Su(var)3-9 Suppressor of variegation 3-9 [Drosophila melanogaster (fruit fly)] - Gene

Summary

Official Symbol: Su(var)3-9provided by FlyBase
Official Full Name: Suppressor of variegation 3-9provided by FlyBase
Primary source: FLYBASE:FBgn0263755
Locus tag: Dmel_CG43664
See related: AllianceGenome:FB:FBgn0263755
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Drosophila melanogaster
Lineage: Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora
Also known as: caa56376 Suvar39 Dm; CG43664; CG6476; Dmel\CG43664; dSu(var)3-9; dSU(VAR)3-9; E(var)3-2; ptn; Su(var); Su(var) 3-9; su(var)3-9; Su(Var)3-9; Su(VAR)3-9; SU(VAR)3-9; Su(var)3-902; Su(var)306; Su(var)310; Su(var)328; Su-var(3)9; Su-var(3)902; Suv 3-9; suv39; SUV39; SUV39H1; Suvar(3)9; Suvar3-9; SuVar3-9; Suvar39
Old locus tag: Dmel_CG6476
Summary: Enables chromatin binding activity; histone H3K9 dimethyltransferase activity; and histone H3K9 trimethyltransferase activity. Involved in several processes, including female germ-line stem cell asymmetric division; negative regulation of response to gamma radiation; and siRNA-mediated pericentric heterochromatin formation. Located in pericentric heterochromatin and polytene chromosome chromocenter. Is expressed in several structures, including adult head; egg chamber; embryonic/larval salivary gland; germarium; and primordial germ cell. Orthologous to several human genes including SUV39H1 (SUV39H1 histone lysine methyltransferase). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs: all
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Genomic context

Location:: 88E7-88E8; 3-56 cM

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
Release 6.54	current	Release 6 plus ISO1 MT (GCF_000001215.4)	3R	NT_033777.3 (15259864..15263458, complement)
Release 5.57	previous assembly	Release 5 (GCF_000001215.2)	3R	NT_033777.2 (11085586..11089180, complement)

Chromosome 3R - NT_033777.3 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SetDB1 and Su(var)3-9 are essential for late stages of larval development of Drosophila melanogaster.
Title: SetDB1 and Su(var)3-9 are essential for late stages of larval development of Drosophila melanogaster.
Live analysis of position-effect variegation in Drosophila reveals different modes of action for HP1a and Su(var)3-9.
Title: Live analysis of position-effect variegation in Drosophila reveals different modes of action for HP1a and Su(var)3-9.
The Organization of Pericentromeric Heterochromatin in Polytene Chromosome 3 of the Drosophilamelanogaster Line with the Rif1(1); SuUR(ES) Su(var)3-9(06) Mutations Suppressing Underreplication.
Title: The Organization of Pericentromeric Heterochromatin in Polytene Chromosome 3 of the Drosophilamelanogaster Line with the Rif1(1); SuUR(ES) Su(var)3-9(06) Mutations Suppressing Underreplication.
SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster.
Title: SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster.
Transcriptome analysis revealed that wge represses eye identity genes independently of Su(var)3-9 and activates TD-related genes by acting together with Su(var)3-9. These findings provide new insights into diverse types of chromatin regulation at progressive steps of cell-fate conversions.
Title: winged eye Induces Transdetermination of Drosophila Imaginal Disc by Acting in Concert with a Histone Methyltransferase, Su(var)3-9.
results suggest that SU(VAR)3-9 targets RRP6 to a subset of heterochromatic loci where RRP6 degrades chromatin-associated non-coding RNAs in a process that is necessary to maintain the packaging of the heterochromatin
Title: An Interaction between RRP6 and SU(VAR)3-9 Targets RRP6 to Heterochromatin and Contributes to Heterochromatin Maintenance in Drosophila melanogaster.
The results showed that on chromosome 4, Su(var)3-9, SETDB1 and HP1a target the same genes.
Title: HP1a, Su(var)3-9, SETDB1 and POF stimulate or repress gene expression depending on genomic position, gene length and expression pattern in Drosophila melanogaster.
H1 plays a key role in silencing by tethering Su(var)3-9 to heterochromatin.
Title: Drosophila H1 regulates the genetic activity of heterochromatin by recruitment of Su(var)3-9.

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Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by FlyBase

Function	Evidence Code	Pubs
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K9 dimethyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K9 dimethyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K9 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K9 methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K9 methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K9 methyltransferase activity	TAS Traceable Author Statement more info	PubMed
enables histone H3K9 trimethyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in chromatin organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin organization	NAS Non-traceable Author Statement more info	PubMed
involved_in chromatin remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromosome organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in female germ-line stem cell asymmetric division	IDA Inferred from Direct Assay more info	PubMed
involved_in heterochromatin formation	HMP more info	PubMed
involved_in heterochromatin formation	IDA Inferred from Direct Assay more info	PubMed
involved_in heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heterochromatin organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of response to gamma radiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in oogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in oogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in pericentric heterochromatin formation	HMP more info	PubMed
involved_in siRNA-mediated pericentric heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in subtelomeric heterochromatin formation	HMP more info	PubMed

Component	Evidence Code	Pubs
located_in chromosome, centromeric region	TAS Traceable Author Statement more info	PubMed
located_in heterochromatin	IDA Inferred from Direct Assay more info	PubMed
located_in heterochromatin	TAS Traceable Author Statement more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in pericentric heterochromatin	IDA Inferred from Direct Assay more info	PubMed
located_in polytene chromosome chromocenter	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: suppressor of variegation 3-9

Names: CG43664-PA; Su(var)3-9-PA; enhancer of variegation 3-2; histone methyltransferase; pitkin; suppressor of variegation 306; suppressor of variegation 310; suppressor of variegation 328

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NT_033777.3 Reference assembly

Range

15259864..15263458 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_079633.3 → NP_524357.2 suppressor of variegation 3-9 [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_524357.2

Status: REVIEWED

UniProtKB/Swiss-Prot

P45975, Q9VFA6

UniProtKB/TrEMBL

I0DHL3

Conserved Domains (4) summary

smart00468
Location:362 → 455

PreSET; N-terminal to some SET domains

smart00317
Location:477 → 609

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

cd00024
Location:217 → 268

CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...

cl21455
Location:41 → 80

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases