Gene Dmel\mt:lrRNA

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General Information

Symbol

Dmel\mt:lrRNA

Species

D. melanogaster

Name

mitochondrial large ribosomal RNA

Annotation symbol

CR34094

Feature type

rRNA_gene

FlyBase ID

FBgn0013686

Gene Model Status

Current

Stock availability

1 publicly available

Also Known As

mtlrRNA, lrRNA, 16S, mtrRNA, 16SrRNA

Genomic Location

Chromosome (arm)

dmel_mitochondrion_genome

Recombination map

Cytogenetic map

Sequence location

dmel_mitochondrion_genome:12,734..14,058 [-]

Genomic Maps

Select View:

Summary Information

Automatically generated summary

See sections below for more information

The gene mitochondrial large ribosomal RNA is referred to in FlyBase by the symbol Dmel\mt:lrRNA (CR34094, FBgn0013686). It is a rRNA_gene from Drosophila melanogaster. It is reported to have molecular function: structural constituent of ribosome. It is reported to be involved in the biological process: pole cell formation. One allele is reported. No phenotypic data is available. It has one annotated transcript. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of very high expression to a trough of very low expression. Peak expression observed within 00-06 and 18-24 hour embryonic stages, during early pupal stages. CAVEAT: These RNA-Seq temporal profiles depend upon RNA-Seq reads that are uniquely placed in the genome. For this reason, genes such as histones, Stellates and many classes of RNA genes that are present in multiple exact or near exact copies in the genome, expression levels may be reported as much lower than their true values. Summary of FlyAtlas Anatomical Expression Data: No FlyAtlas data available because no Affy2 ProbeSet aligns to an exon of mt:lrRNA. Comments on Affy2 ProbeSet: No relevant information because no Affy2 ProbeSet aligns to an exon of mt:lrRNA. Gene sequence location is dmel_mitochondrion_genome:12734..14058.

User Contributed Data

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Recent Updates

Description

What does this section display?

This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms).

What does this section not display?

This section does not currently display links that were removed or gene model changes.

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FB2013_03

FB2013_02

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Detailed Mapping Data

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

Gene Model & Products

Please see the GBrowse view of Dmel\mt:lrRNA for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Comments on Gene Model

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

mt:lrRNA-RA

FBtr0100888

1325

Additional Transcript Data & Comments

Reported size (kB)

Comments

External Data

Crossreferences

Sequences Consistent with the Gene Model

DDBJ /
EMBL /
GenBank

DNA sequence

Name

Mapped Features

Mapped Features have been reorganized, please see this article for details.

Additional mapped features and mutations can be found on GBrowse or related reports.

Type

Symbol & Location

Additional Notes

References

External Data

Linkouts

Crossreferences

Expression Data

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

Reference

See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.

FlyAtlas Anatomy Microarray

FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)

modENCODE Anatomy RNA-Seq

modENCODE Development RNA-Seq

modENCODE Temporal Expression Data (Graveley et al., 2011)

modENCODE Cell Lines RNA-Seq

modENCODE Treatments RNA-Seq

Expression Clusters

A cluster of genes with similar mRNA expression dynamics across development.

(Graveley et al., 2011)

mE1_20_mRNA_expression_cluster_07

External Data & Images

Linkouts

Alleles & Phenotypes

Summary of Allele Phenotypes

Phenotype manifest in

Allele

Classical Alleles ( 0 )

For All Classical Alleles Show

Allele of mt:lrRNA	Class	Mutagen	Stocks	Known lesion

Alleles Carried on Transgenic Constructs ( 1 )

For All Alleles Carried on Transgenic Constructs Show

Allele of mt:lrRNA	Class	Mutagen	Stocks	Known lesion
mt:lrRNA^GL00701		in vitro construct - RNAi in vitro construct - regulatory fusion	1	Yes

Aneuploid Aberrations

Transgenic Constructs & Insertions

Transgenic Constructs

Type of construct

Name

Expression data

UAS construct

P{TRiP.GL00701}

Insertions

Type of insertions

Name

Expression data

Gene Ontology: Function, Process & Cellular Component ( 5 unique terms )

Terms Based on Experimental Evidence ( 0 terms )

Terms Based on Predictions or Assertions ( 5 terms )

Molecular Function

CV term

Evidence

References

structural constituent of ribosome

non-traceable author statement

(Leatherman and Jongens, 2003)

Biological Process

CV term

Evidence

References

pole cell formation

traceable author statement

(Leatherman and Jongens, 2003, Mahowald, 2001, Williamson and Lehmann, 1996)

Cellular Component

CV term

Evidence

References

mitochondrial large ribosomal subunit

non-traceable author statement

(FlyBase, 1992-)

mitochondrion

non-traceable author statement

(FlyBase, 1992-)

P granule

traceable author statement

(Mahowald, 2001, Williamson and Lehmann, 1996)

Sequence Ontology: Class of Gene

mt_gene

rRNA_gene

Interactions & Pathways

Summary of Physical Interactions

Summary of Genetic Interactions

Interacts with

Please look at the allele data for full details of the genetic interactions

mt:lrRNA allele

Gene

References

External Data

Linkouts

Orthologs

OrthoDB Orthologs (0) - based on analysis using Dmel annotation version 5.41

OrthoDB Ortholog Groups

OrthoDB orthology group searches

(Waterhouse et al., 2011, Nucleic Acids Res. 39(Database issue): D283--D288)

Drosophila inclusive ortholog search

No orthologs identified

Dipteran inclusive ortholog search

No orthologs identified

Insect inclusive ortholog search

No orthologs identified

Arthropod inclusive ortholog search

No orthologs identified

Metazoa inclusive ortholog search

No orthologs identified

Orthologs in Drosophila Species (None identified)

No orthologies identified

Orthologs in non-Drosophila Dipterans (None identified)

No non-Drosophilid orthologies identified

Orthologs in non-Dipteran Insects (None identified)

No non-Dipteran orthologies identified

Orthologs in non-Insect Arthropods (None identified)

No non-Insect Arthropod orthologies identified

Orthologs in non-Arthropod Metazoa (None identified)

No non-Arthropod Metazoa orthologies identified

Human Orthologs (0)

Gene

OMIM

HGNC

AAA Orthologs (0) based on analysis using Dmel annotation version 4.3

No orthologs identified

Stocks & Reagents

Stocks Listed in FlyBase ( 1 )

Bloomington

41584

y¹ v¹; P{TRiP.GL00701}attP2

Genomic Clones ( 0 )

cDNA Clones ( 89 )

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 GBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA Clones, Fully Sequenced

BDGP DGC clones

Other clones

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi & Array Information

Linkouts

DRSC - Results from RNAi screens.

•

FBgn0013686

GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents

•

261002

Other Information

Discoverer

Etymology

Identification

Relationship to Other Genes

Source for database identity of

Source for database merge of

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

(Bayraktaroglu, 2000.11.2)

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

(FlyBase, 1996-)

Additional comments

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)

External Crossreferences & Linkouts

Sequence Crossreferences

DDBJ / EMBL / GenBank

•

Entrez Gene - A searchable database of RefSeq genes.

•

261002

Other Crossreferences

Linkouts

DRSC - Results from RNAi screens.

•

FBgn0013686

FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans

•

FBgn0013686

GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents

•

261002

modMine - Data generated by the modENCODE project.

•

FBgn0013686

Synonyms & Secondary IDs ( 32 )

Reported As

Symbol Synonym

16S

(Giribet et al., 2001, Toivonen et al., 2001, Durando et al., 2000, van der Linde et al., 2010)

16S mtRNA

(Schwarze et al., 1998)

16S RNA

(Lipshitz et al., 1993)

16SrRNA

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

16S rRNA

(Aw et al., 2011)

anon-EST:fe1A1

anon-EST:fe1F3

anon-EST:fe2F10

(Fargnoli and Waring, 1984)

CR34094

(FlyBase Genome Annotators, 2005, Ni et al., 2010.12.1)

Lr mtDNA

(Morel et al., 1999)

lrRNA

(Kobayashi and Okada, 1990, Roberti et al., 2006, Ballard, 2000, Stewart and Beckenbach, 2009, Bruni et al., 2012)

mlrRNA

(Mahowald, 2001)

mt 16S rDNA

(Durando et al., 2000)

mt 16S rRNA

(Ding and Lipshitz, 1993)

mt:lrRNA

mt large rRNA

(Clary, 1995.7.11)

mtlRNA

(Hazelrigg, 1998)

mtlrRNA

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

mtlr RNA

(Starz-Gaiano and Lehmann, 2001)

mtrRNA

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

rRNA-16s

(Peralta et al., 2012)

rrnL

(Montagna et al., 2012)

unnamed

(Schmid and Tautz, 1997)

Name Synonym

16S mitochondrial rDNA

(Psaila et al., 2010)

16S ribosomal DNA

(Durando et al., 2000)

anon-fast-evolving-1A1

anon-fast-evolving-1F3

anon-fast-evolving-2F10

Large Subunit rRNA

(Ballard, 2000)

mitochondrial large ribosomal RNA

mitochondrial large rRNA

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

Secondary FlyBase IDs

FBgn0002867
FBgn0025213
FBgn0025251
FBgn0025280

References ( 89 )

Generate a list of

All references relating to this gene ( 89 )

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Recent research papers ( 6 )

Wolff et al., 2013, Heredity 110(1): 57--62: Paternal transmission of mitochondrial DNA as an integral part of mitochondrial inheritance in metapopulations of Drosophila simulans. [FBrf0220230]
Bruni et al., 2012, Mitochondrion 12(5): 492--499: D-MTERF5 is a novel factor modulating transcription in Drosophila mitochondria. [FBrf0219394]
Montagna et al., 2012, PLoS ONE 7(10): e47538: Tick-box for 3'-end formation of mitochondrial transcripts in ixodida, Basal chelicerates and Drosophila. [FBrf0219749]
Oliveira et al., 2012, Molec. Phylog. Evol. 64(3): 533--544: Monophyly, divergence times, and evolution of host plant use inferred from a revised phylogeny of the Drosophila repleta species group. [FBrf0218731]
Peralta et al., 2012, J. Biol. Chem. 287(29): 24174--24185: Coiled Coil Domain-containing Protein 56 (CCDC56) Is a Novel Mitochondrial Protein Essential for Cytochrome c Oxidase Function. [FBrf0218928]
Aw et al., 2011, Mitochondrion 11(5): 756--763: Mitochondrial DNA variants in Drosophila melanogaster are expressed at the level of the organismal phenotype. [FBrf0214676]

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