FlyBase Gene Report: Dmel\Rga

General Information

Symbol

Dmel\Rga

Species

D. melanogaster

Name

Regena

Annotation Symbol

CG2161

Feature Type

protein_coding_gene

FlyBase ID

FBgn0017550

Gene Model Status

Current

Stock Availability

8 publicly available

Gene Snapshot

Contributions welcome

Other Summaries

Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

NOT2, l(3)03834

Key Links

Genomic Location

Cytogenetic map

83B5-83B6

Sequence location

3R:5,607,275..5,613,112 [-]

Recombination map

3-47.5

RefSeq locus

NT_033777 REGION:5607275..5613112

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

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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

enables protein binding

inferred from physical interaction with FLYBASE:Marf1; FB:FBgn0039972

(Zhu et al., 2018)

inferred from physical interaction with UniProtKB:Q8SY33

(assigned by UniProt )

(Braun et al., 2011)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (7 terms)

Terms Based on Experimental Evidence (7 terms)

CV Term

Evidence

References

involved_in female germ-line stem cell population maintenance

inferred from mutant phenotype

(assigned by UniProt )

(Ng et al., 2018)

involved_in mRNA catabolic process

inferred from direct assay

(Bawankar et al., 2013)

involved_in negative regulation of translation

inferred from direct assay

(Bawankar et al., 2013)

involved_in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay

inferred from mutant phenotype

(Arvola et al., 2020)

involved_in nuclear-transcribed mRNA poly(A) tail shortening

inferred from mutant phenotype

(Temme et al., 2010)

involved_in regulation of stem cell population maintenance

inferred from genetic interaction with UniProtKB:Q9VHB0

(assigned by UniProt )

(Ng et al., 2018)

involved_in regulation of transcription, DNA-templated

inferred from mutant phenotype

(assigned by UniProt )

(Frolov et al., 1998)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in nuclear-transcribed mRNA poly(A) tail shortening

inferred from biological aspect of ancestor with PANTHER:PTN000595684

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in regulation of stem cell population maintenance

inferred from biological aspect of ancestor with PANTHER:PTN000595688

(assigned by GO_Central )

(Gaudet et al., 2011)

Cellular Component (5 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

part_of CCR4-NOT complex

inferred from direct assay

(Temme et al., 2010, Temme et al., 2004)

located_in cytosol

inferred from direct assay

(Temme et al., 2010)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

part_of CCR4-NOT core complex

inferred from biological aspect of ancestor with PANTHER:PTN000595684

(assigned by GO_Central )

(Gaudet et al., 2011)

located_in nucleus

inferred from electronic annotation with InterPro:IPR007282

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

non-traceable author statement

(assigned by UniProt )

(Frolov et al., 1998)

located_in P-body

inferred from biological aspect of ancestor with PANTHER:PTN000595684

(assigned by GO_Central )

(Gaudet et al., 2011)

Gene Group (FlyBase)

CCR4-NOT COMPLEX

Protein Family (UniProt)

Belongs to the CNOT2/3/5 family. (Q94547)

Protein Signatures (InterPro)

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

Number of Unique Polypeptides

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

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Rga-RA

FBtr0078741

NM_169080

2902

585

Rga-RB

FBtr0078742

NM_079515

2816

579

Rga-RC

FBtr0345140

NM_001300254

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

Rga-PA

FBpp0078390

60.0

585

5.88

NP_730966

AAF51992

Rga-PB

FBpp0078391

59.3

579

5.88

NP_524239

AAN13250

Rga-PC

FBpp0311361

59.3

579

5.88

NP_001287183

AHN57182

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

InterPro - A database of protein families, domains and functional sites

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

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.

Rga_1

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

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | faint | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

antennal primordium