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General Information
Symbol
roo
Species
D. melanogaster
Feature type
natural_transposable_element
FlyBase ID
FBte0000100
Sequences and Components
Complete element (bp)
Terminal repeat (bp)

429

Component genes
Sequence Accessions
Sequence Ontology (SO)
Insertions and Copy Number
Copy number and comments

80 (Scherer et al., 1982)

146 in euchromatin of Release 3 genome annotation, of which 58 are full length.

Target Site Duplication
Orthologs
Comments

The distribution of structural variation within the roo elements analysed is relatively even with the exception of two hotspots, at coordinates approximately 1kb and 8 kb, both of which are in regions that are expected to be coding. Insertion site data suggest that roo elements are more likely to insert in regions of higher than average denaturation temperatures.

Identified with: RE43210 (BDGP-DGC) <up>FlyBase curator comment: EST subsequently found to be chimeric</up>.

Polymorphic locations of roo insertions have been used for mapping QTL affecting bristle number on the X and 3rd chromosomes.

Transposable elements can be used to reveal cross-over events.

Correlations between the rate of transposition and TE copy number are determined for 412 and roo and are found to be zero.

EST RE43210 is chimeric; the 5' portion corresponds to part of roo, the 3' portion corresponds to part of HMS-Beagle.

Study of TE distribution (P-element, hobo, I-element, copia, mdg1, mdg3, 412, 297 and roo) along chromosome arms shows no global tendency for the TE site occupancy frequency to negatively follow the recombination rate, except for the 3L arm. The tendency for TE insertion number to increase from base to tip of some chromosome arms is simply explicable by a positive relationship with DNA content along the chromosomes. So for all TEs, except hobo, there is no relationship between distribution of TE insertion numbers weighted by DNA content and recombination rate. hobo insertion site number is positively correlated with recombination rate.

The stage- and tissue-dependent expression pattern of roo is conserved between D.melanogaster and D.yakuba.

roo expression in the Drosophila embryo is mediated by internal cis-acting elements of the transposon.

Spontaneous insertions and excisions of mdg1, copia, 412 and roo (excisions are outnumbered by insertions) occur during 65 generations of mass mating under laboratory conditions. Their contribution into variation for transposable element location does not seem great.

The distribution of a number of transposable elements has been studied in 10 Harwich mutation accumulation lines.

Transposition induction of copia-like mobile genetic elements by heavy heat shock is a general phenomenon common for various isogenic lines of Drosophila.

Estimating the genomic numbers of transposable elements demonstrates many families of element are over-represented in heterochromatin.

The spatial and temporal expression patterns of fifteen families of retrotransposons are analysed during embryogenesis and are found to be conserved. Results suggest that all families carry cis-acting elements that control their spatial and temporal expression patterns.

roo mediated ectopic recombination occurs in meiotic cells, intrachromosomal recombination is as frequent as interchromosomal recombination.

Rates of transposition and excision of the roo element have been determined.

Element copy numbers on inversion and standard chromosomes has been determined. The copy number is significantly higher within low frequency inversions than within the corresponding standard chromosome regions.

Heat shock transposition induction can be considered a general property of different copia-like mobile genetic elements.

Polymorphism of transposable elements in inbred lines has been examined: P-element, gypsy, jockey, I-element, mdg1, 412, mdg3 and 297 sites are largely stable, whereas roo and copia sites are polymorphic.

Reduction of fitness, as implied from increase in sterility, accompanies high mobility of roo and copia in a semi-sterile inbred stock.

In a study of the distribution in the genome of 9 families of transposable element among chromosomes 2 and 3 of a natural population, it was found that the elements were distributed randomly in the distal section of chromosome arms, whereas some linkage disequilibrium was detected in proximal regions. Different elements tend to occupy different sites. The more proximal the site, the more likely the element was to show a non-random distribution.

Distribution of 9 families of transposable elements in a natural population was studied and the hypothesis that transposable element abundance is regulated primarily by deleterious fitness consequences of ectopic meiotic exchange was supported. Proximal euchromatin may only infrequently undergo exchange, and elements detected in population surveys of this kind tend to be inserted into sites where there is negligible effect on fitness.

Stability of 11 transposable element families compared by Southern blotting among individuals of lines that had been subjected to 30 generations of sister sib matings. 412, roo, blood, 297, 1731 and G-element all appear stable, whereas copia, hobo, I-element, gypsy and jockey elements show instability.

Nucleotide position -116 of the ct is a hotspot for roo element insertions.

The genomic distribution of transposable elements in somatic tissues and during development is homogeneous.

roo insertions in the 5SrRNA gene locus have generated heterogeneity at the 5SrRNA locus due to the excision of the locus with and without accompanying deletions of flanking sequences.

Described as B104 by Scherer et al. (1981), Scherer et al. (1982) and as roo by Meyerowitz and Hogness (1982). B104 elements were found because they are complementary to abundant poly(A)+ RNA in embryos (Scherer et al., 1981), whereas a roo element was found inserted near the Sgs3 gene (Meyerowitz and Hogness, 1982). The LTR sequence shown here was reported by Scherer et al. (1982) and the map in Lindsley, Zimm, 1992: 1106 is adapted from those of Scherer et al. (1982) and Swaroop et al. (1985).

Other Information
Etymology
External Crossreferences and Linkouts ( 33 )
Synonyms and Secondary IDs (26)
Reported As
Symbol Synonym
BcDNA:RE43210
EG:100G7.4
EG:125H10.4
EG:30B7.1
EG:52C10.3
EG:BACH7M4.3
EG:BACR43E12.2
EG:BACR7A4.1
EG:EG0009.1
anon-EST:Liang-2.23
roo
(Merenciano et al., 2019, Rech et al., 2019, Villanueva-Cañas et al., 2019, Solares et al., 2018, Fanti et al., 2017, Karam et al., 2017, Nefedova and Kim, 2017, Iwasaki et al., 2016, Jiang et al., 2016, Bozzetti et al., 2015, Fu et al., 2015, Kofler et al., 2015, Rahman et al., 2015, Senti et al., 2015, Zhang et al., 2015, Huang et al., 2014, Kim et al., 2014, Minakhina et al., 2014, Mirkovic-Hösle and Förstemann, 2014, Ott et al., 2014, Patil et al., 2014, Sytnikova et al., 2014, Cridland et al., 2013, Czech et al., 2013, Mamillapalli et al., 2013, Muerdter et al., 2013, Ohtani et al., 2013, Thomae et al., 2013, Vagin et al., 2013, Anand and Kai, 2012, Kofler et al., 2012, Linheiro and Bergman, 2012, Sienski et al., 2012, Tan et al., 2012, Díaz-González et al., 2011, Khurana et al., 2011, Méndez-Lago et al., 2011, Nefedova et al., 2011, Pane et al., 2011, Petrov et al., 2011, Lu and Clark, 2010, Patil and Kai, 2010, Potter and Luo, 2010, Specchia et al., 2010, Bartolomé et al., 2009, de la Chaux and Wagner, 2009, Deloger et al., 2009, Fagegaltier et al., 2009, Henikoff et al., 2009, Lau et al., 2009, Li et al., 2009, Malone et al., 2009, Watanabe et al., 2009, Brennecke et al., 2008, Chung et al., 2008, Genissel et al., 2008, Ghildiyal et al., 2008, González et al., 2008, Kawamura et al., 2008, Matyunina et al., 2008, Mugnier et al., 2008, Bergman and Bensasson, 2007, Brennecke et al., 2007, Chen et al., 2007, Domínguez et al., 2007, Gunawardane et al., 2007, Horwich et al., 2007, Lim and Kai, 2007, Minervini et al., 2007, Nishida et al., 2007, Pane et al., 2007, Papaceit et al., 2007, Smith et al., 2007, Vázquez et al., 2007, Zaratiegui, 2007, Bergman et al., 2006, Ganko et al., 2006, Saito et al., 2006, Vagin et al., 2006, Lipatov et al., 2005, Malik and Henikoff, 2005, Maside et al., 2005, Mito et al., 2005)
Secondary FlyBase IDs
  • FBgn0063019
  • FBgn0025962
  • FBgn0011765
  • FBgn0010010
  • FBgn0000155
  • FBtp0011460
References (237)