FlyBase Gene Report: Dmel\Su(var)3-3

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

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]

Other Summaries

Alliance
Auto summary
Gene Group
UniProtKB
Red Book
Interactive Fly

Also Known As

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

Key Links

Genomic Location

Cytogenetic map

Sequence location

3L:20,226,381..20,230,250 [+]

Recombination map

3-47

RefSeq locus

NT_037436 REGION:20226381..20230250

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

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Other Genome Views

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

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (21 terms)

Molecular Function (8 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

enables histone demethylase activity (H3-K4 specific)

inferred from mutant phenotype

(Di Stefano et al., 2007)

enables protein binding

inferred from physical interaction with UniProtKB:Q59E36

(assigned by UniProt )

(Dallman et al., 2004)

Terms Based on Predictions or Assertions (6 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 DNA binding

inferred from electronic annotation with InterPro:IPR009057

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

enables flavin adenine dinucleotide binding

inferred from biological aspect of ancestor with PANTHER:PTN002473317

(assigned by GO_Central )

(Gaudet et al., 2011)

enables histone demethylase activity (H3-dimethyl-K4 specific)

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)

enables transcription factor binding

inferred from biological aspect of ancestor with PANTHER:PTN002473317

(assigned by GO_Central )

(Gaudet et al., 2011)

Biological Process (10 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 gene silencing

inferred from mutant phenotype

(assigned by UniProt )

(Rudolph et al., 2007)

involved_in heterochromatin organization

inferred from mutant phenotype

(Di Stefano et al., 2011)

involved_in histone H3-K4 demethylation

inferred from mutant phenotype

(assigned by UniProt )

(Rudolph et al., 2007)

inferred from mutant phenotype

(Di Stefano et al., 2011, Di Stefano 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 (3 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 oxidation-reduction process

inferred from electronic annotation with InterPro:IPR002937, InterPro:IPR023753

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

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 (3 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 (1 term)

CV Term

Evidence

References

located_in chromatin

inferred from biological aspect of ancestor with PANTHER:PTN002473317

(assigned by GO_Central )

(Gaudet et al., 2011)

Gene Group (FlyBase)

LYSINE SPECIFIC DEMETHYLASE 1 FAMILY

Protein Family (UniProt)

Belongs to the flavin monoamine oxidase family. (Q9VW97)

Protein Signatures (InterPro)

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

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

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 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.

Su(var)3-3_1

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

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

View exonic expression by developmental stage for Dmel\Su(var)3-3

View exonic expression by tissue for Dmel\Su(var)3-3

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

FBgn0260397

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0260397

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG17149

Flygut - An atlas of the Drosophila adult midgut

FBgn0260397

Images

FlyBase Wiki

Image Based Resources

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 )

Disrupted in

Df(3L)ED4858

(Di Stefano et al., 2007)

Phenotypes

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

Lethality

Allele

lethal | male | recessive

Su(var)3-3^ΔN

lethal - all die before end of embryonic stage | recessive

Su(var)3-3¹

partially lethal - majority die | male | recessive

Su(var)3-3^ΔN

partially lethal - majority die | recessive

Su(var)3-3^ΔN

viable

Su(var)3-3^unspecified

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Su(var)3-3^GD9296

viable, with Scer\GAL4^Mef2.PR

Su(var)3-3^GD9296

viable, with Scer\GAL4^pnr-MD237

Su(var)3-3^GD9296

viable, with Scer\GAL4^tin.CΔ4

Su(var)3-3^GD9296

Sterility

Allele

female sterile, with Scer\GAL4^C587, Su(var)3-3^UAS.cDa

Su(var)3-3^ΔN

female sterile, with Scer\GAL4^C587, Su(var)3-3^ΔN

Su(var)3-3^UAS.cDa

male sterile | recessive

Su(var)3-3^ΔN

Other Phenotypes

Allele

flightless | recessive

Su(var)3-3^ΔN

non-suppressor of variegation | dominant, with P{hsp26-pt-T}39C-5

Su(var)3-3^unspecified

some die during embryonic stage | recessive

Su(var)3-3¹

suppressor of variegation, with In(1)y^3P

Su(var)3-3^ΔN

suppressor of variegation, with T(2;3)Sb^V

Su(var)3-3^ΔN

suppressor of variegation | dominant

suppressor of variegation | dominant, with In(1)w^m4

Su(var)3-3^unspecified

visible

Su(var)3-3^ΔN

visible, with Scer\GAL4^69B

Su(var)3-3^VDRC.cUa

visible, with Scer\GAL4^bs.PU

Su(var)3-3^VDRC.cUa

visible | adult stage

Su(var)3-3^ΔN

visible | adult stage, with Scer\GAL4^Act5C.PI

Su(var)3-3^GD9296

visible | adult stage, with Scer\GAL4^en.PU

Su(var)3-3^GD9296

visible | recessive

Su(var)3-3^ΔN

Phenotype manifest in

Allele

anterior crossvein | ectopic, with Scer\GAL4^bs.PU

Su(var)3-3^VDRC.cUa

egg, with Scer\GAL4^C587, Su(var)3-3^UAS.cDa

Su(var)3-3^ΔN

egg, with Scer\GAL4^C587, Su(var)3-3^ΔN

Su(var)3-3^UAS.cDa

female germline cell

Su(var)3-3^ΔN

female germline stem cell | supernumerary

Su(var)3-3^ΔN

female germline stem cell | supernumerary, with Scer\GAL4^C587

Su(var)3-3^NIG.17149R

follicle cell

Su(var)3-3^ΔN

ovariole

Su(var)3-3^ΔN

ovary, with Scer\GAL4^Act5C.PI

Su(var)3-3^GD9296

posterior crossvein

Su(var)3-3^ΔN

wing vein, with Scer\GAL4^Act5C.PI

Su(var)3-3^GD9296

wing vein, with Scer\GAL4^en.PU

Su(var)3-3^GD9296

wing vein | ectopic

Su(var)3-3^ΔN

wing vein | ectopic, with Scer\GAL4^69B

Su(var)3-3^VDRC.cUa

wing vein | ectopic, with Scer\GAL4^bs.PU

Su(var)3-3^VDRC.cUa

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

Alignment

Complementation?

Transgene?

Hsap\KDM1A

14 of 15

Yes

Hsap\KDM1B

3 of 15

Yes

2 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (9)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Kdm1a

13 of 15

Yes

Mmus\Kdm1b

2 of 15

Yes

Mmus\Maoa

2 of 15

Mmus\4930438A08Rik

1 of 15

Mmus\Il4i1

1 of 15

Yes

1 of 15

1 of 15

1 of 15

1 of 15

Rattus norvegicus (Norway rat) (7)

Rnor\Kdm1a

6 of 13

Yes

Rnor\Kdm1b

2 of 13

Yes

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Xenopus tropicalis (Western clawed frog) (6)

Xtro\kdm1a

9 of 12

Yes

Xtro\kdm1b

3 of 12

Yes

1 of 12

1 of 12

1 of 12

1 of 12

Danio rerio (Zebrafish) (7)

Drer\kdm1a

14 of 15

Yes

Drer\LOC100331367

1 of 15

Yes

Drer\mao

1 of 15

Drer\si:ch211-127i16.2

1 of 15

Drer\si:dkey-40g16.6

1 of 15

Drer\si:dkey-275b16.2

1 of 15

Drer\smox

1 of 15

Caenorhabditis elegans (Nematode, roundworm) (6)

Cele\spr-5

11 of 15

Yes

Cele\lsd-1

10 of 15

Yes

Cele\amx-1

4 of 15

Yes

Cele\amx-2

2 of 15

Yes

Cele\amx-3

1 of 15

Cele\hpo-15

1 of 15

Arabidopsis thaliana (thale-cress) (7)

Atha\LDL2

7 of 9

Yes

Atha\FLD

6 of 9

Yes

Atha\LDL1

6 of 9

Yes

Atha\LDL3

4 of 9

Yes

Atha\PAO2

2 of 9

Yes

Atha\PAO3

2 of 9

Yes

Atha\PAO4

2 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\FMS1

4 of 15

Yes

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\lsd1

5 of 12

Yes

Spom\lsd2

5 of 12

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

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila yakuba

Drosophila ananassae

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

Alignment

3 of 10

3 of 10

2 of 10

2 of 10

2 of 10

2 of 10

2 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 ( 2 )

Allele

Disease

Interaction

References

Su(var)3-3^HMS00608

ameliorates frontotemporal dementia and/or amyotrophic lateral sclerosis-1

modeled by Zzzz\poly-GR^PO-100.UAS

(Lu et al., 2019)

modeled by Zzzz\poly-PR^PO-100.UAS

(Lu et al., 2019)

Su(var)3-3^HMS00638

ameliorates amyotrophic lateral sclerosis type 6

modeled by Hsap\FUS^{R521C.UAS.Tag:HA}

(Periz et al., 2015)

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

CLEFT PALATE, PSYCHOMOTOR RETARDATION, AND DISTINCTIVE FACIAL FEATURES; CPRF

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

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 tag coimmunoprecipitation, western blot, molecular sieving, ion exchange chromatography, anti bait coimmunoprecipitation, Identification by mass spectrometry

(Mačinković et al., 2019, Meier et al., 2012)

Su(var)3-3 - HDAC1

anti bait coimmunoprecipitation, western blot, anti tag coimmunoprecipitation

(Lepesant et al., 2020, Mačinković et al., 2019, Rudolph et al., 2007)

Su(var)3-3 - His3

enzymatic study, peptide massfingerprinting

(Rudolph et al., 2007)

Su(var)3-3 - Lint-1

anti tag coimmunoprecipitation, western blot, anti bait coimmunoprecipitation, affinity technology, peptide massfingerprinting, molecular sieving, ion exchange chromatography

(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

anti bait coimmunoprecipitation, western blot, pull down

(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

anti tag coimmunoprecipitation, anti tag western blot, two hybrid

(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

dpp

(Eliazer et al., 2011)

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

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)

suppressible

Su(var)3-3

(Di Stefano et al., 2011)

polybromo

enhanceable

Su(var)3-3

(Curtis et al., 2011)

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.

FBgn0260397

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

40217

MIST (genetic) - An integrated Molecular Interaction Database

Su(var)3-3

MIST (protein-protein) - An integrated Molecular Interaction Database

Su(var)3-3

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

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

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-47

Cytogenetic map

77A3-77A3

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

3-47

(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)

Bloomington

91358

w^*; PBac{WHr}Su(var)3-3^ΔN/TM3, Sb¹

85185

w¹¹¹⁸; PBac{WH}Su(var)3-3^f00678/TM6B, Tb¹

32853

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00638}attP2

36867

y¹ sc^* v¹ sev²¹; P{TRiP.GL01006}attP40

33726

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00608}attP2/TM3, Sb¹

79268

y¹ w^*; TI{CRIMIC.TG4.1}Su(var)3-3^{CR00478-TG4.1}/TM3, Sb¹ Ser¹

VDRC

v106147

P{KK102965}VIE-260B

v25218

w¹¹¹⁸; P{GD9296}v25218

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

LD45081

Other clones

DPiM_LD45081

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.

FBgn0260397

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0260397

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

40217

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)w^m4.

(Garzino et al., 1992)

Suppression of In(1)w^m4 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 ( 44 )

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.

40217

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

Q9VW97

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

FBgn0260397

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

FBgn0260397

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

Su(var)3-3_1

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG17149

Flygut - An atlas of the Drosophila adult midgut

FBgn0260397

FlyMine - An integrated database for Drosophila genomics

FBgn0260397

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

40217

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

TC032014

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

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

Dmel_CG17149

modMine - A data warehouse for the modENCODE project

FBgn0260397

Linkouts

DPiM - Drosophila Protein interaction map

FBgn0260397

DroID - A comprehensive database of gene and protein interactions.

FBgn0260397

DRSC - Results frm RNAi screens

FBgn0260397

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0260397

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

40217

MIST (genetic) - An integrated Molecular Interaction Database

Su(var)3-3

MIST (protein-protein) - An integrated Molecular Interaction Database

Su(var)3-3

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, 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

(Periz et al., 2015)

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

(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 (102)

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

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