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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 HDAC1 |
 Gene summary |
| Gene information | Gene symbol | HDAC1 | Gene ID | 3065 |
| Gene name | histone deacetylase 1 | |
| Synonyms | GON-10|HD1|KDAC1|RPD3|RPD3L1 | |
| Cytomap | 1p35.2-p35.1 | |
| Type of gene | protein-coding | |
| Description | histone deacetylase 1reduced potassium dependency, yeast homolog-like 1 | |
| Modification date | 20200327 | |
| UniProtAcc | ||
| Context | - 32424276(HDAC1 modulates OGG1-initiated oxidative DNA damage repair in the aging brain and Alzheimer's disease) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| HDAC1 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 18854353 |
| HDAC1 | GO:0006476 | protein deacetylation | 17172643|23629966 |
| HDAC1 | GO:0045893 | positive regulation of transcription, DNA-templated | 16762839 |
| HDAC1 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 16762839 |
| HDAC1 | GO:0060766 | negative regulation of androgen receptor signaling pathway | 15919722 |
| HDAC1 | GO:0070932 | histone H3 deacetylation | 12590135 |
| HDAC1 | GO:0070933 | histone H4 deacetylation | 12590135 |
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Gene structures and expression levels for HDAC1 |
| 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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ENSG00000116478
| 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 HDAC1 |
| 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_128975 | chr1 | 32292161:32292218:32302621:32302733:32316665:32316782 | 32302621:32302733 |
| exon_skip_191373 | chr1 | 32326939:32327077:32327406:32327458:32327536:32327674 | 32327406:32327458 |
| exon_skip_196206 | chr1 | 32329068:32329160:32330578:32330686:32330768:32330875 | 32330578:32330686 |
| exon_skip_203608 | chr1 | 32326939:32327077:32327406:32327458:32327536:32327626 | 32327406:32327458 |
| exon_skip_239412 | chr1 | 32326943:32327077:32327406:32327458:32327536:32327626 | 32327406:32327458 |
| exon_skip_30854 | chr1 | 32327536:32327677:32329068:32329160:32330578:32330686 | 32329068:32329160 |
| exon_skip_45406 | chr1 | 32316665:32316782:32324479:32324553:32326939:32327077 | 32324479:32324553 |
| exon_skip_63572 | chr1 | 32332090:32332242:32332701:32332749:32333017:32333079 | 32332701:32332749 |
| 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 HDAC1 |
| 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 |
| ENST00000373548 | 32332701 | 32332749 | Frame-shift |
| ENST00000373548 | 32324479 | 32324553 | In-frame |
| ENST00000373548 | 32329068 | 32329160 | 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 |
| 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 |
| ENST00000373548 | 32330578 | 32330686 | Frame-shift |
| ENST00000373548 | 32332701 | 32332749 | Frame-shift |
| ENST00000373548 | 32324479 | 32324553 | In-frame |
| ENST00000373548 | 32329068 | 32329160 | In-frame |
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Infer the effects of exon skipping event on protein functional features for HDAC1 |
p-ENSG00000116478_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 |
| ENST00000373548 | 2141 | 482 | 32324479 | 32324553 | 366 | 439 | 94 | 118 |
| ENST00000373548 | 2141 | 482 | 32329068 | 32329160 | 722 | 813 | 212 | 243 |
| 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 |
| ENST00000373548 | 2141 | 482 | 32324479 | 32324553 | 366 | 439 | 94 | 118 |
| ENST00000373548 | 2141 | 482 | 32329068 | 32329160 | 722 | 813 | 212 | 243 |
| 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 |
| Q13547 | 94 | 118 | 1 | 482 | Chain | ID=PRO_0000114687;Note=Histone deacetylase 1 |
| Q13547 | 94 | 118 | 88 | 94 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BKX |
| Q13547 | 94 | 118 | 106 | 125 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BKX |
| Q13547 | 94 | 118 | 9 | 321 | Region | Note=Histone deacetylase |
| Q13547 | 94 | 118 | 97 | 99 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BKX |
| Q13547 | 212 | 243 | 223 | 228 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BKX |
| Q13547 | 212 | 243 | 1 | 482 | Chain | ID=PRO_0000114687;Note=Histone deacetylase 1 |
| Q13547 | 212 | 243 | 217 | 219 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BKX |
| Q13547 | 212 | 243 | 234 | 252 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BKX |
| Q13547 | 212 | 243 | 220 | 220 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| Q13547 | 212 | 243 | 9 | 321 | Region | Note=Histone deacetylase |
| 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 |
| Q13547 | 94 | 118 | 1 | 482 | Chain | ID=PRO_0000114687;Note=Histone deacetylase 1 |
| Q13547 | 94 | 118 | 88 | 94 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BKX |
| Q13547 | 94 | 118 | 106 | 125 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BKX |
| Q13547 | 94 | 118 | 9 | 321 | Region | Note=Histone deacetylase |
| Q13547 | 94 | 118 | 97 | 99 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BKX |
| Q13547 | 212 | 243 | 223 | 228 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BKX |
| Q13547 | 212 | 243 | 1 | 482 | Chain | ID=PRO_0000114687;Note=Histone deacetylase 1 |
| Q13547 | 212 | 243 | 217 | 219 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BKX |
| Q13547 | 212 | 243 | 234 | 252 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BKX |
| Q13547 | 212 | 243 | 220 | 220 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| Q13547 | 212 | 243 | 9 | 321 | Region | Note=Histone deacetylase |
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3'-UTR located exon skipping events that lost miRNA binding sites in HDAC1 |
| 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 HDAC1 |
| - 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 HDAC1 |
| 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 HDAC1 |
| 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 HDAC1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for HDAC1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Q13547 | approved|investigational | DB01169 | Arsenic trioxide | small molecule | Q13547 |
| Q13547 | approved|investigational | DB01593 | Zinc | small molecule | Q13547 |
| Q13547 | approved|investigational | DB02546 | Vorinostat | small molecule | Q13547 |
| Q13547 | approved|investigational | DB05015 | Belinostat | small molecule | Q13547 |
| Q13547 | approved|investigational | DB06176 | Romidepsin | small molecule | Q13547 |
| Q13547 | approved|investigational | DB06603 | Panobinostat | small molecule | Q13547 |
| Q13547 | approved|investigational | DB08868 | Fingolimod | small molecule | Q13547 |
| Q13547 | approved|investigational | DB14487 | Zinc acetate | small molecule | Q13547 |
| Q13547 | approved|investigational | DB14533 | Zinc chloride | small molecule | Q13547 |
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RelatedDiseases for HDAC1 |
| 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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