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HDAC11 histone deacetylase 11 [ Homo sapiens (human) ]

Gene ID: 79885, updated on 11-Apr-2024

Summary

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Official Symbol
HDAC11provided by HGNC
Official Full Name
histone deacetylase 11provided by HGNC
Primary source
HGNC:HGNC:19086
See related
Ensembl:ENSG00000163517 MIM:607226; AllianceGenome:HGNC:19086
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
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Genomic context

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Location:
3p25.1
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (13480306..13506416)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (13480765..13506873)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (13521806..13547916)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 3172 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19491 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13521871-13522527 Neighboring gene Sharpr-MPRA regulatory region 12997 Neighboring gene PRR3 pseudogene 1 Neighboring gene HDAC11 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19492 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13557470-13558398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13559772-13560661 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13567399-13568002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13573992-13574615 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13574616-13575238 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13577465-13577965 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13584863-13585400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13591988-13592596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13592597-13593203 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13597673-13598460 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14087 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13600925-13601426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13601427-13601926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13610405-13611364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13612969-13613685 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13618331-13619084 Neighboring gene fibulin 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13619085-13619838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13639373-13639873 Neighboring gene Sharpr-MPRA regulatory region 12774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13663487-13664060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13664061-13664635 Neighboring gene small nucleolar RNA, H/ACA box 93 Neighboring gene uncharacterized LOC100293612 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19493 Neighboring gene long intergenic non-protein coding RNA 620

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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 Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A pan-cancer analysis identifies HDAC11 as an immunological and prognostic biomarker. Li R, et al. FASEB J, 2022 Jul. PMID 35657209
  2. HDAC11 activity contributes to MEK inhibitor escape in uveal melanoma. Sriramareddy SN, et al. Cancer Gene Ther, 2022 Dec. PMID 35332245, Free PMC Article
  3. HDAC11: a multifaceted histone deacetylase with proficient fatty deacylase activity and its roles in physiological processes. Núñez-Álvarez Y, et al. FEBS J, 2022 May. PMID 33891374
  4. HDAC11 Regulates Glycolysis through the LKB1/AMPK Signaling Pathway to Maintain Hepatocellular Carcinoma Stemness. Bi L, et al. Cancer Res, 2021 Apr 15. PMID 33602787
  5. Histone Deacetylase 11 Is a Fatty-Acid Deacylase. Kutil Z, et al. ACS Chem Biol, 2018 Mar 16. PMID 29336543

See all (54) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. HDAC11 Regulates Palmitate-induced NLRP3 Inflammasome Activation by Inducing YAP Expression in THP-1 Cells and PBMCs.
    Title: HDAC11 Regulates Palmitate-induced NLRP3 Inflammasome Activation by Inducing YAP Expression in THP-1 Cells and PBMCs.
  2. HDAC11: A novel target for improved cancer therapy.
    Title: HDAC11: A novel target for improved cancer therapy.
  3. HDAC11 activity contributes to MEK inhibitor escape in uveal melanoma.
    Title: HDAC11 activity contributes to MEK inhibitor escape in uveal melanoma.
  4. HDAC11 negatively regulates antifungal immunity by inhibiting Nos2 expression via binding with transcriptional repressor STAT3.
    Title: HDAC11 negatively regulates antifungal immunity by inhibiting Nos2 expression via binding with transcriptional repressor STAT3.
  5. A pan-cancer analysis identifies HDAC11 as an immunological and prognostic biomarker.
    Title: A pan-cancer analysis identifies HDAC11 as an immunological and prognostic biomarker.
  6. HDAC11: a multifaceted histone deacetylase with proficient fatty deacylase activity and its roles in physiological processes.
    Title: HDAC11: a multifaceted histone deacetylase with proficient fatty deacylase activity and its roles in physiological processes.
  7. HDAC11 Regulates Glycolysis through the LKB1/AMPK Signaling Pathway to Maintain Hepatocellular Carcinoma Stemness.
    Title: HDAC11 Regulates Glycolysis through the LKB1/AMPK Signaling Pathway to Maintain Hepatocellular Carcinoma Stemness.
  8. Long noncoding RNA BCYRN1 promotes prostate cancer progression via elevation of HDAC11.
    Title: Long non‑coding RNA BCYRN1 promotes prostate cancer progression via elevation of HDAC11.
  9. Novel HDAC11 inhibitors suppress lung adenocarcinoma stem cell self-renewal and overcome drug resistance by suppressing Sox2.
    Title: Novel HDAC11 inhibitors suppress lung adenocarcinoma stem cell self-renewal and overcome drug resistance by suppressing Sox2.
  10. HDAC11 is a regulatory molecule in Th2 response and plays a critical role in the restriction of the biased IL-13 expression in CD4(+) T cells of the heart.
    Title: HDAC11 regulates interleukin-13 expression in CD4+ T cells in the heart.
Submit: New GeneRIF Correction See all GeneRIFs (28)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ22237

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor binding TAS
Traceable Author Statement
more info
 PubMed 
enables histone deacetylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone deacetylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromatin organization TAS
Traceable Author Statement
more info
 PubMed 
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
involved_in epigenetic regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in oligodendrocyte development IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of histone deacetylase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of histone deacetylase complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
histone deacetylase 11
NP_001129513.1
NP_001317565.1
NP_079103.2

NCBI Reference Sequences (RefSeq)

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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_001136041.3 → NP_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
    Consensus CDS
    CCDS46760.1
    UniProtKB/Swiss-Prot
    Q96DB2
    Related
    ENSP00000429794.1, ENST00000522202.5
    Conserved Domains (1) summary
    cd09993
    Location:7 → 268
    HDAC_classIV; Histone deacetylase class IV also known as histone deacetylase 11

  2. NM_001330636.2 → NP_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, DC315722, HY351163
    Consensus CDS
    CCDS82738.1
    UniProtKB/TrEMBL
    B5MCQ6, B5MCU6
    Related
    ENSP00000384123.1, ENST00000402271.5
    Conserved Domains (1) summary
    cd09993
    Location:35 → 240
    HDAC_classIV; Histone deacetylase class IV also known as histone deacetylase 11

  3. NM_024827.4 → NP_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
    Consensus CDS
    CCDS2615.1
    UniProtKB/Swiss-Prot
    B4DDK1, Q96DB2, Q9H6I7, Q9H6X3, Q9NTC9
    Related
    ENSP00000295757.3, ENST00000295757.8
    Conserved Domains (1) summary
    cd09993
    Location:35 → 319
    HDAC_classIV; Histone deacetylase class IV also known as histone deacetylase 11

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    13480306..13506416
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    13480765..13506873
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96DB2.1 GenPept UniProtKB/Swiss-Prot:Q96DB2

Gene LinkOut

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