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Gene Dmel\Rpd3

General Information
Symbol	Dmel\Rpd3	Species	D. melanogaster
Name	Rpd3	Annotation symbol	CG7471
Feature type	protein_coding_gene	FlyBase ID	FBgn0015805
Created / Updated	2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)	3L	Recombination map
Cytogenetic map	64B12-64B12	Sequence location	3L:4,626,717..4,629,471 [+]
Map ( GBrowse )	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	This gene is referred to in FlyBase by the symbol Rpd3 (CG7471, FBgn0015805). It has the cytological map location 64B12. Its sequence location is 3L:4626717..4629471. Its molecular function is described as: histone deacetylase activity; transcription corepressor activity; protein binding; histone lysine N-methyltransferase activity (H3-K27 specific); histone lysine N-methyltransferase activity (H3-K9 specific). It is involved in the biological processes: blastoderm segmentation; negative regulation of transcription; chromatin silencing; gene silencing; histone deacetylation; determination of adult life span; histone methylation; dendrite morphogenesis; muscle development; oogenesis. 29 alleles are reported. The phenotypes of these alleles are annotated with 12 unique terms, many of which group under: organ system; adult segment; peripheral nervous system; nervous system; integumentary system; cuticle; adult mesothoracic segment; embryonic tagma; embryonic segment; cephalopharyngeal skeleton. It has one annotated transcript and one annotated polypeptide.
External Summaries
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 64B12-64B12   Limits computationally determined from genome sequence between P{PZ}l(3)rG166rG166 and P{PZ}sinu06524
Experimentally Determined Cytological Location
Cytogenetic map Notes References 64B-64C   (Spierer, 1996.11.6) 64C7-64C8   (Mottus, 1998.8.24) 64C1-64C6   (Johnson, 1997.9.26) 64C1-64C2 (determined by in situ hybridisation)   (Spradling et al., 1999) 64C1-64C6 (determined by in situ hybridisation)   (Johnson et al., 1998) 64C1-64C2 (determined by in situ hybridisation)   (Perrimon et al., 1996) 64B-64C (determined by in situ hybridisation)   (De Rubertis et al., 1996) 64B-64C   (De Rubertis et al., 1996) 64C1-64C2   (BDGP Project Members, 1994-1999)
Experimentally Determined Recombination Data
Location	3- (Sinclair et al., 1983, De Rubertis et al., 1996, Gepner et al., 1996, Spierer, 1996.11.6)
Left of (cM)
Right of (cM)
Notes	Maps near the tip of 3L. (Sinclair et al., 1983)
Molecular Map Data
Gene Order (in direction of increasing cytology) References Gene Order (overall orientation not stated) References
Gene Model & Products
Please see the GBrowse view of Dmel\Rpd3 for information on other features
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Rpd3-RA FBtr0073317  NM_139661   2145   521
Additional Transcript Data & Comments
Reported size (kB)	2.2 (northern blot) (De Rubertis et al., 1996)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kD) Length (aa) Theoretical pI RefSeq ID GenBank protein Rpd3-PA   FBpp0073173   58.3   521   5.51     NP_647918   AAF47924
Additional Polypeptide Data & Comments
Reported size (kD)	520 (aa) (De Rubertis et al., 1996) 521 (aa) (Mottus et al., 2000, Johnson et al., 1998)
Comments
External Data
Linkouts	PANTHER - Protein classification by function, families, and pathways • FBgn0015805
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Histone deacetylase superfamily (IPR000286) Histone deacetylase (IPR003084)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA201209   AA201342   AA201419   AA201513   AA202373   AA202647   AA263321   AA263673   AA264310   AA264929   AA392092   AA392703   AA392801   AA392871   AA392908   AA440171   AA440619   AA440725   AA536503   AA538879   AA539365   AA539604   AA540188   AA540906   AA696898   AA735144   AA735296   AA735340   AA803742   AA816260   AA816588   AA816966   AA820182   AA820333   AA941409   AA941447   AA948799   AA949427   AA949720   AA949860   AA950807   AA979264   AE003482 AAF47924   AF026949 AAC23917   AF086715 AAC61494   AI061694   AI135186   AI256888   AI257423   AI258092   AI258404   AI455114   AI455676   AI456334   AI456826   AI456926   AI512978   AI514371   AI515016   AI516763   AI518370   AI518586   AI518725   AI518989   AI519224   AI519699   AI520028   AI520145   AI533938   AI534443   AI541962   AI542303   AI542991   AI543927   AI546527   AI546554   AQ073107   AY058487 AAL13716   BG635506   BI163285   BI164594   BI173050   BI173540   BI214078   BI231324   BI234681   BI236270   BI242663   BI355128   BI362212   BI372475   BI375781   BI483721   BI485073   BI577870   BI579812   BI632235   BI636790   BI636898   BI637253   BI639621   CK657697   CO266193   CO289682   CO311894   CO317806   CO321959   CZ469061   CZ479671   EC061175   EC066671   EC068547   EC084469   EC194429   EC213711   EC219107   EC225405   EC241365   EC241491   EC243158   EC250620   G00703   Y09258 CAA70455
UniProtKB/Swiss-Prot	Q94517
UniProtKB/TrEMBL
Maps to
Does NOT map to
Identified with	GM14158 (BDGP Project Members, 2000-) LD06915 (Spradling et al., 1999) Dm0562 (BDGP Project Members, 1994-1999, Spradling et al., 1999)
Mapped Features & Mutations
Please see GBrowse or insertion reports for information on insertions of transgenic constructs and features not listed here Type Symbol & Location Additional Notes References point mutation Rpd3[313] 3L:4,627,470..4,627,470 comment=Site of nucleotide substitution in mutant inferred by FlyBase based on reported amino acid change. The mutation is reported at residue R30. The analagous amino acid in the reference sequence is R32. evidence=experimental pr_change=R32C|Rpd3-PA reported_pr_change=R30C na_change=C4627470T (Mottus et al., 2000) point mutation Rpd3[328] 3L:4,627,747..4,627,747 comment=Site of nucleotide substitution in mutant inferred by FlyBase based on reported amino acid change. evidence=experimental pr_change=C98Y|Rpd3-PA reported_pr_change=C98Y na_change=G4627747A (Mottus et al., 2000) point mutation Rpd3[303] 3L:4,627,747..4,627,747 comment=Site of nucleotide substitution in mutant inferred by FlyBase based on reported amino acid change. evidence=experimental pr_change=C98Y|Rpd3-PA reported_pr_change=C98Y na_change=G4627747A (Mottus et al., 2000) point mutation Rpd3[326] 3L:4,628,064..4,628,064 comment=Site of nucleotide substitution in mutant inferred by FlyBase based on reported amino acid change. evidence=experimental pr_change=P204S|Rpd3-PA reported_pr_change=P204S na_change=C4628064T (Mottus et al., 2000)
External Data
Linkouts	DEDB - Drosophila exon database: splicing graphs • 2388
Crossreferences
Expression Data
FlyBase-Curated Data
Transcript and Protein data	Please see the FlyBase Gene Expression Report for details of gene expression from the literature.
Summary of Transcript Expression
Stage Tissue/Position Reference  larval stage  eye-antennal disc (De Rubertis et al., 1996)  embryonic stage,larval stage,adult stage   (De Rubertis et al., 1996)
Marker for
Subcellular Localization
CV Term
Summary of Polypeptide Expression
Stage Tissue/Position Reference
Marker for
Subcellular Localization
CV Term
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0015805 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • FBgn0015805 GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies • FBgn0015805 FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for Rpd3 Stage(s) 4-6 Stage(s) 7-8 Stage(s) 11-12 Stage(s) 13-16
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele viable Rpd315-1 lethal Rpd3CB04302 lethal | recessive Rpd304556 Rpd31-3 Rpd33-10 Rpd3303 Rpd3326 Rpd3328 Rpd34-4 Rpd35-2 Rpd35-5 lethal | polyphasic | recessive Rpd304556 lethal | embryonic stage | maternal effect | poor Rpd304556 lethal | embryonic stage | germ-line clone | pair rule Rpd304556 lethal | embryonic stage | germ-line clone | pair rule | recessive Rpd304556 lethal | larval stage | recessive Rpd3313 Rpd3326 Rpd3def24 Rpd3def8 semi-lethal Rpd304556 semi-lethal | recessive Rpd304556 semi-lethal | dominant | male Rpd3303 Rpd3313 Rpd3326 Rpd3328 Other Phenotypes Allele visible | drug conditional Rpd304556 enhancer of variegation | dominant, with In(1)wm4 Rpd315-1 enhancer of variegation, with In(1)wm4 Rpd315-1 suppressor of variegation | recessive, with In(1)wm4 Rpd304556 Rpd315-1 suppressor of variegation | dominant | female, with In(2R)bwVDe2 Rpd3326 Rpd3328 suppressor of variegation | dominant, with In(1)wm4 Rpd3303 Rpd3313 Rpd3326 Rpd3328 suppressor of variegation | dominant, with In(2R)bwVDe2 Rpd3326 Rpd3328 suppressor of variegation | dominant, with T(2;3)SbV Rpd3326 Rpd3328 long lived Rpd3def24 long lived | dominant | male Rpd304556 Rpd3def24 long lived | dominant | female Rpd304556 mitotic cell cycle defective Rpd35-5 Sterility Allele fertile Rpd315-1 Phenotype manifest in Allele cuticle | maternal effect Rpd304556 segment | maternal effect | pair rule Rpd304556 wing Rpd304556 Rpd3303 macrochaeta Rpd304556 Rpd3303 alula Rpd304556 Rpd3303 sex comb Rpd304556 Rpd3303 wing | drug conditional Rpd304556 embryonic segment | pair rule Rpd304556 embryo | germ-line clone | pair rule Rpd304556 cephalopharyngeal skeleton | germ-line clone Rpd304556 denticle belt | germ-line clone Rpd304556 embryonic epidermis | germ-line clone | pair rule Rpd304556 ommatidium Rpd315-1
Classical Alleles ( 19 )
For All Classical Alleles Show
Allele of Rpd3 Class Mutagen Stocks Known lesion Rpd304556 loss of function, hypomorph P-element activity 1 Yes Rpd31-3 ethyl methanesulfonate 0 -- Rpd315-1 loss of function P-element activity 0 Yes Rpd33-10 ethyl methanesulfonate 0 -- Rpd3303 hypomorph 0 Yes Rpd3313 hypomorph ethyl methanesulfonate 0 Yes Rpd3326 hypomorph ethyl methanesulfonate 0 Yes Rpd3328 hypomorph ethyl methanesulfonate 0 Yes Rpd34-4 ethyl methanesulfonate 0 -- Rpd35-2 ethyl methanesulfonate 0 -- Rpd35-5 ethyl methanesulfonate 0 -- Rpd3CB04302 P-element activity 0 Yes Rpd3EP3672 P-element activity 1 Yes Rpd3X5 P-element activity 0 Yes Rpd3c04194 piggyBac transposase 1 -- Rpd3def24 loss of function Δ2-3 0 Yes Rpd3def8 loss of function Δ2-3 0 Yes Rpd3e01851 piggyBac transposase