HDAC11 (histone deacetylase 11)

Gene

• Entrez ID: 79885
• Gene name: Histone deacetylase 11
• Gene symbol: HDAC11
• Synonyms (NCBI Gene): HD11
• Chromosome: 3
• Chromosome location: 3p25.1
• Summary: 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 200

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT438718	hsa-miR-145-5p	Luciferase reporter assay, qRT-PCR, Western blot	23980205
MIRT438718	hsa-miR-145-5p	Luciferase reporter assay, qRT-PCR, Western blot	23980205
MIRT1042252	hsa-miR-1200	CLIP-seq
MIRT1042253	hsa-miR-1224-3p	CLIP-seq
MIRT1042254	hsa-miR-1245b-5p	CLIP-seq
MIRT1042255	hsa-miR-1972	CLIP-seq
MIRT1042256	hsa-miR-3127-3p	CLIP-seq
MIRT1042257	hsa-miR-3142	CLIP-seq
MIRT1042258	hsa-miR-3667-3p	CLIP-seq
MIRT1042259	hsa-miR-4461	CLIP-seq
MIRT1042260	hsa-miR-4468	CLIP-seq
MIRT1042261	hsa-miR-4511	CLIP-seq
MIRT1042262	hsa-miR-4650-5p	CLIP-seq
MIRT1042263	hsa-miR-486-5p	CLIP-seq
MIRT1042264	hsa-miR-579	CLIP-seq
MIRT1042265	hsa-miR-587	CLIP-seq
MIRT1042266	hsa-miR-646	CLIP-seq
MIRT1042267	hsa-miR-660	CLIP-seq
MIRT1042253	hsa-miR-1224-3p	CLIP-seq
MIRT1042268	hsa-miR-4286	CLIP-seq
MIRT1042269	hsa-miR-4287	CLIP-seq
MIRT1042270	hsa-miR-4313	CLIP-seq
MIRT1042271	hsa-miR-432	CLIP-seq
MIRT1042272	hsa-miR-4469	CLIP-seq
MIRT1042273	hsa-miR-4685-3p	CLIP-seq
MIRT1042274	hsa-miR-4713-5p	CLIP-seq
MIRT1549469	hsa-miR-4254	CLIP-seq
MIRT2008892	hsa-miR-1178	CLIP-seq
MIRT1042253	hsa-miR-1224-3p	CLIP-seq
MIRT1042254	hsa-miR-1245b-5p	CLIP-seq
MIRT2008893	hsa-miR-1285	CLIP-seq
MIRT2008894	hsa-miR-1291	CLIP-seq
MIRT2008895	hsa-miR-1913	CLIP-seq
MIRT2008896	hsa-miR-2355-5p	CLIP-seq
MIRT1042257	hsa-miR-3142	CLIP-seq
MIRT2008897	hsa-miR-3173-5p	CLIP-seq
MIRT2008898	hsa-miR-3187-5p	CLIP-seq
MIRT2008899	hsa-miR-324-3p	CLIP-seq
MIRT2008900	hsa-miR-328	CLIP-seq
MIRT2008901	hsa-miR-4267	CLIP-seq
MIRT2008902	hsa-miR-4292	CLIP-seq
MIRT2008903	hsa-miR-4297	CLIP-seq
MIRT2008904	hsa-miR-4308	CLIP-seq
MIRT2008905	hsa-miR-4420	CLIP-seq
MIRT2008906	hsa-miR-4640-5p	CLIP-seq
MIRT2008907	hsa-miR-4645-5p	CLIP-seq
MIRT1042262	hsa-miR-4650-5p	CLIP-seq
MIRT2008908	hsa-miR-4656	CLIP-seq
MIRT2008909	hsa-miR-4673	CLIP-seq
MIRT2008910	hsa-miR-4726-5p	CLIP-seq
MIRT2008911	hsa-miR-4749-3p	CLIP-seq
MIRT2008912	hsa-miR-612	CLIP-seq
MIRT2008913	hsa-miR-4446-3p	CLIP-seq
MIRT2008895	hsa-miR-1913	CLIP-seq
MIRT2008899	hsa-miR-324-3p	CLIP-seq
MIRT2241264	hsa-miR-4695-3p	CLIP-seq
MIRT2008911	hsa-miR-4749-3p	CLIP-seq
MIRT2241265	hsa-miR-1207-5p	CLIP-seq
MIRT2241266	hsa-miR-4763-3p	CLIP-seq
MIRT2451032	hsa-miR-2392	CLIP-seq
MIRT2451033	hsa-miR-3190	CLIP-seq
MIRT2451034	hsa-miR-3689d	CLIP-seq
MIRT2451035	hsa-miR-4534	CLIP-seq
MIRT1042262	hsa-miR-4650-5p	CLIP-seq
MIRT2451036	hsa-miR-4802-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000118	Component	Histone deacetylase complex	IBA
GO:0000118	Component	Histone deacetylase complex	IDA	11948178
GO:0000118	Component	Histone deacetylase complex	IEA
GO:0004407	Function	Histone deacetylase activity	IBA
GO:0004407	Function	Histone deacetylase activity	IEA
GO:0005515	Function	Protein binding	IPI	26221039, 32296183, 33961781
GO:0005634	Component	Nucleus	IDA	11948178
GO:0005634	Component	Nucleus	IEA
GO:0005886	Component	Plasma membrane	IDA
GO:0006325	Process	Chromatin organization	IEA
GO:0006325	Process	Chromatin organization	TAS	12711221
GO:0016787	Function	Hydrolase activity	IEA
GO:0040029	Process	Epigenetic regulation of gene expression	IBA
GO:0140297	Function	DNA-binding transcription factor binding	IEA
GO:0140297	Function	DNA-binding transcription factor binding	TAS	12711221
GO:0141221	Function	Histone deacetylase activity, hydrolytic mechanism	IDA	11948178
GO:0141221	Function	Histone deacetylase activity, hydrolytic mechanism	IEA

Other IDs

• MIM: 607226
• HGNC: 19086
• e!Ensembl: ENSG00000163517

Protein

• UniProt ID: Q96DB2
• Protein name: Histone deacetylase 11 (HD11) (EC 3.5.1.98)
• Protein 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 c
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00850	Hist_deacetyl	35 → 320	Histone deacetylase domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Weakly expressed in most tissues. Strongly expressed in brain, heart, skeletal muscle, kidney and testis. {ECO:0000269|PubMed:11948178}.
• Sequence:

  MLHTTQLYQHVPETRWPIVYSPRYNITFMGLEKLHPFDAGKWGKVINFLKEEKLLSDSML
  VEAREASEEDLLVVHTRRYLNELKWSFAVATITEIPPVIFLPNFLVQRKVLRPLRTQTGG
  TIMAGKLAVERGWAINVGGGFHHCSSDRGGGFCAYADITLAIKFLFERVEGISRATIIDL
  DAHQGNGHERDFMDDKRVYIMDVYNRHIYPGDRFAKQAIRRKVELEWGTEDDEYLDKVER
  NIKKSLQEHLPDVVVYNAGTDILEGDRLGGLSISPAGIVKRDELVFRMVRGRRVPILMVT
  SGGYQKRTARIIADSILNLFGLGLIGPESPSVSAQNSDTPLLPPAVP

• Sequence length: 347

Pathways

KEGG:

Neutrophil extracellular trap formation
Alcoholism
Viral carcinogenesis

Reactome:

Constitutive Signaling by NOTCH1 PEST Domain Mutants
Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants
Notch-HLH transcription pathway

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CERVICAL CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOARTHRITIS, HIP	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOARTHRITIS, KNEE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adult Hodgkin Lymphoma	Hodgkin Lymphoma	BEFREE	21239696, 28418763		★☆☆☆☆ Found in Text Mining only
Age related macular degeneration	Age-related macular degeneration	BEFREE	29636475		★☆☆☆☆ Found in Text Mining only
Allergic rhinitis (disorder)	Allergic rhinitis	BEFREE	30007011		★☆☆☆☆ Found in Text Mining only
Amyotrophic Lateral Sclerosis	Amyotrophic Lateral Sclerosis	BEFREE	20467334		★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune Diseases	BEFREE	28819166, 29222071		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	31519896		★☆☆☆☆ Found in Text Mining only
Bronchitis	Bronchitis	BEFREE	29302792		★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	35345359	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma	Carcinoma	BEFREE	23024001		★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	36124029, 37903974	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	34308568	Associate	★☆☆☆☆ Found in Text Mining only
Cardiomyopathy, Familial Idiopathic	Cardiomyopathy	BEFREE	30063898		★☆☆☆☆ Found in Text Mining only
Chronic myeloproliferative disorder	Myeloproliferative disorder	BEFREE	21806350, 31750881		★☆☆☆☆ Found in Text Mining only
Colitis Ulcerative	Ulcerative colitis	Pubtator	26278503	Associate	★☆☆☆☆ Found in Text Mining only
Crohn Disease	Crohn Disease	BEFREE	26278503		★☆☆☆☆ Found in Text Mining only
Degenerative polyarthritis	Arthritis	BEFREE	19531758		★☆☆☆☆ Found in Text Mining only
Diabetes	Diabetes	BEFREE	30089714, 30126820		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	BEFREE	29655790, 30089714, 30126820		★☆☆☆☆ Found in Text Mining only
Diabetic Foot	Diabetic foot	Pubtator	33096729	Associate	★☆☆☆☆ Found in Text Mining only
Dyslipidemias	Dyslipidemias	BEFREE	29655790		★☆☆☆☆ Found in Text Mining only
Fibrosis, Liver	Liver Fibrosis	BEFREE	27818223		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	25791281, 37528157	Associate	★☆☆☆☆ Found in Text Mining only
Hepatitis B	Hepatitis b	Pubtator	35478990	Associate	★☆☆☆☆ Found in Text Mining only
Hodgkin Disease	Hodgkin Disease	BEFREE	21239696, 28418763		★☆☆☆☆ Found in Text Mining only
Hodgkin Disease	Hodgkin disease	Pubtator	21239696, 29481474	Associate	★☆☆☆☆ Found in Text Mining only
Inflammatory Bowel Diseases	Inflammatory bowel disease	Pubtator	26278503	Associate	★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	26024595, 31635225		★☆☆☆☆ Found in Text Mining only
Liver neoplasms	Liver neoplasms	BEFREE	26024595		★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	32170113	Associate	★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus Systemic	Systemic lupus erythematosus	Pubtator	25611806	Inhibit	★☆☆☆☆ Found in Text Mining only
Macular Degeneration	Macular degeneration	Pubtator	29636475	Associate	★☆☆☆☆ Found in Text Mining only
Macular dystrophy, corneal type 1	Macular corneal dystrophy	BEFREE	30063898		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	31519896		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of liver	Liver Cancer	BEFREE	30899397		★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	24850177		★☆☆☆☆ Found in Text Mining only
Melanoma	Melanoma	Pubtator	24850177	Associate	★☆☆☆☆ Found in Text Mining only
Metabolic Diseases	Metabolic Diseases	BEFREE	31264832		★☆☆☆☆ Found in Text Mining only
Metabolic Syndrome X	Metabolic Syndrome	BEFREE	29958910		★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Multiple myeloma	Pubtator	25482492	Associate	★☆☆☆☆ Found in Text Mining only
Myeloproliferative disease	Myeloproliferative disorder	BEFREE	31750881		★☆☆☆☆ Found in Text Mining only
Myocarditis	Myocarditis	BEFREE	30063898		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	17201809, 25593028		★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	BEFREE	28252645		★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	Pubtator	28252645	Associate	★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	BEFREE	29958910, 30089714, 30126820		★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	23965899	Associate	★☆☆☆☆ Found in Text Mining only
Pituitary Neoplasms	Pituitary Neoplasms	BEFREE	28782861		★☆☆☆☆ Found in Text Mining only
Primary Myelofibrosis	Myelofibrosis	BEFREE	21806350		★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	28928414		★☆☆☆☆ Found in Text Mining only
Thrombocythemia, Essential	Thrombocythemia	BEFREE	21806350		★☆☆☆☆ Found in Text Mining only
Thyroid Cancer Papillary	Papillary thyroid cancer	Pubtator	26810418	Associate	★☆☆☆☆ Found in Text Mining only
Ulcerative Colitis	Ulcerative colitis	BEFREE	26278503		★☆☆☆☆ Found in Text Mining only
Uveal melanoma	Uveal melanoma	Pubtator	25593028, 35332245	Associate	★☆☆☆☆ Found in Text Mining only