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HDAC11 histone deacetylase 11 [ Homo sapiens (human) ]

Gene ID: 79885, updated on 5-Aug-2018

Summary

Official Symbol
HDAC11provided by HGNC
Official Full Name
histone deacetylase 11provided by HGNC
Primary source
HGNC:HGNC:19086
See related
Ensembl:ENSG00000163517 MIM:607226; Vega:OTTHUMG00000129800
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HD11
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 2009]
Expression
Broad expression in brain (RPKM 17.4), testis (RPKM 14.8) and 22 other tissues See more
Orthologs

Genomic context

See HDAC11 in Genome Data Viewer
Location:
3p25.1
Exon count:
14
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (13478903..13506424)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (13521671..13547924)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene NUP210-HDAC11 intergenic CAGE-defined high expression enhancer Neighboring gene proline-rich protein 3 pseudogene Neighboring gene HDAC11 antisense RNA 1 Neighboring gene fibulin 2 Neighboring gene small nucleolar RNA, H/ACA box 93 Neighboring gene uncharacterized LOC100293612 Neighboring gene long intergenic non-protein coding RNA 620

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
NHGRI GWA Catalog

Pathways from BioSystems

  • Alcoholism, organism-specific biosystem (from KEGG)
    Alcoholism, organism-specific biosystemAlcoholism, also called dependence on alcohol (ethanol), is a chronic relapsing disorder that is progressive and has serious detrimental health outcomes. As one of the primary mediators of the reward...
  • Alcoholism, conserved biosystem (from KEGG)
    Alcoholism, conserved biosystemAlcoholism, also called dependence on alcohol (ethanol), is a chronic relapsing disorder that is progressive and has serious detrimental health outcomes. As one of the primary mediators of the reward...
  • Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants, organism-specific biosystem (from REACTOME)
    Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants, organism-specific biosystemWhen found in cis, HD and PEST domain mutations act synergistically, increasing NOTCH1 transcriptional activity up to ~40-fold, compared with up to ~10-fold and up to ~2-fold increase with HD mutatio...
  • Constitutive Signaling by NOTCH1 PEST Domain Mutants, organism-specific biosystem (from REACTOME)
    Constitutive Signaling by NOTCH1 PEST Domain Mutants, organism-specific biosystemAs NOTCH1 PEST domain is intracellular, NOTCH1 PEST domain mutants are expected to behave as the wild-type NOTCH1 with respect to ligand binding and proteolytic cleavage mediated activation of signal...
  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • Diseases of signal transduction, organism-specific biosystem (from REACTOME)
    Diseases of signal transduction, organism-specific biosystemSignaling processes are central to human physiology (e.g., Pires-da Silva & Sommer 2003), and their disruption by either germ-line and somatic mutation can lead to serious disease. Here, the molecula...
  • NOTCH1 Intracellular Domain Regulates Transcription, organism-specific biosystem (from REACTOME)
    NOTCH1 Intracellular Domain Regulates Transcription, organism-specific biosystemNICD1 produced by activation of NOTCH1 in response to Delta and Jagged ligands (DLL/JAG) presented in trans, traffics to the nucleus where it acts as a transcription regulator. In the nucleus, NICD1 ...
  • Neural Crest Differentiation, organism-specific biosystem (from WikiPathways)
    Neural Crest Differentiation, organism-specific biosystemGene regulatory network model of cranial neural crest cell (CNCC) development, adaped from PMID: 19575671. Most interactions in the model are proposed to regulate transcription of core factors involv...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by NOTCH, organism-specific biosystem (from REACTOME)
    Signaling by NOTCH, organism-specific biosystemThe Notch Signaling Pathway (NSP) is a highly conserved pathway for cell-cell communication. NSP is involved in the regulation of cellular differentiation, proliferation, and specification. For exam...
  • Signaling by NOTCH1, organism-specific biosystem (from REACTOME)
    Signaling by NOTCH1, organism-specific biosystemNOTCH1 functions as both a transmembrane receptor presented on the cell surface and as a transcriptional regulator in the nucleus.NOTCH1 receptor presented on the plasma membrane is activated by a me...
  • Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer, organism-specific biosystem (from REACTOME)
    Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer, organism-specific biosystemMutations in the heterodimerization domain (HD) and PEST domain of NOTCH1 are frequently found in cis in T-cell acute lymphoblastic leukemia. While HD mutations alone result in up to ~10-fold increas...
  • Signaling by NOTCH1 PEST Domain Mutants in Cancer, organism-specific biosystem (from REACTOME)
    Signaling by NOTCH1 PEST Domain Mutants in Cancer, organism-specific biosystemNOTCH1 PEST domain mutations are frequently found in T-cell acute lymphoblastic leukemia (T-ALL). PEST domain mutations interfere with ubiquitination-mediated NOTCH1 downregulation and result in prol...
  • Signaling by NOTCH1 in Cancer, organism-specific biosystem (from REACTOME)
    Signaling by NOTCH1 in Cancer, organism-specific biosystemHuman NOTCH1 was cloned as a chromosome 9 gene, translocated to the T-cell beta receptor (TCBR) promoter on chromosome 7 in T-cell acute lymphoblastic leukemia (T-ALL) (Ellisen et al. 1991). This tra...
  • Signaling events mediated by HDAC Class I, organism-specific biosystem (from Pathway Interaction Database)
    Signaling events mediated by HDAC Class I, organism-specific biosystem
    Signaling events mediated by HDAC Class I
  • Signaling events mediated by HDAC Class II, organism-specific biosystem (from Pathway Interaction Database)
    Signaling events mediated by HDAC Class II, organism-specific biosystem
    Signaling events mediated by HDAC Class II
  • Viral carcinogenesis, organism-specific biosystem (from KEGG)
    Viral carcinogenesis, organism-specific biosystemThere is a strong association between viruses and the development of human malignancies. We now know that at least six human viruses, Epstein-Barr virus (EBV), hepatitis B virus (HBV), hepatitis C vi...
  • Viral carcinogenesis, conserved biosystem (from KEGG)
    Viral carcinogenesis, conserved biosystemThere is a strong association between viruses and the development of human malignancies. We now know that at least six human viruses, Epstein-Barr virus (EBV), hepatitis B virus (HBV), hepatitis C vi...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ22237

Gene Ontology Provided by GOA

Function Evidence Code Pubs
NAD-dependent histone deacetylase activity (H3-K14 specific) IEA
Inferred from Electronic Annotation
more info
 
histone deacetylase activity IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor binding TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
chromatin organization TAS
Traceable Author Statement
more info
PubMed 
histone H3 deacetylation IEA
Inferred from Electronic Annotation
more info
 
histone deacetylation IDA
Inferred from Direct Assay
more info
PubMed 
oligodendrocyte development IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
histone deacetylase complex IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
histone deacetylase 11
NP_001129513.1
NP_001317565.1
NP_079103.2
XP_005265548.1
XP_006713401.1
XP_011532433.1
XP_011532434.2
XP_011532437.1
XP_016862723.1
XP_024309529.1
XP_024309530.1
XP_024309531.1
XP_024309532.1
XP_024309533.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001136041.2NP_001129513.1  histone deacetylase 11 isoform 2

    See identical proteins and their annotated locations for NP_001129513.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AC027124, AK293223, AW291816, BG708402, DB556939
    Consensus CDS
    CCDS46760.1
    UniProtKB/Swiss-Prot
    Q96DB2
    Related
    ENSP00000429794.1, OTTHUMP00000226982, ENST00000522202.5, OTTHUMT00000379260
    Conserved Domains (1) summary
    cd09993
    Location:7268
    HDAC_classIV; Histone deacetylase class IV also known as histone deacetylase 11
  2. NM_001330636.1NP_001317565.1  histone deacetylase 11 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks three exons in the coding region, compared to variant 1. It encodes isoform 3, which lacks an internal in-frame segment and is shorter, compared to isoform 1.
    Source sequence(s)
    AC027124, DA157041, DB449078, DC315722, HY351163
    Consensus CDS
    CCDS82738.1
    UniProtKB/TrEMBL
    B5MCQ6
    Related
    ENSP00000384123.1, ENST00000402271.5
    Conserved Domains (1) summary
    cd09993
    Location:35240
    HDAC_classIV; Histone deacetylase class IV also known as histone deacetylase 11
  3. NM_024827.3NP_079103.2  histone deacetylase 11 isoform 1

    See identical proteins and their annotated locations for NP_079103.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC027124, AW291816, BC009676, DB025431, DB556939
    Consensus CDS
    CCDS2615.1
    UniProtKB/Swiss-Prot
    Q96DB2
    UniProtKB/TrEMBL
    A0A024R2I1
    Related
    ENSP00000295757.3, OTTHUMP00000160231, ENST00000295757.7, OTTHUMT00000252028
    Conserved Domains (1) summary
    cd09993
    Location:35319
    HDAC_classIV; Histone deacetylase class IV also known as histone deacetylase 11

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    13478903..13506424
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024453764.1XP_024309532.1  histone deacetylase 11 isoform X2

    Conserved Domains (1) summary
    cd09993
    Location:7212
    HDAC_classIV; Histone deacetylase class IV also known as histone deacetylase 11
  2. XM_024453761.1XP_024309529.1  histone deacetylase 11 isoform X1

    Conserved Domains (1) summary
    cd09993
    Location:7291
    HDAC_classIV; Histone deacetylase class IV also known as histone deacetylase 11
  3. XM_006713338.1XP_006713401.1  histone deacetylase 11 isoform X4

    Conserved Domains (1) summary
    cd09993
    Location:35240
    HDAC_classIV; Histone deacetylase class IV also known as histone deacetylase 11
  4. XM_011534135.1XP_011532437.1  histone deacetylase 11 isoform X7

    See identical proteins and their annotated locations for XP_011532437.1

    UniProtKB/Swiss-Prot
    Q96DB2
    UniProtKB/TrEMBL
    Q6IA14
    Conserved Domains (1) summary
    cd09993
    Location:1197
    HDAC_classIV; Histone deacetylase class IV also known as histone deacetylase 11
  5. XM_005265491.1XP_005265548.1  histone deacetylase 11 isoform X1

    See identical proteins and their annotated locations for XP_005265548.1

    UniProtKB/TrEMBL
    E7ETT9
    Related
    ENSP00000395188.2, OTTHUMP00000208001, ENST00000437379.2, OTTHUMT00000340090
    Conserved Domains (1) summary
    cd09993
    Location:7291
    HDAC_classIV; Histone deacetylase class IV also known as histone deacetylase 11
  6. XM_024453765.1XP_024309533.1  histone deacetylase 11 isoform X6

    Conserved Domains (1) summary
    cd09993
    Location:7212
    HDAC_classIV; Histone deacetylase class IV also known as histone deacetylase 11
  7. XM_024453762.1XP_024309530.1  histone deacetylase 11 isoform X3

    Conserved Domains (1) summary
    cd09993
    Location:54259
    HDAC_classIV; Histone deacetylase class IV also known as histone deacetylase 11
  8. XM_024453763.1XP_024309531.1  histone deacetylase 11 isoform X5

    Conserved Domains (1) summary
    cl17011
    Location:54103
    Arginase_HDAC; Arginase-like and histone-like hydrolases
  9. XM_011534132.2XP_011532434.2  histone deacetylase 11 isoform X2

    Conserved Domains (1) summary
    cd09993
    Location:7212
    HDAC_classIV; Histone deacetylase class IV also known as histone deacetylase 11
  10. XM_011534131.1XP_011532433.1  histone deacetylase 11 isoform X1

    See identical proteins and their annotated locations for XP_011532433.1

    UniProtKB/TrEMBL
    E7ETT9
    Conserved Domains (1) summary
    cd09993
    Location:7291
    HDAC_classIV; Histone deacetylase class IV also known as histone deacetylase 11
  11. XM_017007234.1XP_016862723.1  histone deacetylase 11 isoform X6

    Conserved Domains (1) summary
    cd09993
    Location:7212
    HDAC_classIV; Histone deacetylase class IV also known as histone deacetylase 11
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