Human Gene HDAC6 (uc004dkr.1) Description and Page Index
  Description: Homo sapiens histone deacetylase 6 (HDAC6), mRNA.
RefSeq Summary (NM_006044): 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 contains an internal duplication of two catalytic domains which appear to function independently of each other. This protein possesses histone deacetylase activity and represses transcription. [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 :: SRR1660805.144770.1, SRR1660803.117327.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000334136.11/ ENSP00000334061.5 RefSeq Select criteria :: based on manual assertion, conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chrX:48,660,471-48,664,871 Size: 4,401 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chrX:48,661,100-48,664,082 Size: 2,983 Coding Exon Count: 5 

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 (chrX:48,660,471-48,664,871)mRNA (may differ from genome)Protein (146 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMGIPubMedStanford SOURCE
UniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): HDAC6
CDC HuGE Published Literature: HDAC6

-  MalaCards Disease Associations
  MalaCards Gene Search: HDAC6
Diseases sorted by gene-association score: chondrodysplasia with platyspondyly, distinctive brachydactyly, hydrocephaly, and microphthalmia* (1320)
* = 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: 49.39 RPKM in Pituitary
Total median expression: 932.75 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 -196.78518-0.380 Picture PostScript Text
3' UTR -282.10789-0.358 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

SCOP Domains:
52768 - Arginase/deacetylase

ModBase Predicted Comparative 3D Structure on Q9BRX7
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 orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0016787 hydrolase activity


-  Descriptions from all associated GenBank mRNAs
  AK302926 - Homo sapiens cDNA FLJ56474 complete cds, highly similar to Histone deacetylase 6.
AL137696 - Homo sapiens mRNA; cDNA DKFZp566E044 (from clone DKFZp566E044).
BC005872 - Homo sapiens histone deacetylase 6, mRNA (cDNA clone IMAGE:3029555), complete cds.
AK024083 - Homo sapiens cDNA FLJ14021 fis, clone HEMBA1002513, highly similar to Histone deacetylase 6.
AJ011972 - Homo sapiens mRNA for histone deacetylase-like protein (JM21).
AB020708 - Homo sapiens KIAA0901 mRNA for KIAA0901 protein.
BC069243 - Homo sapiens histone deacetylase 6, mRNA (cDNA clone MGC:78509 IMAGE:6584427), complete cds.
AK295884 - Homo sapiens cDNA FLJ54798 complete cds, highly similar to Histone deacetylase 6.
BC011498 - Homo sapiens histone deacetylase 6, mRNA (cDNA clone IMAGE:4179066), complete cds.
AK095124 - Homo sapiens cDNA FLJ37805 fis, clone BRSSN2001342, highly similar to Histone deacetylase 6.
JD216210 - Sequence 197234 from Patent EP1572962.
JD208923 - Sequence 189947 from Patent EP1572962.
JD310346 - Sequence 291370 from Patent EP1572962.
KJ902051 - Synthetic construct Homo sapiens clone ccsbBroadEn_11445 HDAC6 gene, encodes complete protein.
BT006649 - Homo sapiens histone deacetylase 6 mRNA, complete cds.
AB385398 - Synthetic construct DNA, clone: pF1KA0901, Homo sapiens HDAC6 gene for histone deacetylase 6, complete cds, without stop codon, in Flexi system.
AF132609 - Homo sapiens histone deacetylase 6 mRNA, complete cds.
BC013737 - Homo sapiens histone deacetylase 6, mRNA (cDNA clone MGC:5339 IMAGE:2984860), complete cds.
AK303012 - Homo sapiens cDNA FLJ56624 complete cds, highly similar to Histone deacetylase 6.
JD022859 - Sequence 3883 from Patent EP1572962.
JD027597 - Sequence 8621 from Patent EP1572962.
JF432329 - Synthetic construct Homo sapiens clone IMAGE:100073516 histone deacetylase 6 (HDAC6) gene, encodes complete protein.
KJ902052 - Synthetic construct Homo sapiens clone ccsbBroadEn_11446 HDAC6 gene, encodes complete protein.
AF174499 - Homo sapiens GR AF-1 specific histone deacetylase mRNA, partial cds.

-  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: BC005872, Q9BRX7, Q9BRX7_HUMAN
UCSC ID: uc004dkr.1
RefSeq Accession: NM_006044
Protein: Q9BRX7

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC005872.1
exon count: 6CDS single in 3' UTR: no RNA size: 1200
ORF size: 441CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 968.00frame shift in genome: no % Coverage: 94.92
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# 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.