FlyBase Gene Report: Dmel\RpS4

General Information

Symbol

Dmel\RpS4

Species

D. melanogaster

Name

Ribosomal protein S4

Annotation Symbol

CG11276

Feature Type

protein_coding_gene

FlyBase ID

FBgn0011284

Gene Model Status

Current

Stock Availability

4 publicly available

Gene Summary

Ribosomal protein S4 (RpS4) encodes a structural constituent of ribosomes. [Date last reviewed: 2019-07-11] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

69F6-69F6

Sequence location

3L:13,041,756..13,044,234 [+]

Recombination map

3-39

RefSeq locus

NT_037436 REGION:13041756..13044234

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 (7 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables structural constituent of ribosome

inferred from high throughput direct assay

(Alonso and Santaren, 2006)

inferred from direct assay

(Anger et al., 2013)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables RNA binding

inferred from electronic annotation with InterPro:IPR002942, InterPro:IPR036986

(InterPro Project Members, 2004-)

enables structural constituent of ribosome

inferred from electronic annotation with InterPro:IPR000876

(InterPro Project Members, 2004-)

traceable author statement

(Marygold et al., 2007)

inferred from biological aspect of ancestor with PANTHER:PTN000171891

(GO Reference Genome Project, 2011-)

Biological Process (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in cytoplasmic translation

inferred by curator from GO:0022626

(Anger et al., 2013, Alonso and Santaren, 2006)

traceable author statement

(Marygold et al., 2007)

involved_in translation

inferred from biological aspect of ancestor with PANTHER:PTN000171891

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR000876

(InterPro Project Members, 2004-)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in cytosolic ribosome

inferred from high throughput direct assay

(Alonso and Santaren, 2006)

inferred from direct assay

(Anger et al., 2013)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

part_of cytosolic small ribosomal subunit

inferred from biological aspect of ancestor with PANTHER:PTN000171891

(GO Reference Genome Project, 2011-)

traceable author statement

(Marygold et al., 2007)

located_in ribosome

inferred from electronic annotation with InterPro:IPR000876

(InterPro Project Members, 2004-)

Gene Group (FlyBase)

CYTOPLASMIC SMALL RIBOSOMAL SUBUNIT

CYTOPLASMIC SMALL RIBOSOMAL SUBUNIT - TESTIS-SPECIFIC VARIANT

Protein Family (UniProt)

Belongs to the eukaryotic ribosomal protein eS4 family. (P41042)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Ribosomal protein S4 (RpS4) encodes a structural constituent of ribosomes. [Date last reviewed: 2019-07-11]

Gene Group (FlyBase)

CYTOPLASMIC SMALL RIBOSOMAL SUBUNIT -: Cytoplasmic ribosomes are found on the endoplasmic reticulum and in the cytosol. They translate all mRNAs produced from nuclear genes and perform the majority of cellular protein synthesis. Ribosomes are formed by two ribonucleoprotein subunits, large and small. The principle function of the small subunit is to bind mRNA. (Adapted from FBrf0205398.)
CYTOPLASMIC SMALL RIBOSOMAL SUBUNIT - TESTIS-SPECIFIC VARIANT -: Cytoplasmic ribosomes are found on the endoplasmic reticulum and in the cytosol. They translate all mRNAs produced from nuclear genes and perform the majority of cellular protein synthesis. Ribosomes are formed by two ribonucleoprotein subunits, large and small. The principle function of the small subunit is to bind mRNA. Tissue expression data from modENCODE has been used to infer the composition of the cytosolic small ribosomal subunit testis-specific variant. (Adapted from FBrf0205398.)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\RpS4 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 P41042)

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

PDB - An information portal to biological macromolecular structures

Comments on Gene Model

Gene model reviewed during 5.45

Gene model reviewed during 5.56

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

RpS4-RA

FBtr0075884

NM_168537

976

261

RpS4-RB

FBtr0075885

NM_079329

1075

261

RpS4-RC

FBtr0346390

NM_001300126

1305

261

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

RpS4-PA

FBpp0075618

29.1

261

10.85

FBpp0075619

29.1

261

10.85

FBpp0312080

29.1

261

10.85

P41042

NP_001287055

AHN58080

Polypeptides with Identical Sequences

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

261 aa isoforms: RpS4-PA, RpS4-PB, RpS4-PC

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

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

PDB - An information portal to biological macromolecular structures

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\RpS4 using the Feature Mapper tool.

External Data

Crossreferences

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

RpS4_1

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).

-1.25

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

day 7 of adulthood -- day 49 of adulthood

adult heart

(Cammarato et al., 2011)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in cytosolic ribosome

inferred from high throughput direct assay

(Alonso and Santaren, 2006)

inferred from direct assay

(Anger et al., 2013)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\RpS4 in JBrowse

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

View exonic expression by developmental stage for Dmel\RpS4

View exonic expression by tissue for Dmel\RpS4

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

39484/tissue=All

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

FBgn0011284

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0011284

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

FBgn0011284

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

CG11276

Flygut - An atlas of the Drosophila adult midgut

FBgn0011284

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 0 )

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 RpS4

Transgenic constructs containing regulatory region of RpS4

Aberrations (Deficiencies and Duplications) ( 2 )

Inferred from experimentation ( 2 )

Gene disrupted in

Df(3L)Exel6261

(Ryder, 2004.4.26)

Df(3L)VW1

(Marygold et al., 2007)

Inferred from location ( 0 )

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 before end of pupal stage, with Scer\GAL4^pnr-MD237

RpS4^GD13437

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

RpS4^GD13437

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

RpS4^GD13437

partially lethal, with Scer\GAL4^tin.CΔ4

RpS4^GD13437

Other Phenotypes

Allele

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

RpS4^GD13437

Phenotype manifest in

Allele

larval somatic muscle cell, with Scer\GAL4^Mef2.PR

RpS4^GD13437

sarcomere, with Scer\GAL4^Mef2.PR

RpS4^GD13437

Z disc, with Scer\GAL4^Mef2.PR

RpS4^GD13437

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) (3)

Hsap\RPS4X

14 of 14

Yes

Hsap\RPS4Y1

12 of 14

Yes

Hsap\RPS4Y2

11 of 14

Yes

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (3)

Rnor\Rps4x

13 of 14

Yes

Rnor\Rps4y2

13 of 14

Yes

Rnor\Rps4x-ps9

1 of 14

Yes

Mus musculus (laboratory mouse) (2)

Mmus\Rps4x

12 of 14

Yes

Mmus\Gm15013

9 of 14

Yes

Xenopus tropicalis (Western clawed frog) (1)

Xtro\rps4x

10 of 13

Yes

Danio rerio (Zebrafish) (1)

Drer\rps4x

14 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\rps-4

14 of 14

Yes

Anopheles gambiae (African malaria mosquito) (1)

Agam\AgaP_AGAP006871

12 of 12

Yes

Arabidopsis thaliana (thale-cress) (3)

Atha\AT2G17360

13 of 13

Yes

Atha\AT5G58420

13 of 13

Yes

Atha\AT5G07090

12 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\RPS4A

13 of 13

Yes

Scer\RPS4B

13 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (3)

Spom\rps401

12 of 12

Yes

Spom\rps402

12 of 12

Yes

Spom\rps403

12 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:RpS4. 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 ( 1 )

Allele

Disease

Interaction

References

RpS4^HMS05869

exacerbates cancer

modeled by Rbf^HMS03004

(Parkhitko et al., 2021)

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?

RPS4X; ribosomal protein S4 X-linked

14 of 14

312760

RPS4Y1; ribosomal protein S4 Y-linked 1

12 of 14

470000

RPS4Y2; ribosomal protein S4 Y-linked 2

11 of 14

400030

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

RpS4 - Rack1

cosedimentation, electron microscopy

(Anger et al., 2013)

RpS4 - RpL10

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL10Ab

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL11

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL12

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL13

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL13A

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL14

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL15

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL17

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL18

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL18A

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL19

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL21

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL22

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL23

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL23A

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL24

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL26

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL27

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL27A

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL28

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL29

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL3

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL30

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL31

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL32

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL34a

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL35

cosedimentation, electron microscopy

(Anger et al., 2013)

RpS4 - RpL35A

cosedimentation, electron microscopy

(Anger et al., 2013)

RpS4 - RpL36

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL36A

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL37-1

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL37A

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL38

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL39

cosedimentation, electron microscopy

(Anger et al., 2013)

RpS4 - RpL4

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL40

cosedimentation, electron microscopy

(Anger et al., 2013)

RpS4 - RpL41

cosedimentation, electron microscopy

(Anger et al., 2013)

RpS4 - RpL5

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL6

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL7

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL7A

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL8

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpL9

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpLP0

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpLP1

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpLP2

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS10a

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS11

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS12

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS13

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS14a

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS14b

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS15

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS15Aa

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS16

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS17

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS18

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS19a

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS2

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS20

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS21

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS23

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS24

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS25

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS26

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS27

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS27A

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS28b

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS29

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS3

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS30

cosedimentation, electron microscopy

(Anger et al., 2013)

RpS4 - RpS3A

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS5a

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS6

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS7

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS8

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - RpS9

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - S6kII

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

RpS4 - clu

anti tag coimmunoprecipitation, western blot, anti bait coimmunoprecipitation, peptide massfingerprinting, anti tag western blot

(Sen and Cox, 2016)

RpS4 - eEF2

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - kra

anti bait coimmunoprecipitation, Identification by mass spectrometry

(Wang et al., 2006)

RpS4 - melt

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

RpS4 - sta

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RpS4 - vig2

cosedimentation, Identification by mass spectrometry, electron microscopy

(Anger et al., 2013)

RNA-protein

Physical Interaction

Assay

References

RpS4 - 18SrRNA

cosedimentation, electron microscopy

(Anger et al., 2013)

RpS4 - 28SrRNA

cosedimentation, electron microscopy

(Anger et al., 2013)

RpS4 - 2SrRNA

cosedimentation, electron microscopy

(Anger et al., 2013)

RpS4 - 5.8SrRNA

cosedimentation, electron microscopy

(Anger et al., 2013)

RpS4 - 5SrRNA

cosedimentation, electron microscopy

(Anger et al., 2013)

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

Linkouts

BioGRID - A database of protein and genetic interactions.

64829

DroID - A comprehensive database of gene and protein interactions.

FBgn0011284

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

39484

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Ribosome

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-39

Cytogenetic map

69F6-69F6

Sequence location

3L:13,041,756..13,044,234 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

69F6-69F6

Limits computationally determined from genome sequence between P{lacW}RpS12^s2783 and P{PZ}l(3)04220⁰⁴²²⁰&P{lacW}l(3)j10B6^j10B6

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

cDNA clone hybridises to two sites: 1B1-1B2 and 3A3-3A6. Sequence analysis is required to assign RpS4 to either site.

(Yokokura et al., 1993)

Experimentally Determined Recombination Data

Location

3-39

(FlyBase, 2016)

3-34.0

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (4)

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

Bloomington

82945

y¹ v¹; P{TRiP.HMS05869}attP2

11276R-2

v106654

v35718

w¹¹¹⁸; P{GD13437}v35718

Genomic Clones (9)

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

cDNA Clones (810)

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

RE57333

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.

FBgn0011284

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0011284

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Nishiyama et al., 2007)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Haploinsufficient locus.

(Cook et al., 2012)

RNAi screen using dsRNA made from templates generated with primers directed against this gene results in aberrantly short, monopolar spindles when assayed in S2 cells. This phenotype can be observed when the screen is performed with or without Cdc27 dsRNA.

(Goshima et al., 2007)

Likely Minute gene.

(Marygold et al., 2007)

A deletion removing RpS4 and RpS12 shows Minute phenotypes, whereas deletions removing RpS12 but no other cytoplasmic ribosomal protein-encoding genes do not show Minute phenotypes, suggesting that RpS4 is a Minute gene.

(Marygold et al., 2007)

RNAi generated by PCR using primers directed to this gene causes a cell growth and viability phenotype when assayed in Kc167 and S2R⁺ cells.

(Boutros et al., 2004)

Area matching Drosophila ribosomal S4 protein gene, Acc No. D16257. Probable intron.

(Davies, 2001.3.15)

RpS4 cDNA is cloned and sequenced, a high degree of sequence similarity with mammalian RpS4 proteins suggests the proteins are encoded by homologous genes that have very similar biochemical activities.

(Yokokura et al., 1993)

Relationship to Other Genes

Source for database merge of

Additional comments

"RpS4" likely corresponds to "M(3)69E".

(Marygold et al., 2007)

It is not possible to say whether "M(3)69E" corresponds to "RpS12" or "RpS4", or whether the genetically-defined "M(3)69E" locus is a composite of both ribosomal protein genes.

(Deal and Cook, 2002.1.22)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (10)

Reported As

Symbol Synonym

CG11276

(Kolkhof et al., 2017, Rosa-Ferreira et al., 2015, Fukuoh et al., 2014, Schertel et al., 2013, Jaspers et al., 2012, Cammarato et al., 2011, Müller et al., 2010, Keleman et al., 2009.8.5, Perkins et al., 2009, Worringer et al., 2009, Goshima et al., 2007, Marygold et al., 2007, Cermelli et al., 2006, Huang et al., 2005)

RPS4

(Pinnola et al., 2007, Wang et al., 2006, Bergen et al., 1998, Yokokura et al., 1993)

Rp S4

(Alonso and Santaren, 2006)

S4e

(Anger et al., 2013)

SX4

(Brogna et al., 2002)

anon-EST:Posey270

rpS4

(Nishiyama et al., 2007, Yokokura, 1994.1.13)

Name Synonyms

Ribosomal protein S4

(Jaspers et al., 2012, Cammarato et al., 2011)

ribosomal protein S4

(Sen and Cox, 2016)

Secondary FlyBase IDs

FBgn0025296

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 62 )

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.

39484

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.

P41042

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

P41042

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

X2JGM9

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.

P41042

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

39484/tissue=All

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

FBgn0011284

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

FBgn0011284

FlyMine - An integrated database for Drosophila genomics

FBgn0011284

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

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

dme:Dmel_CG11276

MARRVEL_MODEL - MARRVEL (model organism gene)

39484

PDB - An information portal to biological macromolecular structures

Linkouts

BioGRID - A database of protein and genetic interactions.

64829

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

FBgn0011284

DroID - A comprehensive database of gene and protein interactions.

FBgn0011284

DRSC - Results frm RNAi screens

FBgn0011284

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

RpS4_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0011284

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0011284

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

CG11276

Flygut - An atlas of the Drosophila adult midgut

FBgn0011284

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0011284

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC013431

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Ribosome

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

39484

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

References (91)

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

-1.25

Report Sections