FlyBase Gene Report: Dmel\Su(var)3-9

SET DOMAIN LYSINE METHYLTRANSFERASES -: SET domain lysine methyltransferases (KMTs) catalyze the addition of methyl groups to lysine residues. SET domain KMTs possess a domain that was original characterized in the D.mel KMTs Su(var)3-9, E(z) and trx. (Adapted from FBrf0216343).

Protein Function (UniProtKB)

Histone methyltransferase that specifically trimethylates 'Lys-9' of histone H3 using monomethylated H3 'Lys-9' as substrate. H3 'Lys-9' trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting Su(var)205/HP1 to methylated histones. Mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric regions. Involved in heterochromatic gene silencing including the modification of position-effect-variegation.

(UniProt, P45975)

Summary (Interactive Fly)

involved in gene silencing - a modifier of position effect variegation - methylates histone H3 thus providing a mark for the association of HP1 to heterochromatin

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the GBrowse view of Dmel\Su(var)3-9 or the JBrowse view of Dmel\Su(var)3-9 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 5.42

Genes with CDS overlap: eIF-2gamma and Su(var)3-9 share promoter, first exon and N-terminal coding sequences (80 residues); overlapping structure not conserved outside of insects (see FBrf0189765).

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

Gene model reviewed during 5.55

Sequence Ontology: Class of Gene

nuclear_gene

(FlyBase Genome Annotators, 2012)

protein_coding_gene

(FlyBase Genome Annotators, 2012)

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Su(var)3-9-RA

FBtr0310385

NM_079633

2386

635

Additional Transcript Data and Comments

Reported size (kB)

2.4, 2.0 (northern blot)

(Tschiersch et al., 1994)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

RefSeq ID

GenBank

Su(var)3-9-PA

FBpp0302536

71.8

635

8.35

NP_524357

AAF55154

Polypeptides with Identical Sequences

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

Additional Polypeptide Data and Comments

Reported size (kDa)

635, 475 (aa); 51 (kD predicted)

(Tschiersch et al., 1994)

Comments

Has 80 N-terminal amino acids in common with the 475aa Su(var)3-9 protein. Genetic evidence suggests that this protein carries out the genetically defined functions of the gene.

(Tschiersch et al., 1994)

External Data

Subunit Structure (UniProtKB)

Interacts with Su(var)205 and Su(var)3-7. Probably associates with Rpd3.

(UniProt, P45975)

Domain

Although the SET domain contains the active site of enzymatic activity, both pre-SET and post-SET domains are required for methyltransferase activity. The SET domain also participates in stable binding to heterochromatin (By similarity). In the pre-SET domain, Cys residues bind 3 zinc ions that are arranged in a triangular cluster; some of these Cys residues contribute to the binding of two zinc ions within the cluster.

(UniProt, P45975)

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)3-9 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)3-9_1

Linkouts

Gene Ontology (25 terms)

Molecular Function (4 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

chromatin binding

inferred from direct assay

(Sienski et al., 2015)

histone methyltransferase activity

inferred from direct assay

(Ebert et al., 2004, Eskeland et al., 2004)

inferred from direct assay

(assigned by UniProt )

(Czermin et al., 2001)

histone methyltransferase activity (H3-K9 specific)

inferred from direct assay

(Czermin et al., 2001)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

histone methyltransferase activity

non-traceable author statement

(Ner et al., 2002)

histone methyltransferase activity (H3-K9 specific)

inferred from biological aspect of ancestor with PANTHER:PTN000526939

(assigned by GO_Central )

(Gaudet et al., 2011)

traceable author statement

(McNairn and Gilbert, 2003, Simms et al., 2003)

zinc ion binding

inferred from electronic annotation with InterPro:IPR003606, InterPro:IPR007728

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

Biological Process (17 terms)

Terms Based on Experimental Evidence (16 terms)

CV Term

Evidence

References

chromatin organization

inferred from mutant phenotype

(Ner et al., 2002)

chromatin silencing

inferred from high throughput mutant phenotype

(Donaldson et al., 2002)

chromatin silencing at centromere

inferred from high throughput mutant phenotype

(Donaldson et al., 2002)

chromatin silencing at telomere

inferred from high throughput mutant phenotype

(Donaldson et al., 2002)

chromosome organization

inferred from mutant phenotype

(Demakova et al., 2007)

DNA methylation

inferred from mutant phenotype

(Kunert et al., 2003)

female germ-line stem cell asymmetric division

inferred from direct assay

(Yoon et al., 2008)

gene silencing

inferred from mutant phenotype

(Schotta et al., 2002)

heterochromatin assembly

inferred from mutant phenotype

(Andreyeva et al., 2007)

heterochromatin organization

inferred from mutant phenotype

(Sienski et al., 2015)

heterochromatin organization involved in chromatin silencing

inferred from mutant phenotype

(Fagegaltier et al., 2009)

histone H3-K9 methylation

inferred from direct assay

(Czermin et al., 2001)

inferred from mutant phenotype

(Gracheva et al., 2009, Ebert et al., 2004)

histone methylation

inferred from direct assay

(Eskeland et al., 2004)

histone modification

inferred from mutant phenotype

(Ner et al., 2002)

negative regulation of response to gamma radiation

inferred from mutant phenotype

(Zhang et al., 2008)

oogenesis

inferred from mutant phenotype

(Kuhfittig et al., 2001)

inferred from direct assay

(Yoon et al., 2008)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

chromatin organization

non-traceable author statement

(Schneider et al., 2002)

gene silencing

traceable author statement

(assigned by UniProt )

(Czermin et al., 2001)

histone lysine methylation

inferred from biological aspect of ancestor with PANTHER:PTN000526939

(assigned by GO_Central )

(Gaudet et al., 2011)

histone methylation

traceable author statement

(Simms et al., 2003)

Cellular Component (4 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

heterochromatin

inferred from direct assay

(Swenson et al., 2016)

polytene chromosome chromocenter

inferred from direct assay

(Koryakov et al., 2011)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

chromosome, centromeric region

traceable author statement

(McNairn and Gilbert, 2003, Zhimulev and Belyaeva, 2003)

heterochromatin

traceable author statement

(McNairn and Gilbert, 2003, Zhimulev and Belyaeva, 2003)

nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000526939

(assigned by GO_Central )

(Gaudet et al., 2011)

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 4

organism

• yolk plasma | posterior

(Lecuyer et al., 2007)

embryonic stage 5

pole cell

(Lecuyer et al., 2007)

oogenesis

egg chamber

(Yoon et al., 2008)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 12

organism | intense

Comment: 0-9 hr AEL

(Tschiersch et al., 1994)

embryonic stage 13 -- adult stage

organism | faint

(Tschiersch et al., 1994)

RT-PCR

Stage

Tissue/Position (including subcellular localization)

Reference

oogenesis

egg chamber | intense

(Yoon et al., 2008)

germarium | faint

(Yoon et al., 2008)

Additional Descriptive Data

The 2.4 kb transcript is detected in all developmental stages by Northern blot, but it is enriched at 0-9 hr of embryogenesis.

(Tschiersch et al., 1994)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

distribution deduced from reporter or direct label

Stage

Tissue/Position (including subcellular localization)

Reference

third instar larval stage

embryonic/larval salivary gland

• euchromatin | restricted

(Schotta et al., 2002)

embryonic/larval salivary gland

• telomeric heterochromatin & chromocenter

(Schotta et al., 2002)

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

Additional Descriptive Data

A fusion of eGFP and the Su(var)3-9 protein concentrates primarily at the chromocenters and telomeric heterochromatin with a few foci in the euchromatin of larval salivary gland chromosomes.

(Schotta et al., 2002)

Marker for

Subcellular Localization

CV Term

Evidence

References

heterochromatin

inferred from direct assay

(Swenson et al., 2016)

polytene chromosome chromocenter

inferred from direct assay

(Koryakov et al., 2011)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Su(var)3-9 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)3-9

View exonic expression by tissue for Dmel\Su(var)3-9

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

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

CG6476

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, and Transgenic Constructs

Classical and Insertion Alleles ( 67 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 17 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Su(var)3-9

Transgenic constructs containing regulatory region of Su(var)3-9

Deletions and Duplications ( 4 )

Disrupted in

Df(3R)ED5678

(Marygold et al., 2007)

Df(3R)ED5692

(Marygold et al., 2007)

Df(3R)ED10574

(Marygold et al., 2007)

Df(3R)Exel7323

(Ryder, 2004.4.26)

Phenotypes

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

Lethality

Allele

lethal, with Scer\GAL4^Act5C.PI

Su(var)3-9^KK108870

lethal, with Scer\GAL4^en.PU

Su(var)3-9^KK108870

lethal, with Scer\GAL4^ey.PH

Su(var)3-9^KK108870

lethal, with Scer\GAL4^nub.PK

Su(var)3-9^KK108870

lethal - all die before end of embryonic stage | dominant | maternal effect

Su(var)3-9^ptn

viable

Sterility

Allele

fertile

Su(var)3-9^unspecified

Other Phenotypes

Allele

decreased fecundity | recessive

Su(var)3-9⁶

enhancer of variegation

enhancer of variegation, with Dp(3;Y)BL2

Su(var)3-9^+t11.5

enhancer of variegation, with In(1)w^m4h

enhancer of variegation, with In(3L)BL1

Su(var)3-9^+t11.5

enhancer of variegation, with P{hsp26-pt-T}39C-12

Su(var)3-9⁶

enhancer of variegation, with P{hsp26-pt-T}gw^39C-33

Su(var)3-9⁶

enhancer of variegation, with T(2;3)V21-P{lacW}92E.x3

Su(var)3-9^+t11.5

enhancer of variegation | dominant, with In(1)rst³

Su(var)3-9^ptn

enhancer of variegation | dominant, with In(1)sc⁸

Su(var)3-9^ptn

enhancer of variegation | dominant, with In(1)sc^S1

Su(var)3-9^ptn

enhancer of variegation | dominant, with In(1)w^m4h

Su(var)3-9^ptn

enhancer of variegation | dominant, with In(1)w^m51b

Su(var)3-9^ptn

enhancer of variegation | dominant, with P{hsp26-pt-T}39C-12

Su(var)3-9⁶

enhancer of variegation | dominant, with P{hsp26-pt-T}118E-25-5

Su(var)3-9⁶

enhancer of variegation | dominant, with T(1;2)N^264-10

Su(var)3-9^ptn

enhancer of variegation | dominant, with T(1;4)N^264-12

Su(var)3-9^ptn

enhancer of variegation | dominant, with T(1;4)w^m258-21

Su(var)3-9^ptn

non-suppressor of variegation

Su(var)3-9⁶

non-suppressor of variegation | dominant, with P{hsp26-pt-T}8-M76

Su(var)3-9²

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

non-suppressor of variegation | dominant, with P{hsp26-pt-T}39C-66

Su(var)3-9²

non-suppressor of variegation | dominant, with P{RS3}pan^CB-5204-3

Su(var)3-9⁶

non-suppressor of variegation | dominant, with P{RS5}5-HA-1902

Su(var)3-9⁶

non-suppressor of variegation | dominant, with P{RS5}5-HA-1992

Su(var)3-9⁶

non-suppressor of variegation | dominant, with T(2;3)V21-P{lacW}92E.x3

Su(var)3-9⁶

some die during embryonic stage | dominant | maternal effect | maternal effect

Su(var)3-9^ptn

suppressor of variegation

suppressor of variegation, with Dp(1;f)γ878

Su(var)3-9¹⁶⁹⁹

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

suppressor of variegation, with In(2R)bw^VDe2

Su(var)3-9¹

suppressor of variegation, with P{hsp26-pt-T}39C-3

Su(var)3-9⁶

suppressor of variegation, with P{hsp26-pt-T}39C-27

Su(var)3-9⁶

suppressor of variegation, with P{hsp26-pt-T}118E-10

Su(var)3-9⁶

suppressor of variegation, with P{T1(-FRT)}T190-177

Su(var)3-9⁶

suppressor of variegation, with P{T1}T190-177

Su(var)3-9⁶

suppressor of variegation, with P{w⁺(FRT.attP.1360)}1198

Su(var)3-9⁶

suppressor of variegation, with P{wA^R}A

Su(var)3-9¹

suppressor of variegation | dominant

Su(var)3-9⁶

suppressor of variegation | dominant, with P{hsp26-pt-T}8-M76

Su(var)3-9⁶

suppressor of variegation | dominant, with P{hsp26-pt-T}39C-2

Su(var)3-9⁶

suppressor of variegation | dominant, with P{hsp26-pt-T}39C-3

Su(var)3-9¹⁶⁹⁹

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

suppressor of variegation | dominant, with P{hsp26-pt-T}39C-27

Su(var)3-9¹⁶⁹⁹

suppressor of variegation | dominant, with P{hsp26-pt-T}39C-66

Su(var)3-9⁶

suppressor of variegation | dominant, with P{hsp26-pt-T}118E-10

Su(var)3-9⁶

suppressor of variegation | dominant, with P{hsp26-pt-T}118E-28a, P{hsp26-pt-T}118E-28b

Su(var)3-9⁶

suppressor of variegation | dominant, with P{lacW}50C.x6

Su(var)3-9¹

suppressor of variegation | dominant, with P{SUPor-P}B079

Su(var)3-9¹⁶⁹⁹

suppressor of variegation | dominant, with T(1;4)w^m258-21

Su(var)3-9¹

suppressor of variegation | recessive, with Dp(?;2)bw^D

Su(var)3-9¹⁶⁹⁹

visible | adult stage, with Scer\GAL4^GMR.PF

Su(var)3-9^KK108870

Phenotype manifest in

Allele

cephalopharyngeal skeleton | maternal effect

Su(var)3-9^ptn

chromatin | maternal effect

Su(var)3-9^ptn

dorsal arm of pharyngeal sclerite

Su(var)3-9^ptn

dorsal bridge

Su(var)3-9^ptn

embryo | embryonic stage 4 | maternal effect

Su(var)3-9^ptn

eye, with Scer\GAL4^GMR.PF

Su(var)3-9^KK108870

follicle cell

Su(var)3-9^ptn

nurse cell & nucleus

Su(var)3-9^ptn

oocyte nucleus

Su(var)3-9^ptn

polytene chromosome

Su(var)3-9⁶

polytene chromosome chromocenter

Su(var)3-9⁶

ventral arm of pharyngeal sclerite

Su(var)3-9^ptn

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v7.1)

Homo sapiens (Human) (6)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\SUV39H1

4 of 15

Yes

Hsap\SUV39H2

4 of 15

Yes

Hsap\EHMT1

1 of 15

Hsap\EHMT2

1 of 15

Hsap\PRSS48

1 of 15

Yes

Hsap\SETMAR

1 of 15

Model Organism Orthologs (via DIOPT v7.1)

Mus musculus (laboratory mouse) (7)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Suv39h1

4 of 15

Yes

Mmus\Suv39h2

4 of 15

Yes

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Yes

Rattus norvegicus (Norway rat) (5)

Rnor\Suv39h2

4 of 13

Yes

Rnor\Suv39h1

3 of 13

Yes

Rnor\Ehmt1

1 of 13

Rnor\Ehmt2

1 of 13

Rnor\Setmar

1 of 13

Xenopus tropicalis (Western clawed frog) (3)

Xtro\suv39h2

3 of 12

Yes

Xtro\ehmt1

1 of 12

Xtro\ehmt2

1 of 12

Danio rerio (Zebrafish) (10)

Drer\suv39h1a

5 of 15

Yes

4 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Caenorhabditis elegans (Nematode, roundworm) (14)

Cele\eif-2gamma

1 of 15

Yes

Cele\set-6

1 of 15

Yes

Cele\set-11

1 of 15

Yes

Cele\set-13

1 of 15

Yes

Cele\set-15

1 of 15

Yes

Cele\set-19

1 of 15

Yes

Cele\set-20

1 of 15

Yes

Cele\set-21

1 of 15

Yes

Cele\set-23

1 of 15

Yes

Cele\set-25

1 of 15

Yes

Cele\set-32

1 of 15

Yes

Cele\set-33

1 of 15

Yes

Cele\svh-1

1 of 15

Yes

Cele\try-1

1 of 15

Yes

Arabidopsis thaliana (thale-cress) (0)

No records found.

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\GCD11

1 of 15

Yes

Scer\SET2

1 of 15

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\clr4

2 of 12

Yes

Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091902DX )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila melanogaster

fruit fly

Dmel\Su(var)3-9

Drosophila suzukii

Spotted wing Drosophila

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA19622

Drosophila persimilis

Dper\GL12073

Drosophila willistoni

Dwil\GK12089

Drosophila virilis

Dvir\GJ24041

Drosophila mojavensis

Dmoj\GI24667

Drosophila grimshawi

Dgri\GH18750

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG0915016J )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Mdoa\17016444

Glossina morsitans

Tsetse fly

Gmor\GMOY011471

Glossina morsitans

Tsetse fly

Gmor\GMOY009260

Lucilia cuprina

Australian sheep blowfly

Lcup\FF38_04390

Mayetiola destructor

Hessian fly

Mdes\Mdes002338

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL010826

Anopheles darlingi

American malaria mosquito

Adar\ADAC003826

Anopheles gambiae

Malaria mosquito

Agam\AGAP003597

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ019323

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ019325

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W00ZI )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA011500

Danaus plexippus

Monarch butterfly

Dple\DPOGS203219-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL006496

Apis florea

Little honeybee

Aflo\2152280964

Apis mellifera

Western honey bee

Amel\GB47635

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP17863

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP17862

Bombus terrestris

Buff-tailed bumblebee

Bter\15206376

Linepithema humile

Argentine ant

Lhum\LH17627

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:001d58

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG019793

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG000765

Dendroctonus ponderosae

Mountain pine beetle

Dpod\YQE_08059

Tribolium castaneum

Red flour beetle

Tcas\TC001103

Pediculus humanus

Human body louse

Phum\PHUM490650

Rhodnius prolixus

Kissing bug

Rpro\RPRC015292

Cimex lectularius

Bed bug

Clec\CLEC002826

Cimex lectularius

Bed bug

Clec\CLEC002827

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI003098

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI006256

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI003589

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI002814

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_00097

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_16525

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X03TA )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strigamia maritima

European centipede

Smar\SMAR015743

Ixodes scapularis

Black-legged tick

Isca\ISCW011810

Stegodyphus mimosarum

African social velvet spider

Smim\KFM77086.1

Stegodyphus mimosarum

African social velvet spider

Smim\KFM68855.1

Tetranychus urticae

Two-spotted spider mite

Turt\tetur35g00260

Tetranychus urticae

Two-spotted spider mite

Turt\tetur04g08120

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_231062

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0624 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Eif2g

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000000736

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000004255

Gallus gallus

Domestic chicken

Ggal\EIF2S3

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v7.1)

Drosophila melanogaster (Fruit fly) (14)

Gene Symbol

Score

Source

Alignment

2 of 10

G9a

2 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

egg

1 of 10

NSD

1 of 10

Send2

1 of 10

Ser6

1 of 10

Set2

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 ( 3 )

Allele

Disease

Interaction

References

Su(var)3-9¹

exacerbates Alzheimer's disease

modeled by Hsap\MAPT^R406W.UAS

(Frost et al., 2014)

Su(var)3-9¹⁷

ameliorates cancer

modeled by Dl^UAS.cDa, lola^GS88A8, psq^GS88A8

(Ferres-Marco et al., 2006)

Su(var)3-9²

exacerbates Alzheimer's disease

modeled by Hsap\MAPT^R406W.UAS

(Frost et al., 2014)

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?

SUV39H1; suppressor of variegation 3-9 homolog 1

4 of 15

300254

SUV39H2; suppressor of variegation 3-9 homolog 2

4 of 15

606503

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.

Dmel gene

Ortholog showing functional complementation

Supporting References

Su(var)3-9

Hsap\SUV39H1

(Schotta et al., 2002)

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)3-9 - HDAC1

anti tag coimmunoprecipitation, western blot, affinity chromatography technology

(Boeke et al., 2010, Czermin et al., 2001)

Su(var)3-9 - HP1b

pull down, anti tag western blot

(Lee et al., 2019)

Su(var)3-9 - HP1c

pull down, anti tag western blot

(Lee et al., 2019)

Su(var)3-9 - Hers

anti bait coimmunoprecipitation, western blot, pull down, autoradiography, cosedimentation

(Ito et al., 2012)

Su(var)3-9 - His1

anti bait coimmunoprecipitation, anti tag western blot, pull down, western blot, anti tag coimmunoprecipitation, autoradiography

(Kavi et al., 2016, Lu et al., 2013)

Su(var)3-9 - His3

enzymatic study, autoradiography

(Lu et al., 2013, Rudolph et al., 2007, Schotta et al., 2002)

Su(var)3-9 - JIL-1

pull down, autoradiography, anti tag coimmunoprecipitation, anti tag western blot, affinity chromatography technology, western blot, enzymatic study

(Boeke et al., 2010)

Su(var)3-9 - Rm62

affinity chromatography technology, Identification by mass spectrometry, anti bait coimmunoprecipitation, anti tag western blot, pull down, autoradiography

(Boeke et al., 2011)

Su(var)3-9 - Rrp6

anti tag coimmunoprecipitation, anti tag western blot

(Eberle et al., 2015)

Su(var)3-9 - Su(var)205

pull down, autoradiography, affinity chromatography technology, western blot, two hybrid, anti bait coimmunoprecipitation, anti tag western blot, anti tag coimmunoprecipitation, peptide massfingerprinting

(Lee et al., 2019, Alekseyenko et al., 2014, Lu et al., 2013, Ito et al., 2012, Boeke et al., 2010, Abel et al., 2009, Schotta et al., 2002)

Su(var)3-9 - Su(var)3-3

anti bait coimmunoprecipitation, western blot

(Rudolph et al., 2007)

Su(var)3-9 - Su(var)3-7

two hybrid

(Schotta et al., 2002)

Su(var)3-9 - ft

anti tag coimmunoprecipitation, peptide massfingerprinting

(Kwon et al., 2013)

Su(var)3-9 - wge

anti tag coimmunoprecipitation, western blot

(Masuko et al., 2018)

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

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

suppressible

Su(var)3-9

(Locke et al., 1993)

crm

enhanceable

Su(var)3-9

(Gibert et al., 2011)

crm

suppressible

Su(var)3-9

(Gibert et al., 2011)

ct|lncRNA:flam

suppressible

Su(var)3-9

(Guida et al., 2016)

Dl|lola|psq

suppressible

Su(var)3-9

(Ferres-Marco et al., 2006)

egg

suppressible

Su(var)3-9

(Brower-Toland et al., 2009)

enhanceable

(Ito et al., 2012)

suppressible

(Deng et al., 2007, Zhang et al., 2006)

lid

suppressible

Su(var)3-9

(Di Stefano et al., 2011)

w|Su(var)205

enhanceable

Su(var)3-9

(Li et al., 2003)

External Data

Subunit Structure (UniProtKB)

Interacts with Su(var)205 and Su(var)3-7. Probably associates with Rpd3.

(UniProt, P45975 )

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0263755

MIST (genetic) - An integrated Molecular Interaction Database

Su(var)3-9

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

Su(var)3-9

Pathways

Gene Group - Pathway Membership (FlyBase)

External Data

Linkouts

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

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

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-56

Cytogenetic map

88E7-88E8

Sequence location

3R:15,259,864..15,263,458 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

88E7-88E8

Limits computationally determined from genome sequence between P{lacW}Hsc70-4^L3929 and P{lacW}MRG15^j6A3

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-56

(FlyBase, 2016, Donaldson et al., 2002)

3-55.8

(Comeron et al., 2012)

3-56.4 +/- 0.7

(Wustmann et al., 1989, Reuter et al., 1986)

3-56.4

Left of (cM)

Right of (cM)

Notes

Genetic map position of Su(var)3-9³⁰⁶ mutation on Gl Sb H chromosome is at 57.9 and on the cv-c Sb chromosome locus is at 56.4. Genetic map position of Su(var)3-9³¹⁰ mutation on Gl Sb H chromosome is at 56.7 and on the cv-c Sb chromosome locus is at 56.5. Genetic map position of Su(var)3-9³²⁸ mutation on Gl Sb H chromosome is at 57.3 and on the cv-c Sb chromosome locus is at 56.4. Genetic map position of Su(var)3-9³⁴⁰ mutation on Gl Sb H chromosome is at 55.6 and on the cv-c Sb chromosome locus is at 56.9. Genetic map position of Su(var)3-9³²² mutation on Gl Sb H chromosome is at 57.8 and on the cv-c Sb chromosome locus is at 56.4. Genetic map position of Su(var)3-9³³⁶ mutation on Gl Sb H chromosome is at 54.9 and on the cv-c Sb chromosome locus is at 56.2.

(Locke et al., 1993)

Stocks and Reagents

Stocks (12)

Bloomington

6209

In(1)w^m4; Su(var)3-9¹/TM3, Sb¹ Ser¹

6210

In(1)w^m4; Su(var)3-9²/TM3, Sb¹ Ser¹

32914

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00704}attP2

33401

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00279}attP2

43661

y¹ sc^* v¹ sev²¹; P{TRiP.GL01471}attP40

Kyoto

108675

Su(var)3-9¹/TM3, Sb¹ Ser¹

108676

Su(var)3-9²/TM3, Sb¹ Ser¹

104393

w^*; P{GawB}Su(var)3-9^NP3153 / TM6, Sb¹ Tb¹

VDRC

v101494

P{KK108870}VIE-260B

v39378

w¹¹¹⁸; P{GD15258}v39378

v33834

w¹¹¹⁸; P{GD15421}v33834/TM3

v39377

w¹¹¹⁸; P{GD15258}v39377/CyO

Genomic Clones (18)

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

cDNA Clones (47)

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

RE16601

Other clones

FI20106

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.

FBgn0263755

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

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

41483

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Sienski et al., 2015, Boeke et al., 2010)

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for database merge of

Additional comments

The CG6476 annotation has been split into two CG43664 (which corresponds to Su(var)3-9) and CG43665 (which corresponds to eIF-2γ) in release 5.43 of the genome annotation.

(FlyBase Genome Annotators, 2012)

The "pitkin^D" mutation maps within Su(var)3-9 at 88E, not at 67C as previously reported (FBrf0134644). The locus at 67C described in FBrf0134644 is a separate "modifier of dominant female sterility".

(Ebert et al., 2004)

FlyBase curator comment: Su(var)3-9^ptn was reported to be allelic to two P-element insertion alleles at 67C (l(3)S089004^S089004 and l(3)S089004^S089302) in FBrf0134644. However, FBrf0180260 demonstrates that Su(var)3-9^ptn is an allele of Su(var)3-9 (at 88E) and that the l(3)S089004^S089004 and l(3)S089004^S089302 alleles at 67C represent a separate "modifier of dominant female sterility" locus.

(Kuhfittig et al., 2001)

The genomic region around Su(var)3-9 encodes two classes of transcript (2.4kb and 2.0kb), which show a 330bp overlap at their 5' ends, producing an overlap of 80 amino acids at the N-terminal ends of the encoded proteins. The encoded proteins are otherwise different in sequence. The 2.4kb transcript encodes Su(var)3-9 and the 2.0kb transcript encodes eIF-2γ.

(Tschiersch et al., 1994)

Other Comments

Haploinsufficient locus.

(Cook et al., 2012)

DNA-protein interactions: genome-wide binding profile assayed for Su(var)3-9 protein in Kc167 cells; see Chromatin_types_NKI collection report. Individual protein-binding experiments listed under "Samples" at GEO_GSE22069 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22069).

(Filion et al., 2010)

The organisation of nucleosomes over the entire histone complex region is altered in Su(var)3-9 mutants and there is a concomitant increase in expression of the histone genes.

(Ner et al., 2002)

Su(var)3-9 has a central role in heterochromatin-induced gene silencing.

(Schotta et al., 2002)

Su(var)3-9 is required for normal development of the female germ line.

(Kuhfittig et al., 2001)

Variegation of bw^D suppressed.

(Csink and Henikoff, 1996)

Phenotype of w^bl is unchanged by Su(var)3-9.

(Csink et al., 1994)

Su(var)3-9 is a haplo suppressor and a triplo enhancer and a non-essential gene. The suppressor effect of mutations dominate over enhancer mutations of over 40 different haplo-dependent enhancer genes. Results indicate that Su(var)3-9 plays an important role in the regulation of gene inactivation through heterochromatinization in position effect variegation (PEV). Su(var)3-9 mutations are epistatic to E(var)2-88.

(Tschiersch et al., 1994)

Su(var) mutants have dramatic effects on chromosome morphology and gene expression but negligible effects on nuclease sensitivity of the w gene chromatin: changes due to alterations in chromosomal packaging.

(Hayashi et al., 1990)

Origin and Etymology

Discoverer

Etymology

The gene is named after "Pitkin", the principal figure in Robert Ascher's movie "A Stitch in Time", who caused perplexing confusions by overdoing almost everything.

(Kuhfittig et al., 2001)

Identification

External Crossreferences and Linkouts ( 31 )

Sequence Crossreferences

NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

41483

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

P45975

Other crossreferences

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

FBgn0263755

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

Su(var)3-9_1

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

CG6476

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

41483

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

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

Dmel_CG43664

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

Lysine

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

SIRT1 negatively regulates rRNA expression

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0263755

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

Interactive Fly

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

Lysine degradation

MIST (genetic) - An integrated Molecular Interaction Database

Su(var)3-9

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

Su(var)3-9

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

SIRT1 negatively regulates rRNA expression

Synonyms and Secondary IDs (34)

Reported As

Symbol Synonym

CG43664

(Ni et al., 2010.12.1)

CG6476

(Boltengagen et al., 2016, Keleman et al., 2009.8.5)

E(var)3-2

SUV39

(Colmenares et al., 2017, Gerber and Shilatifard, 2003)

SUV39H1

(McNairn and Gilbert, 2003)

Su(VAR)3-9

(Doheny et al., 2008)

Su(Var)3-9

(Petruk et al., 2013, Mikhaylova and Nurminsky, 2011, Shevelyov et al., 2009, Stabell et al., 2003, Naumova et al., 1999)

Su(var)

(Scaria et al., 2008)

Su(var) 3-9

(Bhadra et al., 2007)

Su(var)3-9

(Berlandi et al., 2019, Chang et al., 2019, Glenn and Geyer, 2019, Lee et al., 2019, Martins et al., 2019, Seller et al., 2019, Shimaji et al., 2019, Sidorenko et al., 2019, Deshpande and Meller, 2018, Hughes et al., 2018, Lee et al., 2018, Masuko et al., 2018, Amaral et al., 2017, Caridi et al., 2017, Colmenares et al., 2017, Teixeira et al., 2017, Tsurumi et al., 2017, Bayona-Feliu et al., 2016, Boltengagen et al., 2016, Guida et al., 2016, Kavi et al., 2016, Timms et al., 2016, Aradska et al., 2015, Boija and Mannervik, 2015, Dent et al., 2015, Dietz et al., 2015, Meller et al., 2015, Sienski et al., 2015, Alekseyenko et al., 2014, Boyle et al., 2014, Comoglio and Paro, 2014, Eissenberg and Elgin, 2014, Frost et al., 2014, Gonzalez et al., 2014, Ost et al., 2014, Ross et al., 2014, Wang et al., 2014, Wang et al., 2014, Xu et al., 2014, Zhang et al., 2014, Debruhl et al., 2013, Elgin and Reuter, 2013, Huang et al., 2013, Kwon et al., 2013, Kwon et al., 2013, Lu et al., 2013, Sentmanat et al., 2013, Silva-Sousa and Casacuberta, 2013, Vasanthi et al., 2013, Antao et al., 2012, Cook et al., 2012, Ferree and Prasad, 2012, Figueiredo et al., 2012, Hazelett et al., 2012, Ito et al., 2012, Japanese National Institute of Genetics, 2012.5.21, Nowak et al., 2012, Sakoparnig et al., 2012, Sawamura, 2012, Sentmanat and Elgin, 2012, Sim et al., 2012, Stern et al., 2012, Szabad et al., 2012, Abramov et al., 2011, Boeke et al., 2011, Cryderman et al., 2011, Di Stefano et al., 2011, Friedman et al., 2011, Gibert et al., 2011, Kappes et al., 2011, Koryakov et al., 2011, Wang et al., 2011, Yan et al., 2011, Deng et al., 2010, Gan et al., 2010, Lee et al., 2010, Lemos et al., 2010, Moshkovich and Lei, 2010, Skora and Spradling, 2010, Abel et al., 2009, Brower-Toland et al., 2009, Fagegaltier et al., 2009, Gracheva et al., 2009, Hofmann et al., 2009, Lu et al., 2009, Paredes and Maggert, 2009, Peng and Karpen, 2009, Phalke et al., 2009, Vogel et al., 2009, Andreyeva et al., 2008, Cai et al., 2008, Chiolo et al., 2008, Ciurciu et al., 2008, de Wit et al., 2008, Doheny et al., 2008, Kent, 2008, Lin et al., 2008, Nisha et al., 2008, Pindyurin et al., 2008, Sakaguchi et al., 2008, Scaria et al., 2008, Yasuhara and Wakimoto, 2008, Yoon et al., 2008, Zhang et al., 2008, Zhou et al., 2008, Andreyeva et al., 2007, Bai et al., 2007, Budde, 2007, Demakova et al., 2007, Deng et al., 2007, Goldberg et al., 2007, Greil et al., 2007, Haigh and Lloyd, 2007, Haynes et al., 2007, Johansson et al., 2007, Lecuyer et al., 2007, Li et al., 2007, Maines et al., 2007, Marygold et al., 2007, Mohan et al., 2007, Nurminsky, 2007, Peng and Karpen, 2007, Seum et al., 2007, Seum et al., 2007, Stuart et al., 2007, Xing et al., 2007, Zaratiegui, 2007, Haynes et al., 2006, Koryakov et al., 2006, Krauss et al., 2006, Mis et al., 2006, Moorman et al., 2006, Moorman et al., 2006, Pickersgill et al., 2006, Qi et al., 2006, Shi et al., 2006, Talbert and Henikoff, 2006, de Wit et al., 2005, Dillon et al., 2005, Kalmykova et al., 2005, Krauss et al., 2005, Lam et al., 2005, Bazin et al., 2004, Delattre et al., 2004, Taylor-Harding et al., 2004, Fahrner and Baylin, 2003, Shareef et al., 2003, Weissmann et al., 2003, Balasov, 2002, Czermin et al., 2002, Joanis and Lloyd, 2002, Krauss and Reuter, 2000, Tschiersch et al., 1994)

Su(var)3-902

(Netter et al., 1998)

Su(var)306

Su(var)310

Su(var)328

Su-var(3)9

(Popkova et al., 2001, Wustmann et al., 1989, Reuter et al., 1986)

Su-var(3)902

(Fauvarque and Dura, 1993)

SuVar3-9

(Slattery et al., 2014, Ahmad, 2004, Workman and Abmayr, 2004)

Suv 3-9

(Abel et al., 2009)

Suvar(3)9

(Henikoff, 1996)

Suvar3-9

(Birchler et al., 2004)

Suvar39

(Lund and van Lohuizen, 2004)

caa56376 Suvar39 Dm

(Alvarez-Venegas and Avramova, 2002)

dSU(VAR)3-9

(Eskeland et al., 2004)

dSu(var)3-9

(Ciurciu et al., 2008)

ptn

(Kuhfittig et al., 2001)

su(var)3-9

(Hong and Choi, 2016, Lo et al., 2016, Eberle et al., 2015, Vujatovic et al., 2012, Kroiss et al., 2009, Brehm et al., 2004, Pai et al., 2004)

Name Synonyms

Enhancer of variegation 3-2

(Tschiersch et al., 1994)

Su(var)3-9

(Cryderman et al., 2005)

Suppressor of variegation 3-9

(Comoglio and Paro, 2014, Lee et al., 2014, Garcia and Stathopoulos, 2011, Xing et al., 2007)

Suppressor of variegation 306

Suppressor of variegation 310

Suppressor of variegation 328

histone methyltransferase

(Vogel et al., 2009)