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FB2026_01
,
released March 12, 2026
SuVar3-9, Su-var(3)9, SUV39, ptn
involved in gene silencing - a modifier of position effect variegation - methylates histone H3 thus providing a mark for the association of HP1 to heterochromatin
Please see 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
AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.
Low-frequency RNA-Seq exon junction(s) not annotated.
Gene model reviewed during 5.55
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).
Gene model reviewed during 5.42
2.4, 2.0 (northern blot)
There is only one protein coding transcript and one polypeptide associated with this gene
635, 475 (aa); 51 (kD predicted)
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.
Interacts with Su(var)205 and Su(var)3-7. Probably associates with HDAC1/Rpd3. Interacts with Rrp6; the interaction promotes association of Rrp6 with a subset of genomic loci (PubMed:26389589).
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.
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.
The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).
The 2.4 kb transcript is detected in all developmental stages by Northern blot, but it is enriched at 0-9 hr of embryogenesis.
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.
JBrowse - Visual display of RNA-Seq signals
View Dmel\Su(var)3-9 in JBrowse3-55.8
3-56.4 +/- 0.7
3-54.7 +/- 1.4
3-56.4
3-54.7
3-55.6
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.
Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
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 JBrowse for alignment of the cDNAs and ESTs to the gene model.
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.
polyclonal
Haploinsufficient locus.
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).
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.
Su(var)3-9 has a central role in heterochromatin-induced gene silencing.
Su(var)3-9 is required for normal development of the female germ line.
Variegation of bwD suppressed.
Phenotype of wbl is unchanged by Su(var)3-9.
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.
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.
homozygous viable
Source for merge of: Su(var)3-9 Su(var)330
Source for merge of: Su(var)3-9 Su(var)311
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.
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".
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.
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.
FlyBase curator comment: The Su(var)311 gene entry in FlyBase (FBgn0004115) was made for the 'Su(var)311' mutation described in FBrf0051451, where it is stated to map to 3-55.6 and FBrf0039952 is referenced for the screen that generated this suppressor of variegation mutation. In FBrf0155808 (another paper by the same lab as FBrf0051451), the suppressor of variegation mutation '311' (corresponding to the Su(var)3-9[311] allele, FBal0144511, in FlyBase) is stated to belong to the Su(var)3-9 complementation group, and again, FBrf0039952 is referenced for the screen that generated the 311 suppressor of variegation mutation. The genetic location of Su(var)3-9 is 3-56. Given this information, the Su(var)311 gene has been merged with the Su(var)3-9 gene in FlyBase, and the Su(var)311 mutation described in FBrf0051451 must correspond to the Su(var)3-9[311] allele.
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.
