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Gene Dmel\Su(var)3-9

General Information
Symbol	Dmel\Su(var)3-9	Species	D. melanogaster
Name	Suppressor of variegation 3-9	Annotation symbol	CG43664
Feature type	protein_coding_gene	FlyBase ID	FBgn0263755
Gene Model Status	Current	Stock availability	5 publicly available
Also Known As	SuVar3-9, Su-var(3)9
Genomic Location
Chromosome (arm)	3R	Recombination map	3-56.4
Cytogenetic map	88E7-88E8	Sequence location	3R:11,085,586..11,089,196 [-]
Genomic Maps Select View:Gene Models/EvidenceExpression/RegulationMegaViewGene Disruptions, Stocks and Reagents modENCODE GBrowse	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	The gene Suppressor of variegation 3-9 is referred to in FlyBase by the symbol Dmel\Su(var)3-9 (CG43664, FBgn0263755). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: histone methyltransferase activity (H3-K9 specific); histone methyltransferase activity. There is experimental evidence for 14 unique biological process terms, many of which group under: cellular component organization or biogenesis; biological regulation; organelle organization; macromolecule modification; negative regulation of cellular biosynthetic process; chromosome organization; gene silencing; multicellular organism reproduction; macromolecule methylation; gamete generation. 76 alleles are reported. The phenotypes of these alleles are annotated with: dorsal bridge; ventral arm of pharyngeal sclerite; dorsal arm of pharyngeal sclerite; polytene chromosome; follicle cell; oocyte nucleus; polytene chromosome chromocenter. It has one annotated transcript and one annotated polypeptide. Protein features are: Chromo domain; Chromo domain, conserved site; Chromo domain-like; Chromo domain/shadow; Histone H3-K9 methyltransferase; Post-SET domain; Pre-SET domain; Pre-SET zinc-binding sub-group; Protein synthesis factor, GTP-binding; SET domain. Gene sequence location is 3R:11085586..11089196.
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
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FB2011_10
FB2012_01	New/Merged/Split Record This record was either newly added to FlyBase for this release or is the result of merging or splitting existing records in this release
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 88E7-88E8   Limits computationally determined from genome sequence between P{lacW}Hsc70-4L3929 and P{lacW}MRG15j6A3
Experimentally Determined Cytological Location
Cytogenetic map Notes References
Experimentally Determined Recombination Data
Location	3-56.4   3-56.4 +/- 0.7 (Reuter et al., 1986, Wustmann et al., 1989) 3-56 (Donaldson et al., 2002)
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)
Gene Model & Products
Please see the GBrowse 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
Comments on Gene Model
	Gene model reviewed during 5.42 Gene split based on protein alignment (BLASTX) data.
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Su(var)3-9-RA FBtr0310385     2402   635
Additional Transcript Data & 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 protein Su(var)3-9-PA   FBpp0302536   71.8   635   8.35
Additional Polypeptide Data & 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
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Chromo domain, conserved site (IPR023779) Chromo domain (IPR023780) Protein synthesis factor, GTP-binding (IPR000795) Chromo domain/shadow (IPR000953) SET domain (IPR001214) Pre-SET zinc-binding sub-group (IPR003606) Post-SET domain (IPR003616) Pre-SET domain (IPR007728) Histone H3-K9 methyltransferase (IPR011381) Chromo domain-like (IPR016197)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA802714   AJ290956 CAB93768   BF487476   BI216670   BI356560   BI363137   BQ102783   BT125886   CO184157   CO287016   CO297348   CO331101   EC064458   EC200809   EC207163   GH941697   GH943214   GH943440   GH943545   GH945000   GH945038   GH945435   GH946460   GH946738   GH947706   GH953006   GH953212   GH954136   GH954559   GH954818   GH955283   GH956701   GH959929   GH960596   GH962824   GH964940   GH964987   GH966501   GH967380   GH968351   GH970978   GH971929   GH974668   GH976843   GH977426   GH978819   GH979576   GH980008   GH981160   GH982842   GH984169   X80070 CAA56376
UniProtKB/Swiss-Prot	P45975
UniProtKB/TrEMBL
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References
External Data
Linkouts
Crossreferences
Expression Data
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) northern blot Stage Tissue/Position (including subcellular localization) Reference embryonic stage 1 -- 12   organism | intense   (Tschiersch et al., 1994) Comment:0-9 hr AEL embryonic stage 13 -- adult stage   organism | faint   (Tschiersch et al., 1994)
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
Notes
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)
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
Notes
High-Throughput Expression Data
or
See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes. [an error occurred while processing this directive] modENCODE Temporal Expression Data (Graveley et al., 2011) FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
Expression Clusters
	A cluster of genes with similar mRNA expression dynamics across development. (The modENCODE Consortium, 2010) mE2_34_mRNA_expression_cluster_08
External Data & Images
Linkouts
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal | dominant | embryonic stage | maternal effect Su(var)3-9ptn viable Su(var)3-91 Su(var)3-92 Su(var)3-93 Su(var)3-94 Su(var)3-95 Su(var)3-96 Su(var)3-97 Su(var)3-98 Su(var)3-99 Su(var)3-910 Su(var)3-911 Su(var)3-912 Su(var)3-913 Su(var)3-9306 Su(var)3-91699 Su(var)3-9unspecified Sterility Allele fertile Su(var)3-9unspecified Other Phenotypes Allele enhancer of variegation Su(var)3-9+t11.5 Su(var)3-9ptn.hs.T:Avic\GFP-EGFP enhancer of variegation, with In(1)wm4h Su(var)3-9+t11.5 Su(var)3-9hs.T:Hsap\MYC 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}gw39C-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, with Tp(3;Y)BL2 Su(var)3-9+t11.5 enhancer of variegation | dominant, with In(1)rst3 Su(var)3-9ptn enhancer of variegation | dominant, with In(1)sc8 Su(var)3-9ptn enhancer of variegation | dominant, with In(1)scS1 Su(var)3-9ptn enhancer of variegation | dominant, with In(1)wm4h Su(var)3-9ptn enhancer of variegation | dominant, with In(1)wm51b Su(var)3-9ptn 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)N264-10 Su(var)3-9ptn enhancer of variegation | dominant, with T(1;4)N264-12 Su(var)3-9ptn enhancer of variegation | dominant, with T(1;4)wm258-21 Su(var)3-9ptn non-suppressor of variegation Su(var)3-96 non-suppressor of variegation | dominant, with P{RS3}panCB-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 suppressor of variegation Su(var)3-96 Su(var)3-9P17 Su(var)3-9P25 suppressor of variegation, with Dp(1;f)γ878 Su(var)3-91699 suppressor of variegation, with In(1)wm4 Su(var)3-91 Su(var)3-9336 Su(var)3-9340 suppressor of variegation, with In(2R)bwVDe2 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{wAR}wA Su(var)3-91 suppressor of variegation | dominant Su(var)3-96 suppressor of variegation | dominant, with In(1)wm4 Su(var)3-96 Su(var)3-9306 Su(var)3-9310 Su(var)3-9311 Su(var)3-9319 Su(var)3-9322 Su(var)3-9328 Su(var)3-9330 Su(var)3-9336 Su(var)3-9340 Su(var)3-91699 suppressor of variegation | dominant, with In(1)wm4h Su(var)3-91 Su(var)3-92 Su(var)3-93 Su(var)3-94 Su(var)3-95 Su(var)3-96 Su(var)3-97 Su(var)3-98 Su(var)3-99 Su(var)3-910 Su(var)3-911 Su(var)3-912 Su(var)3-913 Su(var)3-914 Su(var)3-915 Su(var)3-916 Su(var)3-917 Su(var)3-918 Su(var)3-919 Su(var)3-920 Su(var)3-91699 Su(var)3-9unspecified 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 Su(var)3-91699 suppressor of variegation | dominant, with P{hsp26-pt-T}39C-27 Su(var)3-91699 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)wm258-21 Su(var)3-91 suppressor of variegation | recessive, with Dp(?;2)bwD Su(var)3-91699 Phenotype manifest in Allele cephalopharyngeal skeleton | maternal effect Su(var)3-9ptn chromatin | maternal effect Su(var)3-9ptn dorsal arm of pharyngeal sclerite Su(var)3-9ptn dorsal bridge Su(var)3-9ptn follicle cell Su(var)3-9ptn nurse cell & nucleus Su(var)3-9ptn oocyte nucleus Su(var)3-9ptn polytene chromosome Su(var)3-96 polytene chromosome chromocenter Su(var)3-96 syncytial blastoderm embryo | maternal effect Su(var)3-9ptn ventral arm of pharyngeal sclerite Su(var)3-9ptn
Classical Alleles ( 60 )
For All Classical Alleles Show
Allele of Su(var)3-9 Class Mutagen Stocks Known lesion Su(var)3-91 loss of function allele ethyl methanesulfonate 2 -- Su(var)3-92 loss of function allele ethyl methanesulfonate 2 Yes Su(var)3-9NP3153 1 -- Su(var)3-910 loss of function allele ethyl methanesulfonate 0 Yes Su(var)3-911 ethyl methanesulfonate 0 Yes Su(var)3-912 ethyl methanesulfonate 0 Yes Su(var)3-913 hypomorphic allele - genetic evidence ethyl methanesulfonate 0 Yes Su(var)3-914 PM hybrid dysgenesis 0 Yes Su(var)3-915 X ray 0 -- Su(var)3-91699 ethyl methanesulfonate 0 Yes Su(var)3-916 loss of function allele X ray 0 Yes Su(var)3-917 loss of function allele X ray 0 Yes Su(var)3-918 X ray 0 -- Su(var)3-919 X ray 0 -- Su(var)3-920 loss of function allele X ray 0 -- Su(var)3-921 hypomorphic allele - genetic evidence 0 Yes Su(var)3-922 hypomorphic allele - genetic evidence 0 Yes Su(var)3-923 0 Yes Su(var)3-924 0 -- Su(var)3-925 hypomorphic allele - genetic evidence 0 Yes Su(var)3-926 0 -- Su(var)3-927 0 Yes Su(var)3-928 0 -- Su(var)3-929 0 -- Su(var)3-9306 ethyl methanesulfonate Delta2-3 0 -- Su(var)3-930 0 Yes Su(var)3-9310 ethyl methanesulfonate Delta2-3 0 -- Su(var)3-9311 ethyl methanesulfonate 0 -- Su(var)3-9319 ethyl methanesulfonate 0 Yes Su(var)3-931 0 Yes Su(var)3-9322 Delta2-3 0 -- Su(var)3-9328 Delta2-3 0 -- Su(var)3-932 loss of function allele 0 Yes Su(var)3-9330 ethyl methanesulfonate 0 Yes Su(var)3-9336 Delta2-3 0 -- Su(var)3-933 0 -- Su(var)3-9340 Delta2-3 0 -- Su(var)3-934 0 Yes Su(var)3-935 0 -- Su(var)3-93 ethyl methanesulfonate 0 Yes Su(var)3-94 loss of function allele ethyl methanesulfonate 0 Yes Su(var)3-95 ethyl methanesulfonate 0 Yes Su(var)3-96 ethyl methanesulfonate X ray 0 Yes Su(var)3-97 X ray 0 Yes Su(var)3-98 loss of function allele ethyl methanesulfonate 0 Yes Su(var)3-99 ethyl methanesulfonate 0 Yes Su(var)3-9evo 0 -- Su(var)3-9P17-r12 0 -- Su(var)3-9P17-r2 0 -- Su(var)3-9P17 P-element activity 0 Yes Su(var)3-9P25-r2 0 -- Su(var)3-9P25 P-element activity 0 Yes Su(var)3-9ptn hypermorphic allele - genetic evidence, antimorphic allele - genetic evidence, gain of function allele X ray 0 Yes Su(var)3-9t1 0 -- Su(var)3-9t2 0 -- Su(var)3-9t3 0 -- Su(var)3-9t4 0 -- Su(var)3-9t5 0 -- Su(var)3-9t6 0 -- Su(var)3-9unspecified 0 --
Alleles Carried on Transgenic Constructs ( 16 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Su(var)3-9 Class Mutagen Stocks Known lesion Su(var)3-9+t11.5 in vitro construct - genomic fragment 0 Yes Su(var)3-910kb.T:Avic\GFP-EGFP in vitro construct - coding region fusion 0 Yes Su(var)3-9dsRNA.cGa in vitro construct - RNAi 0 Yes Su(var)3-9GD15258 in vitro construct - regulatory fusion in vitro construct - RNAi 0 Yes Su(var)3-9GD15421 in vitro construct - regulatory fusion in vitro construct - RNAi 0 Yes Su(var)3-9HMS00279 in vitro construct - regulatory fusion in vitro construct - RNAi 0 Yes Su(var)3-9HMS00704 in vitro construct - regulatory fusion in vitro construct - RNAi 0 Yes Su(var)3-9hs.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes Su(var)3-9hs.T:Ecol\dam,T:Hsap\MYC in vitro construct - coding region fusion in vitro construct - regulatory fusion 0 Yes Su(var)3-9hs.T:Hsap\MYC in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes Su(var)3-9KK108870 in vitro construct - regulatory fusion in vitro construct - RNAi 0 Yes Su(var)3-9NTerm.hs.T:Avic\GFP-EGFP in vitro construct - regulatory fusion 0 Yes Su(var)3-9ptn.hs.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - amino acid replacement 0 Yes Su(var)3-9Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes Su(var)3-9Δchromo.hs.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - deletion 0 Yes Su(var)3-9ΔSET.hs.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - deletion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(3R)Exel7323 (Ryder, 2004.4.26)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data heat-shock construct P{GS.ry+hs(Su(var)3-9cDNA)EGFP} NA P{hs-Su(var)3-9.Myc} NA P{hs-Su(var)3-9ptn.EGFP} NA P{Su(var)3-9-EGFP.NTerm} NA P{Su(var)3-9-EGFP.Δchromo} NA P{Su(var)3-9-EGFP.ΔSET} NA UAS construct P{GD15258} NA P{GD15421} NA P{KK108870} NA P{TRiP.HMS00279} NA P{TRiP.HMS00704} NA P{TRiP.JF01404} NA P{UAS-Su(var)3-9.EGFP} NA characterization construct P{(ry+),11.5kb} NA P{GS.ry+(10kbSu(var)3-9)EGFP} NA P{Su(var)3-9::trx-EGFP} NA
Insertions
	Type of insertions Name Expression data insertion of enhancer trap binary system P{GawB}Su(var)3-9NP3153 No miscellaneous insertions H{}Su(var)3-9306 NA H{}Su(var)3-9310 NA H{}Su(var)3-9322 NA H{}Su(var)3-9328 NA H{}Su(var)3-9336 NA H{}Su(var)3-9340 NA P{}Su(var)3-914 NA P{}Su(var)3-9P17 NA P{}Su(var)3-9P25 NA P{lacW-ΔS089302rv1}l(3)S089004S089302rv1 NA P{lacW-ΔS089302rv6}l(3)S089004S089302rv6 NA P{lacW-ΔS089302rv7}l(3)S089004S089302rv7 NA P{lacW-ΔS089302rv9}l(3)S089004S089302rv9 NA
Gene Ontology: Function, Process & Cellular Component ( 24 unique terms )
Terms Based on Experimental Evidence ( 17 terms )
Molecular Function
CV term Evidence References
histone methyltransferase activity inferred from direct assay (Eskeland et al., 2004, Ebert et al., 2004) inferred from direct assay (assigned by UniProtKB) (Czermin et al., 2001) histone methyltransferase activity (H3-K9 specific) inferred from direct assay (Czermin et al., 2001)
Biological Process
CV term Evidence References
chromatin organization inferred from mutant phenotype (Ner et al., 2002) chromatin silencing inferred from mutant phenotype (Donaldson et al., 2002) chromatin silencing at centromere inferred from mutant phenotype (Donaldson et al., 2002) chromatin silencing at telomere inferred from 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 division inferred from direct assay (Yoon et al., 2008) gene silencing inferred from mutant phenotype (Schotta et al., 2002) heterochromatin formation inferred from mutant phenotype (Andreyeva et al., 2007) 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 (Ebert et al., 2004, Gracheva et al., 2009) histone methylation inferred from direct assay (Eskeland et al., 2004) histone modification inferred from mutant phenotype (Ner et al., 2002) oogenesis inferred from direct assay (Yoon et al., 2008) inferred from mutant phenotype (Kuhfittig et al., 2001)
Cellular Component
CV term Evidence References
polytene chromosome chromocenter inferred from direct assay (Koryakov et al., 2011)
Terms Based on Predictions or Assertions ( 12 terms )
Molecular Function
CV term Evidence References
chromatin binding non-traceable author statement (Swiss-Prot Project Members, 1995.9.1) GTPase activity inferred from electronic annotation with InterPro:IPR000795 (FlyBase Curators et al., 2004-) GTP binding inferred from electronic annotation with InterPro:IPR000795 (FlyBase Curators et al., 2004-) histone methyltransferase activity non-traceable author statement (Ner et al., 2002) histone methyltransferase activity (H3-K9 specific) non-traceable author statement (Ebert et al., 2003) traceable author statement (McNairn and Gilbert, 2003, Simms et al., 2003) zinc ion binding inferred from electronic annotation with InterPro:IPR003606, InterPro:IPR007728 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
chromatin organization non-traceable author statement (Schneider et al., 2002) gene silencing non-traceable author statement (Ebert et al., 2003) histone methylation traceable author statement (Simms et al., 2003)
Cellular Component
CV term Evidence References
chromosome, centromeric region traceable author statement (McNairn and Gilbert, 2003, Zhimulev and Belyaeva, 2003) heterochromatin non-traceable author statement (Swiss-Prot Project Members, 1995.9.1) traceable author statement (McNairn and Gilbert, 2003, Zhimulev and Belyaeva, 2003) nucleus inferred from electronic annotation with InterPro:IPR000953, InterPro:IPR003606, InterPro:IPR007728, InterPro:IPR011381 (FlyBase Curators et al., 2004-) non-traceable author statement (Swiss-Prot Project Members, 1995.9.1)
Sequence Ontology: Class of Gene
	nuclear_gene (FlyBase Genome Annotators, 2012) protein_coding_gene (FlyBase Genome Annotators, 2012)
Interactions & Pathways
Summary of Physical Interactions
Protein-protein
Interacting group Assay References
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions Su(var)3-9 allele Gene References Su(var)3-9306 B (Locke et al., 1993) Su(var)3-9310 B (Locke et al., 1993) Su(var)3-9322 B (Locke et al., 1993) Su(var)3-9328 B (Locke et al., 1993) Su(var)3-9ptn l(3)S089004 (Kuhfittig et al., 2001) unspecified B (Locke et al., 1993) JIL-1 (Zhang et al., 2006)
External Data
Linkouts
Orthologs
Genome-wide drosophilid orthologs	Dana\GF11769 Dere\eIF-2γ Dgri\GH18750 Dmoj\GI24667 Dper\GL12073 Dpse\GA19622 Dsec\GM25792 Dsim\GD20368 Dvir\GJ24041 Dwil\GK12089 Dyak\GE26397
Curated drosophilid orthologs	Dere\Su(var)3-9 (Krauss, 2000.6.1) Dnst\Su(var)3-9 (Krauss, 2005.7.19) Dpse\GA19622
Linkouts
Stocks & Reagents
Stocks Listed in FlyBase ( 5 )
Bloomington	6209 In(1)wm4; Su(var)3-91/TM3, Sb1 Ser1 6210 In(1)wm4; Su(var)3-92/TM3, Sb1 Ser1
Kyoto	108675 Su(var)3-91/TM3, Sb1 Ser1 108676 Su(var)3-92/TM3, Sb1 Ser1 104393 w*; P{GawB}Su(var)3-9NP3153 / TM6, Sb1 Tb1
Genomic Clones ( 2 )
	BACR13A02 BACR32A03 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 50 )
	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	RE16601
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	AT22281 GM06202 RE23877 RE42737 RE47877
Other clones	65707 83228 CK01.64A.G7 EC27245 EK064625 EK216751 EK298022 RP004072590 RP004100107 RP004107927 RP004112554 RP004119306 RP004133529 RP004136391 RP004201024 RP004205564 RP004216881 RP004217550 RP004219762 RP004230967 RP004234992 RP004235593 RP004236431 RP004243817 RP004248970 RP004249414 RP004250827 RP004254572 RP004256898 RP004263284 RP004291470 RP004309214 RP004359209 RP004405299 RP004419901 RP004456309 RP004467896 RP004478594 RP004497081 RP004497498 RP004521081 RP004542948 RP004551830 UUGC0170
RNAi & Array Information
Linkouts
Antibody Information
	polyclonal (Boeke et al., 2010)
Other Information
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
Relationship to Other Genes
Source for database identity 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 "pitkinD" 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)3-9ptn was reported to be allelic to two P-element insertion alleles at 67C (l(3)S089004S089004 and l(3)S089004S089302) in FBrf0134644. However, FBrf0180260 demonstrates that Su(var)3-9ptn is an allele of Su(var)3-9 (at 88E) and that the l(3)S089004S089004 and l(3)S089004S089302 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
	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 bwD suppressed. (Csink and Henikoff, 1996) Phenotype of wbl 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)
External Crossreferences & Linkouts
Sequence Crossreferences
	DDBJ / EMBL / GenBank • AJ290956 CAA56376 CAB93768 X80070 Entrez Gene - A searchable database of RefSeq genes. • 41843 UniProtKB/Swiss-Prot • P45975
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Chromo domain, conserved site (IPR023779) Chromo domain (IPR023780) Protein synthesis factor, GTP-binding (IPR000795) Chromo domain/shadow (IPR000953) SET domain (IPR001214) Pre-SET zinc-binding sub-group (IPR003606) Post-SET domain (IPR003616) Pre-SET domain (IPR007728) Histone H3-K9 methyltransferase (IPR011381) Chromo domain-like (IPR016197)
Linkouts
Synonyms & Secondary IDs ( 31 )
Reported As
Symbol Synonym	caa56376 Suvar39 Dm (Alvarez-Venegas and Avramova, 2002) CG6476 (Keleman et al., 2009.8.5, ) dSU(VAR)3-9 (Eskeland et al., 2004) E(var)3-2   ptn (Kuhfittig et al., 2001) Su(var) (Scaria et al., 2008) Su(var)3-9 (Lam et al., 2005, Krauss and Reuter, 2000, Krauss et al., 2005, Budde, 2007, Goldberg et al., 2007, Li et al., 2007, Zaratiegui, 2007, Boeke et al., 2011, Yan et al., 2011, Cryderman et al., 2011, Koryakov et al., 2011, Gan et al., 2010, Di Stefano et al., 2011, Seum et al., 2007, Sakaguchi et al., 2008, Nisha et al., 2008, Talbert and Henikoff, 2006, Qi et al., 2006, Demakova et al., 2007, Moorman et al., 2006, Moorman et al., 2006, Doheny et al., 2008, Joanis and Lloyd, 2002, Haigh and Lloyd, 2007, Stuart et al., 2007, Nurminsky, 2007, Haynes et al., 2007, Kalmykova et al., 2005, Haynes et al., 2006, Maines et al., 2007, Mis et al., 2006, Peng and Karpen, 2007, Koryakov et al., 2006, Bai et al., 2007, Chiolo et al., 2008, Lin et al., 2008, Kent, 2008, Lecuyer et al., 2007, Fahrner and Baylin, 2003, Taylor-Harding et al., 2004, Deng et al., 2007, Xing et al., 2007, Andreyeva et al., 2007, Yasuhara and Wakimoto, 2008, Seum et al., 2007, Greil et al., 2007, Johansson et al., 2007, Mohan et al., 2007, Zhang et al., 2008, Cai et al., 2008, Delattre et al., 2004, Pindyurin et al., 2008, Lu et al., 2009, Vogel et al., 2009, Peng and Karpen, 2009, Abel et al., 2009, Brower-Toland et al., 2009, Phalke et al., 2009, Shareef et al., 2003, Hofmann et al., 2009, Gracheva et al., 2009, Shi et al., 2006, Pickersgill et al., 2006, Bazin et al., 2004, Czermin et al., 2002, Paredes and Maggert, 2009, Fagegaltier et al., 2009, Scaria et al., 2008, Yoon et al., 2008, Balasov, 2002, de Wit et al., 2008, de Wit et al., 2005, Skora and Spradling, 2010, Zhou et al., 2008, Lemos et al., 2010, Moshkovich and Lei, 2010, Krauss et al., 2006, Marygold et al., 2007, Tschiersch et al., 1994, Kappes et al., 2011) SU(VAR)3-9 (Yasuhara and Wakimoto, 2006, Naumann et al., 2005, de la Cruz et al., 2005, Ebert et al., 2003, Grewal and Elgin, 2007, Cryderman et al., 2007, Seum et al., 2007, Koryakov et al., 2007, Rudolph et al., 2007, Cryderman et al., 2008, Li et al., 2002, Pindyurin et al., 2007, Fanti et al., 2008, Czermin et al., 2001, Hines et al., 2009, Seeger et al., 2005, van Steensel et al., 2010, Boeke et al., 2010, Huang et al., 2010, Filion et al., 2010) Su(Var)3-9 (Stabell et al., 2003, Naumova et al., 1999, Shevelyov et al., 2009) su(var)3-9 (Brehm et al., 2004, Pai et al., 2004, Kroiss et al., 2009) Su(var) 3-9 (Bhadra et al., 2007) Su(var)3-902 (Netter et al., 1998) Su(var)306   Su(var)310   Su(var)328   Suv 3-9 (Abel et al., 2009) SUV39 (Gerber and Shilatifard, 2003) SUV39H1 (McNairn and Gilbert, 2003) SuVar3-9 (Ahmad, 2004, Workman and Abmayr, 2004) Suvar3-9 (Birchler et al., 2004) Suvar39 (Lund and van Lohuizen, 2004) Su-var(3)9 (Popkova et al., 2001, Wustmann et al., 1989, Reuter et al., 1986) Suvar(3)9 (Henikoff, 1996) Su-var(3)902 (Fauvarque and Dura, 1993)
Name Synonym	Enhancer of variegation 3-2 (Tschiersch et al., 1994) histone methyltransferase (Vogel et al., 2009) pitkin (Kuhfittig et al., 2001) Su(var)3-9 (Cryderman et al., 2005) Suppressor of variegation 3-9 (Xing et al., 2007) Suppressor of variegation 306   Suppressor of variegation 310   Suppressor of variegation 328
Secondary FlyBase IDs
	FBgn0003600 FBgn0003624 FBgn0004560 FBgn0014846 FBgn0263739
References ( 238 )
Generate a list of	All references relating to this gene ( 238 )
List References by type	Research paper  ( 135 ) Supplementary material  ( 2 ) Review  ( 59 ) Personal communication to FlyBase  ( 4 ) Abstract  ( 29 ) FlyBase analysis  ( 3 ) Conference report  ( 2 ) Protein sequence record  ( 1 ) DNA/RNA sequence record  ( 2 ) Book  ( 1 )
Recent research papers ( 17 )
	Boeke et al., 2011, PLoS ONE 6(6): e20761 The RNA Helicase Rm62 Cooperates with SU(VAR)3-9 to Re-Silence Active Transcription in Drosophila melanogaster. [FBrf0213941] Chiolo et al., 2011, Cell 144(5): 732--744 Double-Strand Breaks in Heterochromatin Move Outside of a Dynamic HP1a Domain to Complete Recombinational Repair. [FBrf0213146] Cryderman et al., 2011, Transcription 2(2): 95--99 Heterochromatin protein 1a is required for an open chromatin structure. [FBrf0213370] Di Stefano et al., 2011, Genes Dev. 25(1): 17--28 Functional antagonism between histone H3K4 demethylases in vivo. [FBrf0212709] Gibert et al., 2011, PLoS Genet. 7(1): e1001280 Segregating Variation in the Polycomb Group Gene cramped Alters the Effect of Temperature on Multiple Traits. [FBrf0212864] Kappes et al., 2011, Genes Dev. 25(7): 673--678 The DEK oncoprotein is a Su(var) that is essential to heterochromatin integrity. [FBrf0213363] Koryakov et al., 2011, Chromosome Res. 19(2): 235--249 The SUUR protein is involved in binding of SU(VAR)3-9 and methylation of H3K9 and H3K27 in chromosomes of Drosophila melanogaster. [FBrf0213472] Riddle et al., 2011, Genome Res. 21(2): 147--163 Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. [FBrf0213099] Yan et al., 2011, FASEB J. 25(1): 232--241 Unphosphorylated STAT and heterochromatin protect genome stability. [FBrf0212715] Boeke et al., 2010, PLoS ONE 5(4): e10042 Phosphorylation of SU(VAR)3-9 by the chromosomal kinase JIL-1. [FBrf0210532] Filion et al., 2010, Cell 143(2): 212--224 Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. [FBrf0212051] Gan et al., 2010, Cell Res. 20(7): 763--783 Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq. [FBrf0211191] Huang et al., 2010, J. Cell Sci. 123(16): 2853--2861 Drosophila CAF-1 regulates HP1-mediated epigenetic silencing and pericentric heterochromatin stability. [FBrf0211452] Lemos et al., 2010, Proc. Natl. Acad. Sci. U.S.A. 107(36): 15826--15831 Epigenetic effects of polymorphic Y chromosomes modulate chromatin components, immune response, and sexual conflict. [FBrf0211775] Moshkovich and Lei, 2010, PLoS Genet. 6(3): e1000880 HP1 Recruitment in the Absence of Argonaute Proteins in Drosophila. [FBrf0210291] Skora and Spradling, 2010, Proc. Natl. Acad. Sci. U.S.A. 107(16): 7389--7394 Epigenetic stability increases extensively during Drosophila follicle stem cell differentiation. [FBrf0210662] van Steensel et al., 2010, Genome Res. 20(2): 190--200 Bayesian network analysis of targeting interactions in chromatin. [FBrf0209848] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2010 Show reviews ...