FlyBase Gene Report: Dmel\mt:lrRNA

General Information

Symbol

Dmel\mt:lrRNA

Species

D. melanogaster

Name

mitochondrial large ribosomal RNA

Annotation Symbol

CR34094

Feature Type

mt_LSU_rRNA_gene

FlyBase ID

FBgn0013686

Gene Model Status

Current

Stock Availability

1 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

mtlrRNA, 16S, lrRNA, 16S rRNA, mitochondrial large rRNA

Key Links

Genomic Location

Cytogenetic map

Sequence location

mitochondrion_genome:12,735..14,058 [-]

Recombination map

RefSeq locus

NC_024511 REGION:12735..14058

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

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

NCBI

UCSC

Ensembl

Function

Gene Ontology (GO) Annotations (6 terms)

Molecular Function (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables structural constituent of ribosome

inferred from direct assay

(Wredenberg et al., 2013)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

enables structural constituent of ribosome

inferred from electronic annotation with Rfam:RF02540

(RNAcentral, 2018-)

non-traceable author statement

(Leatherman and Jongens, 2003)

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 mitochondrial translation

inferred by curator from GO:0005762

(Wredenberg et al., 2013)

involved_in pole cell formation

traceable author statement

(Leatherman and Jongens, 2003, Williamson and Lehmann, 1996)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

part_of mitochondrial large ribosomal subunit

inferred from direct assay

(Wredenberg et al., 2013)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

located_in P granule

traceable author statement

(Williamson and Lehmann, 1996)

located_in ribosome

inferred from electronic annotation with Rfam:RF02540

(RNAcentral, 2018-)

Gene Group (FlyBase)

MITOCHONDRIAL LARGE RIBOSOMAL COMPONENTS

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

MITOCHONDRIAL LARGE RIBOSOMAL COMPONENTS -: Mitochondrial ribosomes are found in the mitochondrial matrix and translate genes involved in oxidative phosphorylation encoded by the mitochondrial genome. Ribosomes are formed by two ribonucleoprotein subunits, large and small. The principle function of the large subunit is to bind tRNA during the synthesis of polypeptides. (Adapted from FBrf0205398).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\mt:lrRNA 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

RNA 2D structure (Predicted by RNAcentral) (RNAcentral entry URS000048AC6D)

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

mt:lrRNA-RA

FBtr0100888

1324

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

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\mt:lrRNA 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

part_of mitochondrial large ribosomal subunit

inferred from direct assay

(Wredenberg et al., 2013)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\mt:lrRNA in JBrowse

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

View exonic expression by developmental stage for Dmel\mt:lrRNA

View exonic expression by tissue for Dmel\mt:lrRNA

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

261002/tissue=All

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

FBgn0013686

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

FBgn0013686

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 ( 1 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of mt:lrRNA

Transgenic constructs containing regulatory region of mt:lrRNA

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:mt:lrRNA. 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

esyN Network Diagram

Show neighbor-neighbor interactions:

Off

Show/hide secondary interactors
(data from AllianceMine provided by esyN)

Select Layout:

Force Directed

Circle

Concentric

Legend:

Protein

RNA

Selected Interactor(s)

Other 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

mt:lrRNA - mTerf3

anti tag coimmunoprecipitation, primer specific pcr

(Wredenberg et al., 2013)

Summary of Genetic Interactions

esyN Network Diagram

Other 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

mt_LSU_rRNA_gene

mt_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

mitochondrion_genome

Recombination map

Cytogenetic map

Sequence location

mitochondrion_genome:12,735..14,058 [-]

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

41584

y¹ v¹; P{TRiP.GL00701}attP2

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

DRSC - Results frm RNAi screens

FBgn0013686

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

New annotation (CR34094) in release 4.3 of the genome annotation.

(FlyBase Genome Annotators, 2005)

mt:lrRNA has an essential role in pole cell formation.

(Iida and Kobayashi, 1998)

Contrary to a previous report (FBrf0072967), localization of mt:lrRNA depends on osk function even at the anterior pole.

(Kobayashi et al., 1995)

Steady state levels of mt:lrRNA decrease as adult Drosophila age, and this change correlates with the shape of the life span curve.

(Calleja et al., 1993)

Maternal 16S rRNA localises to the pole region of the embryo.

(Ding and Lipshitz, 1993)

The mitochondrial large ribosomal RNA gene maps to the mitochondrial DNA, between mt:srRNA and mt:ND1. It has previously been proposed that extra-mitochondrial mtlr-RNA is a component of the functional polar plasm: it induces pole cell formation in UV irradiated embryos (FBrf0049573). mtlr-RNA is enriched in germ plasm and is tightly associated with polar granules. Mutations in seven posterior group genes affects location of extra-mitochondrial mtlr, but alleles of nos have no effect (Ding, Whittaker and Lipschitz, unpublished data), suggesting that mtlr-RNA, like nos RNA, depends on the function of posterior group genes for its localization in the polar plasm.

(Kobayashi et al., 1993)

A mt:lrRNA cDNA has been cloned and sequenced.

(Kobayashi and Okada, 1990)

During oogenesis RNA from mt:srRNA, mt:lrRNA, mt:ND2, mt:CoI, mt:CoII, mt:CoIII, mt:ND4, mt:ND5 and mt:Cyt-b shows fluctuations in RNA density after stage 9 in follicle and nurse cells.There is a correlation between the mtRNA level and the cell volume and/or the nuclear DNA content suggesting a global extra-mitochondrial, transcriptional control mechanism.

(Tourmente et al., 1990)

mt:lrRNA RNA has been cloned and sequenced.

(Benkel et al., 1988)

Relationship to Other Genes

Source for database merge of

Source for merge of: mt:lrRNA anon- EST:fe1F3 anon- EST:fe2F10

(FlyBase, 1996-)

Source for merge of: mt:lrRNA anon- EST:fe1A1

(Bayraktaroglu, 2000.11.2)

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (34)

Reported As

Symbol Synonym

16S

(Clemente et al., 2022, Branco et al., 2017, Bratic et al., 2016, Baggio et al., 2014, Da-Rè et al., 2014, Bratic et al., 2011, van der Linde et al., 2010, Giribet et al., 2001, Toivonen et al., 2001, Durando et al., 2000)

16S RNA

(Lipshitz et al., 1993)

16S mtRNA

(Schwarze et al., 1998)

16S rRNA

(Salminen and Vale, 2020, Matsushima et al., 2017, Aw et al., 2011)

16SrRNA

(Parker and Kornfield, 1996, Calleja et al., 1993)

(Fargnoli and Waring, 1984)

CR34094

(Palu and Thummel, 2016, Ni et al., 2010.12.1, FlyBase Genome Annotators, 2005)

LSU rRNA

(Chen et al., 2012)

Lr mtDNA

(Morel et al., 1999)

anon-EST:fe1A1

anon-EST:fe1F3

anon-EST:fe2F10

lrRNA

(Camus et al., 2023, Tsai et al., 2016, Jaiswal et al., 2015, Bruni et al., 2012, Stewart and Beckenbach, 2009, Roberti et al., 2006, Ballard, 2000, Kobayashi and Okada, 1990)

mlrRNA

(Mahowald, 2001)

mt 16S rDNA

(Durando et al., 2000)

mt 16S rRNA

(Ding and Lipshitz, 1993)

mt large rRNA

(Clary, 1995.7.11)

mt16S

(Gnainsky et al., 2021)

mt:lrRNA

(Liu et al., 2024, Baker et al., 2021, Cho et al., 2020, Davie et al., 2018, Barry and Thummel, 2016)

mtlRNA

(Hazelrigg, 1998)

mtlr RNA

(Starz-Gaiano and Lehmann, 2001)

mtlrRNA

(Hurd et al., 2016, Psaila et al., 2010, Amikura et al., 2005, Santos and Lehmann, 2004, Extavour and Akam, 2003, Leatherman and Jongens, 2003, Amikura et al., 2001, Matova and Cooley, 2001, Iida and Kobayashi, 2000, Saffman and Lasko, 1999, Iida and Kobayashi, 1998, Amikura et al., 1997, Rongo et al., 1997, Iida and Kobayashi, 1996, Kobayashi et al., 1995)

mtrRNA

(Wang et al., 2006, Goto et al., 2001)

rRNA-16s

(Peralta et al., 2012)

rrnL

(Montagna et al., 2012)

Name Synonyms

16S mitochondrial rDNA

(Psaila et al., 2010)

16S ribosomal DNA

(Durando et al., 2000)

Large Subunit rRNA

(Ballard, 2000)

anon-fast-evolving-1A1

anon-fast-evolving-1F3

anon-fast-evolving-2F10

mitochondrial 16S rRNA

(Wredenberg et al., 2013)

mitochondrial large rRNA

(Psaila et al., 2010, Leatherman and Jongens, 2003)

mitochondrial large ribosomal RNA

Secondary FlyBase IDs

FBgn0002867
FBgn0025213
FBgn0025251
FBgn0025280

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 21 )

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.

261002

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

RNAcentral - A comprehensive ncRNA sequence collection representing all ncRNA types from a broad range of organisms

URS000048AC6D_7227

Other crossreferences

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

261002/tissue=All

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

FBgn0013686

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

FBgn0013686

FlyMine - An integrated database for Drosophila genomics

FBgn0013686

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

dme:Dmel_CR34094

MARRVEL_MODEL - MARRVEL (model organism gene)

261002

Linkouts

DRSC - Results frm RNAi screens

FBgn0013686

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0013686

References (115)

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

NA

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