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HDAC11 histone deacetylase 11 [ Homo sapiens (human) ]

Gene ID: 79885, updated on 15-Jul-2024

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; 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

See HDAC11 in Genome Data Viewer
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

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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 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

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_001136041.3NP_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:7268
    HDAC_classIV; Histone deacetylase class IV also known as histone deacetylase 11
  2. NM_001330636.2NP_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:35240
    HDAC_classIV; Histone deacetylase class IV also known as histone deacetylase 11
  3. NM_024827.4NP_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:35319
    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)