FlyBase Gene Report: Dmel\HDAC11

General Information

Symbol

Dmel\HDAC11

Species

D. melanogaster

Name

Histone deacetylase 11

Annotation Symbol

CG31119

Feature Type

protein_coding_gene

FlyBase ID

FBgn0051119

Gene Model Status

Current

Stock Availability

4 publicly available

Enzyme Name (EC)

histone deacetylase (3.5.1.98)

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

HDACX

Key Links

Genomic Location

Cytogenetic map

96B1-96B1

Sequence location

3R:24,854,496..24,856,243 [-]

Recombination map

3-86

RefSeq locus

NT_033777 REGION:24854496..24856243

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (4 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables histone deacetylase activity, hydrolytic mechanism

inferred from sequence or structural similarity with UniProtKB:Q96DB2

(Gene Ontology Curators, 2002-)

enables histone deacetylase activity

inferred from electronic annotation with InterPro:IPR044150

(InterPro Project Members, 2004-)

inferred from biological aspect of ancestor with PANTHER:PTN008143312

(GO Reference Genome Project, 2011-)

non-traceable author statement

(Feller et al., 2015)

Biological Process (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in epigenetic regulation of gene expression

inferred from biological aspect of ancestor with PANTHER:PTN008143312

(GO Reference Genome Project, 2011-)

Cellular Component (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

part_of histone deacetylase complex

inferred from biological aspect of ancestor with PANTHER:PTN000066374

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

RPD3/HDA1 LYSINE DEACETYLASES

Protein Family (UniProt)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

histone deacetylase activity, hydrolytic mechanism

N(6)-acetyl-L-lysyl-[histone] + H2O = L-lysyl-[histone] + acetate (3.5.1.98)

RHEA 58196:

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).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\HDAC11 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

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q9VC26)

If you don't see a structure in the viewer, 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.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Gene model reviewed during 5.39

Gene model reviewed during 5.47

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

HDAC11-RA

FBtr0084734

NM_170173

1129

343

HDAC11-RB

FBtr0305045

NM_001260367

1692

343

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

UniProt

RefSeq ID

GenBank

HDAC11-PA

FBpp0084109

39.1

343

8.27

FBpp0293582

39.1

343

8.27

Q9VC26

NP_001247296

AFH06613

Polypeptides with Identical Sequences

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

343 aa isoforms: HDAC11-PA, HDAC11-PB

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

InterPro - A database of protein families, domains and functional sites

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q9VC26

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\HDAC11 using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

HdacX_1

Linkouts

Expression Data

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.19

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\HDAC11 in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\HDAC11

View exonic expression by tissue for Dmel\HDAC11

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

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

326120/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0051119

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0051119

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0051119

Flygut - An atlas of the Drosophila adult midgut

FBgn0051119

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 0 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 7 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of HDAC11

Transgenic constructs containing regulatory region of HDAC11

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(3R)Exel6200

(Ryder, 2004.4.26)

Inferred from location ( 6 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Other Phenotypes

Allele

long lived | dominant

HDAC11^RNAi.UAS

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (11)

Hsap\HDAC11

14 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (11)

Rnor\Hdac11

14 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (11)

Mmus\Hdac11

13 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (6)

Xtro\hdac11

5 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (11)

Drer\hdac11

13 of 14

Yes

Drer\hdac12

3 of 14

Yes

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (10)

Cele\hda-11

14 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (5)

Agam\AgaP_AGAP001736

12 of 12

Yes

2 of 12

2 of 12

2 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (14)

Atha\HDA2

13 of 13

Yes

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

Yes

Atha\HDA14

2 of 13

Atha\HDA15

2 of 13

Atha\hda17

2 of 13

Yes

Atha\HDA18

2 of 13

Atha\AT4G09784

1 of 13

Atha\AT5G61050

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (5)

Scer\HDA1

2 of 13

Yes

Scer\HOS1

2 of 13

Yes

Scer\HOS2

2 of 13

Yes

Scer\HOS3

2 of 13

Yes

Scer\RPD3

2 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (3)

Spom\clr3

2 of 12

Yes

Spom\clr6

2 of 12

Yes

Spom\hos2

2 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:HDAC11. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (9)

4 of 13

4 of 13

4 of 13

4 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

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 ( 2 )

Allele

Disease

Interaction

References

HDAC11^RNAi.UAS

exacerbates neurodegenerative disease

modeled by Zzzz\CGG^90.UAS.EGFP

(Todd et al., 2010)

HDAC11^{UAS.Tag:V5,Tag:polyHis}

ameliorates neurodegenerative disease

modeled by Zzzz\CGG^90.UAS.EGFP

(Todd et al., 2010)

Disease Associations of Human Orthologs (via DIOPT v9.1 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?

HDAC11; histone deacetylase 11

14 of 14

607226

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

Interaction Browsers

Summary of Genetic Interactions

Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0051119

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Notch-HLH transcription pathway

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-86

Cytogenetic map

96B1-96B1

Sequence location

3R:24,854,496..24,856,243 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

96B1-96B1

Limits computationally determined from genome sequence between P{PZ}crb⁰⁷²⁰⁷&P{PZ}BRWD3⁰⁵⁸⁴² and P{EP}CycB3^EP3127

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-86

(FlyBase, 2016)

3-84.8

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (4)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

32480

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00483}attP2

31119R-2

31119R-3

v108098

Genomic Clones (15)

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

cDNA Clones (13)

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 JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

Other clones

IP11169

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.

FBgn0051119

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

LD16278

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0051119

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

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

(Foglietti et al., 2006)

New annotation (CG31119) in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: HdacX CG31119

(Foglietti et al., 2006)

Source for identity of: HDAC11 HdacX

(FlyBase, 2009-)

Nomenclature comments

Renamed from 'HdacX' to 'HDAC11' (which is a synonym) to be consistent with the naming convention of the other D. melanogaster HDAC genes (i.e. named after the mammalian orthologs).

(FlyBase, 2009-)

Etymology

Synonyms and Secondary IDs (10)

Reported As

Symbol Synonym

CG31119

(Ni et al., 2010.12.1, Todd et al., 2010, Keleman et al., 2009.8.5, Pallos et al., 2008, Foglietti et al., 2006)

DHDACX

(Foglietti et al., 2006)

HDAC11

(Willnow and Teleman, 2024, Yamaguchi et al., 2021, Shimaji et al., 2019, Perry et al., 2017, Boyle et al., 2014, Slattery et al., 2014, Nègre et al., 2011, Todd et al., 2010, Pallos et al., 2008)

HDACX

(Ho et al., 2014, Milon et al., 2012, Nègre et al., 2011)

Hdac11

(Pallos et al., 2008)

HdacX

(Japanese National Institute of Genetics, 2012.5.21)

dHDAC11

(Todd et al., 2010)

dmHDA403

(Pandey et al., 2002)

Name Synonyms

CG31119

Histone deacetylase 11

Histone deacetylase X

Secondary FlyBase IDs

Datasets (1)

Study focus (1)

Experimental Role

Project

Project Type

Title

bait_protein

modENCODE_regulation_chromatin

genome binding

Genome-wide localization of chromatin factors by ChIP-chip and ChIP-Seq.

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 31 )

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.

326120

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.

Q9VC26

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Q9VC26

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.

Q9VC26

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

326120/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0051119

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0051119

FlyMine - An integrated database for Drosophila genomics

FBgn0051119

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG31119

MARRVEL_MODEL - MARRVEL (model organism gene)

326120

Linkouts

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0051119

DroID - A comprehensive database of gene and protein interactions.

FBgn0051119

DRSC - Results frm RNAi screens

FBgn0051119

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

HdacX_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0051119

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0051119

Flygut - An atlas of the Drosophila adult midgut

FBgn0051119

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0051119

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC007473

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Notch-HLH transcription pathway

References (31)

The following external sites may use different assemblies or annotations than FlyBase.

-0.19

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