Open Close
General Information
Symbol
Dmel\Su(var)3-3
Species
D. melanogaster
Name
Suppressor of variegation 3-3
Annotation Symbol
CG17149
Feature Type
FlyBase ID
FBgn0260397
Gene Model Status
Stock Availability
Gene Snapshot
Suppressor of variegation 3-3 (Su(var)3-3) encodes a member of the Lysine specific demethylase (LSD1/KDM1) family. It can function both as a transcriptional co-repressor and a co-activator. It demethylates histone H3K4-me2 and -me1 residues, and promotes heterochromatin formation by facilitating H3K9 methylation mediated by the product of Su(var)3-9. It is involved in fertility, wing patterning formation and bristle specification. [Date last reviewed: 2019-09-26]
Also Known As
dLsd1, lsd1, Suvar(3)3, Su-var(3)3, Histone demethylase
Key Links
Genomic Location
Cytogenetic map
Sequence location
3L:20,226,381..20,230,250 [+]
Recombination map
3-47
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
Belongs to the flavin monoamine oxidase family. (Q9VW97)
Summaries
Gene Group (FlyBase)
LYSINE SPECIFIC DEMETHYLASE 1 FAMILY -
Human LSD1 (Lysine specific demethylase 1) is the founding member of a class of enzymes that remove histone H3K4 or H3K9 modifications by an oxidative demethylation reaction in which flavin is a cofactor. (Adapted from FBrf0195283).
Protein Function (UniProtKB)
Probable histone demethylase that specifically demethylates 'Lys-4' of histone H3, a specific tag for epigenetic transcriptional activation, thereby acting as a corepressor. Required for heterochromatic gene silencing. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Demethylates both mono- and tri-methylated 'Lys-4' of histone H3. May also demethylate 'Lys-9' of histone H3, Plays a role in the repression of neuronal genes.
(UniProt, Q9VW97)
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
Su(var)3-3
Homozygotes strongly semilethal in males; weakly so in females; homozygous females sterile; produce no eggs. Homozygous males have spread-wing phenotype and reduced fertility. Survival sensitive to the presence of the Y chromosome as well as to the presence of 0.1 M butyrate in the medium.
Summary (Interactive Fly)
homolog of the human LSD1 amine oxidase - demethylates H3K4me2 and H3K4me1 and facilitates subsequent H3K9 methylation by SU(VAR)3-9 - dictates the distinction between euchromatic and heterochromatic domains during early embryogenesis
Gene Model and Products
Number of Transcripts
3
Number of Unique Polypeptides
2

Please see the GBrowse view of Dmel\Su(var)3-3 or the JBrowse view of Dmel\Su(var)3-3 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
Gene model reviewed during 5.43
Gene model reviewed during 5.45
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0074825
3681
890
FBtr0074826
3615
890
FBtr0332693
3555
870
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
FBpp0074594
98.4
890
7.88
FBpp0074595
98.4
890
7.88
FBpp0304939
95.9
870
7.33
Polypeptides with Identical Sequences

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

890 aa isoforms: Su(var)3-3-PA, Su(var)3-3-PB
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)
Component of a complex that contains at least Rpd3, CoRest and Su(var)3-3/Hdm.
(UniProt, Q9VW97)
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\Su(var)3-3 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 (21 terms)
Molecular Function (8 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from physical interaction with UniProtKB:Q59E36
(assigned by UniProt )
Terms Based on Predictions or Assertions (6 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN002473317
(assigned by GO_Central )
inferred from electronic annotation with InterPro:IPR009057
(assigned by InterPro )
inferred from biological aspect of ancestor with PANTHER:PTN002473317
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN002473317
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000743742
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN002473317
(assigned by GO_Central )
Biological Process (10 terms)
Terms Based on Experimental Evidence (7 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
(assigned by UniProt )
inferred from mutant phenotype
inferred from mutant phenotype
(assigned by UniProt )
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN002473317
(assigned by GO_Central )
inferred from electronic annotation with InterPro:IPR002937, InterPro:IPR023753
(assigned by InterPro )
inferred from biological aspect of ancestor with PANTHER:PTN002473317
(assigned by GO_Central )
Cellular Component (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from direct assay
inferred from direct assay
(assigned by UniProt )
inferred from physical interaction with FLYBASE:inferred from high throughput direct assayC1; FB:FBgn0015805
inferred from physical interaction with FLYBASE:CoRest; FB:FBgn0261573
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN002473317
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN002473317
(assigned by GO_Central )
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
organism

Comment: maternally deposited

Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Su(var)3-3 is expressed uniformly throughout the developing wing in both vein and intervein cells in stage P7 pupal wings.
Su(var)3-3 is expressed throughout the germarium and is predominantly localized in the nucleus. Expression appears highest in the germline stem cells, but is also present in the escort cells and follicle cells of the germarium.
Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
inferred from direct assay
(assigned by UniProt )
inferred from physical interaction with FLYBASE:inferred from high throughput direct assayC1; FB:FBgn0015805
inferred from physical interaction with FLYBASE:CoRest; FB:FBgn0261573
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Su(var)3-3 in GBrowse 2
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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
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 ( 31 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 8 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Su(var)3-3
Transgenic constructs containing regulatory region of Su(var)3-3
Deletions and Duplications ( 1 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Sterility
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (6)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
14 of 15
Yes
Yes
2 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
No
1 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?
13 of 15
Yes
Yes
2 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
Rattus norvegicus (Norway rat) (4)
5 of 13
Yes
Yes
2 of 13
No
Yes
1 of 13
No
Yes
1 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (5)
8 of 12
Yes
Yes
3 of 12
No
Yes
1 of 12
No
Yes
1 of 12
No
Yes
1 of 12
No
No
Danio rerio (Zebrafish) (5)
14 of 15
Yes
Yes
1 of 15
No
Yes
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (5)
9 of 15
Yes
Yes
8 of 15
No
Yes
4 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (4)
6 of 9
Yes
Yes
6 of 9
Yes
Yes
6 of 9
Yes
Yes
4 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
1 of 15
Yes
No
Schizosaccharomyces pombe (Fission yeast) (2)
7 of 12
Yes
Yes
4 of 12
No
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091902JT )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
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) ( EOG091505WH )
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
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W09M8 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman 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
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Nasonia vitripennis
Parasitic wasp
Tribolium castaneum
Red flour beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Zootermopsis nevadensis
Nevada dampwood termite
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X09I8 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Tetranychus urticae
Two-spotted spider mite
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G04NO )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (6)
2 of 10
2 of 10
1 of 10
1 of 10
1 of 10
1 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 ( 0 )
    Allele
    Disease
    Interaction
    References
    Comments on Models/Modifiers Based on Experimental Evidence ( 0 )
     
    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.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    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

    Please see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    Assay
    References
    RNA-protein
    Physical Interaction
    Assay
    References
    Summary of Genetic Interactions
    esyN Network Diagram
    esyN Network Key:
    Suppression
    Enhancement

    Please look at the allele data for full details of the genetic interactions
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Subunit Structure (UniProtKB)
    Component of a complex that contains at least Rpd3, CoRest and Su(var)3-3/Hdm.
    (UniProt, Q9VW97 )
    Linkouts
    DroID - A comprehensive database of gene and protein interactions.
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    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
    3-47
    Cytogenetic map
    Sequence location
    3L:20,226,381..20,230,250 [+]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    77A3-77A3
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location
    3-46.6 +/- 0.2
    3-46.7 +/- 2.3
    3-46.6
    Left of (cM)
    Right of (cM)
    Notes
    Mapping on 3L based on its absence from induced C(3R)RM derivatives of Su(var)3-3-bearing chromosomes.
    Stocks and Reagents
    Stocks (7)
    Genomic Clones (10)
     

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

    cDNA Clones (35)
     

    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 identity of: Hdm CG17149
    Source for database merge of
    Source for merge of: Su(var)3-3 Hdm
    Additional comments
    The "Su(var)3-3" gene was previously mistakenly merged with the CG17147 gene in FlyBase. This error has been corrected and CG17147 has been split out into a separate gene from Su(var)3-3. The "Su(var)3-3" gene actually corresponds to the "CG17149" annotation.
    Other Comments
    lid and Su(var)3-3 have opposing functions in the establishment of euchromatin and heterochromatin boundaries; Su(var)3-3 promotes heterochromatin formation, while lid promotes euchromatin formation.
    Su(var)3-3 and Wow represent different complementation groups based on their effects on w mutations and fertility/viability.
    No additive effect of mutant alleles with mod alleles on suppression of position effect variegation at In(1)wm4.
    Suppression of In(1)wm4 position effect variegation by Su(var)3-3 was reversed by a supernumerary copy of Su(var)3-7.
    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 46 )
    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/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
    UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
    Other crossreferences
    BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
    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
    FlyMine - An integrated database for Drosophila genomics
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
    KEGG Genes - Molecular building blocks of life in the genomic space.
    modMine - A data warehouse for the modENCODE project
    Linkouts
    DPiM - Drosophila Protein interaction map
    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
    Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    MIST (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Synonyms and Secondary IDs (19)
    Reported As
    Symbol Synonym
    Dmel\LSD1
    Hdm
    Name Synonyms
    Flavoprotein
    Histone demethylase
    histone lysine-specific demethylase 1
    lysine-specific demethylase 1
    Secondary FlyBase IDs
    • FBgn0259698
    • FBgn0003594
    • FBgn0036954
    • FBgn0036955
    Datasets (0)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    References (95)