FlyBase Gene Report: Dmel\28SrRNA

General Information

Symbol

Dmel\28SrRNA

Species

D. melanogaster

Name

28SrRNA

Annotation Symbol

Feature Type

cytosolic_rRNA_28S_gene

FlyBase ID

FBgn0061474

Gene Model Status

Not Applicable

Stock Availability

1 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Also Known As

28S, 28S rDNA, 28S ribosomal RNA, 28S RNA, 28SRNA

Function

Gene Ontology (GO) Annotations (0 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

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

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Transcript Data

Annotated Transcripts

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Polypeptides with Identical Sequences

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\28SrRNA using the Feature Mapper tool.

External Data

Crossreferences

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).

NA

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\28SrRNA in JBrowse

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

View exonic expression by developmental stage for Dmel\28SrRNA

View exonic expression by tissue for Dmel\28SrRNA

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

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 1 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 2 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of 28SrRNA

Transgenic constructs containing regulatory region of 28SrRNA

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

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.

Phenotype manifest in

Allele

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) (0)

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:28SrRNA. 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

RNA-protein

Physical Interaction

Assay

References

28SrRNA - Rack1

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL10

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL10Ab

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL11

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL12

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL13

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL13A

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL14

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL15

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL17

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL18

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL18A

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL19

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL21

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL22

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL23

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL23A

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL24

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL26

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL27

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL27A

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL28

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL29

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL3

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL30

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL31

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL32

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL34a

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL35

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL35A

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL36

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL36A

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL37-1

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL37A

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL38

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL39

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL4

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL40

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL41

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL5

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL6

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL7

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL7A

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL8

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpL9

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpLP0

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpLP1

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpLP2

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS10a

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS11

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS12

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS13

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS14a

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS14b

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS15

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS15Aa

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS16

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS17

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS18

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS19a

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS2

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS20

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS21

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS23

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS24

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS25

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS26

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS27

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS27A

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS28b

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS29

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS3

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS30

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS3A

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS4

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS5a

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS6

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS7

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS8

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - RpS9

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - eEF2

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - sta

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - vig2

cosedimentation, electron microscopy

(Anger et al., 2013)

RNA-RNA

Physical Interaction

Assay

References

28SrRNA - 18SrRNA

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - 2SrRNA

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - 5.8SrRNA

cosedimentation, electron microscopy

(Anger et al., 2013)

28SrRNA - 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

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

cytosolic_rRNA_28S_gene

gene_array_member

nuclear_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

Cytogenetic map

Sequence location

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (1)

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

Bloomington

62077

y¹; P{SUPor-P}28SrRNA^KV00547

Genomic Clones (0)

cDNA Clones (0)

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

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)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Extrachromosomal circular DNA (eccDNA) is present throughout the fly's life cycle. The eccDNA population contains circular multimers of tandemly repeated genes, including 28SrRNA.

(Cohen et al., 2003)

Relationship to Other Genes

Source for database merge of

Source for merge of: 28SrRNA BEST:HL02093 BEST:HL02977 BEST:HL03427

(FlyBase, 1996-)

Source for merge of: 28SrRNA NEST:bs30g02 BEST:LD41653

(FlyBase, 1996-)

Source for merge of: 28SrRNA NEST:bs10c09 NEST:bs15g08 NEST:bs17g11

(FlyBase, 1996-)

Encoded by

Ybb

Component gene(s)

28SrRNA:CR45837

28SrRNA:CR45844

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (18)

Reported As

Symbol Synonym

28S

(Miwa et al., 2020, Gerstberger et al., 2017, Wei et al., 2013, van der Linde et al., 2010, Fichelson et al., 2009, Tortoriello et al., 2009, Paredes and Maggert, 2008, Demakova et al., 2007, Ye and Eickbush, 2006, Mateos and Markow, 2005, Sage and Csink, 2003, Giribet et al., 2001, van Steensel et al., 2001, Eickbush et al., 2000, van Steensel and Henikoff, 2000)

28S DNA

(Plata et al., 2009)

28S RNA

(Ding and Lipshitz, 1993, Jakubczak et al., 1991)

28S rDNA

(Cohen et al., 2003, Ye et al., 2002, Talbert and Henikoff, 2000, Smoller et al., 1991)

28S rRNA

(Luo et al., 2020, Raje et al., 2018, He et al., 2015, Tafer et al., 2010, Zhang et al., 2008, Stage and Eickbush, 2007, Colon-Ramos et al., 2006, Averbeck and Eickbush, 2005, Bhadra et al., 2000, Giordano et al., 1999, Reim et al., 1999, Belyaeva et al., 1998, Friedrich and Tautz, 1997, Rae, 1996.10.2, Mandal, 1992.2.28, Tautz, 1990.3.15)

28SRNA

(Garcia-Arraez et al., 2019)

28SrRNA

(Higareda Alvear et al., 2021, Guan and Grigoriev, 2020, Gao et al., 2011)

28s rRNA

(Brogna et al., 2002)

BEST:HL02093

BEST:HL02977

BEST:HL03427

BEST:LD41653

Mgn570

(Brown et al., 2014)

NEST:bs10c09

NEST:bs15g08

NEST:bs17g11

NEST:bs30g02

Name Synonyms

28S rRNA

(Cao et al., 2011)

28S ribosomal RNA

(Remsen, 1998.4.9, Solignac, 1993.2.2, Solignac, 1993.2.2)

28SrRNA

Secondary FlyBase IDs

FBgn0045782
FBgn0045792
FBgn0045793
FBgn0045794
FBgn0045992
FBgn0046040
FBgn0046048
FBgn0046072

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 44 )

Sequence Crossreferences

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

References (72)

NA

Report Sections