FlyBase Gene Report: Dmel\Rcd4

General Information

Symbol

Dmel\Rcd4

Species

D. melanogaster

Name

Reduction in Cnn dots 4

Annotation Symbol

CG17295

Feature Type

protein_coding_gene

FlyBase ID

FBgn0032034

Gene Model Status

Current

Stock Availability

8 publicly available

Gene Summary

Reduction in Cnn dots 4 (Rcd4) encodes a protein involved in the regulation of the number of centrosomes per cell. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
UniProtKB
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

29B4-29B4

Sequence location

2L:8,382,861..8,383,657 [+]

Recombination map

2-31

RefSeq locus

NT_033779 REGION:8382861..8383657

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (4 terms)

Molecular Function (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables protein binding

inferred from physical interaction with UniProtKB:A1Z8X3

(Panda et al., 2020)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (2 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

involved_in centriole assembly

inferred from mutant phenotype

(Panda et al., 2020)

involved_in centriole replication

inferred from mutant phenotype

(Dobbelaere et al., 2008)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in centriole

inferred from direct assay

(Dobbelaere et al., 2008)

inferred from direct assay

(Panda et al., 2020)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

Protein Family (UniProt)

Belongs to the PPP1R35 family. (Q9VLM6)

Protein Signatures (InterPro)

Protein phosphatase 1 regulatory subunit 35, C-terminal

Summaries

Gene Snapshot

Reduction in Cnn dots 4 (Rcd4) encodes a protein involved in the regulation of the number of centrosomes per cell. [Date last reviewed: 2019-03-14]

Protein Function (UniProtKB)

Participates in the later stages of centriole assembly through the interaction with Ana3 leading to the centriole to centrosome conversion in somatic cells.

(UniProt, Q9VLM6)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Rcd4 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

Structure

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q9VLM6)

If you don't see a structure in the viewer, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Gene model reviewed during 5.45

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Rcd4-RA

FBtr0079652

NM_135377

733

199

Rcd4-RB

FBtr0303472

NM_001201793

681

199

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

UniProt

RefSeq ID

GenBank

Rcd4-PA

FBpp0079268

22.2

199

10.17

FBpp0292524

22.2

199

10.17

Q9VLM6

NP_001188722

ADV36972

Polypeptides with Identical Sequences

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

199 aa isoforms: Rcd4-PA, Rcd4-PB

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Subunit Structure (UniProtKB)

Interacts with Ana3; this complex is recruited to daughter centrioles before their conversion to centrosomes.

(UniProt, Q9VLM6)

Crossreferences

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

Protein phosphatase 1 regulatory subunit 35, C-terminal

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q9VLM6

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Rcd4 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

Testis-specificity index

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).

-0.15

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in centriole

inferred from direct assay

(Dobbelaere et al., 2008)

inferred from direct assay

(Panda et al., 2020)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Rcd4 in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\Rcd4

View exonic expression by tissue for Dmel\Rcd4

Bulk Downloads

RNA-Seq RPKM values for all genes

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

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

34158/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0032034

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0032034

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0032034

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG17295

Flygut - An atlas of the Drosophila adult midgut

FBgn0032034

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 7 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 9 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Rcd4

Transgenic constructs containing regulatory region of Rcd4

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 4 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

lethal - all die during P-stage, with Scer\GAL4^Mef2.PR

Rcd4^GD9341

partially lethal (with Df(2L)ED626)

Rcd4²

partially lethal | recessive

Rcd4²

partially lethal - majority die, with Scer\GAL4^pnr-MD237

Rcd4^GD9341

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Rcd4^GD9341

Sterility

Allele

female sterile (with Df(2L)ED626)

female sterile (with Rcd4¹)

Rcd4²

female sterile (with Rcd4²)

Rcd4¹

female sterile | recessive

male fertile, with Rcd4², Scer\GAL4^elav-C155

Rcd4^UASp.EGFP

male fertile, with Rcd4^UASp.EGFP, Scer\GAL4^elav-C155

Rcd4²

Other Phenotypes

Allele

abnormal body color, with Scer\GAL4^pnr-MD237

Rcd4^GD9341

abnormal mitotic cell cycle | embryonic stage | maternal effect, with Rcd4¹, Scer\GAL4^elav-C155

Rcd4^UASp.EGFP

abnormal mitotic cell cycle | embryonic stage | maternal effect, with Rcd4², Scer\GAL4^elav-C155

Rcd4^UASp.EGFP

abnormal mitotic cell cycle | embryonic stage | maternal effect, with Rcd4^UASp.EGFP, Scer\GAL4^elav-C155

abnormal pain response | adult stage, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Rcd4^GD9341

short lived (with Df(2L)ED626)

short lived (with Rcd4¹)

Rcd4²

short lived (with Rcd4²)

Rcd4¹

short lived | recessive

some die during P-stage (with Df(2L)ED626)

Rcd4²

some die during P-stage | recessive

Rcd4²

some die during pupal stage, with Scer\GAL4^pnr-MD237

Rcd4^GD9341

uncoordinated (with Df(2L)ED626)

uncoordinated (with Rcd4¹)

Rcd4²

uncoordinated (with Rcd4²)

Rcd4¹

uncoordinated | recessive

visible, with Scer\GAL4^pnr-MD237

Rcd4^GD9341

Phenotype manifest in

Allele

actin filament bundle

axoneme | absent

Rcd4¹

centriole | absent | male

Rcd4²

chordotonal neuron

ciliary rootlet | absent

femoral chordotonal organ

Johnston organ

mesonotum, with Scer\GAL4^pnr-MD237

Rcd4^GD9341

mitotic spindle | embryonic stage | maternal effect, with Rcd4¹, Scer\GAL4^elav-C155

Rcd4^UASp.EGFP

mitotic spindle | embryonic stage | maternal effect, with Rcd4², Scer\GAL4^elav-C155

Rcd4^UASp.EGFP

mitotic spindle | embryonic stage | maternal effect, with Rcd4^UASp.EGFP, Scer\GAL4^elav-C155

primary spermatocyte

Rcd4²

spindle pole centrosome | embryonic stage | maternal effect, with Rcd4¹, Scer\GAL4^elav-C155

Rcd4^UASp.EGFP

spindle pole centrosome | embryonic stage | maternal effect, with Rcd4², Scer\GAL4^elav-C155

Rcd4^UASp.EGFP

spindle pole centrosome | embryonic stage | maternal effect, with Rcd4^UASp.EGFP, Scer\GAL4^elav-C155

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (0)

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (0)

Mus musculus (laboratory mouse) (0)

Xenopus tropicalis (Western clawed frog) (0)

Danio rerio (Zebrafish) (0)

Caenorhabditis elegans (Nematode, roundworm) (0)

Anopheles gambiae (African malaria mosquito) (1)

Agam\AgaP_AGAP009620

4 of 12

Yes

Arabidopsis thaliana (thale-cress) (0)

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Rcd4. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (0)

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 0 )

Human Ortholog

Disease

Evidence

References

Modifiers Based on Experimental Evidence ( 0 )

Allele

Disease

Interaction

References

Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)

Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.

Homo sapiens (Human)

Gene name

Score

OMIM

OMIM Phenotype

DO term

Complementation?

Transgene?

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

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

Rcd4 - ana3

pull down, western blot, anti tag coimmunoprecipitation, Identification by mass spectrometry

(Panda et al., 2020)

Summary of Genetic Interactions

Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Subunit Structure (UniProtKB)

Interacts with Ana3; this complex is recruited to daughter centrioles before their conversion to centrosomes.

(UniProt, Q9VLM6 )

Linkouts

BioGRID - A database of protein and genetic interactions.

60282

DroID - A comprehensive database of gene and protein interactions.

FBgn0032034

MIST (protein-protein) - An integrated Molecular Interaction Database

34158

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-31

Cytogenetic map

29B4-29B4

Sequence location

2L:8,382,861..8,383,657 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

29B4-29B4

Limits computationally determined from genome sequence between P{EP}EP646^EP646&P{lacW}RpS13^k09614 and P{lacW}l(2)k12914^k12914&P{lacW}Akap200^k07118a

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-31

(FlyBase, 2016)

2-27.7

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (8)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

15375

w^*; P{EPgy2}Rcd4^EY01780

Kyoto

123300

w¹¹¹⁸; P{RS3}Rcd4^CB-0729-3

NIG-Fly

17295R-6

P{NIG.17295R}6

M2L-0738

y¹ w¹¹¹⁸; Rcd4^SK1 P{neoFRT}40A/CyO-Tb

M2L-0739

y¹ w¹¹¹⁸; Rcd4^SK2 P{neoFRT}40A/CyO-Tb

2LG-0583

y² VhaAC39-1^cho-1 v¹; P{U6-Rcd4.NIG.sgRNA}attP40/CyO

VDRC

v106376

P{KK110603}VIE-260B

v25251

w¹¹¹⁸; P{GD9341}v25251

Genomic Clones (14)

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

cDNA Clones (7)

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.

cDNA clones, fully sequenced

BDGP DGC clones

SD16838

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.

FBgn0032034

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

GH07303

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0032034

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

New stable cell line derived from S2-ThermoFischer : Centriolar proteins were tagged with GFP at either the N- or C- terminus and used to create stable S2 cell lines. S2 cell lines constitutively expressing the following constructs were created: asl-GFP, Sas-6-GFP, ana1-GFP, GFP-ana1, Cep135-GFP, ana3-GFP, Rcd4-GFP, ana2-GFP, GFP-asl.
(Tian et al., 2021)
New stable cell line derived from S2-ThermoFischer : Stable cell lines established expressing GFP-tagged ana3 or Rcd4 under the control of the Act5C promoter.
(Panda et al., 2020)

Other Comments

Rcd4 is involved in centriole duplication and is required for efficient recruitment of pericentriolar material.

(Dobbelaere et al., 2008)

Relationship to Other Genes

Source for database merge of

Source for merge of: CG17295 BcDNA:SD16838

(FlyBase, 1996-)

Additional comments

Source for merge of CG17295 BcDNA:SD16838 was a shared cDNA ( date:030728 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Source for identity of: Rcd4 CG17295

(Dobbelaere et al., 2008)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (6)

Reported As

Symbol Synonym

BcDNA:SD16838

CG17295

(National Institute of Genetics Fly Stocks, 2022-, Hosono et al., 2015, Japanese National Institute of Genetics, 2012.5.21, Keleman et al., 2009.8.5, Dobbelaere et al., 2008, FlyBase Curators, 2008-)

Rcd4

(National Institute of Genetics Fly Stocks, 2022-, Fatalska et al., 2021, Tian et al., 2021, Hall et al., 2019, Jana et al., 2016, Dzhindzhev et al., 2014, Stevens et al., 2010, Dobbelaere et al., 2008)

rcd4

(Panda et al., 2020)

Name Synonyms

CG17295

Reduction in Cnn Dots 4

(Dobbelaere et al., 2008)

Reduction in Cnn dots 4

Secondary FlyBase IDs

FBgn0062872

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 32 )

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.

34158

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/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

Q9VLM6

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

Q9VLM6

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

Q9VLM6

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

34158/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0032034

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0032034

FlyMine - An integrated database for Drosophila genomics

FBgn0032034

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

Protein phosphatase 1 regulatory subunit 35, C-terminal

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG17295

MARRVEL_MODEL - MARRVEL (model organism gene)

34158

Linkouts

BioGRID - A database of protein and genetic interactions.

60282

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0032034

DroID - A comprehensive database of gene and protein interactions.

FBgn0032034

DRSC - Results frm RNAi screens

FBgn0032034

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0032034

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0032034

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG17295

Flygut - An atlas of the Drosophila adult midgut

FBgn0032034

MIST (protein-protein) - An integrated Molecular Interaction Database

34158

References (28)

The following external sites may use different assemblies or annotations than FlyBase.

-0.15

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