Human Gene HDAC1 (ENST00000373548.8_5) from GENCODE V47lift37
  Description: histone deacetylase 1 (from RefSeq NM_004964.3)
Gencode Transcript: ENST00000373548.8_5
Gencode Gene: ENSG00000116478.13_10
Transcript (Including UTRs)
   Position: hg19 chr1:32,757,684-32,799,227 Size: 41,544 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg19 chr1:32,757,771-32,798,645 Size: 40,875 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:32,757,684-32,799,227)mRNA (may differ from genome)Protein (482 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: Q6IT96_HUMAN
DESCRIPTION: RecName: Full=Histone deacetylase; EC=3.5.1.98;
CATALYTIC ACTIVITY: Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Belongs to the histone deacetylase family. HD Type 1 subfamily.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: HDAC1
Diseases sorted by gene-association score: atrichia with papular lesions (12), rett syndrome (10), retinoblastoma (9), valproate embryopathy, susceptibility to (4), hiv-1 (3), breast cancer (3), endometrial stromal sarcoma (2), colorectal cancer (2), leukemia, acute myeloid (0)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 91.05 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1570.34 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -37.8087-0.434 Picture PostScript Text
3' UTR -157.40582-0.270 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000286 - His_deacetylse
IPR003084 - His_deacetylse_1
IPR023801 - His_deacetylse_dom

Pfam Domains:
PF00850 - Histone deacetylase domain

SCOP Domains:
52768 - Arginase/deacetylase

ModBase Predicted Comparative 3D Structure on Q6IT96
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGD   SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004407 histone deacetylase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0032041 NAD-dependent histone deacetylase activity (H3-K14 specific)
GO:0046872 metal ion binding
GO:0051059 NF-kappaB binding

Biological Process:
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0016575 histone deacetylation
GO:0070932 histone H3 deacetylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  AK225555 - Homo sapiens mRNA for histone deacetylase 1 variant, clone: KDN05801.
AK296308 - Homo sapiens cDNA FLJ51981 complete cds, highly similar to Histone deacetylase 1.
AK313061 - Homo sapiens cDNA, FLJ93538.
D50405 - Homo sapiens mRNA for RPD3 protein, complete cds.
E11455 - cDNA encoding human transcriptional control protein,RPDL.
BC000301 - Homo sapiens histone deacetylase 1, mRNA (cDNA clone MGC:8378 IMAGE:2820260), complete cds.
AK299792 - Homo sapiens cDNA FLJ60860 complete cds, highly similar to Histone deacetylase 1.
U50079 - Human histone deacetylase HD1 mRNA, complete cds.
AY627042 - Homo sapiens histone deacetylase 1 mRNA, complete cds.
CU674144 - Synthetic construct Homo sapiens gateway clone IMAGE:100018338 5' read HDAC1 mRNA.
AB451430 - Homo sapiens HDAC1 mRNA for histone deacetylase 1, partial cds, clone: FLJ08148AAAF.
AB463736 - Synthetic construct DNA, clone: pF1KB7736, Homo sapiens HDAC1 gene for histone deacetylase 1, without stop codon, in Flexi system.
AB451297 - Homo sapiens HDAC1 mRNA for histone deacetylase 1, complete cds, clone: FLJ08148AAAN.
DQ891398 - Synthetic construct clone IMAGE:100004028; FLH176575.01X; RZPDo839E11122D histone deacetylase 1 (HDAC1) gene, encodes complete protein.
DQ894577 - Synthetic construct Homo sapiens clone IMAGE:100009037; FLH176571.01L; RZPDo839E11121D histone deacetylase 1 (HDAC1) gene, encodes complete protein.
KJ891340 - Synthetic construct Homo sapiens clone ccsbBroadEn_00734 HDAC1 gene, encodes complete protein.
CR541717 - Homo sapiens full open reading frame cDNA clone RZPDo834A0629D for gene HDAC1, histone deacetylase 1; complete cds, incl. stopcodon.
AK299241 - Homo sapiens cDNA FLJ51764 complete cds, highly similar to Histone deacetylase 1.
BX648055 - Homo sapiens mRNA; cDNA DKFZp686H12203 (from clone DKFZp686H12203).
JD193723 - Sequence 174747 from Patent EP1572962.
JD126725 - Sequence 107749 from Patent EP1572962.
JD210360 - Sequence 191384 from Patent EP1572962.
JD391676 - Sequence 372700 from Patent EP1572962.
JD444334 - Sequence 425358 from Patent EP1572962.
JD339772 - Sequence 320796 from Patent EP1572962.
JD116414 - Sequence 97438 from Patent EP1572962.
JD384573 - Sequence 365597 from Patent EP1572962.
JD296431 - Sequence 277455 from Patent EP1572962.
JD254523 - Sequence 235547 from Patent EP1572962.
JD168324 - Sequence 149348 from Patent EP1572962.
JD188924 - Sequence 169948 from Patent EP1572962.
LF838626 - JP 2016530232-A/21: Biomarkers of miR-34 Activity.
JD323447 - Sequence 304471 from Patent EP1572962.
JD537036 - Sequence 518060 from Patent EP1572962.
JD411016 - Sequence 392040 from Patent EP1572962.
JD315075 - Sequence 296099 from Patent EP1572962.
JD358464 - Sequence 339488 from Patent EP1572962.
JD156427 - Sequence 137451 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_wntPathway - WNT Signaling Pathway
h_mta3Pathway - Downregulated of MTA-3 in ER-negative Breast Tumors
h_ranbp2Pathway - Sumoylation by RanBP2 Regulates Transcriptional Repression
h_prc2Pathway - The PRC2 Complex Sets Long-term Gene Silencing Through Modification of Histone Tails
h_g1Pathway - Cell Cycle: G1/S Check Point
h_pitx2Pathway - Multi-step Regulation of Transcription by Pitx2
h_carm-erPathway - CARM1 and Regulation of the Estrogen Receptor
h_HuntingtonPathway - Inhibition of Huntington's disease neurodegeneration by histone deacetylase inhibitors
h_vdrPathway - Control of Gene Expression by Vitamin D Receptor
h_mef2dPathway - Role of MEF2D in T-cell Apoptosis
h_tertpathway - Overview of telomerase protein component gene hTert Transcriptional Regulation

-  Other Names for This Gene
  Alternate Gene Symbols: D3DPP9, ENST00000373548.1, ENST00000373548.2, ENST00000373548.3, ENST00000373548.4, ENST00000373548.5, ENST00000373548.6, ENST00000373548.7, hCG_41610 , HDAC1 , NM_004964, Q6IT96, Q6IT96_HUMAN, uc318kvz.1, uc318kvz.2
UCSC ID: ENST00000373548.8_5
RefSeq Accession: NM_004964.3
Protein: Q6IT96

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.