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General Information
Symbol
Dmel\HDAC4
Species
D. melanogaster
Name
Histone deacetylase 4
Annotation Symbol
CG1770
Feature Type
FlyBase ID
FBgn0041210
Gene Model Status
Stock Availability
Enzyme Name (EC)
Histone deacetylase (3.5.1.98)
Gene Snapshot
Histone deacetylase 4 (HDAC4) encodes a Class IIa histone deacetylase that modulates gene expression by associating with transcriptional factors. It is regulated by nucleocytoplasmic shuttling and contributes to embryogenesis, muscle development, circadian function, energy balance and memory. [Date last reviewed: 2019-03-07]
Also Known As

dHDAC4, HDAC4a, HDAC

Key Links
Genomic Location
Cytogenetic map
Sequence location
X:13,262,687..13,285,632 [-]
Recombination map

1-42

RefSeq locus
NC_004354 REGION:13262687..13285632
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
-
Molecular Function (GO)
[Detailed GO annotations]
Catalytic Activity (EC)
Experimental Evidence
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (3.5.1.98)
Predictions / Assertions
-
Summaries
Gene Group (FlyBase)
RPD3/HDA1 LYSINE DEACETYLASES -
The RPD3/HDA1 family are Zn2+-dependent lysine deacetylases that share a common catalytic core domain. (Adapted from FBrf0159755).
SUMO TRANSFERASES -
SUMO transferases catalyze the transfer of SUMO from either E2 or E3 enzyme to a substrate.
Pathway (FlyBase)
Insulin-like Receptor Signaling Pathway Core Components -
The Insulin-like Receptor (IR) signaling pathway in Drosophila is initiated by the binding of an insulin-like peptides to the Insulin-like receptor (InR). (Adapted from FBrf0232297, FBrf0230017 and FBrf0229989.)
Gene Model and Products
Number of Transcripts
8
Number of Unique Polypeptides
6

Please see the GBrowse view of Dmel\HDAC4 or the JBrowse view of Dmel\HDAC4 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Comments on Gene Model

Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated

Gene model reviewed during 5.39

Gene model reviewed during 5.46

Gene model reviewed during 5.56

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0073798
5182
1181
FBtr0301298
6312
1252
FBtr0301299
5299
1203
FBtr0308576
5487
1242
FBtr0333331
6876
1269
FBtr0333332
6510
1181
FBtr0333333
6559
1205
FBtr0333334
6248
1205
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0073629
126.0
1181
8.11
FBpp0290513
134.2
1252
7.79
FBpp0290514
128.6
1203
7.18
FBpp0300800
133.1
1242
7.79
FBpp0305523
136.2
1269
7.95
FBpp0305524
126.0
1181
8.11
FBpp0305525
129.0
1205
8.27
FBpp0305526
129.0
1205
8.27
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

1181 aa isoforms: HDAC4-PB, HDAC4-PH
1205 aa isoforms: HDAC4-PI, HDAC4-PJ
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\HDAC4 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (15 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from direct assay
inferred from mutant phenotype
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from sequence or structural similarity with UniProtKB:P56524
Biological Process (8 terms)
Terms Based on Experimental Evidence (8 terms)
CV Term
Evidence
References
inferred from expression pattern
inferred from direct assay
inferred from mutant phenotype
inferred from direct assay
inferred from mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (4 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
inferred from direct assay
inferred from direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR017320
(assigned by InterPro )
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

In early embryos (< 1 hour AEL) HDAC4 is expressed ubiquitously, and concentrated around the nuclei. At about 2 hours of development expression is decreased, and is refined to a broad anterior domain. Seven stripes appear at cellularization, between 70% and 24% egg length, the broad anterior stripe is lessened in intensity. During gastrulation, anoter seven stripes appear between the first seven, and these are maintainted through embryonic stage 11. The 3 kB transcript is predominant in larvae, while the 5.5 kB transcript is predominant in embryos and adults.

Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

A single confocal plane through the Kenyon cells

at the level of the calyx (asterisk) shows HDAC4 is predominantly localized to the calyx and cytoplasm. In a subset of cells, nuclear HDAC4 expression is observed, which always co-localizes with Mef2.

Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
inferred from direct assay
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\HDAC4 in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 22 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 11 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of HDAC4
Transgenic constructs containing regulatory region of HDAC4
Deletions and Duplications ( 0 )
Phenotypes
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (6)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
10 of 15
Yes
Yes
 
10 of 15
Yes
Yes
9 of 15
No
Yes
5 of 15
No
Yes
3 of 15
No
No
 
3 of 15
No
No
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (6)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
10 of 15
Yes
Yes
9 of 15
No
Yes
6 of 15
No
Yes
5 of 15
No
Yes
3 of 15
No
No
3 of 15
No
No
Rattus norvegicus (Norway rat) (6)
9 of 13
Yes
Yes
8 of 13
No
Yes
5 of 13
No
Yes
2 of 13
No
Yes
2 of 13
No
No
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (5)
5 of 12
Yes
Yes
4 of 12
No
Yes
3 of 12
No
Yes
1 of 12
No
Yes
1 of 12
No
No
Danio rerio (Zebrafish) (7)
10 of 15
Yes
Yes
7 of 15
No
Yes
5 of 15
No
Yes
4 of 15
No
Yes
3 of 15
No
No
2 of 15
No
No
1 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (7)
8 of 15
Yes
Yes
3 of 15
No
No
2 of 15
No
No
2 of 15
No
No
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
Arabidopsis thaliana (thale-cress) (4)
2 of 9
Yes
No
2 of 9
Yes
No
2 of 9
Yes
No
1 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (2)
5 of 15
Yes
No
1 of 15
No
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
4 of 12
Yes
No
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091901IS )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG0915018G )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W09ID )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X09EC )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0EQO )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (1)
5 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 1 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v7.1 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Functional Complementation Data
    Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
    Interactions
    Summary of Physical Interactions
    esyN Network Diagram
    Interactions Browser
    Summary of Genetic Interactions
    esyN Network Diagram
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Insulin-like Receptor Signaling Pathway Core Components -
    The Insulin-like Receptor (IR) signaling pathway in Drosophila is initiated by the binding of an insulin-like peptides to the Insulin-like receptor (InR). (Adapted from FBrf0232297, FBrf0230017 and FBrf0229989.)
    Metabolic Pathways
    External Data
    Linkouts
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    X
    Recombination map

    1-42

    Cytogenetic map
    Sequence location
    X:13,262,687..13,285,632 [-]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    11E8-11E9
    Limits computationally determined from genome sequence between P{EP}EP1461 and P{EP}CG1640EP1626
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (16)
    Genomic Clones (15)
     

    Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

    cDNA Clones (32)
     

    Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.

    cDNA clones, fully sequences
    BDGP DGC clones
    Other clones
    Drosophila Genomics Resource Center cDNA clones

    For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

    cDNA Clones, End Sequenced (ESTs)
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    Antibody Information
    Laboratory Generated Antibodies
     
    Commercially Available Antibodies
     
    Other Information
    Relationship to Other Genes
    Source for database identify of
    Source for database merge of

    Source for merge of: HDAC4 CG1770

    Source for merge of: HDAC4 HDAC4a

    Additional comments

    Source for merge of HDAC4 HDAC4a was sequence comparison ( date:030604 ).

    Other Comments

    HDAC4 is a repressor of long-term memory and modulates normal memory formation.

    S2 cells which have been treated with dsRNA made from templates generated with primers directed against HDAC4 show no significant inhibition of cell growth.

    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 101 )
    Sequence Crossreferences
    NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
    GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
    RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
    UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
    Other crossreferences
    Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
    Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
    Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
    Flygut - An atlas of the Drosophila adult midgut
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    KEGG Genes - Molecular building blocks of life in the genomic space.
    modMine - A data warehouse for the modENCODE project
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    DRSC - Results frm RNAi screens
    FLIGHT - Cell culture data for RNAi and other high-throughput technologies
    FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
    FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
    FlyMine - An integrated database for Drosophila genomics
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Synonyms and Secondary IDs (11)
    Datasets (1)
    Study focus (1)
    Experimental Role
    Project
    Project Type
    Title
    • bait_protein
    Genome-wide localization of chromatin factors by ChIP-chip and ChIP-Seq.
    References (89)