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    HDAC5 histone deacetylase 5 [ Homo sapiens (human) ]

    Gene ID: 10014, updated on 10-Dec-2024

    Summary

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    Official Symbol
    HDAC5provided by HGNC
    Official Full Name
    histone deacetylase 5provided by HGNC
    Primary source
    HGNC:HGNC:14068
    See related
    Ensembl:ENSG00000108840 MIM:605315; AllianceGenome:HGNC:14068
    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
    HD5; NY-CO-9
    Summary
    Histones play a critical role in transcriptional regulation, cell cycle progression, and developmental events. Histone acetylation/deacetylation alters chromosome structure and affects transcription factor access to DNA. The protein encoded by this gene belongs to the class II histone deacetylase/acuc/apha family. It possesses histone deacetylase activity and represses transcription when tethered to a promoter. It coimmunoprecipitates only with HDAC3 family member and might form multicomplex proteins. It also interacts with myocyte enhancer factor-2 (MEF2) proteins, resulting in repression of MEF2-dependent genes. This gene is thought to be associated with colon cancer. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in skin (RPKM 14.0), ovary (RPKM 13.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HDAC5 in Genome Data Viewer
    Location:
    17q21.31
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (44076753..44123641, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (44929260..44976146, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (42154121..42201009, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene LSM12 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8571 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8572 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42146518-42147445 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42147446-42148372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12251 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:42149300-42150225 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42152642-42153376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42154394-42154933 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:42159496-42160695 Neighboring gene glucose-6-phosphatase catalytic subunit 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42169749-42170254 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42172728-42173488 Neighboring gene Sharpr-MPRA regulatory region 9416 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:42176231-42176442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42182651-42183302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42189382-42189882 Neighboring gene uncharacterized LOC105371789 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8573 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8574 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8575 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42202517-42203016 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42215327-42215850 Neighboring gene RNA, U6 small nuclear 131, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8576 Neighboring gene Sharpr-MPRA regulatory region 5 Neighboring gene homologous recombination factor with OB-fold Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12254

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Role of HDAC5 Epigenetics in Chronic Craniofacial Neuropathic Pain. Hui SE, et al. Int J Mol Sci, 2024 Jun 23. PMID 38999998, Free PMC Article
    2. Neutralizing negative epigenetic regulation by HDAC5 enhances human haematopoietic stem cell homing and engraftment. Huang X, et al. Nat Commun, 2018 Jul 16. PMID 30013077, Free PMC Article
    3. Histone deacetylase 5 promotes the proliferation and invasion of lung cancer cells. Zhong L, et al. Oncol Rep, 2018 Oct. PMID 30066893
    4. HDAC5 Expression in Urothelial Carcinoma Cell Lines Inhibits Long-Term Proliferation but Can Promote Epithelial-to-Mesenchymal Transition. Jaguva Vasudevan AA, et al. Int J Mol Sci, 2019 Apr 30. PMID 31052182, Free PMC Article
    5. Abnormal methylation of histone deacetylase genes: implications on etiology and epigenetic therapy of astrocytomas. Gomes MV, et al. Anticancer Res, 2011 Apr. PMID 21508384

    See all (218) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Role of HDAC5 Epigenetics in Chronic Craniofacial Neuropathic Pain.
      Title: Role of HDAC5 Epigenetics in Chronic Craniofacial Neuropathic Pain.
    2. Histone Trimethylations and HDAC5 Regulate Spheroid Subpopulation and Differentiation Signaling of Human Adipose-Derived Stem Cells.
      Title: Histone Trimethylations and HDAC5 Regulate Spheroid Subpopulation and Differentiation Signaling of Human Adipose-Derived Stem Cells.
    3. NFYB increases chemosensitivity in glioblastoma by promoting HDAC5-mediated transcriptional inhibition of SHMT2.
      Title: NFYB increases chemosensitivity in glioblastoma by promoting HDAC5-mediated transcriptional inhibition of SHMT2.
    4. HDAC5 Loss Enhances Phospholipid-Derived Arachidonic Acid Generation and Confers Sensitivity to cPLA2 Inhibition in Pancreatic Cancer.
      Title: HDAC5 Loss Enhances Phospholipid-Derived Arachidonic Acid Generation and Confers Sensitivity to cPLA2 Inhibition in Pancreatic Cancer.
    5. METTL3-mediated N6-methyladenosine modification and HDAC5/YY1 promote IFFO1 downregulation in tumor development and chemo-resistance.
      Title: METTL3-mediated N6-methyladenosine modification and HDAC5/YY1 promote IFFO1 downregulation in tumor development and chemo-resistance.
    6. HDAC5 inactivates CYR61-regulated CD31/mTOR axis to prevent the occurrence of preeclampsia.
      Title: HDAC5 inactivates CYR61-regulated CD31/mTOR axis to prevent the occurrence of preeclampsia.
    7. HDAC5-mediated Smad7 silencing through MEF2A is critical for fibroblast activation and hypertrophic scar formation.
      Title: HDAC5-mediated Smad7 silencing through MEF2A is critical for fibroblast activation and hypertrophic scar formation.
    8. Epigenetic master regulators HDAC1 and HDAC5 control pathobiont Enterobacteria colonization in ileal mucosa of Crohn's disease patients.
      Title: Epigenetic master regulators HDAC1 and HDAC5 control pathobiont Enterobacteria colonization in ileal mucosa of Crohn's disease patients.
    9. HDAC5, negatively regulated by miR-148a-3p, promotes colon cancer cell migration.
      Title: HDAC5, negatively regulated by miR-148a-3p, promotes colon cancer cell migration.
    10. HDAC5 modulates PD-L1 expression and cancer immunity via p65 deacetylation in pancreatic cancer.
      Title: HDAC5 modulates PD-L1 expression and cancer immunity via p65 deacetylation in pancreatic cancer.
    Submit: New GeneRIF Correction See all GeneRIFs (84)

    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
    Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.
    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

    • FLJ90614

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA polymerase II-specific DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables chromatin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 histone deacetylase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein kinase C binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein lysine deacetylase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    contributes_to transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription corepressor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in B cell activation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in B cell differentiation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in cellular response to insulin stimulus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in cellular response to lipopolysaccharide 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 inflammatory response TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of DNA-templated transcription TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of cell migration involved in sprouting angiogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of gene expression, epigenetic NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of myotube differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of DNA-binding transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of myotube differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of protein binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to cocaine IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to xenobiotic stimulus IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    part_of histone deacetylase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of histone deacetylase complex TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    histone deacetylase 5
    Names
    antigen NY-CO-9
    NP_001015053.1
    NP_001369322.1
    NP_005465.2
    XP_011522451.1
    XP_047291003.1
    XP_047291004.1
    XP_047291005.1
    XP_047291006.1
    XP_047291007.1
    XP_047291008.1
    XP_047291009.1
    XP_047291010.1
    XP_047291011.1
    XP_047291012.1
    XP_047291013.1
    XP_054170588.1
    XP_054170589.1
    XP_054170590.1
    XP_054170591.1
    XP_054170592.1
    XP_054170593.1
    XP_054170594.1
    XP_054170595.1
    XP_054170596.1
    XP_054170597.1
    XP_054170598.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001015053.2 → NP_001015053.1  histone deacetylase 5 isoform 3

      See identical proteins and their annotated locations for NP_001015053.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) represents the longer transcript and encodes the longer isoform (3).
      Source sequence(s)
      AB011172, AC023855, BC051824, CN290533
      Consensus CDS
      CCDS32663.1
      UniProtKB/Swiss-Prot
      Q9UQL6
      Related
      ENSP00000225983.5, ENST00000225983.10
      Conserved Domains (2) summary
      cd10164
      Location:69 → 165
      ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
      cd10007
      Location:680 → 1096
      HDAC5; Histone deacetylase 5

    2. NM_001382393.1 → NP_001369322.1  histone deacetylase 5 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AB011172, AC023855, BC051824
      Consensus CDS
      CCDS45696.1
      UniProtKB/Swiss-Prot
      C9JFV9, O60340, O60528, Q96DY4, Q9UQL6
      Related
      ENSP00000468004.1, ENST00000586802.5
      Conserved Domains (2) summary
      cd10164
      Location:68 → 164
      ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
      cd10007
      Location:679 → 1095
      HDAC5; Histone deacetylase 5

    3. NM_005474.5 → NP_005465.2  histone deacetylase 5 isoform 1

      See identical proteins and their annotated locations for NP_005465.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) uses an alternate in-frame splice site compared to variant 3. The resulting isoform (1) has the same N- and C-termini but is 1 aa shorter compared to isoform 3.
      Source sequence(s)
      AB011172, AC023855, BC051824, BM564861
      Consensus CDS
      CCDS45696.1
      UniProtKB/Swiss-Prot
      C9JFV9, O60340, O60528, Q96DY4, Q9UQL6
      Related
      ENSP00000507606.1, ENST00000682912.1
      Conserved Domains (2) summary
      cd10164
      Location:68 → 164
      ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
      cd10007
      Location:679 → 1095
      HDAC5; Histone deacetylase 5

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      44076753..44123641 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047435054.1 → XP_047291010.1  histone deacetylase 5 isoform X6

    2. XM_047435052.1 → XP_047291008.1  histone deacetylase 5 isoform X5

    3. XM_047435050.1 → XP_047291006.1  histone deacetylase 5 isoform X3

    4. XM_011524149.3 → XP_011522451.1  histone deacetylase 5 isoform X4

      Conserved Domains (2) summary
      cd10007
      Location:671 → 1087
      HDAC5; Histone deacetylase 5
      cl23765
      Location:69 → 156
      iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits

    5. XM_047435048.1 → XP_047291004.1  histone deacetylase 5 isoform X2

    6. XM_047435051.1 → XP_047291007.1  histone deacetylase 5 isoform X3

    7. XM_047435049.1 → XP_047291005.1  histone deacetylase 5 isoform X2

    8. XM_047435047.1 → XP_047291003.1  histone deacetylase 5 isoform X1

    9. XM_047435053.1 → XP_047291009.1  histone deacetylase 5 isoform X9

    10. XM_047435056.1 → XP_047291012.1  histone deacetylase 5 isoform X7

    11. XM_047435055.1 → XP_047291011.1  histone deacetylase 5 isoform X7

    12. XM_047435057.1 → XP_047291013.1  histone deacetylase 5 isoform X8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      44929260..44976146 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314620.1 → XP_054170595.1  histone deacetylase 5 isoform X6

    2. XM_054314619.1 → XP_054170594.1  histone deacetylase 5 isoform X5

    3. XM_054314616.1 → XP_054170591.1  histone deacetylase 5 isoform X3

    4. XM_054314618.1 → XP_054170593.1  histone deacetylase 5 isoform X4

    5. XM_054314614.1 → XP_054170589.1  histone deacetylase 5 isoform X2

    6. XM_054314617.1 → XP_054170592.1  histone deacetylase 5 isoform X3

    7. XM_054314615.1 → XP_054170590.1  histone deacetylase 5 isoform X2

    8. XM_054314613.1 → XP_054170588.1  histone deacetylase 5 isoform X1

    9. XM_054314622.1 → XP_054170597.1  histone deacetylase 5 isoform X7

    10. XM_054314621.1 → XP_054170596.1  histone deacetylase 5 isoform X7

    11. XM_054314623.1 → XP_054170598.1  histone deacetylase 5 isoform X8

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_139205.1: Suppressed sequence

      Description
      NM_139205.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UQL6.2 GenPept UniProtKB/Swiss-Prot:Q9UQL6

    Gene LinkOut

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

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