A Database of Drosophila Genes & Genomes

FB2013_03, released May 7th, 2013
 

Dmel\roo

General Information
Symbol Dmel\roo Species D.melanogaster
Name roo element FlyBase ID FBte0000100
Feature type natural transposable element
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Description
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FB2013_03
FB2013_02
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hide Sequences & Components
Complete element (bp)
8.7kb
 
9092
(Kaminker et al., 2002)
Terminal repeat (bp)
429
 
Reference sequence transposon_sequence_set.embl.txt.gz
Component genes
roo\ORF
 
hide Sequence Accessions
DDBJ/EMBL/GenBank
 
hide Sequence Ontology (SO)
Transposon type
LTR_retrotransposon
(Kaminker et al., 2002, Mugnier et al., 2008, Lipatov et al., 2005)
transposable_element
(Kaminker et al., 2002, Mugnier et al., 2008)
hide Insertions & 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.
(Kaminker et al., 2002)
Search for
Target Site Duplication
Size (bp)
5
(Linheiro and Bergman, 2012, )
hide Orthologs
Curated drosophilid orthologs
(Biemont and Cizeron, 1999)
 
(Biemont and Cizeron, 1999)
 
hide 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.
(Kaminker et al., 2002)
Identified with: RE43210 (BDGP-DGC) <up>FlyBase curator comment: EST subsequently found to be chimeric</up>.
(BDGP Project Members, 2000-)
Polymorphic locations of roo insertions have been used for mapping QTL affecting bristle number on the X and 3rd chromosomes.
(Nuzhdin et al., 1999, Long et al., 1995)
Transposable elements can be used to reveal cross-over events.
(Furman and Bukharina, 1998)
Correlations between the rate of transposition and TE copy number are determined for 412 and roo and are found to be zero.
(Nuzhdin et al., 1997)
EST RE43210 is chimeric; the 5' portion corresponds to part of roo, the 3' portion corresponds to part of HMS-Beagle.
(FlyBase, 1996-)
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.
(Hoogland and Biemont, 1996)
The stage- and tissue-dependent expression pattern of roo is conserved between D.melanogaster and D.yakuba.
(Bronner and Jaeckle, 1995)
roo expression in the Drosophila embryo is mediated by internal cis-acting elements of the transposon.
(Bronner et al., 1995)
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.
(Kozhemiakina and Furman, 1995)
The distribution of a number of transposable elements has been studied in 10 Harwich mutation accumulation lines.
(Nuzhdin and Mackay, 1995)
Transposition induction of copia-like mobile genetic elements by heavy heat shock is a general phenomenon common for various isogenic lines of Drosophila.
(Anikeeva et al., 1994)
Estimating the genomic numbers of transposable elements demonstrates many families of element are over-represented in heterochromatin.
(Charlesworth et al., 1994)
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.
(Ding and Lipshitz, 1994)
roo mediated ectopic recombination occurs in meiotic cells, intrachromosomal recombination is as frequent as interchromosomal recombination.
(Lim and Simmons, 1994)
Rates of transposition and excision of the roo element have been determined.
(Nuzhdin and Mackay, 1994)
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.
(Sniegowski and Charlesworth, 1994)
Heat shock transposition induction can be considered a general property of different copia-like mobile genetic elements.
(Zabanov et al., 1994)
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.
(Aleksandrova and Alexandrov, 1992)
Reduction of fitness, as implied from increase in sterility, accompanies high mobility of roo and copia in a semi-sterile inbred stock.
(Alexandrov and Alexandrova, 1992)
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.
(Charlesworth et al., 1992)
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.
(Charlesworth et al., 1992)
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.
(di Franco et al., 1992)
The genomic distribution of transposable elements in somatic tissues and during development is homogeneous.
(di Franco et al., 1989)
Nucleotide position -116 of the ct is a hotspot for roo element insertions.
(Tchurikov et al., 1989)
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.
(Tschudi et al., 1982)
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).
 
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Sequence Crossreferences
DDBJ/EMBL/GenBank
 
Other Crossreferences
hide Synonyms & Secondary IDs ( 26 )
Reported As
Symbol Synonym
73C1S
(Louis et al., 1997)
anon-EST:Liang-2.23
 
B 104
(Fortunati and Junakovic, 1999)
B104
(Arnold et al., 2004)
B104/roo
(Syomin et al., 2002)
B104/Roo
(Frame et al., 2001)
B104B
(Jiang and Gibson, 1992, FlyBase, 1996-)
BcDNA:RE43210
 
clone 2.23
(Liang and Biggin, 1998)
E239.9-1
(Tulin et al., 2002, Shimizu, 1994.6.29, )
EG:30B7.1
 
EG:52C10.3
 
EG:100G7.4
(Benos, 2000.2.6)
EG:125H10.4
 
EG:BACH7M4.3
(Benos, 1999.12.16)
EG:BACR7A4.1
(Benos, 1999.12.13)
EG:BACR43E12.2
(Benos, 2000.2.5)
EG:EG0009.1
 
Ro
(Kapitonov and Jurka, 2003)
roo
(Watanabe et al., 2009, Henikoff et al., 2009, Saito et al., 2006, Zaratiegui, 2007, Vagin et al., 2006, Díaz-González et al., 2011, Ganko et al., 2006, Linheiro and Bergman, 2012, Pane et al., 2011, Domínguez et al., 2007, Minervini et al., 2007, Lim and Kai, 2007, Gunawardane et al., 2007, Lau et al., 2009, Mito et al., 2005, Vázquez et al., 2007, Petrov et al., 2011, Smith et al., 2007, Brennecke et al., 2007, Horwich et al., 2007, Kawamura et al., 2008, Deloger et al., 2009, Mugnier et al., 2008, Papaceit et al., 2007, de la Chaux and Wagner, 2009, Ghildiyal et al., 2008, Nefedova et al., 2011, Matyunina et al., 2008, Brennecke et al., 2008, Bergman and Bensasson, 2007, Chen et al., 2007, González et al., 2008, Chung et al., 2008, Genissel et al., 2008, Lipatov et al., 2005, Anand and Kai, 2012, Malone et al., 2009, Pane et al., 2007, Li et al., 2009, Maside et al., 2005, Nishida et al., 2007, Malik and Henikoff, 2005, Fagegaltier et al., 2009, Bartolomé et al., 2009, Lu and Clark, 2010, Bergman et al., 2006, Méndez-Lago et al., 2011, Potter and Luo, 2010, Specchia et al., 2010, Patil and Kai, 2010, Tan et al., 2012, Khurana et al., 2011, Sienski et al., 2012)
ROO
(Bai et al., 2008, Czech et al., 2008, Zhou et al., 2009)
Roo
(Makunin and Yurlova, 2010, Makunin and Yurlova, 2010, Zamparini et al., 2011, Franchini et al., 2004, Wang and Elgin, 2011, Rincon-Arano et al., 2012)
ROO_I
(Gunawardane et al., 2007)
roo/B104
(Lerat et al., 2003, Vieira et al., 2002, Biemont et al., 1999, Ding and Lipshitz, 1994)
Roo/B104
(Rizzon et al., 2002)
Name Synonym
roo
(Mugnier et al., 2008, Lipatov et al., 2005)
roo element
(Vázquez et al., 2007, Chen et al., 2007, Genissel et al., 2008)
Secondary FlyBase IDs
  • FBgn0000155
  • FBgn0010010
  • FBgn0011765
  • FBgn0025962
  • FBgn0063019
  • FBtp0011460
hide References ( 199 )
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hide Recent research papers ( 13 )
Anand and Kai, 2012, EMBO J. 31(4): 870--882
The tudor domain protein Kumo is required to assemble the nuage and to generate germline piRNAs in Drosophila. [FBrf0217541]
Linheiro and Bergman, 2012, PLoS ONE 7(2): e30008
Whole Genome Resequencing Reveals Natural Target Site Preferences of Transposable Elements in Drosophila melanogaster. [FBrf0217478]
Rincon-Arano et al., 2012, Cell 151(6): 1214--1228
UpSET Recruits HDAC Complexes and Restricts Chromatin Accessibility and Acetylation at Promoter Regions. [FBrf0220189]
Sienski et al., 2012, Cell 151(5): 964--980
Transcriptional silencing of transposons by piwi and maelstrom and its impact on chromatin state and gene expression. [FBrf0220033]
Tan et al., 2012, Hum. Mol. Genet. 21(1): 57--65
Retrotransposon activation contributes to fragile X premutation rCGG-mediated neurodegeneration. [FBrf0216915]
Díaz-González et al., 2011, Genet. Res. (Camb.) 93(03): 181--187
Long-term evolution of the roo transposable element copy number in mutation accumulation lines of Drosophila melanogaster. [FBrf0213827]
Khurana et al., 2011, Cell 147(7): 1551--1563
Adaptation to P Element Transposon Invasion in Drosophila melanogaster. [FBrf0217035]
Méndez-Lago et al., 2011, Mol. Biol. Evol. 28(7): 1967--1971
A Large Palindrome With Interchromosomal Gene Duplications in the Pericentromeric Region of the D. melanogaster Y Chromosome. [FBrf0214341]
Nefedova et al., 2011, Virus Genes 42(2): 297--306
Integration specificity of LTR-retrotransposons and retroviruses in the Drosophila melanogaster genome. [FBrf0213545]
Pane et al., 2011, EMBO J. 30(22): 4601--4615
The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline. [FBrf0217070]
Petrov et al., 2011, Mol. Biol. Evol. 28(5): 1633--1644
Population genomics of transposable elements in Drosophila melanogaster. [FBrf0214125]
Wang and Elgin, 2011, Proc. Natl. Acad. Sci. U.S.A. 108(52): 21164--21169
Drosophila Piwi functions downstream of piRNA production mediating a chromatin-based transposon silencing mechanism in female germ line. [FBrf0217081]
Zamparini et al., 2011, Development 138(18): 4039--4050
Vreteno, a gonad-specific protein, is essential for germline development and primary piRNA biogenesis in Drosophila. [FBrf0214783]
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