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General Information
Symbol
Dmel\Rga
Species
D. melanogaster
Name
Regena
Annotation Symbol
CG2161
Feature Type
FlyBase ID
FBgn0017550
Gene Model Status
Stock Availability
Gene Snapshot
Also Known As

NOT2, l(3)03834

Key Links
Genomic Location
Cytogenetic map
Sequence location
3R:5,607,275..5,613,112 [-]
Recombination map

3-47.5

RefSeq locus
NT_033777 REGION:5607275..5613112
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (13 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from physical interaction with FLYBASE:Marf1; FB:FBgn0039972
inferred from physical interaction with UniProtKB:Q8SY33
(assigned by UniProt )
Terms Based on Predictions or Assertions (0 terms)
Biological Process (7 terms)
Terms Based on Experimental Evidence (7 terms)
CV Term
Evidence
References
inferred from mutant phenotype
(assigned by UniProt )
inferred from direct assay
inferred from direct assay
inferred from mutant phenotype
inferred from genetic interaction with UniProtKB:Q9VHB0
(assigned by UniProt )
inferred from mutant phenotype
(assigned by UniProt )
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000595684
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000595688
(assigned by GO_Central )
Cellular Component (5 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from direct assay
located_in cytosol
inferred from direct assay
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000595684
(assigned by GO_Central )
located_in nucleus
inferred from electronic annotation with InterPro:IPR007282
(assigned by InterPro )
non-traceable author statement
(assigned by UniProt )
located_in P-body
inferred from biological aspect of ancestor with PANTHER:PTN000595684
(assigned by GO_Central )
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the CNOT2/3/5 family. (Q94547)
Summaries
Gene Group (FlyBase)
CCR4-NOT COMPLEX -
The CCR4-NOT complex is a conserved multi-subunit complex implicated in various cellular processes to regulated gene expression. It is best characterised in its role as the main enzyme responsible for the deadenylation of mRNA. The conserved core of the complex is composed of two modules: the NOT module and a catalytic module comprising two deadenylases, twin and Pop2. (Adapted from FBrf0221179 and FBrf0231273).
Protein Function (UniProtKB)
Component of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation (PubMed:20504953, PubMed:23303381). Additional complex functions may be a consequence of its influence on mRNA expression (PubMed:23303381). Essential for viability (PubMed:9475742). Acts as a suppressor of position effect variegation (PEV) at the white locus and regulates the expression of several unrelated genes (PubMed:9475742). Plays a role in germline stem cell differentiation in the ovaries (PubMed:29887366).
(UniProt, Q94547)
Gene Model and Products
Number of Transcripts
3
Number of Unique Polypeptides
2

Please see the JBrowse view of Dmel\Rga 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

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

Gene model reviewed during 5.46

Gene model reviewed during 5.55

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0078741
2902
585
FBtr0078742
2816
579
FBtr0345140
2514
579
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0078390
60.0
585
5.88
FBpp0078391
59.3
579
5.88
FBpp0311361
59.3
579
5.88
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

579 aa isoforms: Rga-PB, Rga-PC
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Component of the CCR4-NOT complex composed of at least Pop2/Caf1-55, Ccr4, Not1, Rga/Not2, and Not3.

(UniProt, Q94547)
Crossreferences
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\Rga using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
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
organism

Comment: maternally deposited

antennal primordium

Comment: reported as procephalic ectoderm primordium

central brain primordium

Comment: reported as procephalic ectoderm primordium

visual primordium

Comment: reported as procephalic ectoderm primordium

dorsal head epidermis primordium

Comment: reported as procephalic ectoderm primordium

lateral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

ventral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
located_in cytosol
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Rga in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 1-3
  • Stages(s) 4-6
  • Stages(s) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 12 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Rga
Transgenic constructs containing regulatory region of Rga
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation
Inferred from location
Phenotypes
Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
11 of 15
Yes
Yes
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
11 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (1)
7 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
5 of 12
Yes
No
Danio rerio (Zebrafish) (1)
9 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (2)
10 of 15
Yes
Yes
2 of 15
No
No
Arabidopsis thaliana (thale-cress) (2)
6 of 9
Yes
Yes
5 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
8 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
6 of 12
Yes
Yes
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG091908X2 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091506EF )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W06GO )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X06CC )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0C7Y )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (3)
6 of 10
2 of 10
2 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Model Summary Ribbon
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 1 )
Allele
Disease
Evidence
References
Potential Models Based on Orthology ( 0 )
Human Ortholog
Disease
Evidence
References
Modifiers Based on Experimental Evidence ( 1 )
Allele
Disease
Interaction
References
Disease Associations of Human Orthologs (via DIOPT v8.0 and OMIM)
Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
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.
Interactions
Summary of Physical Interactions
esyN Network Diagram
Show neighbor-neighbor interactions:
Select Layout:
Legend:
Protein
RNA
Selected Interactor(s)
Interactions Browser

Please see the Physical Interaction reports below for full details
protein-protein
Physical Interaction
Assay
References
RNA-protein
Physical Interaction
Assay
References
Summary of Genetic Interactions
esyN Network Diagram
esyN Network Key:
Suppression
Enhancement

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
External Data
Subunit Structure (UniProtKB)
Component of the CCR4-NOT complex composed of at least Pop2/Caf1-55, Ccr4, Not1, Rga/Not2, and Not3.
(UniProt, Q94547 )
Linkouts
BioGRID - A database of protein and genetic interactions.
DroID - A comprehensive database of gene and protein interactions.
InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
MIST (protein-protein) - An integrated Molecular Interaction Database
Pathways
Signaling Pathways (FlyBase)
Metabolic Pathways
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)
3R
Recombination map

3-47.5

Cytogenetic map
Sequence location
3R:5,607,275..5,613,112 [-]
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
83B5-83B6
Limits computationally determined from genome sequence between P{PZ}Snr101319&P{PZ}Itp-r83A05616 and P{lacW}Atus1938
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
83B4-83B5
(determined by in situ hybridisation)
Experimentally Determined Recombination Data
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (8)
Genomic Clones (19)
 
cDNA Clones (69)
 

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
Other clones
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.

cDNA Clones, End Sequenced (ESTs)
RNAi and Array Information
Linkouts
DRSC - Results frm RNAi screens
GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
Antibody Information
Laboratory Generated Antibodies
 
Commercially Available Antibodies
 
Other Information
Relationship to Other Genes
Source for database identify of

Source for identity of: Rga CG2161

Source for database merge of
Additional comments
Other Comments

Candidate stable intronic sequence RNA (sisRNA), named as "sisR-1", identified within CDS of this gene.

Rga modulates the expression of the w locus and several other unrelated genes.

Origin and Etymology
Discoverer
Etymology

The gene is named "Regena" - "Regulator of gene activity" as it affects the expression of numerous genes.

Identification
External Crossreferences and Linkouts ( 50 )
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.
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
UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
Other crossreferences
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
KEGG Genes - Molecular building blocks of life in the genomic space.
modMine - A data warehouse for the modENCODE project
Linkouts
BioGRID - A database of protein and genetic interactions.
DPiM - Drosophila Protein interaction map
DroID - A comprehensive database of gene and protein interactions.
DRSC - Results frm RNAi screens
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
FlyMine - An integrated database for Drosophila genomics
InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
MIST (protein-protein) - An integrated Molecular Interaction Database
Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
Synonyms and Secondary IDs (12)
Datasets (0)
Study focus (0)
Experimental Role
Project
Project Type
Title
References (87)