FB2022_03, released June 9, 2022

Gene: Dmel\HDAC1

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General Information
Symbol
Dmel\HDAC1
Species
D. melanogaster
Name
Histone deacetylase 1
Annotation Symbol
CG7471
Feature Type
protein_coding_gene
FlyBase ID
FBgn0015805
Gene Model Status
Current
Stock Availability
17 publicly available
Enzyme Name (EC)
Histone deacetylase (3.5.1.98)
Gene Summary
Catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4) (PubMed:11571273, PubMed:28245922, PubMed:12408863). Histone deacetylation may constitute a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events (PubMed:11571273, PubMed:8955276, PubMed:15545624, PubMed:15306652). For instance, deacetylation of histone H3 may be a prerequisite for the subsequent recruitment of the histone methyltransferase Su(var)3-9 to histones (PubMed:11571273). Involved in position-effect variegation (PEV) (PubMed:11571273). In the larval brain, part of a regulatory network including the transcriptional repressors klu, dpn and E(spl)mgamma-HLH which is required for type II neuroblast self-renewal and for maintaining erm in an inactive state in intermediate neural progenitors (INP) (PubMed:28245922). (UniProt, Q94517)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

Rpd3, dHDAC1, dRPD3, HDAC, l(3)04556

Key Links
Genomic Location
Cytogenetic map
64B12-64B12
Sequence location
Recombination map
3-12
RefSeq locus
NT_037436 REGION:4626734..4629467
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (35 terms)
Molecular Function (4 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
enables histone deacetylase activity
inferred from direct assay
(Miotto et al., 2006, Cho et al., 2005, Barlow et al., 2001, Huang and Kadonaga, 2001)
inferred from mutant phenotype
(Feller et al., 2015)
enables protein binding
inferred from physical interaction with UniProtKB:Q24459
(assigned by UniProt )
(Tie et al., 2003)
inferred from physical interaction with FLYBASE:Smyd4-2; FB:FBgn0036282
(Thompson and Travers, 2008)
inferred from physical interaction with FLYBASE:mip120; FB:FBgn0033846
(Lewis et al., 2004)
enables transcription corepressor activity
inferred from physical interaction with FLYBASE:kay; FB:FBgn0001297
(Miotto et al., 2006)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
enables histone deacetylase activity
non-traceable author statement
(Courey and Jia, 2001)
inferred from biological aspect of ancestor with PANTHER:PTN002239566
(assigned by GO_Central )
(Gaudet et al., 2011)
inferred from sequence or structural similarity with HGNC:4852
(De Rubertis et al., 1996)
inferred from sequence or structural similarity with SGD:S000005274
(De Rubertis et al., 1996)
enables NAD-independent histone deacetylase activity
non-traceable author statement
(Feller et al., 2015)
enables transcription corepressor activity
non-traceable author statement
(Courey and Jia, 2001)
Biological Process (20 terms)
Terms Based on Experimental Evidence (18 terms)
CV Term
Evidence
References
involved_in blastoderm segmentation
inferred from mutant phenotype
(Mannervik and Levine, 1999)
involved_in chromosome condensation
inferred from mutant phenotype
(Nikalayevich and Ohkura, 2015)
involved_in dendrite guidance
inferred from mutant phenotype
(Tea et al., 2010)
involved_in determination of adult lifespan
inferred from mutant phenotype
(Rogina et al., 2002)
involved_in heterochromatin assembly
inferred from mutant phenotype
(Zhu et al., 2008, Tie et al., 2001)
inferred from genetic interaction with FLYBASE:Pc; FB:FBgn0003042
(Chang et al., 2001)
inferred from physical interaction with FLYBASE:Pc; FB:FBgn0003042
(Chang et al., 2001)
inferred from genetic interaction with FLYBASE:inferred from high throughput direct assayC3; FB:FBgn0025825
(Zhu et al., 2008)
involved_in histone deacetylation
inferred from mutant phenotype
(Feller et al., 2015, Tea et al., 2010, Pile et al., 2002)
involved_in negative regulation of axonogenesis
inferred from mutant phenotype
(Tea et al., 2010)
involved_in negative regulation of gene expression
inferred from mutant phenotype
(assigned by UniProt )
(Janssens et al., 2017)
involved_in negative regulation of histone H3-K27 methylation
inferred from mutant phenotype
(assigned by UniProt )
(Janssens et al., 2017)
involved_in negative regulation of histone methylation
inferred from mutant phenotype
(assigned by UniProt )
(Janssens et al., 2017)
involved_in negative regulation of response to gamma radiation
inferred from mutant phenotype
(Zhang et al., 2008)
involved_in negative regulation of smoothened signaling pathway
inferred from mutant phenotype
(Zhang et al., 2013)
inferred from physical interaction with FLYBASE:ci; FB:FBgn0004859
(Zhang et al., 2013)
involved_in negative regulation of transcription by RNA polymerase II
inferred from direct assay
(Miotto et al., 2006)
involved_in negative regulation of transcription, DNA-templated
inferred from genetic interaction with FLYBASE:ttk; FB:FBgn0003870
(Chen et al., 2009)
inferred from expression pattern
(Pile and Wassarman, 2000)
involved_in regulation of histone acetylation
inferred from mutant phenotype
(Zhang et al., 2013)
involved_in regulation of neuroblast proliferation
inferred from mutant phenotype
(assigned by UniProt )
(Janssens et al., 2017)
inferred from genetic interaction with UniProtKB:M9PF84
(assigned by UniProt )
(Janssens et al., 2017)
inferred from genetic interaction with UniProtKB:Q01070
(assigned by UniProt )
(Janssens et al., 2017)
inferred from genetic interaction with UniProtKB:Q26263
(assigned by UniProt )
(Janssens et al., 2017)
involved_in regulation of neuron differentiation
inferred from mutant phenotype
(assigned by UniProt )
(Janssens et al., 2017)
involved_in regulation of transcription, DNA-templated
inferred from direct assay
(Cho et al., 2005)
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
involved_in determination of adult lifespan
traceable author statement
(Helfand and Rogina, 2003)
involved_in histone deacetylation
non-traceable author statement
(Courey and Jia, 2001)
involved_in negative regulation of transcription, DNA-templated
non-traceable author statement
(Courey and Jia, 2001)
involved_in oogenesis
traceable author statement
(Courey and Jia, 2001)
involved_in regulation of transcription by RNA polymerase II
inferred from biological aspect of ancestor with PANTHER:PTN000835657
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (11 terms)
Terms Based on Experimental Evidence (9 terms)
CV Term
Evidence
References
located_in chromatin
inferred from direct assay
(Pile and Wassarman, 2000)
part_of ESC/E(Z) complex
inferred from direct assay
(Czermin et al., 2002)
part_of Myb complex
inferred from direct assay
(Lewis et al., 2004)
located_in nucleus
inferred from direct assay
(Miotto et al., 2006, Cho et al., 2005, Czermin et al., 2002, Tie et al., 2001, Pile and Wassarman, 2000)
part_of NuRD complex
inferred from physical interaction with FLYBASE:Mi-2; FB:FBgn0262519
(Murawsky et al., 2001)
located_in polytene chromosome interband
inferred from direct assay
(Wang et al., 2008)
located_in polytene chromosome
inferred from direct assay
(Burgio et al., 2008)
part_of Sin3-type complex
inferred from direct assay
(Spain et al., 2010)
part_of transcription repressor complex
inferred from physical interaction with FLYBASE:Su(var)3-3; FB:FBgn0260397
(Dallman et al., 2004)
inferred from physical interaction with FLYBASE:CoRest; FB:FBgn0261573
(Dallman et al., 2004)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
part_of histone deacetylase complex
inferred from biological aspect of ancestor with PANTHER:PTN002239566
(assigned by GO_Central )
(Gaudet et al., 2011)
part_of NuRD complex
non-traceable author statement
(Pile and Wassarman, 2000)
part_of Sin3 complex
non-traceable author statement
(Pile and Wassarman, 2000)
Gene Group (FlyBase)
Pathway (FlyBase)
Protein Family (UniProt)
Belongs to the histone deacetylase family. HD type 1 subfamily. (Q94517)
Protein Signatures (InterPro)
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
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (3.5.1.98)
Summaries
Gene Group (FlyBase)
NUCLEOSOME REMODELING DEACETYLASE COMPLEX -
The nucleosome remodelling and deacetylase (NuRD) complex couples chromatin remodelling and histone deacetylation to mediate transcriptional repression. (Adapted from FBrf0228973 and FBrf0228920).
RPD3/HDA1 LYSINE DEACETYLASES -
The RPD3/HDA1 family are Zn2+-dependent lysine deacetylases that share a common catalytic core domain. (Adapted from FBrf0159755).
Pathway (FlyBase)
Negative Regulators of Hedgehog Signaling Pathway -
Negative regulators of hedgehog signaling down-regulate the pathway, resulting in the repression of transcription of hh-responsive genes.
Protein Function (UniProtKB)
Catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4) (PubMed:11571273, PubMed:28245922, PubMed:12408863). Histone deacetylation may constitute a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events (PubMed:11571273, PubMed:8955276, PubMed:15545624, PubMed:15306652). For instance, deacetylation of histone H3 may be a prerequisite for the subsequent recruitment of the histone methyltransferase Su(var)3-9 to histones (PubMed:11571273). Involved in position-effect variegation (PEV) (PubMed:11571273). In the larval brain, part of a regulatory network including the transcriptional repressors klu, dpn and E(spl)mgamma-HLH which is required for type II neuroblast self-renewal and for maintaining erm in an inactive state in intermediate neural progenitors (INP) (PubMed:28245922).
(UniProt, Q94517)
Summary (Interactive Fly)

histone deacetylase. functioning in gene silencing - interacts with Groucho - required for starvation stress resistance - interacts with insulin signaling in Drosophila longevity extension

Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\HDAC1 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
Structure New Section
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q94517)

If you don't see the viewer to the right, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Comments on Gene Model

Gene model reviewed during 5.46

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.56

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
HDAC1-RA
FBtr0073317
NM_139661
2124
521
Additional Transcript Data and Comments
Reported size (kB)

2.2 (northern blot)

(De Rubertis et al., 1996)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
HDAC1-PA
FBpp0073173
58.3
521
5.51
Q94517
NP_647918
AAF47924
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)

521 (aa)

(Mottus et al., 2000, Johnson et al., 1998)

520 (aa)

(De Rubertis et al., 1996)
Comments
External Data
Subunit Structure (UniProtKB)

Component of a form of the Esc/E(z) complex present specifically during early embryogenesis which is composed of Caf1-55, esc, E(z), Su(z)12, Pcl and HDAC1 (PubMed:12533794, PubMed:12408863, PubMed:12697833). The Esc/E(z) complex may also associate with Pcl and HDAC1 during early embryogenesis (PubMed:12697833). This complex is distinct from the PRC1 complex, which contains many other PcG proteins like Pc, Ph, Psc, Su(z)2 (PubMed:12533794). The 2 complexes however cooperate and interact together during the first 3 hours of development to establish PcG silencing (PubMed:12533794). Interacts with the histone methyltransferase Su(var)3-9 (PubMed:11571273). Component of a complex that contains at least HDAC1, CoRest and Su(var)3-3/Hdm (PubMed:15306652). Component of the DREAM complex at least composed of Myb, Caf1-55, mip40, mip120, mip130, E2f2, Dp, Rbf, Rbf2, lin-52, HDAC1 and l(3)mbt (PubMed:15545624). Interacts with the chromatin-remodeler Mi-2 (PubMed:18250149).

(UniProt, Q94517)
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
UniProt
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\HDAC1 using the Feature Mapper tool.

External Data
Crossreferences
Linkouts
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that the Fly Cell Atlas project found the gene expressed in that cell type. Darker colors mean that more cells of that cell type express the gene:
 low
high 
Colorless tiles indicate that there is no scRNAseq data for the gene in that cell type.
Colored tiles in ribbon indicate that expression data (RNA and/or protein) has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
Colored tiles in the ribbon indicate the average RNA expression level of the gene at the indicated stages:
 low
high 
as determined by RNA-seq (RPKM) using whole organism samples modENCODE, Brown et al., 2014. 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
embryonic stage
presumptive embryonic/larval central nervous system
(Zhu et al., 2008)
embryonic/larval central nervous system
(Zhu et al., 2008)
embryonic stage 1 -- 3
organism

Comment: maternally deposited

(Fisher et al., 2012)
embryonic stage 4 -- 6
organism | intense | ubiquitous
(Fisher et al., 2012)
embryonic stage 7 -- 8
organism | intense | ubiquitous
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 9 -- 10
organism | intense | ubiquitous
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 11 -- 12
anterior midgut primordium
(Fisher et al., 2012)
central brain primordium
(Fisher et al., 2012)
Malpighian tubule primordium
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
posterior midgut primordium
(Fisher et al., 2012)
ventral nerve cord primordium
(Fisher et al., 2012)
embryonic stage 13 -- 16
embryonic brain
(Fisher et al., 2012)
embryonic/larval midgut
(Fisher et al., 2012)
embryonic/larval nervous system
(Fisher et al., 2012)
gonad
(Fisher et al., 2012)
larval ventral nerve cord
(Fisher et al., 2012)
larval stage
embryonic/larval central nervous system
(Zhu et al., 2008)
embryonic/larval brain
(Zhu et al., 2008)
wing disc
(Zhu et al., 2008)
adult stage | female
ovariole
(Zhu et al., 2008)
day 1 of adulthood
testis | restricted

Comment: apical tip

(Gan et al., 2010)
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage & larval stage & adult stage
(De Rubertis et al., 1996)
larval stage
eye-antennal disc
(De Rubertis et al., 1996)
Additional Descriptive Data

Gcn5 transcript is localized to the apical tip of the adult testis.

(Gan et al., 2010)

Rpd3 transcripts are more abundant during development than HDAC3 transcripts.

(Zhu et al., 2008)

Transcripts are observed in RNA from embryos, larvae, and adults on northern blots. An insertion 1.8kb upstream of the Rpd3 gene causes a substantial reduction in transcript levels in the eye-antennal disc.

(De Rubertis et al., 1996)
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 4
organism
• nucleus
(Chen et al., 1999)
embryonic stage 9 -- 10
embryonic head | restricted
• nucleus
(Chen et al., 1999)
oogenesis
nurse cell
• nucleus
(Chen et al., 1999)
follicle cell
• nucleus
(Chen et al., 1999)
western blot
Stage
Tissue/Position (including subcellular localization)
Reference
S2 cell-line
(Tea et al., 2010)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in chromatin
inferred from direct assay
(Pile and Wassarman, 2000)
part_of ESC/E(Z) complex
inferred from direct assay
(Czermin et al., 2002)
part_of Myb complex
inferred from direct assay
(Lewis et al., 2004)
located_in nucleus
inferred from direct assay
(Miotto et al., 2006, Cho et al., 2005, Czermin et al., 2002, Tie et al., 2001, Pile and Wassarman, 2000)
part_of NuRD complex
inferred from physical interaction with FLYBASE:Mi-2; FB:FBgn0262519
(Murawsky et al., 2001)
located_in polytene chromosome interband
inferred from direct assay
(Wang et al., 2008)
located_in polytene chromosome
inferred from direct assay
(Burgio et al., 2008)
part_of Sin3-type complex
inferred from direct assay
(Spain et al., 2010)
part_of transcription repressor complex
inferred from physical interaction with FLYBASE:Su(var)3-3; FB:FBgn0260397
(Dallman et al., 2004)
inferred from physical interaction with FLYBASE:CoRest; FB:FBgn0261573
(Dallman et al., 2004)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\HDAC1 in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
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
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 7-8
  • Stages(s) 11-12
  • Stages(s) 13-16
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 22 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 19 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of HDAC1
Transgenic constructs containing regulatory region of HDAC1
Aberrations (Deficiencies and Duplications) ( 4 )
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
lethal
lethal, with Scer\GAL4Act5C.PI
lethal, with Scer\GAL4Act.PU
lethal, with Scer\GAL4Tub.PU
lethal | larval stage | recessive
lethal | recessive
lethal - all die before end of larval stage | recessive
lethal - all die before end of pupal stage
lethal - all die before end of pupal stage (with HDAC13-10)
lethal - all die before end of pupal stage (with HDAC1X5)
lethal - all die before end of second instar larval stage
lethal - all die before end of second instar larval stage (with HDAC13-10)
lethal - all die before end of second instar larval stage (with HDAC15-5)
lethal - all die during embryonic stage | germline clone
lethal - all die during embryonic stage | germline clone | recessive
lethal - all die during P-stage, with Scer\GAL4Mef2.PR
partially lethal | male limited, with Scer\GAL4r4
partially lethal - majority die
partially lethal - majority die, with Scer\GAL4pnr-MD237
partially lethal - majority die | dominant | male
partially lethal - majority die | nutrition conditional (with HDAC1303)
partially lethal - majority die | nutrition conditional (with HDAC1313)
partially lethal - majority die | nutrition conditional (with HDAC1326)
partially lethal - majority die | nutrition conditional (with HDAC1328)
partially lethal - majority die | nutrition conditional (with HDAC104556)
partially lethal - majority die | recessive
viable
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4tin.CΔ4
Sterility
Allele
fertile
fertile, with Scer\GAL4Mef2.PR
Other Phenotypes
Allele
abnormal heat stress response | adult stage, with Scer\GAL4tin.CΔ4
abnormal mitotic cell cycle
abnormal mitotic cell cycle | somatic clone
abnormal mitotic cell cycle | somatic clone (with HDAC13-10)
abnormal mitotic cell cycle | somatic clone (with HDAC1X5)
abnormal neuroanatomy | larval stage
abnormal neuroanatomy | somatic clone
abnormal oxidative stress response | adult stage
abnormal oxidative stress response | adult stage, with Scer\GAL4arm.PU
abnormal oxidative stress response | adult stage, with Scer\GAL4tin.CΔ4
abnormal oxidative stress response | adult stage | male limited, with Scer\GAL4UAS.cHa, Scer\GAL4tin.CΔ4
abnormal size | adult stage, with Scer\GAL4ey.PH
abnormal starvation stress response | adult stage, with Scer\GAL4fat
abnormal starvation stress response | adult stage, with Scer\GAL4tin.CΔ4
abnormal taste perception, with Scer\GAL4fuss-MI13731-GAL4
decreased cell number | somatic clone
decreased cell number | somatic clone (with HDAC13-10)
decreased cell number | somatic clone (with HDAC1X5)
decreased occurrence of cell division | larval stage (with HDAC13-10)
decreased occurrence of cell division | larval stage (with HDAC1X5)
enhancer of variegation, with In(1)wm4
enhancer of variegation, with P{UAS-lacZ.Abd-B.24F6}GCD-6/+:
enhancer of variegation | dominant, with In(1)wm4
flightless, with Scer\GAL4Mef2.PR
increased cell death, with Scer\GAL4bbg-C96
increased cell death | somatic clone
increased memory | adult stage, with Scer\GAL4Mef2.247.Switch
long lived
long lived, with Scer\GAL4arm.PU
long lived, with Scer\GAL4tin.CΔ4
long lived, with Scer\GAL4UAS.cHa, Scer\GAL4tin.CΔ4
long lived | dominant | female
long lived | dominant | male
pair rule phenotype
pair rule phenotype | embryonic stage | germline clone
pair rule phenotype | embryonic stage | germline clone | recessive
pair rule phenotype | germline clone
pair rule phenotype | maternal effect
short lived | nutrition conditional (with HDAC1303)
short lived | nutrition conditional (with HDAC1313)
short lived | nutrition conditional (with HDAC1326)
short lived | nutrition conditional (with HDAC1328)
short lived | nutrition conditional (with HDAC104556)
some die during embryonic stage | germline clone
some die during embryonic stage | maternal effect
some die during embryonic stage | recessive
some die during larval stage | recessive
some die during pupal stage
some die during pupal stage, with Scer\GAL4pnr-MD237
some die during pupal stage (with HDAC13-10)
some die during pupal stage (with HDAC1X5)
some die during second instar larval stage
some die during second instar larval stage (with HDAC13-10)
some die during second instar larval stage (with HDAC15-5)
suppressor of variegation
suppressor of variegation | dominant, with In(1)wm4
suppressor of variegation | dominant, with In(2R)bwVDe2
suppressor of variegation | dominant, with P{hsp26-pt-T}39C-5
suppressor of variegation | dominant, with T(2;3)SbV
suppressor of variegation | dominant | female, with In(2R)bwVDe2
suppressor of variegation | recessive, with In(1)wm4
visible, with Scer\GAL4bbg-C96
visible, with Scer\GAL4pnr-MD237
visible | adult stage, with Scer\GAL4en.PU
visible | adult stage, with Scer\GAL4ey.PH
visible | adult stage, with Scer\GAL4nub.PK
visible | drug conditional
Phenotype manifest in
Allele
adult antennal lobe projection neuron DL1 adPN | somatic clone
adult fat body | nutrition conditional, with Scer\GAL4Cg.PA
adult heart
adult heart, with Scer\GAL4tin.CΔ4
adult heart, with Scer\GAL4UAS.cHa, Scer\GAL4tin.CΔ4
alula
cephalopharyngeal skeleton | germline clone
chromosome | adult stage | female, with Scer\GAL4VP16.mat.αTub67C
cuticle | maternal effect
denticle belt | germline clone
embryo | germline clone
embryonic epidermis | germline clone
embryonic segment
eye, with Scer\GAL4ey.PH
eye, with Scer\GAL4GMR.PF
ganglion mother cell | larval stage
macrochaeta
mesothoracic tergum, with Scer\GAL4pnr-MD237
ommatidium
ommatidium, with Scer\GAL4GMR.PF
oocyte, with Scer\GAL4VP16.mat.αTub67C
posterior crossvein, with Scer\GAL4en.PU
projection neuron | somatic clone
segment | maternal effect
sex comb
wing
wing, with Scer\GAL4bbg-C96
wing | drug conditional
wing blade, with Scer\GAL4nub.PK
wing disc
wing disc, with Scer\GAL4bbg-C96
wing disc | somatic clone
wing disc | somatic clone (with HDAC13-10)
wing disc | somatic clone (with HDAC1X5)
wing vein, with Scer\GAL4en.PU
wing vein, with Scer\GAL4nub.PK
wing vein L5, with Scer\GAL4nub.PK
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (11)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\HDAC1
14 of 15
Yes
Yes
Hsap\HDAC2
13 of 15
No
Yes
1  
Hsap\HDAC3
4 of 15
No
No
Hsap\HDAC8
2 of 15
No
Yes
Hsap\HDAC4
1 of 15
No
No
8  
Hsap\HDAC5
1 of 15
No
No
Hsap\HDAC6
1 of 15
No
No
3  
Hsap\HDAC7
1 of 15
No
No
Hsap\HDAC9
1 of 15
No
No
Hsap\HDAC10
1 of 15
No
No
1  
Hsap\HDAC11
1 of 15
No
No
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (12)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Hdac1
13 of 15
Yes
Yes
Mmus\Hdac2
12 of 15
No
Yes
Mmus\Hdac3
4 of 15
No
No
Mmus\Hdac8
2 of 15
No
Yes
Mmus\Gm10093
1 of 15
No
Yes
Mmus\Hdac4
1 of 15
No
No
Mmus\Hdac5
1 of 15
No
No
Mmus\Hdac6
1 of 15
No
No
Mmus\Hdac7
1 of 15
No
No
Mmus\Hdac9
1 of 15
No
No
Mmus\Hdac10
1 of 15
No
No
Mmus\Hdac11
1 of 15
No
No
Rattus norvegicus (Norway rat) (12)
Rnor\Hdac1
12 of 13
Yes
Yes
Rnor\Hdac2
12 of 13
Yes
Yes
Rnor\Hdac1l
10 of 13
No
Yes
Rnor\Hdac3
4 of 13
No
No
Rnor\Hdac8
2 of 13
No
Yes
Rnor\Hdac4
1 of 13
No
No
Rnor\Hdac5
1 of 13
No
No
Rnor\Hdac6
1 of 13
No
No
Rnor\Hdac9
1 of 13
No
No
Rnor\Hdac10
1 of 13
No
No
Rnor\Hdac11
1 of 13
No
No
Rnor\LOC103689963
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (8)
Xtro\hdac2
8 of 12
Yes
Yes
Xtro\hdac1
7 of 12
No
Yes
Xtro\hdac3
3 of 12
No
No
Xtro\hdac8
2 of 12
No
Yes
Xtro\hdac4
1 of 12
No
No
Xtro\hdac6
1 of 12
No
No
Xtro\hdac7
1 of 12
No
No
Xtro\hdac9
1 of 12
No
No
Danio rerio (Zebrafish) (11)
Drer\hdac1
8 of 15
Yes
Yes
Drer\hdac3
4 of 15
No
No
Drer\hdac4
1 of 15
No
No
Drer\hdac5
1 of 15
No
No
Drer\hdac6
1 of 15
No
No
Drer\hdac7b
1 of 15
No
No
Drer\hdac8
1 of 15
No
Yes
Drer\hdac9b
1 of 15
No
No
Drer\hdac10
1 of 15
No
No
Drer\hdac11
1 of 15
No
No
Drer\phka1a
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (10)
Cele\hda-1
10 of 15
Yes
Yes
Cele\hda-3
7 of 15
No
Yes
Cele\hda-2
4 of 15
No
No
Cele\F43G6.4
2 of 15
No
Yes
Cele\F43G6.17
2 of 15
No
No
Cele\hda-5
2 of 15
No
No
Cele\hda-4
1 of 15
No
No
Cele\hda-6
1 of 15
No
No
Cele\hda-10
1 of 15
No
No
Cele\hda-11
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (5)
Atha\HD1
8 of 9
Yes
Yes
Atha\HDA6
6 of 9
No
Yes
Atha\HDA9
2 of 9
No
No
Atha\HDA7
1 of 9
No
Yes
Atha\hda10
1 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (5)
Scer\RPD3
11 of 15
Yes
Yes
Scer\HOS2
3 of 15
No
No
Scer\HOS1
2 of 15
No
Yes
Scer\HDA1
1 of 15
No
No
Scer\HOS3
1 of 15
No
Yes
Schizosaccharomyces pombe (Fission yeast) (2)
Spom\clr6
9 of 12
Yes
Yes
Spom\hos2
1 of 12
No
No
Other Organism Orthologs (via OrthoDB)
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (4)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
HDAC3
5 of 10
HDAC4
2 of 10
HDAC6
2 of 10
HDAC11
2 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 ( 9 )
    Disease Associations of Human Orthologs (via DIOPT v8.0 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    HDAC1; histone deacetylase 1
    14 of 15
    601241
        HDAC2; histone deacetylase 2
        13 of 15
        605164
             
            HDAC3; histone deacetylase 3
            4 of 15
            605166
                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
                Show neighbor-neighbor interactions:
                Select Layout:
                Legend:
                Protein
                RNA
                Selected Interactor(s)
                Interactions Browser
                View in Interactions Browser
                Please see the Physical Interaction reports below for full details
                protein-protein
                Physical Interaction
                Assay
                References
                HDAC1 - CDK2AP1
                anti bait coimmunoprecipitation, western blot
                (Reddy et al., 2010)
                HDAC1 - CG13367
                anti tag coimmunoprecipitation, anti tag western blot, molecular weight estimation by staining, affinity chromatography technology, molecular sieving
                (Lee et al., 2009)
                HDAC1 - CG15356
                anti bait coimmunoprecipitation, Identification by mass spectrometry, western blot
                (Moshkin et al., 2009)
                HDAC1 - CG1620
                experimental knowledge based
                (Guruharsha et al., 2011)
                HDAC1 - CG3815
                anti bait coimmunoprecipitation, western blot, Identification by mass spectrometry, affinity chromatography technology, molecular sieving, molecular weight estimation by staining
                (Lee et al., 2009, Moshkin et al., 2009)
                HDAC1 - CG5973
                experimental knowledge based
                (Guruharsha et al., 2011)
                HDAC1 - CG8745
                experimental knowledge based
                (Guruharsha et al., 2011)
                HDAC1 - Caf1-55
                pull down, western blot, anti tag coimmunoprecipitation, Identification by mass spectrometry, molecular sieving, molecular weight estimation by staining, autoradiography, ion exchange chromatography
                (Mugat et al., 2020, Zhang et al., 2016, Tie et al., 2003, Czermin et al., 2002, Tie et al., 2001)
                HDAC1 - Charon
                anti tag coimmunoprecipitation, western blot
                (Morris et al., 2016)
                HDAC1 - CoRest
                anti bait coimmunoprecipitation, Identification by mass spectrometry, tandem affinity purification, anti tag coimmunoprecipitation, western blot, experimental knowledge based, pull down, molecular sieving, coimmunoprecipitation
                (Takakura et al., 2021, Mačinković et al., 2019, Guruharsha et al., 2011, Dallman et al., 2004)
                HDAC1 - Dsor1
                anti tag coimmunoprecipitation, peptide massfingerprinting
                (Friedman et al., 2011)
                HDAC1 - Dsp1
                anti bait coimmunoprecipitation, western blot
                (Kim et al., 2007)
                HDAC1 - E(z)
                pull down, autoradiography, western blot, ion exchange chromatography, anti bait coimmunoprecipitation
                (Tie et al., 2003, Czermin et al., 2002, Tie et al., 2001)
                HDAC1 - G9a
                anti tag coimmunoprecipitation, western blot
                (Mačinković et al., 2019)
                HDAC1 - Gug
                anti tag coimmunoprecipitation, anti tag western blot, anti bait coimmunoprecipitation, western blot
                (Zhang et al., 2013, Wang et al., 2008)
                HDAC1 - His4
                enzymatic study, autoradiography
                (Scharf et al., 2009)
                HDAC1 - Hr78
                two hybrid array
                (Shokri et al., 2019)
                HDAC1 - Iswi
                anti tag coimmunoprecipitation, western blot, tandem affinity purification
                (Burgio et al., 2008)
                HDAC1 - Jra
                anti bait coimmunoprecipitation, anti tag western blot, western blot, pull down, autoradiography
                (Kim et al., 2007, Kim et al., 2005)
                HDAC1 - Kdm5
                ion exchange chromatography, molecular sieving, affinity chromatography technology, Identification by mass spectrometry, anti bait coimmunoprecipitation, western blot, anti tag coimmunoprecipitation, anti tag western blot, molecular weight estimation by staining
                (Gajan et al., 2016, Lee et al., 2009, Moshkin et al., 2009)
                HDAC1 - Lint-1
                anti tag coimmunoprecipitation, western blot, anti bait coimmunoprecipitation, affinity technology, peptide massfingerprinting, experimental knowledge based
                (Meier et al., 2012, Guruharsha et al., 2011)
                HDAC1 - MBD-like
                experimental knowledge based, molecular sieving, molecular weight estimation by staining
                (Zhang et al., 2016, Guruharsha et al., 2011)
                HDAC1 - MEP-1
                molecular sieving, molecular weight estimation by staining, anti bait coimmunoprecipitation, western blot, Identification by mass spectrometry
                (Mugat et al., 2020, Reddy et al., 2010)
                HDAC1 - MRG15
                molecular sieving, western blot, anti tag coimmunoprecipitation, anti tag western blot, molecular weight estimation by staining, affinity chromatography technology
                (Lee et al., 2009)
                HDAC1 - MTA1-like
                experimental knowledge based, anti tag coimmunoprecipitation, molecular weight estimation by staining, molecular sieving
                (Mugat et al., 2020, Zhang et al., 2016, Guruharsha et al., 2011)
                HDAC1 - Mapmodulin
                experimental knowledge based
                (Guruharsha et al., 2011)
                HDAC1 - Mi-2
                molecular sieving, molecular weight estimation by staining, anti bait coimmunoprecipitation, western blot, anti tag coimmunoprecipitation, Identification by mass spectrometry
                (Mugat et al., 2020, Fasulo et al., 2012, Reddy et al., 2010, Kunert et al., 2009, Murawska et al., 2008)
                HDAC1 - Nap1
                anti bait coimmunoprecipitation, western blot, Identification by mass spectrometry
                (Moshkin et al., 2009)
                HDAC1 - Pc
                anti bait coimmunoprecipitation, autoradiography, western blot
                (Tie et al., 2016, Poux et al., 2001)
                HDAC1 - Pcl
                anti bait coimmunoprecipitation, western blot, pull down, autoradiography
                (Tie et al., 2003)
                HDAC1 - Pten
                anti tag coimmunoprecipitation, Identification by mass spectrometry
                (Vinayagam et al., 2016)
                HDAC1 - Rbf
                anti tag coimmunoprecipitation, western blot
                (Taylor-Harding et al., 2004)
                HDAC1 - Rbf2
                anti tag coimmunoprecipitation, western blot
                (Taylor-Harding et al., 2004)
                HDAC1 - Rrp6
                coimmunoprecipitation, anti tag western blot, anti tag coimmunoprecipitation, western blot
                (Eberle et al., 2015)
                HDAC1 - S6kII
                anti tag coimmunoprecipitation, Identification by mass spectrometry
                (Vinayagam et al., 2016)
                HDAC1 - Sfmbt
                anti tag coimmunoprecipitation, peptide massfingerprinting
                (Alfieri et al., 2013)
                HDAC1 - Sin3A
                anti tag coimmunoprecipitation, western blot, peptide massfingerprinting, experimental knowledge based
                (Guruharsha et al., 2011, Spain et al., 2010)
                HDAC1 - Sirt1
                pull down, autoradiography, anti bait coimmunoprecipitation, western blot
                (Furuyama et al., 2004)
                HDAC1 - Smyd4-2
                pull down, autoradiography, anti tag coimmunoprecipitation, anti tag western blot
                (Thompson and Travers, 2008)
                HDAC1 - Stat92E
                anti bait coimmunoprecipitation, western blot
                (Kim et al., 2007)
                HDAC1 - Su(H)
                anti bait coimmunoprecipitation, western blot
                (Moshkin et al., 2009)
                HDAC1 - Su(var)3-3
                anti bait coimmunoprecipitation, western blot, coimmunoprecipitation, anti tag coimmunoprecipitation
                (Lepesant et al., 2020, Mačinković et al., 2019, Rudolph et al., 2007, Dallman et al., 2004)
                HDAC1 - Su(var)3-9
                anti tag coimmunoprecipitation, western blot, affinity chromatography technology
                (Boeke et al., 2010, Czermin et al., 2001)
                HDAC1 - Su(z)12
                ion exchange chromatography, western blot, anti bait coimmunoprecipitation
                (Tie et al., 2003, Czermin et al., 2002)
                HDAC1 - Trl
                anti tag coimmunoprecipitation, peptide massfingerprinting
                (Nakayama et al., 2012)
                HDAC1 - Tsc1
                anti tag coimmunoprecipitation, Identification by mass spectrometry
                (Vinayagam et al., 2016)
                HDAC1 - Ubx
                bimolecular fluorescence complementation, fluorescence microscopy
                (Bischof et al., 2018)
                HDAC1 - abd-A
                bimolecular fluorescence complementation, fluorescence microscopy
                (Bischof et al., 2018)
                HDAC1 - arx
                pull down, Identification by mass spectrometry, anti tag coimmunoprecipitation, western blot, luminescence based mammalian interactome mapping
                (Mugat et al., 2020)
                HDAC1 - bon
                anti bait coimmunoprecipitation, western blot
                (Ito et al., 2012)
                HDAC1 - chm
                anti tag coimmunoprecipitation, anti tag western blot
                (Miotto et al., 2006)
                HDAC1 - ci
                anti tag coimmunoprecipitation, anti tag western blot
                (Zhang et al., 2013)
                HDAC1 - esc
                anti tag coimmunoprecipitation, western blot, ion exchange chromatography, peptide massfingerprinting, anti bait coimmunoprecipitation, pull down, autoradiography, anti tag western blot
                (Tie et al., 2003, Czermin et al., 2002, Poux et al., 2001, Tie et al., 2001)
                HDAC1 - escl
                anti bait coimmunoprecipitation, western blot
                (Kurzhals et al., 2008)
                HDAC1 - fru
                anti bait coimmunoprecipitation, western blot
                (Ito et al., 2012)
                HDAC1 - fuss
                anti tag coimmunoprecipitation, anti tag western blot
                (Rass et al., 2019)
                HDAC1 - gig
                anti tag coimmunoprecipitation, Identification by mass spectrometry
                (Vinayagam et al., 2016)
                HDAC1 - gro
                pull down, western blot, autoradiography, anti tag coimmunoprecipitation, anti bait coimmunoprecipitation, peptide massfingerprinting
                (Choi et al., 2005, Chen et al., 1999)
                HDAC1 - kay
                pull down, autoradiography, anti tag coimmunoprecipitation, anti tag western blot, western blot
                (Miotto et al., 2006, Kim et al., 2005)
                HDAC1 - l(3)mbt
                coimmunoprecipitation, western blot
                (Scharf et al., 2009)
                HDAC1 - mip120
                anti bait coimmunoprecipitation, western blot
                (Lewis et al., 2004)
                HDAC1 - msl-3
                anti bait coimmunoprecipitation, western blot, enzymatic study
                (Buscaino et al., 2003)
                HDAC1 - nej
                anti bait coimmunoprecipitation, western blot
                (Tie et al., 2016)
                HDAC1 - nerfin-1
                anti tag coimmunoprecipitation, anti tag western blot
                (Guo et al., 2019)
                HDAC1 - ova
                anti tag coimmunoprecipitation, western blot
                (Walther et al., 2020)
                HDAC1 - piwi
                anti bait coimmunoprecipitation, western blot
                (Mugat et al., 2020)
                HDAC1 - rictor
                anti tag coimmunoprecipitation, Identification by mass spectrometry
                (Vinayagam et al., 2016)
                HDAC1 - simj
                anti bait coimmunoprecipitation, western blot
                (Kunert et al., 2009)
                HDAC1 - upSET
                anti bait coimmunoprecipitation, western blot
                (Rincon-Arano et al., 2012)
                Summary of Genetic Interactions
                esyN Network Diagram
                esyN Network Key:
                Suppression
                Enhancement
                View in Interactions Browser
                Please look at the allele data for full details of the genetic interactions
                Starting gene(s)
                Interaction type
                Interacting gene(s)
                Reference
                HDAC1|Snr1
                suppressible
                brm
                (Zraly et al., 2004)
                HDAC1|pnr
                enhanceable
                CtBP
                (Biryukova and Heitzler, 2008)
                HDAC1
                enhanceable
                htt
                (Dietz et al., 2015)
                HDAC1|ttk
                enhanceable
                Mi-2
                (Murawsky et al., 2001)
                HDAC1
                suppressible
                pros
                (Tea et al., 2010)
                HDAC1
                suppressible
                Sirt1
                (Rogina and Helfand, 2004)
                Starting gene(s)
                Interaction type
                Interacting gene(s)
                Reference
                bcd|Bin1
                enhanceable
                HDAC1
                (Singh et al., 2005)
                chm
                suppressible
                HDAC1
                (Miotto et al., 2006)
                Dl|lola|psq
                suppressible
                HDAC1
                (Ferres-Marco et al., 2006)
                dom
                suppressible
                HDAC1
                (Ellis et al., 2015)
                H
                suppressible
                HDAC1
                (Müller et al., 2005)
                H
                enhanceable
                HDAC1
                (Müller et al., 2005)
                hep
                enhanceable
                HDAC1
                (Miotto et al., 2006)
                Iswi
                enhanceable
                HDAC1
                (Burgio et al., 2008)
                mamo
                enhanceable
                HDAC1
                (Nakamura et al., 2020)
                net
                enhanceable
                HDAC1
                (Marenda et al., 2004)
                Pc
                suppressible
                HDAC1
                (Chang et al., 2001)
                Pc
                enhanceable
                HDAC1
                (Chang et al., 2001)
                pnr
                enhanceable
                HDAC1
                (Biryukova and Heitzler, 2008)
                pnr|CtBP
                enhanceable
                HDAC1
                (Biryukova and Heitzler, 2008)
                Ras85D|sev
                suppressible
                HDAC1
                (Maixner et al., 1998)
                run
                suppressible
                HDAC1
                (Wheeler et al., 2002)
                sd
                suppressible
                HDAC1
                (Canudas et al., 2005)
                sens
                suppressible
                HDAC1
                (Anderson et al., 2011)
                Snr1
                enhanceable
                HDAC1
                (Zraly et al., 2004)
                tefu
                suppressible
                HDAC1
                (Rimkus et al., 2008)
                External Data
                Subunit Structure (UniProtKB)
                Component of a form of the Esc/E(z) complex present specifically during early embryogenesis which is composed of Caf1-55, esc, E(z), Su(z)12, Pcl and HDAC1 (PubMed:12533794, PubMed:12408863, PubMed:12697833). The Esc/E(z) complex may also associate with Pcl and HDAC1 during early embryogenesis (PubMed:12697833). This complex is distinct from the PRC1 complex, which contains many other PcG proteins like Pc, Ph, Psc, Su(z)2 (PubMed:12533794). The 2 complexes however cooperate and interact together during the first 3 hours of development to establish PcG silencing (PubMed:12533794). Interacts with the histone methyltransferase Su(var)3-9 (PubMed:11571273). Component of a complex that contains at least HDAC1, CoRest and Su(var)3-3/Hdm (PubMed:15306652). Component of the DREAM complex at least composed of Myb, Caf1-55, mip40, mip120, mip130, E2f2, Dp, Rbf, Rbf2, lin-52, HDAC1 and l(3)mbt (PubMed:15545624). Interacts with the chromatin-remodeler Mi-2 (PubMed:18250149).
                (UniProt, Q94517 )
                Linkouts
                BioGRID - A database of protein and genetic interactions.
                DroID - A comprehensive database of gene and protein interactions.
                MIST (genetic) - An integrated Molecular Interaction Database
                MIST (protein-protein) - An integrated Molecular Interaction Database
                Pathways
                Genomic Location and Detailed Mapping Data
                Chromosome (arm)
                3L
                Recombination map
                3-12
                Cytogenetic map
                64B12-64B12
                Sequence location
                FlyBase Computed Cytological Location
                Cytogenetic map
                Evidence for location
                64B12-64B12
                Limits computationally determined from genome sequence between P{PZ}l(3)rG166rG166 and P{PZ}sinu06524
                Experimentally Determined Cytological Location
                Cytogenetic map
                Notes
                References
                64B-64C
                (De Rubertis et al., 1996, Spierer, 1996.11.6)
                64C7-64C8
                (Mottus, 1998.8.24)
                64C1-64C6
                (Johnson, 1997.9.26)
                64C1-64C2
                (determined by in situ hybridisation)
                (Spradling et al., 1999, Perrimon et al., 1996)
                64C1-64C6
                (determined by in situ hybridisation)
                (Johnson et al., 1998)
                64B-64C
                (determined by in situ hybridisation)
                (De Rubertis et al., 1996)
                64C1-64C2
                (BDGP Project Members, 1994-1999)
                Experimentally Determined Recombination Data
                Location

                3-12

                (FlyBase, 2016)

                3-10.8

                (Comeron et al., 2012)

                3-

                (De Rubertis et al., 1996, Gepner et al., 1996, Spierer, 1996.11.6, Sinclair et al., 1983)
                Left of (cM)
                Right of (cM)
                Notes

                Maps near the tip of 3L.

                (Sinclair et al., 1983)
                Stocks and Reagents
                Stocks (17)
                Genomic Clones (25)
                cDNA Clones (185)
                 

                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 sequenced
                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)
                BDGP DGC clones
                Other clones
                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
                 

                polyclonal

                (Takakura et al., 2021, Walther et al., 2020, Chen et al., 2008, Murawska et al., 2008, Chen et al., 1999)
                Commercially Available Antibodies
                 
                Other Information
                Relationship to Other Genes
                Source for database identify of

                Source for identity of: HDAC1 Rpd3

                (FlyBase, 2009-)
                Source for database merge of

                Source for merge of: Rpd3 l(3)04556

                (Maixner et al., 1998)

                Source for merge of: Rpd3 Su(var)328 Su(var)326

                (Mottus et al., 2000)

                Source for merge of: Rpd3 l(3)64Cc

                (Murawsky et al., 2001)
                Additional comments

                Renamed from 'Rpd3' to 'HDAC1' (a popular synonym) to be consistent with the naming convention of the other D. melanogaster HDAC genes (i.e. named after the mammalian orthologs).

                (FlyBase, 2009-)
                Other Comments

                DNA-protein interactions: genome-wide binding profile assayed for Rpd3 protein in Kc167 cells; see Chromatin_types_NKI collection report. Individual protein-binding experiments listed under "Samples" at GEO_GSE22069 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22069).

                (Filion et al., 2010)

                Gene expression is increased in response to the presence of two copies of Scer\GAL4hs.PB.

                (Liu and Lehmann, 2008)

                S2 cell populations treated with dsRNA made from templates generated with primers directed against Rpd3 show inhibition of cell growth due to a G2 arrest.

                (Foglietti et al., 2006)

                chm and Rpd3 act as antagonistic cofactors of Jra and kay proteins to modulate JNK-dependent transcription during thorax metamorphosis and JNK-induced apoptosis.

                (Miotto et al., 2006)

                dsRNA has been made from templates generated with primers directed against this gene. RNAi of Rpd3 results in increased arborization of ddaD and ddaE neurons, defects in muscle, defects in dendrite morphogenesis and reproducible defects in da dendrite development.

                (Parrish et al., 2006)

                Rpd3 may be a component of the silencing complex for chromatin modification on specific regulatory regions of the homeotic genes.

                (Chang et al., 2001)

                The Rpd3 and Caf1 proteins are contained within a complex that includes also PcG proteins esc and E(z).

                (Tie et al., 2001)

                Rpd3 is required for PRE-mediated silencing in vivo.

                (Tie et al., 2001)

                Specific missense mutations in Rpd3 suppress the silencing of genes subject to PEV, perhaps by acting as antimorphs that poisen the deacetylase complex.

                (Mottus et al., 2000)

                Mutational analysis indicates that the Rpd3 histone deacetylase acts as a global transcriptional regulator.

                (Mottus et al., 2000)

                gro and Rpd3 appear to form a complex in vivo and interact directly via the glycine/proline rich (GP) domain.

                (Chen et al., 1999)

                Rpd3 is required for gro mediated repression and has a role in early pattern formation.

                (Chen et al., 1999)

                The Rpd3 histone deacetylase is required for segmentation of the Drosophila embryo.

                (Mannervik and Levine, 1999)

                Loss of Rpd3 results in increased genomic silencing, which decreases the distance from heterochromatin.

                (De Rubertis et al., 1996)

                Identified during a genetic analysis designed to identify mutations in the Dhc64C gene.

                (Gepner et al., 1996)

                The autosomal "FLP-DFS" technique (using the P{ovoD1-18} P{FRT(whs)} P{hsFLP} chromosomes) has been used to identify the specific maternal effect phenotype for the zygotic lethal mutation.

                (Perrimon et al., 1996)

                The presence of Rpd3 does not have any discernible effect on wzm, wzl, wzvl, wzh or wcres, this was not checked in X/0 males.

                (Peterson et al., 1994)
                Origin and Etymology
                Discoverer
                Etymology
                Identification
                External Crossreferences and Linkouts ( 60 )
                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 Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
                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/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
                UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
                Other crossreferences
                AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
                BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
                Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
                DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
                EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
                FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
                FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
                Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
                Flygut - An atlas of the Drosophila adult midgut
                Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
                GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
                iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
                InterPro - A database of protein families, domains and functional sites
                KEGG Genes - Molecular building blocks of life in the genomic space.
                MARRVEL_MODEL - MARRVEL (model organism gene)
                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
                FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
                FlyMine - An integrated database for Drosophila genomics
                Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
                KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
                MIST (genetic) - An integrated Molecular Interaction Database
                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 (40)
                Reported As
                Symbol Synonym
                CG7471
                (Hosono et al., 2015, Nikalayevich and Ohkura, 2015, Ni et al., 2011.7.19, Ni et al., 2010.12.1, Reddy et al., 2010, Spain et al., 2010, Chen et al., 2008, Haussmann et al., 2008, Ni et al., 2008, Foglietti et al., 2006, Aggarwal and Calvi, 2004)
                DHDAC1
                (Foglietti et al., 2006)
                DRpd3
                (Miotto et al., 2006)
                DmHDAC1
                (Mottus et al., 1999)
                DmRpd3
                (Prasad and Rao, 2018)
                E(var)3-64BC
                (Wallrath, 1998)
                HDAC
                (Padmanabhan et al., 2006, Guenther and Lazar, 2001, Saurin et al., 2001, Jones and Kadonaga, 2000)
                HDAC-1
                (Lee et al., 1999)
                HDAC1
                (Buhlman et al., 2021, Evans et al., 2021, Gavory et al., 2021, Keegan and Hughes, 2021, Martin et al., 2021, Ramirez Moreno et al., 2021, Nakamura et al., 2020, Sato and Yamamoto, 2020, Wei et al., 2020, Blice-Baum et al., 2019, Hall et al., 2019, Shokri et al., 2019, Das et al., 2018, Gene Disruption Project members, 2018-, Dobson et al., 2017, L Black et al., 2016, Morimoto et al., 2016, Nakajima et al., 2016, Schertel et al., 2015, Bhaskar et al., 2014, Boyle et al., 2014, Mannervik, 2014, Slattery et al., 2014, Yamamoto et al., 2014, Petruk et al., 2013, Yamamoto and Koganezawa, 2013, Ito et al., 2012, Milon et al., 2012, Pushpavalli et al., 2012, Nègre et al., 2011, Fiesel et al., 2010, Biryukova and Heitzler, 2008, Biryukova and Heitzler, 2008, Chen et al., 2008, Doheny et al., 2008, Matyunina et al., 2008, Qi et al., 2008, Grewal and Elgin, 2007, Choi et al., 2005, Segal et al., 2004, Song et al., 2004, Parsons et al., 2003, Song et al., 2003, Wang and Brock, 2003, Bornemann et al., 2002, Chang et al., 2002, Grewal and Elgin, 2002, Czermin et al., 2001, Huang, 2001, Bornemann et al., 2000, Mottus et al., 2000, Ng and Bird, 2000, Johnson, 1997.9.26)
                Hdac
                (Zhang et al., 2008)
                Hdac1
                (Alfieri et al., 2013, Doheny et al., 2008, Lin et al., 2008, Zhang et al., 2008, Zhu et al., 2008, Zraly et al., 2004, Chang et al., 2001)
                Hdac1/Rpd3
                (Janssens et al., 2017)
                RPD3
                (Walther et al., 2020, Sneppen and Ringrose, 2019, Rennie et al., 2018, Ghezzi et al., 2017, Perry et al., 2017, Gajan et al., 2016, Tie et al., 2016, Eberle et al., 2015, Ellis et al., 2015, Comoglio and Paro, 2014, Ho et al., 2014, Messina et al., 2014, Moshkin et al., 2013, Fasulo et al., 2012, Nègre et al., 2011, Schuettengruber et al., 2011, Boeke et al., 2010, Filion et al., 2010, Reddy et al., 2010, Spain et al., 2010, Swaminathan and Pile, 2010, van Steensel et al., 2010, Clapier and Cairns, 2009, Tie et al., 2009, Doheny et al., 2008, Kurzhals et al., 2008, Rimkus et al., 2008, Stielow et al., 2008, Rudolph et al., 2007, Schwartz and Pirrotta, 2007, Bouazoune and Brehm, 2006, Guarente, 2006, Chopra and Mishra, 2005, Farkas et al., 2005, Nusinow and Panning, 2005, Tie et al., 2005, Lehmann, 2004, Marhold et al., 2004, Farkas et al., 2003, Pile et al., 2002, Tie, 2002, Ballestar et al., 2001, Poux et al., 2001, Brehm et al., 2000, Pile and Wassarman, 2000, Wassarman and Pile, 2000, Breiling et al., 1999, Horard et al., 1999, Maixner et al., 1998, Tsai et al., 1998, De Rubertis et al., 1996, Spierer, 1996.11.6)
                Rpd3
                (Muraoka et al., 2021, Parkhitko et al., 2021, Raun et al., 2021, Sureka and Mishra, 2021, Takakura et al., 2021, Yamaguchi et al., 2021, Das and Bhadra, 2020, Gamez et al., 2020, Kitani-Morii and Noto, 2020, Lepesant et al., 2020, Mugat et al., 2020, Vaid et al., 2020, Angulo et al., 2019, Guo et al., 2019, Molaei et al., 2019, Shimaji et al., 2019, Suda et al., 2019, Bischof et al., 2018, Ghezzi et al., 2017, Janssens et al., 2017, Lin et al., 2017, Maini et al., 2017, Sharma et al., 2017, Brewer-Jensen et al., 2016, Nakajima et al., 2016, Schwartz et al., 2016, Woods and Rogina, 2016, Dietz et al., 2015, Ghasemi et al., 2015, Kang et al., 2015, Kaul et al., 2015, Nikalayevich and Ohkura, 2015, Bhaskar et al., 2014, Alfieri et al., 2013, Debruhl et al., 2013, Fitzsimons et al., 2013, Moshkin et al., 2013, Puram and Bonni, 2013, Ranjini and Ramachandra, 2013, Rohrbaugh et al., 2013, Silver-Morse and Li, 2013, Zhang et al., 2013, Eleftherianos and Castillo, 2012, Ito et al., 2012, Ito et al., 2012, Japanese National Institute of Genetics, 2012.5.21, Nakayama et al., 2012, Rincon-Arano et al., 2012, Williams et al., 2012, Anderson et al., 2011, Burgio et al., 2011, Farkaš et al., 2011, Fitzsimons and Scott, 2011, Friedman et al., 2011, Guan et al., 2011, Joyce et al., 2011, Kim et al., 2011, Kirilly et al., 2011, Klusza and Deng, 2011, Neumüller et al., 2011, Toku et al., 2011, Walrad et al., 2011, Gan et al., 2010, Huang et al., 2010, Kong et al., 2010, Kong et al., 2010, Lorbeck et al., 2010, Mourikis et al., 2010, Swaminathan and Pile, 2010, Swaminathan et al., 2010, Tea et al., 2010, Walrad et al., 2010, Winkler et al., 2010, Zhang et al., 2010, Ayroles et al., 2009, Chen et al., 2009, Lee et al., 2009, Nie et al., 2009, Suzuki et al., 2009, Bajpe et al., 2008, Biryukova and Heitzler, 2008, Branco et al., 2008, Burgio et al., 2008, Cao et al., 2008, Chen et al., 2008, Chihara et al., 2008, González et al., 2008, Liu and Lehmann, 2008, Martinez and Arnosti, 2008, McElroy et al., 2008, Nisha et al., 2008, Pallos et al., 2008, Schmidt et al., 2008, Wang et al., 2008, Zhao et al., 2008, Buszczak et al., 2007, Chihara et al., 2007, Latouche et al., 2007, Tsai and Wang, 2007, Wang and Tsai, 2007, Xing et al., 2007, Holmes et al., 2006, Longo and Kennedy, 2006, Moorman et al., 2006, Moorman et al., 2006, Morozova et al., 2006, Parrish et al., 2006, Payankaulam et al., 2006, Shi et al., 2006, Shirangi et al., 2006, Cho et al., 2005, Harbison et al., 2005, Kohzaki and Murakami, 2005, Machida et al., 2005, Dallman et al., 2004, Wang and Brock, 2003, Czermin et al., 2002, Gim et al., 2001)
                Rpd3/HDAC
                (Kozlova and Thummel, 2000)
                Su(var)3-26
                (Doheny et al., 2008)
                Su(var)3-64B
                (Elgin and Reuter, 2013)
                Su(var)326
                (Peterson et al., 1994, Sinclair et al., 1983)
                Su(var)328
                (Sinclair et al., 1983)
                dHDAC-1
                (Fritsch et al., 1999)
                dHDAC1
                (Morris et al., 2016, Crump et al., 2011, Thompson and Travers, 2008, Kim et al., 2007, Kim et al., 2005, Barlow et al., 2001, Bornemann et al., 2001, Breiling et al., 2001, Huang and Kadonaga, 2001, Tweedie et al., 1999, Johnson et al., 1998)
                dRPD3
                (Vidaurre and Chen, 2021, Lee et al., 2010, Kunert et al., 2009, Murawska et al., 2008, Zhao et al., 2008, Korenjak and Brehm, 2005, Eberharter and Becker, 2004, Taylor-Harding et al., 2004, O'Connor and Simon, 1999, Tsukiyama and Wu, 1997)
                dRpd3
                (Meier et al., 2012, Scharf et al., 2009, Murawsky et al., 2001)
                dmHDA401
                (Pandey et al., 2002)
                drpd3
                (Canudas et al., 2005)
                hdac1
                (Zhu et al., 2008, Canudas et al., 2005)
                l(3)04556
                (Singh et al., 2005, Maixner et al., 1998)
                l(3)64Cc
                (Gepner et al., 1996)
                rpd3
                (Das et al., 2021, Onishi et al., 2021, Samata et al., 2020, Kopp and Park, 2019, Rass et al., 2019, Lin et al., 2018, Woods et al., 2017, Helenius et al., 2016, Liaw, 2016, Woods et al., 2016, Dequéant et al., 2015, Frankel et al., 2015, Kopp et al., 2015, Hainaut et al., 2012, Iliadi et al., 2012, Zhang et al., 2010, Moshkin et al., 2009, Griswold et al., 2008, Lin et al., 2008, McClure and Schubiger, 2008, Reenan and Rogina, 2008, Zhang et al., 2008, Claycomb and Orr-Weaver, 2005, Struffi and Arnosti, 2005, Bauer et al., 2004, Rogina and Helfand, 2004, Rogina et al., 2002, Courey and Jia, 2001, Pile et al., 2001, Chen and Courey, 2000)
                rpd3
                (Helfand and Rogina, 2003)
                Name Synonyms
                Histone Deacetylase 1
                (Chihara et al., 2008)
                Histone Deacetylase 1 (HDAC1)
                (Chihara et al., 2007)
                Histone Deacetylase-1
                (Zhu et al., 2008)
                Histone deacetylase 1
                (Yamamoto et al., 2014)
                Rpd3
                (Branco et al., 2008, Wang et al., 2008, Zhao et al., 2008, Xing et al., 2007)
                Rpd3 histone deacetylase
                (Payankaulam et al., 2006, Kohzaki and Murakami, 2005)
                Suppressor of variegation 326
                histone deacetylase
                (Kim et al., 2005)
                histone deacetylase 1
                (Doheny et al., 2008)
                histone deacetylase RPD3
                (Romey-Glüsing et al., 2018)
                reduced potassium dependency 3
                (Lee et al., 2009)
                Secondary FlyBase IDs
                • FBgn0003632
                • FBgn0003634
                • FBgn0010843
                • FBgn0016893
                Datasets (4)
                Study focus (4)
                Experimental Role
                Project
                Project Type
                Title
                • transgene_used
                FBGSE22069
                Protein profiling reveals five principal chromatin types in Drosophila cells.
                • bait_protein
                modENCODE_chromatin_proteins_cells
                Genome-wide localization of chromosomal proteins in cell lines by ChIP-chip and ChIP-Seq.
                • bait_protein
                modENCODE_chromatin_proteins_flies
                Genome-wide localization of chromosomal proteins in fly tissues by ChIP-chip and ChIP-Seq.
                • bait_protein
                modENCODE_regulation_chromatin
                Genome-wide localization of chromatin factors by ChIP-chip and ChIP-Seq.
                Study result (0)
                Result
                Result Type
                Title
                References (415)