FB2021_06, released December 14, 2021

Gene: Dmel\Su(var)3-3

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General Information
Symbol
Dmel\Su(var)3-3
Species
D. melanogaster
Name
Suppressor of variegation 3-3
Annotation Symbol
CG17149
Feature Type
protein_coding_gene
FlyBase ID
FBgn0260397
Gene Model Status
Current
Stock Availability
8 publicly available
Enzyme Name (EC)
[Histone-H3]-N(6),N(6)-dimethyl-L-lysine(4) FAD-dependent demethylase (1.14.99.66)
Gene Summary
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] (FlyBase Gene Snapshot)
All Summaries
Also Known As

dLsd1, Lsd1, Suvar(3)3, Su-var(3)3, Histone demethylase

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
3-47
RefSeq locus
NT_037436 REGION:20226381..20230250
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 (17 terms)
Molecular Function (6 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
enables histone H3-di/monomethyl-lysine-4 FAD-dependent demethylase activity
inferred from mutant phenotype
(Di Stefano et al., 2007)
enables histone H3-methyl-lysine-4 demethylase activity
inferred from mutant phenotype
(Dietz et al., 2015)
enables protein binding
inferred from physical interaction with UniProtKB:Q59E36
(assigned by UniProt )
(Dallman et al., 2004)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
enables chromatin binding
inferred from biological aspect of ancestor with PANTHER:PTN002473317
(assigned by GO_Central )
(Gaudet et al., 2011)
enables flavin adenine dinucleotide binding
inferred from biological aspect of ancestor with PANTHER:PTN002473317
(assigned by GO_Central )
(Gaudet et al., 2011)
enables oxidoreductase activity
inferred from biological aspect of ancestor with PANTHER:PTN000743742
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (9 terms)
Terms Based on Experimental Evidence (7 terms)
CV Term
Evidence
References
involved_in chromatin organization
inferred from mutant phenotype
(Di Stefano et al., 2007)
involved_in heterochromatin boundary formation
inferred from genetic interaction with FLYBASE:htt; FB:FBgn0027655
(Dietz et al., 2015)
involved_in heterochromatin organization
inferred from mutant phenotype
(Di Stefano et al., 2011)
involved_in histone H3-K4 demethylation
inferred from mutant phenotype
(Di Stefano et al., 2011, Di Stefano et al., 2007)
inferred from mutant phenotype
(assigned by UniProt )
(Rudolph et al., 2007)
involved_in imaginal disc-derived wing vein specification
inferred from mutant phenotype
(Curtis et al., 2011, Di Stefano et al., 2011)
involved_in oogenesis
inferred from mutant phenotype
(Di Stefano et al., 2011, Di Stefano et al., 2007)
involved_in positive regulation of DNA methylation-dependent heterochromatin assembly
inferred from mutant phenotype
(Yu et al., 2015)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in negative regulation of transcription by RNA polymerase II
inferred from biological aspect of ancestor with PANTHER:PTN002473317
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in positive regulation of transcription by RNA polymerase II
inferred from biological aspect of ancestor with PANTHER:PTN002473317
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
located_in nucleus
inferred from direct assay
(Eliazer et al., 2011)
inferred from direct assay
(assigned by UniProt )
(Rudolph et al., 2007)
part_of transcription repressor complex
inferred from physical interaction with FLYBASE:inferred from high throughput direct assayC1; FB:FBgn0015805
(Dallman et al., 2004)
inferred from physical interaction with FLYBASE:CoRest; FB:FBgn0261573
(Dallman et al., 2004)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the flavin monoamine oxidase family. (Q9VW97)
Protein Signatures (InterPro)
Catalytic Activity (EC)
Experimental Evidence
A [histone H3]-N(6),N(6)-dimethyl-L-lysine(4) + 2 acceptor + 2 H(2)O = a [histone H3]-L-lysine(4) + 2 formaldehyde + 2 reduced acceptor (1.14.99.66)
Predictions / Assertions
-
Summaries
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]
Gene Group (FlyBase)
LSD1 FAMILY HISTONE DEMETHYLASES -
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 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
gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Su(var)3-3-RA
FBtr0074825
NM_140937
3681
890
Su(var)3-3-RB
FBtr0074826
NM_168835
3615
890
Su(var)3-3-RC
FBtr0332693
NM_001275171
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
Su(var)3-3-PA
FBpp0074594
98.4
890
7.88
NP_649194
AAF49052
Su(var)3-3-PB
FBpp0074595
98.4
890
7.88
NP_730497
AAF49051
Su(var)3-3-PC
FBpp0304939
95.9
870
7.33
NP_001262100
AGB94793
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 HDAC1/Rpd3, CoRest and Su(var)3-3/Hdm.

(UniProt, Q9VW97)
Crossreferences
InterPro - A database of protein families, domains and functional sites
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
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
embryonic stage 1 -- 3
organism

Comment: maternally deposited

(Fisher et al., 2012)
embryonic stage 4 -- 6
organism
(Fisher et al., 2012)
embryonic stage 7 -- 8
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 9 -- 10
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 11 -- 12
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 13 -- 16
organism | ubiquitous
(Fisher et al., 2012)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
pupal stage P7
wing | ubiquitous
(Curtis et al., 2011)
adult stage | female
germarium
(Eliazer et al., 2011)
oogenesis
female germline stem cell
(Eliazer et al., 2011)
follicle cell
(Eliazer et al., 2011)
escort cell
(Eliazer et al., 2011)
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
day 5 of adulthood & male -- day 7 of adulthood & male
spermatozoon
(Dorus et al., 2006)
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.

(Curtis et al., 2011)

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.

(Eliazer et al., 2011)
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in nucleus
inferred from direct assay
(Eliazer et al., 2011)
inferred from direct assay
(assigned by UniProt )
(Rudolph et al., 2007)
part_of transcription repressor complex
inferred from physical interaction with FLYBASE:inferred from high throughput direct assayC1; FB:FBgn0015805
(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\Su(var)3-3 in GBrowse 2
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
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 31 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 10 )
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
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(3L)ED4858
(Di Stefano et al., 2007)
Inferred from location ( 0 )
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
lethal | male | recessive
lethal - all die during embryonic stage | recessive
partially lethal | recessive
partially lethal - majority die | male | recessive
partially lethal - majority die | recessive
viable
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
viable, with Scer\GAL4tin.CΔ4
Sterility
Allele
female semi-sterile | female, with Scer\GAL4tj.PU
female sterile, with Scer\GAL4C587, Su(var)3-3UAS.cDa
female sterile, with Scer\GAL4C587, Su(var)3-3ΔN
female sterile | recessive
male semi-sterile | recessive
male sterile | recessive
Other Phenotypes
Allele
abnormal cell number | female, with Scer\GAL4tj.PU
decreased fecundity | female, with Scer\GAL4tj.PU
flightless | recessive
increased cell death | oogenesis | oogenesis, with Scer\GAL4C587
increased cell number | cell non-autonomous | oogenesis | somatic clone
increased cell number | oogenesis | oogenesis, with Scer\GAL4C587
non-suppressor of variegation | dominant, with P{hsp26-pt-T}39C-5
some die during embryonic stage | recessive
suppressor of variegation, with In(1)y3P
suppressor of variegation, with T(2;3)SbV
suppressor of variegation | dominant
suppressor of variegation | dominant, with In(1)wm4
suppressor of variegation | dominant, with In(1)wm4h
visible
visible, with Scer\GAL469B
visible, with Scer\GAL4bs.PU
visible | adult stage
visible | adult stage, with Scer\GAL4Act5C.PI
visible | adult stage, with Scer\GAL4en.PU
visible | male | recessive
visible | recessive
Phenotype manifest in
Allele
anterior crossvein | ectopic, with Scer\GAL4bs.PU
cell projection | decreased number | oogenesis, with Scer\GAL4C587
egg, with Scer\GAL4C587, Su(var)3-3UAS.cDa
egg, with Scer\GAL4C587, Su(var)3-3ΔN
egg chamber | decreased number, with Scer\GAL4C587
escort cell, with Scer\GAL4C587
female germline cell
female germline stem cell | cell non-autonomous | increased number | oogenesis | somatic clone
female germline stem cell | increased number
female germline stem cell | increased number, with Scer\GAL4C587
female germline stem cell | increased number | oogenesis, with Scer\GAL4C587
follicle cell
follicle cell, with Scer\GAL4tj.PU
germarium | somatic clone
nurse cell, with Scer\GAL4tj.PU
ovariole
ovariole, with Scer\GAL4Act5C.PI
ovariole, with Scer\GAL4tj.PU
ovary
ovary, with Scer\GAL4Act5C.PI
posterior crossvein
wing
wing vein, with Scer\GAL4Act5C.PI
wing vein, with Scer\GAL4en.PU
wing vein | ectopic
wing vein | ectopic, with Scer\GAL469B
wing vein | ectopic, with Scer\GAL4bs.PU
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (7)
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\KDM1A
14 of 15
Yes
Yes
Hsap\KDM1B
3 of 15
No
Yes
Hsap\MAOA
2 of 15
No
No
Hsap\IL4I1
1 of 15
No
No
Hsap\MAOB
1 of 15
No
No
Hsap\PAOX
1 of 15
No
No
Hsap\SMOX
1 of 15
No
No
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (9)
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\Kdm1a
13 of 15
Yes
Yes
Mmus\Kdm1b
2 of 15
No
Yes
Mmus\Maoa
2 of 15
No
No
Mmus\4930438A08Rik
1 of 15
No
No
Mmus\Il4i1
1 of 15
No
Yes
Mmus\Lao1
1 of 15
No
No
Mmus\Maob
1 of 15
No
No
Mmus\Paox
1 of 15
No
No
Mmus\Smox
1 of 15
No
No
Rattus norvegicus (Norway rat) (7)
Rnor\Kdm1a
6 of 13
Yes
Yes
Rnor\Kdm1b
2 of 13
No
Yes
Rnor\Maoa
2 of 13
No
No
Rnor\Il4i1
1 of 13
No
No
Rnor\Lao1
1 of 13
No
No
Rnor\Maob
1 of 13
No
No
Rnor\RGD1308564
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (6)
Xtro\kdm1a
9 of 12
Yes
Yes
Xtro\kdm1b
3 of 12
No
Yes
Xtro\il4i1
1 of 12
No
No
Xtro\maoa
1 of 12
No
No
Xtro\maob
1 of 12
No
No
Xtro\smox
1 of 12
No
No
Danio rerio (Zebrafish) (7)
Drer\kdm1a
14 of 15
Yes
Yes
Drer\LOC100331367
1 of 15
No
Yes
Drer\mao
1 of 15
No
No
Drer\si:ch211-127i16.2
1 of 15
No
No
Drer\si:dkey-40g16.6
1 of 15
No
No
Drer\si:dkey-275b16.2
1 of 15
No
No
Drer\smox
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (6)
Cele\spr-5
11 of 15
Yes
Yes
Cele\lsd-1
10 of 15
No
Yes
Cele\amx-1
4 of 15
No
Yes
Cele\amx-2
2 of 15
No
Yes
Cele\amx-3
1 of 15
No
No
Cele\hpo-15
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (7)
Atha\LDL2
7 of 9
Yes
Yes
Atha\FLD
6 of 9
No
Yes
Atha\LDL1
6 of 9
No
Yes
Atha\LDL3
4 of 9
No
Yes
Atha\PAO2
2 of 9
No
Yes
Atha\PAO3
2 of 9
No
Yes
Atha\PAO4
2 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\FMS1
4 of 15
Yes
No
Schizosaccharomyces pombe (Fission yeast) (2)
Spom\lsd1
5 of 12
Yes
Yes
Spom\lsd2
5 of 12
Yes
Yes
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG091902JT )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00010662
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00008099
Drosophila simulans
Dsim\GD14861
Drosophila sechellia
Dsec\GM22263
Drosophila erecta
Dere\GG16089
Drosophila yakuba
Dyak\GE19651
Drosophila yakuba
Dyak\GE28814
Drosophila ananassae
Dana\GF25315
Drosophila pseudoobscura pseudoobscura
Dpse\GA14350
Drosophila persimilis
Dper\GL25121
Drosophila willistoni
Dwil\GK16943
Drosophila virilis
Dvir\GJ11550
Drosophila mojavensis
Dmoj\GI11530
Drosophila grimshawi
Dgri\GH16339
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
Mdoa\17020623
Glossina morsitans
Tsetse fly
Gmor\GMOY009793
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_00679
Mayetiola destructor
Hessian fly
Mdes\Mdes008566
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL011415
Anopheles darlingi
American malaria mosquito
Adar\ADAC010092
Anopheles gambiae
Malaria mosquito
Agam\AGAP011661
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ002197
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W09M8 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA011023
Bombyx mori
Silkmoth
Bmor\BGIBMGA011022
Danaus plexippus
Monarch butterfly
Dple\DPOGS203174-PA
Danaus plexippus
Monarch butterfly
Dple\DPOGS203173-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL005792
Heliconius melpomene
Postman butterfly
Hmel\HMEL013878
Apis florea
Little honeybee
Aflo\3326142324
Apis mellifera
Western honey bee
Amel\GB48386
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP10786
Bombus terrestris
Buff-tailed bumblebee
Bter\15213497
Linepithema humile
Argentine ant
Lhum\LH19739
Linepithema humile
Argentine ant
Lhum\LH19745
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:0024dc
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:0024df
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG023095
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG023096
Tribolium castaneum
Red flour beetle
Tcas\TC032014
Tribolium castaneum
Red flour beetle
Tcas\TC032013
Pediculus humanus
Human body louse
Phum\PHUM107180
Pediculus humanus
Human body louse
Phum\PHUM106950
Rhodnius prolixus
Kissing bug
Rpro\RPRC004092
Rhodnius prolixus
Kissing bug
Rpro\RPRC007388
Cimex lectularius
Bed bug
Clec\CLEC011497
Cimex lectularius
Bed bug
Clec\CLEC013092
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI009334
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI40226
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_07217
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_00889
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_00885
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
Smar\SMAR006137
Strigamia maritima
European centipede
Smar\SMAR013509
Ixodes scapularis
Black-legged tick
Isca\ISCW019383
Ixodes scapularis
Black-legged tick
Isca\ISCW004580
Stegodyphus mimosarum
African social velvet spider
Smim\KFM79884.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur27g01970
Tetranychus urticae
Two-spotted spider mite
Turt\tetur501g00010
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_39808
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
Spur\Sp-Aof2
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Aof1
Strongylocentrotus purpuratus
Purple sea urchin
Spur\SPU_014537gn
Ciona intestinalis
Vase tunicate
Cint\LOC100187100
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000007205
Gallus gallus
Domestic chicken
Ggal\KDM1B
Gallus gallus
Domestic chicken
Ggal\KDM1A
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (8)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
CG6034
3 of 10
CG8032
3 of 10
CG5653
2 of 10
CG7460
2 of 10
CG7737
2 of 10
CG10561
2 of 10
shps
2 of 10
Ppox
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 ( 2 )
    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?
    KDM1A; lysine demethylase 1A
    14 of 15
    609132
      KDM1B; lysine demethylase 1B
      3 of 15
      613081
          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
          Su(var)3-3 - CoRest
          anti bait coimmunoprecipitation, Identification by mass spectrometry, coimmunoprecipitation, western blot, molecular sieving, ion exchange chromatography, anti tag coimmunoprecipitation
          (Mačinković et al., 2019, Meier et al., 2012, Dallman et al., 2004)
          Su(var)3-3 - HDAC1
          coimmunoprecipitation, western blot, anti tag coimmunoprecipitation, anti bait coimmunoprecipitation
          (Lepesant et al., 2020, Mačinković et al., 2019, Rudolph et al., 2007, Dallman et al., 2004)
          Su(var)3-3 - His3
          enzymatic study, peptide massfingerprinting
          (Rudolph et al., 2007)
          Su(var)3-3 - Lint-1
          anti bait coimmunoprecipitation, western blot, molecular sieving, ion exchange chromatography, anti tag coimmunoprecipitation, affinity technology, peptide massfingerprinting
          (Meier et al., 2012)
          Su(var)3-3 - Scm
          tandem affinity purification, Identification by mass spectrometry
          (Kang et al., 2015)
          Su(var)3-3 - Snr1
          pull down, western blot, anti bait coimmunoprecipitation
          (Curtis et al., 2011)
          Su(var)3-3 - Su(var)205
          anti bait coimmunoprecipitation, western blot, anti tag coimmunoprecipitation, peptide massfingerprinting
          (Alekseyenko et al., 2014, Rudolph et al., 2007)
          Su(var)3-3 - Su(var)3-9
          anti bait coimmunoprecipitation, western blot
          (Rudolph et al., 2007)
          Su(var)3-3 - ova
          two hybrid, anti tag coimmunoprecipitation, anti tag western blot
          (Yang et al., 2019)
          Su(var)3-3 - piwi
          anti bait coimmunoprecipitation, western blot
          (Lepesant et al., 2020)
          Su(var)3-3 - srp
          anti tag coimmunoprecipitation, western blot
          (Lepesant et al., 2020)
          RNA-protein
          Physical Interaction
          Assay
          References
          Su(var)3-3 - pum
          tandem affinity purification, quantitative reverse transcription pcr
          (Miles et al., 2015)
          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
          Su(var)3-3
          suppressible
          APC7
          (Eliazer et al., 2014)
          Su(var)3-3
          suppressible
          barr
          (Eliazer et al., 2014)
          Su(var)3-3
          suppressible
          CG11779
          (Eliazer et al., 2014)
          Su(var)3-3
          suppressible
          dpp
          (Eliazer et al., 2011)
          Su(var)3-3
          suppressible
          en
          (Eliazer et al., 2014)
          Su(var)3-3
          suppressible
          Fkbp39
          (Eliazer et al., 2014)
          Su(var)3-3
          suppressible
          Gfat1
          (Eliazer et al., 2014)
          Su(var)3-3
          suppressible
          hh
          (Eliazer et al., 2014)
          Su(var)3-3
          suppressible
          Hnf4
          (Eliazer et al., 2014)
          Su(var)3-3
          enhanceable
          htt
          (Dietz et al., 2015)
          Su(var)3-3
          suppressible
          Kdm5
          (Di Stefano et al., 2011)
          Su(var)3-3
          suppressible
          ken
          (Eliazer et al., 2014)
          Su(var)3-3
          suppressible
          piwi
          (Lepesant et al., 2020)
          Su(var)3-3
          suppressible
          raw
          (Eliazer et al., 2014)
          Su(var)3-3
          enhanceable
          srp
          (Lepesant et al., 2020)
          Su(var)3-3
          suppressible
          Su(H)
          (Di Stefano et al., 2011)
          Starting gene(s)
          Interaction type
          Interacting gene(s)
          Reference
          mor
          enhanceable
          Su(var)3-3
          (Curtis et al., 2011)
          mor
          suppressible
          Su(var)3-3
          (Curtis et al., 2011)
          N
          suppressible
          Su(var)3-3
          (Di Stefano et al., 2011)
          polybromo
          enhanceable
          Su(var)3-3
          (Curtis et al., 2011)
          srp
          enhanceable
          Su(var)3-3
          (Lepesant et al., 2020)
          External Data
          Subunit Structure (UniProtKB)
          Component of a complex that contains at least HDAC1/Rpd3, CoRest and Su(var)3-3/Hdm.
          (UniProt, Q9VW97 )
          Linkouts
          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
          Signaling Pathways (FlyBase)
          Metabolic Pathways
          FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
          External Data
          Genomic Location and Detailed Mapping Data
          Chromosome (arm)
          3L
          Recombination map
          3-47
          Cytogenetic map
          77A3-77A3
          Sequence location
          FlyBase Computed Cytological Location
          Cytogenetic map
          Evidence for location
          77A3-77A3
          Experimentally Determined Cytological Location
          Cytogenetic map
          Notes
          References
          Experimentally Determined Recombination Data
          Location

          3-47

          (FlyBase, 2016)

          3-43.5

          (Comeron et al., 2012)

          3-46.6 +/- 0.2

          (Reuter et al., 1986)

          3-46.7 +/- 2.3

          (Reuter et al., 1983)

          3-46.6

          Left of (cM)
          (Reuter et al., 1986)
          Right of (cM)
          (Reuter et al., 1986)
          Notes

          Mapping on 3L based on its absence from induced C(3R)RM derivatives of Su(var)3-3-bearing chromosomes.

          (Reuter et al., 1986)
          Stocks and Reagents
          Stocks (8)
          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 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
           

          monoclonal

          (Lee and Spradling, 2014)

          polyclonal

          (Eliazer et al., 2011)
          Commercially Available Antibodies
           
          Other Information
          Relationship to Other Genes
          Source for database identify of

          Source for identity of: Hdm CG17149

          (Singh, 2007.3.5)
          Source for database merge of

          Source for merge of: Su(var)3-3 Hdm

          (Rudolph et al., 2007)
          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.

          (FlyBase, 1996-)
          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.

          (Di Stefano et al., 2011)

          Su(var)3-3 and Wow represent different complementation groups based on their effects on w mutations and fertility/viability.

          (Birchler et al., 1994)

          No additive effect of mutant alleles with mod alleles on suppression of position effect variegation at In(1)wm4.

          (Garzino et al., 1992)

          Suppression of In(1)wm4 position effect variegation by Su(var)3-3 was reversed by a supernumerary copy of Su(var)3-7.

          (Reuter et al., 1990)
          Origin and Etymology
          Discoverer
          Etymology
          Identification
          External Crossreferences and Linkouts ( 48 )
          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
          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
          Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
          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
          FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
          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)
          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
          DroID - A comprehensive database of gene and protein interactions.
          DRSC - Results frm RNAi screens
          Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
          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 (20)
          Reported As
          Symbol Synonym
          CG17149
          (Holowatyj et al., 2015, Curtis et al., 2011, Ni et al., 2011.7.19, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Haussmann et al., 2008, Matthews, 2008.4.15, Di Stefano et al., 2007, Hueber et al., 2007, Rudolph et al., 2007, Singh, 2007.3.5, Dorus et al., 2006)
          Dmel/HDM
          (Singh and Elefant, 2007)
          Dmel/LSD1
          (Singh and Elefant, 2007)
          Dmel\LSD1
          (Singh, 2007.3.5)
          Hdm
          LSD1
          (L Black et al., 2016, Boija and Mannervik, 2015, Kory et al., 2015, Periz et al., 2015, Robert et al., 2015)
          Lsd1
          (Gulati et al., 2020, Zhang and Cai, 2020, Zraly et al., 2020, Yamashiro and Siomi, 2018, Eliazer et al., 2014, Wylie et al., 2014, Petruk et al., 2013, Eliazer et al., 2011, Di Stefano et al., 2007)
          SU(VAR)3-3
          (Ho et al., 2014, Greer and Shi, 2012, Rudolph et al., 2007)
          Su(Var)3-3
          (Ramirez Moreno et al., 2021, Periz et al., 2015)
          Su(var)3-3
          (Vidaurre and Chen, 2021, Meyer-Nava et al., 2020, Gao et al., 2019, Lu et al., 2019, Gene Disruption Project members, 2018-, Boija and Mannervik, 2015, Holowatyj et al., 2015, Kang et al., 2015, Robert et al., 2015, Alekseyenko et al., 2014, Comoglio and Paro, 2014, Ost et al., 2014, Czech et al., 2013, Elgin and Reuter, 2013, Petruk et al., 2013, Rudolph et al., 2013, Sen et al., 2013, Williams et al., 2012, Friedman et al., 2011, Baig et al., 2010, Gan et al., 2010, Curtis et al., 2008, Doheny et al., 2008, Joanis and Lloyd, 2002)
          Su-var(3)3
          (Wustmann et al., 1989, Reuter et al., 1986)
          Suvar(3)3
          (Bashaw and Baker, 1996, Reuter and Spierer, 1992)
          dLSD1
          (Yang and Xi, 2017, Yu et al., 2015, Alekseyenko et al., 2014)
          dLsd1
          (Jafari and Alenius, 2021, Lepesant et al., 2020, Yang et al., 2019, Dietz et al., 2015, Ost et al., 2014, Rudolph et al., 2013, Meier et al., 2012, Di Stefano et al., 2011, Curtis et al., 2008, Di Stefano et al., 2007)
          lsd1
          (Zhaunova et al., 2016, Lee and Spradling, 2014, Tie et al., 2014, Czech et al., 2013, Curtis et al., 2011)
          Name Synonyms
          CG17149
          (Singh, 2007.3.5)
          Flavoprotein
          (Dallman et al., 2004)
          Histone demethylase
          (Singh and Elefant, 2007)
          Suppressor of variegation 3-3
          (Yamashiro and Siomi, 2018, Comoglio and Paro, 2014, Baig et al., 2010)
          histone lysine-specific demethylase 1
          (Eliazer et al., 2011)
          lysine-specific demethylase 1
          (Lee and Spradling, 2014)
          Secondary FlyBase IDs
          • FBgn0259698
          • FBgn0003594
          • FBgn0036954
          • FBgn0036955
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          References (111)