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    HDAC11 histone deacetylase 11 [ Homo sapiens (human) ]

    Gene ID: 79885, updated on 9-Dec-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
    mouse all
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    Genomic context

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    See HDAC11 in Genome Data Viewer
    Location:
    3p25.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (13480306..13506416)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (13480765..13506873)
    RS_2024_09 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. Histone Deacetylase 11 Is a Fatty-Acid Deacylase. Kutil Z, et al. ACS Chem Biol, 2018 Mar 16. PMID 29336543
    2. From immunity to tolerance through HDAC. Georgopoulos K. Nat Immunol, 2009 Jan. PMID 19088734
    3. MGCD0103, a novel isotype-selective histone deacetylase inhibitor, has broad spectrum antitumor activity in vitro and in vivo. Fournel M, et al. Mol Cancer Ther, 2008 Apr. PMID 18413790
    4. HDAC11 is a novel drug target in carcinomas. Deubzer HE, et al. Int J Cancer, 2013 May 1. PMID 23024001
    5. Multiple histone deacetylases repress tumor suppressor gene ARHI in breast cancer. Feng W, et al. Int J Cancer, 2007 Apr 15. PMID 17230502

    See all (57) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. [Progress on the involvement of HDAC11 in the regulation of mammalian oocyte maturation and early embryonic development].
      Title: [Progress on the involvement of HDAC11 in the regulation of mammalian oocyte maturation and early embryonic development].
    2. 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.
    3. HDAC11: A novel target for improved cancer therapy.
      Title: HDAC11: A novel target for improved cancer therapy.
    4. HDAC11 activity contributes to MEK inhibitor escape in uveal melanoma.
      Title: HDAC11 activity contributes to MEK inhibitor escape in uveal melanoma.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (29)

    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)

    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 H3K14 deacetylase activity, hydrolytic mechanism IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K4 deacetylase activity, hydrolytic mechanism IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K9 deacetylase activity, hydrolytic mechanism IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H4K12 deacetylase activity, hydrolytic mechanism IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H4K16 deacetylase activity, hydrolytic mechanism IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H4K5 deacetylase activity, hydrolytic mechanism IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H4K8 deacetylase activity, hydrolytic mechanism IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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