon_skip_164738 | chr11 | 46092183:46092223:46117922:46118114:46118742:46118800 | 46117922:46118114 |
| exon_skip_187161 | chr11 | 46079134:46079166:46083555:46083611:46084166:46084296 | 46083555:46083611 |
| exon_skip_195810 | chr11 | 46079134:46079166:46083555:46083611:46084166:46084302 | 46083555:46083611 |
| exon_skip_215794 | chr11 | 46084166:46084302:46092183:46092223:46120935:46121104 | 46092183:46092223 |
| exon_skip_223310 | chr11 | 45938219:45938312:45946076:45946098:45948886:45948946 | 45946076:45946098 |
| exon_skip_23080 | chr11 | 45933985:45934225:45935121:45935157:45935636:45935739 | 45935121:45935157 |
| exon_skip_23130 | chr11 | 45938219:45938312:45948886:45948946:45949402:45949481 | 45948886:45948946 |
| exon_skip_231321 | chr11 | 45979863:45979966:46049400:46049497:46076754:46076819 | 46049400:46049497 |
| exon_skip_237937 | chr11 | 45936494:45936569:45938157:45938312:45946076:45946098 | 45938157:45938312 |
| exon_skip_270423 | chr11 | 45933985:45934225:45935121:45935246:45935636:45935739 | 45935121:45935246 |
| exon_skip_279169 | chr11 | 46084193:46084302:46090455:46090581:46092183:46092223 | 46090455:46090581 |
| exon_skip_296215 | chr11 | 45938219:45938312:45945840:45946003:45948886:45948946 | 45945840:45946003 |
| exon_skip_3940 | chr11 | 46092183:46092223:46117922:46118145:46118742:46118800 | 46117922:46118145 |
| exon_skip_40026 | chr11 | 45953527:45953625:45965315:45965608:45969815:45969901 | 45965315:45965608 |
| exon_skip_55617 | chr11 | 46084193:46084302:46090455:46090581:46092183:46092205 | 46090455:46090581 |
| exon_skip_61873 | chr11 | 45938157:45938312:45945840:45946098:45948886:45948946 | 45945840:45946098 |
| exon_skip_66744 | chr11 | 45938157:45938312:45945840:45946003:45948886:45948946 | 45945840:45946003 |
| exon_skip_80087 | chr11 | 46092183:46092223:46118742:46118800:46119724:46119787 | 46118742:46118800 |
| 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 PHF21A |
| 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 |
| ENST00000418153 | 45936494 | 45936569 | Frame-shift |
| ENST00000418153 | 45945840 | 45946003 | Frame-shift |
| ENST00000418153 | 45938157 | 45938312 | In-frame |
| ENST00000418153 | 45965315 | 45965608 | 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 |
| ENST00000418153 | 45945840 | 45946003 | 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 |
| ENST00000418153 | 46092183 | 46092223 | 3UTR-3UTR |
| ENST00000418153 | 45936494 | 45936569 | Frame-shift |
| ENST00000418153 | 45945840 | 45946003 | Frame-shift |
| ENST00000418153 | 45938157 | 45938312 | In-frame |
| ENST00000418153 | 45965315 | 45965608 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PHF21A |
p-ENSG00000135365_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 |
| ENST00000418153 | 2747 | 680 | 45965315 | 45965608 | 900 | 1192 | 233 | 330 |
| ENST00000418153 | 2747 | 680 | 45938157 | 45938312 | 1650 | 1804 | 483 | 534 |
| 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 |
| ENST00000418153 | 2747 | 680 | 45965315 | 45965608 | 900 | 1192 | 233 | 330 |
| ENST00000418153 | 2747 | 680 | 45938157 | 45938312 | 1650 | 1804 | 483 | 534 |
| 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 |
| Q96BD5 | 233 | 330 | 1 | 680 | Chain | ID=PRO_0000226767;Note=PHD finger protein 21A |
| Q96BD5 | 483 | 534 | 429 | 483 | Alternative sequence | ID=VSP_017449;Note=In isoform 2. GRPPKYNAVLGFGALTPTSPQSSHPDSPENEKTETTFTFPAPVQPVSLPSPTSTD->ANEEHWPK;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11214970,ECO:0000303|PubMed:12032298,ECO:0000303|PubMed:14702039;Dbxref=PMID:1 |
| Q96BD5 | 483 | 534 | 504 | 507 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2PUY |
| Q96BD5 | 483 | 534 | 515 | 517 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2PUY |
| Q96BD5 | 483 | 534 | 1 | 680 | Chain | ID=PRO_0000226767;Note=PHD finger protein 21A |
| Q96BD5 | 483 | 534 | 512 | 514 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2PUY |
| Q96BD5 | 483 | 534 | 530 | 538 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2PUY |
| Q96BD5 | 483 | 534 | 486 | 680 | Region | Note=Required for transcriptional repression |
| Q96BD5 | 483 | 534 | 492 | 494 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2PUY |
| Q96BD5 | 483 | 534 | 488 | 535 | Zinc finger | Note=PHD-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00146 |
| 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 |
| Q96BD5 | 233 | 330 | 1 | 680 | Chain | ID=PRO_0000226767;Note=PHD finger protein 21A |
| Q96BD5 | 483 | 534 | 429 | 483 | Alternative sequence | ID=VSP_017449;Note=In isoform 2. GRPPKYNAVLGFGALTPTSPQSSHPDSPENEKTETTFTFPAPVQPVSLPSPTSTD->ANEEHWPK;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11214970,ECO:0000303|PubMed:12032298,ECO:0000303|PubMed:14702039;Dbxref=PMID:1 |
| Q96BD5 | 483 | 534 | 504 | 507 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2PUY |
| Q96BD5 | 483 | 534 | 515 | 517 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2PUY |
| Q96BD5 | 483 | 534 | 1 | 680 | Chain | ID=PRO_0000226767;Note=PHD finger protein 21A |
| Q96BD5 | 483 | 534 | 512 | 514 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2PUY |
| Q96BD5 | 483 | 534 | 530 | 538 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2PUY |
| Q96BD5 | 483 | 534 | 486 | 680 | Region | Note=Required for transcriptional repression |
| Q96BD5 | 483 | 534 | 492 | 494 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2PUY |
| Q96BD5 | 483 | 534 | 488 | 535 | Zinc finger | Note=PHD-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00146 |
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3'-UTR located exon skipping events that lost miRNA binding sites in PHF21A |
| 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 PHF21A |
| - 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 PHF21A |
| 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 PHF21A |
| 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 PHF21A |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| TC | RBM6 | exon_skip_106801 | -4.362576e-01 | 8.859671e-08 |
| TC | RALYL | exon_skip_106801 | 4.518926e-01 | 2.643864e-08 |
| TC | NUP42 | exon_skip_223310 | 4.381787e-01 | 1.190124e-07 |
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RelatedDrugs for PHF21A |
| 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 PHF21A |
| 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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