Human Gene HDAC4 (uc010zoa.1) Description and Page Index
  Description: Homo sapiens histone deacetylase 4 (HDAC4), mRNA.
RefSeq Summary (NM_006037): Histones play a critical role in transcriptional regulation, cell cycle progression, and developmental events. Histone acetylation/deacetylation alters chromosome structure and affects transcription factor access to DNA. The protein encoded by this gene belongs to class II of the histone deacetylase/acuc/apha family. It possesses histone deacetylase activity and represses transcription when tethered to a promoter. This protein does not bind DNA directly, but through transcription factors MEF2C and MEF2D. It seems to interact in a multiprotein complex with RbAp48 and HDAC3. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AB006626.2 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on conservation ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr2:240,016,312-240,220,334 Size: 204,023 Total Exon Count: 16 Strand: -
Coding Region
   Position: hg19 chr2:240,016,679-240,219,867 Size: 203,189 Coding Exon Count: 16 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:240,016,312-240,220,334)mRNA (may differ from genome)Protein (763 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMGIOMIMPubMed
Stanford SOURCEUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): HDAC4
CDC HuGE Published Literature: HDAC4
Positive Disease Associations: Body Weight , Triglycerides
Related Studies:
  1. Body Weight
    , , . [PubMed 0]
  2. Triglycerides
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: HDAC4
Diseases sorted by gene-association score: chromosome 2q37 deletion syndrome* (625), 2q37 microdeletion syndrome* (100), developmental dyspraxia (18), brachydactyly, type e (16), brachydactyly (15), muscle hypertrophy (13), neuronal intranuclear inclusion disease (7), pseudohypoparathyroidism ia (7), breast cancer (2), autism spectrum disorder (1)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 19.59 RPKM in Colon - Sigmoid
Total median expression: 225.99 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -179.80467-0.385 Picture PostScript Text
3' UTR -135.60367-0.369 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
IPR023801 - His_deacetylse_dom
IPR024643 - Hist_deacetylase_Gln_rich_N
IPR017320 - Histone_deAcase_II_euk

Pfam Domains:
PF12203 - Glutamine rich N terminal domain of histone deacetylase 4

SCOP Domains:
52768 - Arginase/deacetylase

ModBase Predicted Comparative 3D Structure on B7Z8G5
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004407 histone deacetylase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding

Biological Process:
GO:0006325 chromatin organization
GO:0016575 histone deacetylation

Cellular Component:
GO:0000118 histone deacetylase complex


-  Descriptions from all associated GenBank mRNAs
  LF383625 - JP 2014500723-A/191128: Polycomb-Associated Non-Coding RNAs.
AB006626 - Homo sapiens KIAA0288 mRNA for KIAA0288 protein.
BC039904 - Homo sapiens histone deacetylase 4, mRNA (cDNA clone MGC:47583 IMAGE:6067363), complete cds.
AF132607 - Homo sapiens histone deacetylase 4 mRNA, complete cds.
AB384455 - Synthetic construct DNA, clone: pF1KA0288, Homo sapiens HDAC4 gene for histone deacetylase 4, complete cds, without stop codon, in Flexi system.
AK310603 - Homo sapiens cDNA, FLJ17645.
AK308791 - Homo sapiens cDNA, FLJ98832.
AK303368 - Homo sapiens cDNA FLJ51174 complete cds, highly similar to Histone deacetylase 4.
MA619202 - JP 2018138019-A/191128: Polycomb-Associated Non-Coding RNAs.
AK302719 - Homo sapiens cDNA FLJ51157 complete cds, highly similar to Histone deacetylase 4.
CU691798 - Synthetic construct Homo sapiens gateway clone IMAGE:100021031 5' read HDAC4 mRNA.
AK021826 - Homo sapiens cDNA FLJ11764 fis, clone HEMBA1005685.
AK303467 - Homo sapiens cDNA FLJ59806 complete cds, highly similar to Histone deacetylase 4.
AK303617 - Homo sapiens cDNA FLJ51177 complete cds, highly similar to Histone deacetylase 4.
AK310488 - Homo sapiens cDNA, FLJ17530.
AK311582 - Homo sapiens cDNA, FLJ18624.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_ranbp2Pathway - Sumoylation by RanBP2 Regulates Transcriptional Repression
h_carm-erPathway - CARM1 and Regulation of the Estrogen Receptor

-  Other Names for This Gene
  Alternate Gene Symbols: AK303368, B7Z8G5, B7Z8G5_HUMAN, NM_006037, NP_006028
UCSC ID: uc010zoa.1
RefSeq Accession: NM_006037
Protein: B7Z8G5

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK303368.1
exon count: 16CDS single in 3' UTR: no RNA size: 2744
ORF size: 2292CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4458.00frame shift in genome: no % Coverage: 99.96
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 394# strange splices: 0
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.