This gene encodes a class IV histone deacetylase. The encoded protein is localized to the nucleus and may be involved in regulating the expression of interleukin 10. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Apr 2009] See more...

Aliases for HDAC11 Gene

Aliases for HDAC11 Gene

  • Histone Deacetylase 11 2 3 4 5
  • EC 3.5.1.98 4 52
  • HD11 3 4

External Ids for HDAC11 Gene

Previous GeneCards Identifiers for HDAC11 Gene

  • GC03P013451

Summaries for HDAC11 Gene

Entrez Gene Summary for HDAC11 Gene

  • This gene encodes a class IV histone deacetylase. The encoded protein is localized to the nucleus and may be involved in regulating the expression of interleukin 10. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Apr 2009]

GeneCards Summary for HDAC11 Gene

HDAC11 (Histone Deacetylase 11) is a Protein Coding gene. Diseases associated with HDAC11 include Bicipital Tenosynovitis and Subungual Glomus Tumor. Among its related pathways are RNA Polymerase II Transcription Initiation And Promoter Clearance and Signaling by NOTCH1. Gene Ontology (GO) annotations related to this gene include hydrolase activity and histone deacetylase activity. An important paralog of this gene is HDAC1.

UniProtKB/Swiss-Prot Summary for HDAC11 Gene

  • Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes.

Tocris Summary for HDAC11 Gene

  • Histone deacetylases (HDACs) are a group of enzymes closely related to sirtuins. They catalyze acetyl group removal from lysine residues in histones and non-histone proteins, causing transcriptional repression. HDACs are usually components of multiprotein complexes.

Gene Wiki entry for HDAC11 Gene

Additional gene information for HDAC11 Gene

No data available for CIViC Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HDAC11 Gene

Genomics for HDAC11 Gene

GeneHancer (GH) Regulatory Elements for HDAC11 Gene

Promoters and enhancers for HDAC11 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J013475 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 500.7 -1.1 -1092 5.8 FOXK2 ZNF217 CTCF ZSCAN5C NRF1 USF1 POLR2G SP1 PHF8 ZFX HDAC11-AS1 HDAC11 RF00017-3921 FBLN2 lnc-NUP210-2 ENSG00000223398
GH03J013532 Enhancer 1.6 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 16.7 +57.5 57476 9.2 ZNF217 CTCF TCF12 FOS ZFX ZIC2 CLOCK KLF4 RFX1 CUX1 HDAC11 HDAC11-AS1 LINC00620 WNT7A FBLN2 piR-36332
GH03J013513 Enhancer 1.2 Ensembl ENCODE CraniofacialAtlas dbSUPER 17 +34.4 34426 2.9 ZNF217 USF1 ZFX CLOCK RFX1 KLF4 RBM25 MYC MBD2 NR3C1 HDAC11 HDAC11-AS1 LINC00620 WNT7A piR-36332 piR-57460-470
GH03J013001 Promoter/Enhancer 1.9 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 10.1 -466.6 -466611 22.6 ZBTB40 CTCF SIN3A USF1 SP1 GTF2E2 JUND PHB2 FOS ZNF10 IQSEC1 HDAC11 HDAC11-AS1 CAND2 NUP210 RPL32 lnc-CAND2-2 lnc-RPL32-3
GH03J013546 Promoter/Enhancer 1.6 Ensembl ENCODE CraniofacialAtlas dbSUPER 11.2 +67.2 67193 1.8 FOS PHB2 ZIC2 ZNF263 ZBTB11 AFF1 TRIM28 TARDBP HES1 TOE1 HDAC11 HDAC11-AS1 VN1R20P FBLN2 piR-36332
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HDAC11 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HDAC11

Top Transcription factor binding sites by QIAGEN in the HDAC11 gene promoter:
  • CUTL1
  • Lmo2
  • SREBP-1a
  • SREBP-1b
  • SREBP-1c

Genomic Locations for HDAC11 Gene

Genomic Locations for HDAC11 Gene
chr3:13,479,724-13,506,424
(GRCh38/hg38)
Size:
26,701 bases
Orientation:
Plus strand
chr3:13,521,224-13,547,924
(GRCh37/hg19)
Size:
26,701 bases
Orientation:
Plus strand

Genomic View for HDAC11 Gene

Genes around HDAC11 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HDAC11 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HDAC11 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HDAC11 Gene

Proteins for HDAC11 Gene

  • Protein details for HDAC11 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96DB2-HDA11_HUMAN
    Recommended name:
    Histone deacetylase 11
    Protein Accession:
    Q96DB2
    Secondary Accessions:
    • B4DDK1
    • Q9H6I7
    • Q9H6X3
    • Q9NTC9

    Protein attributes for HDAC11 Gene

    Size:
    347 amino acids
    Molecular mass:
    39183 Da
    Quaternary structure:
    • Interacts with HDAC6.
    Miscellaneous:
    • Its activity is inhibited by trapoxin, a known histone deacetylase inhibitor.
    SequenceCaution:
    • Sequence=BAB15127.1; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305}; Sequence=CAB70712.1; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for HDAC11 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HDAC11 Gene

Selected DME Specific Peptides for HDAC11 Gene

Q96DB2:
  • IIDLDAHQGNGHE
  • EKLHPFD
  • RGGGFCA

Post-translational modifications for HDAC11 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for HDAC11 Gene

Gene Families for HDAC11 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • FDA approved drug targets
  • Predicted intracellular proteins

Protein Domains for HDAC11 Gene

Blocks:
  • Histone deacetylase superfamily signature
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for HDAC11 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ55185, highly similar to Histone deacetylase 11 (B4DDK1_HUMAN)
  • Histone deacetylase 11 (HDA11_HUMAN)
  • HDAC11 protein (Q6IA14_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96DB2

UniProtKB/Swiss-Prot:

HDA11_HUMAN :
  • Belongs to the histone deacetylase family.
Family:
  • Belongs to the histone deacetylase family.
genes like me logo Genes that share domains with HDAC11: view

Function for HDAC11 Gene

Molecular function for HDAC11 Gene

UniProtKB/Swiss-Prot Function:
Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + N(6)-acetyl-L-lysyl-[histone] = acetate + L-lysyl-[histone]; Xref=Rhea:RHEA:58196, Rhea:RHEA-COMP:9845, Rhea:RHEA-COMP:11338, ChEBI:CHEBI:15377, ChEBI:CHEBI:29969, ChEBI:CHEBI:30089, ChEBI:CHEBI:61930; EC=3.5.1.98;.

Enzyme Numbers (IUBMB) for HDAC11 Gene

Phenotypes From GWAS Catalog for HDAC11 Gene

Gene Ontology (GO) - Molecular Function for HDAC11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004407 histone deacetylase activity IDA,IEA 11948178
GO:0005515 protein binding IPI 26221039
GO:0008134 transcription factor binding TAS 12711221
GO:0016787 hydrolase activity IEA --
GO:0032041 NAD-dependent histone deacetylase activity (H3-K14 specific) IEA --
genes like me logo Genes that share ontologies with HDAC11: view
genes like me logo Genes that share phenotypes with HDAC11: view

Animal Models for HDAC11 Gene

MGI Knock Outs for HDAC11:

Animal Model Products

CRISPR Products

miRNA for HDAC11 Gene

miRTarBase miRNAs that target HDAC11

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HDAC11

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HDAC11 Gene

Localization for HDAC11 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HDAC11 Gene

Nucleus. Note=Predominantly nuclear.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HDAC11 gene
Compartment Confidence
nucleus 5
plasma membrane 4
cytosol 3
extracellular 2
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 1
endosome 1
lysosome 1
peroxisome 0

Gene Ontology (GO) - Cellular Components for HDAC11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000118 histone deacetylase complex IDA 11948178
GO:0005634 nucleus IEA,IDA 11948178
GO:0005886 plasma membrane IDA --
genes like me logo Genes that share ontologies with HDAC11: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HDAC11 Gene

Pathways & Interactions for HDAC11 Gene

genes like me logo Genes that share pathways with HDAC11: view

Pathways by source for HDAC11 Gene

2 KEGG pathways for HDAC11 Gene
15 Qiagen pathways for HDAC11 Gene
  • BRCA1 Pathway
  • Cyclins and Cell Cycle Regulation
  • DNA Methylation and Transcriptional Repression
  • Estrogen Pathway
  • G1-S Phase Transition
1 Cell Signaling Technology pathway for HDAC11 Gene
2 GeneTex pathways for HDAC11 Gene

Gene Ontology (GO) - Biological Process for HDAC11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization TAS 12711221
GO:0014003 oligodendrocyte development IEA --
GO:0016575 histone deacetylation IDA 11948178
GO:0070932 histone H3 deacetylation IEA --
genes like me logo Genes that share ontologies with HDAC11: view

No data available for SIGNOR curated interactions for HDAC11 Gene

Drugs & Compounds for HDAC11 Gene

(13) Drugs for HDAC11 Gene - From: DrugBank, ApexBio, DGIdb, and Tocris

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Belinostat Approved, Investigational Pharma Target, inhibitor Histone deacetylase (HDAC)inhibitors 45
Panobinostat Approved, Investigational Pharma Target, inhibitor, Inhibition Histone deacetylase (HDAC)inhibitors 142
Romidepsin Approved, Investigational Pharma inhibitor Histone deacetylase (HDAC)inhibitors 97
Vorinostat Approved, Investigational Pharma inhibitor HDAC inhibitor, Histone deacetylase (HDAC)inhibitors 264
AR-42 Investigational Pharma 0

(1) Additional Compounds for HDAC11 Gene - From: Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Valproic acid, sodium salt
1069-66-5

(3) Tocris Compounds for HDAC11 Gene

Compound Action Cas Number
Apicidin Potent histone deacetylase inhibitor 183506-66-3
PCI 34051 Potent and selective HDAC8 inhibitor 950762-95-5
Valproic acid, sodium salt Histone deacetylase inhibitor 1069-66-5

(1) ApexBio Compounds for HDAC11 Gene

Compound Action Cas Number
JNJ-26481585 Potent HDAC inhibitor 875320-29-9
genes like me logo Genes that share compounds with HDAC11: view

Drug Products

Transcripts for HDAC11 Gene

mRNA/cDNA for HDAC11 Gene

3 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
21 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HDAC11

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HDAC11 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b · 8c ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15a · 15b · 15c · 15d
SP1: - - - -
SP2: - - - - - -
SP3: - - - -
SP4: - - - - - - - - - - - -
SP5: - - -
SP6: -
SP7: - - - - - - - - - - - -
SP8: - - - - - - -
SP9: - - - - - - - - - - - - - - -
SP10: -
SP11: - - - - - - - - - -
SP12: - - - - - - -
SP13:

Relevant External Links for HDAC11 Gene

GeneLoc Exon Structure for
HDAC11

Expression for HDAC11 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HDAC11 Gene

Protein differential expression in normal tissues from HIPED for HDAC11 Gene

This gene is overexpressed in Liver (41.3), Frontal cortex (10.4), and Spinal cord (9.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for HDAC11 Gene



Protein tissue co-expression partners for HDAC11 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HDAC11

SOURCE GeneReport for Unigene cluster for HDAC11 Gene:

Hs.744132

mRNA Expression by UniProt/SwissProt for HDAC11 Gene:

Q96DB2-HDA11_HUMAN
Tissue specificity: Weakly expressed in most tissues. Strongly expressed in brain, heart, skeletal muscle, kidney and testis.

Evidence on tissue expression from TISSUES for HDAC11 Gene

  • Nervous system(4.6)
  • Intestine(4.3)
genes like me logo Genes that share expression patterns with HDAC11: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for HDAC11 Gene

Orthologs for HDAC11 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HDAC11 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HDAC11 31 30
  • 99.89 (n)
OneToOne
dog
(Canis familiaris)
Mammalia HDAC11 31 30
  • 89.34 (n)
OneToOne
cow
(Bos Taurus)
Mammalia HDAC11 31 30
  • 87.99 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Hdac11 17 31 30
  • 87.42 (n)
rat
(Rattus norvegicus)
Mammalia Hdac11 30
  • 87.42 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia HDAC11 31
  • 73 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia HDAC11 31
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves HDAC11 31 30
  • 69.25 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia HDAC11 31
  • 75 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii hdac11 31 30
  • 69.09 (n)
OneToMany
HDAC11 (3 of 3) 31
  • 60 (a)
OneToMany
HDAC11 (2 of 3) 31
  • 27 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001736 30
  • 58.91 (n)
fruit fly
(Drosophila melanogaster)
Insecta HdacX 31 30
  • 56.06 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea hda-11 31 30
  • 50.92 (n)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HOS2 31
  • 18 (a)
OneToMany
HOS1 31
  • 14 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons HDA2 30
  • 56.59 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.12177 30
rice
(Oryza sativa)
Liliopsida Os06g0571100 30
  • 58.98 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 54 (a)
OneToOne
Species where no ortholog for HDAC11 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for HDAC11 Gene

ENSEMBL:
Gene Tree for HDAC11 (if available)
TreeFam:
Gene Tree for HDAC11 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HDAC11: view image

Paralogs for HDAC11 Gene

(1) SIMAP similar genes for HDAC11 Gene using alignment to 16 proteins:

  • HDA11_HUMAN
  • B5MC52_HUMAN
  • B5MCQ6_HUMAN
  • B5MCS3_HUMAN
  • B5MCU6_HUMAN
  • B5MCV5_HUMAN
  • B5MD06_HUMAN
  • C9J2I7_HUMAN
  • C9J528_HUMAN
  • C9JBI4_HUMAN
  • C9JEC8_HUMAN
  • C9JMH0_HUMAN
  • E7ETT9_HUMAN
  • F5H6R5_HUMAN
  • F8WF94_HUMAN
  • Q6IA14_HUMAN
genes like me logo Genes that share paralogs with HDAC11: view

Variants for HDAC11 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HDAC11 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
744743 Likely Benign: not provided 13,504,667(+) C/A MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for HDAC11 Gene

Structural Variations from Database of Genomic Variants (DGV) for HDAC11 Gene

Variant ID Type Subtype PubMed ID
nsv1011766 CNV gain 25217958
nsv470416 CNV loss 18288195
nsv955316 CNV deletion 24416366

Variation tolerance for HDAC11 Gene

Residual Variation Intolerance Score: 28.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.40; 8.75% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HDAC11 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HDAC11

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HDAC11 Gene

Disorders for HDAC11 Gene

MalaCards: The human disease database

(2) MalaCards diseases for HDAC11 Gene - From: DISEASES

Disorder Aliases PubMed IDs
bicipital tenosynovitis
subungual glomus tumor
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for HDAC11

genes like me logo Genes that share disorders with HDAC11: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HDAC11 Gene

Publications for HDAC11 Gene

  1. Cloning and functional characterization of HDAC11, a novel member of the human histone deacetylase family. (PMID: 11948178) Gao L … Atadja P (The Journal of biological chemistry 2002) 2 3 4 54
  2. Hundreds of variants clustered in genomic loci and biological pathways affect human height. (PMID: 20881960) Lango Allen H … Hirschhorn JN (Nature 2010) 3 41 54
  3. Mutational analyses of WNT7A and HDAC11 as candidate tumour suppressor genes in sporadic malignant pancreatic endocrine tumours. (PMID: 17201809) Lindberg D … Westin G (Clinical endocrinology 2007) 3 23 54
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54

Products for HDAC11 Gene

Sources for HDAC11 Gene