A Database of Drosophila Genes & Genomes

FB2013_03, released May 7th, 2013
 

Dmel\copia

General Information
Symbol Dmel\copia Species D.melanogaster
Name copia element FlyBase ID FBte0000023
Feature type natural transposable element
hide Recent Updates
Description
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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).
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FB2013_03
FB2013_02
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hide Sequences & Components
Complete element (bp)
5146
 
Terminal repeat (bp)
276
 
Reference sequence transposon_sequence_set.embl.txt.gz
Component genes
copia\GIP
 
hide Sequence Accessions
DDBJ/EMBL/GenBank
 
hide Sequence Ontology (SO)
Transposon type
LTR_retrotransposon
(Kaminker et al., 2002, Mugnier et al., 2008, Alonso-Gonzalez et al., 2003, Dimitri et al., 2003, Klenov et al., 2007, Lipatov et al., 2005, Athauda et al., 2006)
transposable_element
(Kaminker et al., 2002, Mugnier et al., 2008)
hide Insertions & Copy Number
Copy number
and comments
60 (Finnegan et al., 1978; Potter et al., 1979)
 
5143 in euchromatin of Release 3 genome annotation, of which 30 are full length.
(Kaminker et al., 2002)
Search for
Target Site Duplication
Size (bp)
5
 
hide Orthologs
Curated drosophilid orthologs
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
 
(Cabre, 1996.3.28, )
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
 
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
 
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Cabre, 1996.3.28, )
(Biemont and Cizeron, 1999)
 
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
 
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
 
 
 
(Biemont and Cizeron, 1999)
 
(Jordan and McDonald, 1998)
(Biemont and Cizeron, 1999)
 
(Biemont and Cizeron, 1999)
 
 
(Biemont and Cizeron, 1999)
hide Comments
Dwil\copia is virtually identical in sequence to copia despite melanogaster and willistoni being separated from a common ancestor by approximately 50 million years. Although copia is abundant in all melanogaster group species it displays a patchy distribution in willistoni. A recent horizontal transfer of copia from melanogaster to willistoni is indicated.
(Jordan et al., 1999)
Age dependence of the copia transposition rate in males is positively associated with copia transcript abundance in testes. This type of age dependence indicates that copia transpositions do not occur in stem cells. Clusters of transpositions have been detected indicating pre-meiotic transposition. The physiological state of the host may affect expression and transposition of copia.
(Filatov et al., 1998)
Transposable elements can be used to reveal cross-over events.
(Furman and Bukharina, 1998)
No transposition was detected in progeny after heat shock of parents.
(Arnault et al., 1997)
Ufo has an effect on copia mRNA levels.
(Bhadra et al., 1997)
A lower proportion of copia, mdg1 and 412 element insertion sites on the X chromosome, from various populations of D.melanogaster and D.simulans, in comparison with autosomes suggests that selection against the detrimental effects of TE insertions in the major force containing TE copies in populations.
(Biemont et al., 1997)
Dhyd\lola-like encodes a transcription factor that binds and interacts with an 18bp target DNA sequence within the copia enhancer sequences to activate transcription in Schneider cells.
(Cavarec et al., 1997)
Using copia LTR as a model, it is demonstrated that a regulatory region contained within the elements untranslated leader region (ULR) consists of multiple copies of an 8bp motif (TTGTGAAA) with similarity to the core sequence of the SV40 enhancer. Naturally occurring variation number of these motifs correlates with the enhancer strength of the ULR. Results indicate that inter-element selection may favour the evolution of more active enhancers within permissive genetic backgrounds.
(McDonald et al., 1997)
Correlations between the rate of transposition and TE copy number are determined for copia and are found to be either zero or positive.
(Nuzhdin et al., 1997)
High rates of germ line copia transposition occur only in males by tissue-specific control of RNA levels (copia is transcribed at much higher levels in male germinal tissues that in the equivalent female tissue). Data suggests that transposition of copia is regulated at the RNA level and only occurs in tissues containing more than a relatively high threshold level of copia RNA.
(Pasyukova et al., 1997)
Used in an investigation to address the relationship between retrotransposons and retroviruses and the coadaptation of these retroelements to their host genomes. Results indicate retrotransposons are heterogeneous in contrast to retroviruses, suggesting different modes of evolution by slippage-like mechanisms.
(Terzian et al., 1997)
One of a class of genes with TATA-less promoters that have the conserved DPE sequence.
(Burke and Kadonaga, 1996)
The behaviour of the retrotransposons copia, Dsim\copia and mdg1 has been analysed in hybrids between D.melanogaster and D.simulans. No somatic transposition events were detected in hybrid larvae.
(Garcia-Guerreiro, 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)
Endogenous transposable elements show more instability in sublines injected with exogenous viral particles than in transgenic sublines containing a foreign viral insert, all transposable elements are not equally sensitive to such genomic stress.
(Jouan-Dufournel et al., 1996)
Larval copia RNA levels are variable among Drosophila species, transcripts are detected in D.melanogaster, but not in D.simulans, D.mauritiana, D.sechellia, D.yakuba, D.erecta or D.willistoni. Size variation mapping to the LTR and ULR in naturally occurring copia elements is likely generated by duplication and is of functional significance. Ecol\CAT reporter gene constructs indicate that regulatory sequences that influence copia expression are located within the elements 5' LTR and adjacent ULR.
(Matyunina et al., 1996)
copia transposition rate is positively and nonlinearly associated with copia copy number. Results postulate that the number of copia virus-like particles, necessary for copia transposition, could depend nonlinearly on copia copy number.
(Nuzhdin et al., 1996)
Excision of the copia retrotransposon can be influenced by heat shock.
(Baldrich et al., 1995)
The distribution of copia elements in heterochromatin has been studied by in situ hybridisation to mitotic chromosomes.
(Carmena and Gonzalez, 1995)
Phylogenetic analysis indicates that although D.melanogaster copia elements are distinct from those of D.simulans and D.mauritiana, the copia elements of these latter two species are not distinguishable from one another.
(Csink and Mcdonald, 1995)
Experiments designed to compare the insertion patterns of copia and mdg1 revealed that crossing to marker strains led to heterogeneity in insertion patterns of the copia elements, with no significant polymorphism of the mdg1 insertions.
(Garcia-Guerreiro and Biemont, 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)
copia activity appears to be restricted to males. The X chromosome is the preferential target for copia insertions.
(Pasyukova and Nuzhdin, 1995)
The distribution of transposable elements within heterochromatin indicates that they are major structural components of the heterochromatin.
(Pimpinelli et al., 1995)
The chromosomal distribution of a number of retrotransposons in an isolated population of D.melanogaster (from Ishigaki Island, Okinawa, Japan) has been determined.
(Suh et al., 1995)
The distribution of copia elements across the chromosomes has been analysed in individuals from a natural population of D.melanogaster.
(Biemont et al., 1994)
copia enancer sequences are responsible for high level expression of copia in transient transfection assays using D.hydei- and D.melanogaster-derived cells. A 50kD factor that binds the enhancer sequences is identified by mobility shift assays and UV crosslinking experiments.
(Cavarec 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)
The copia and 412 transposable elements increase in copy number in aged adult tissue due to the activation of reverse transcriptase.
(Driver and Vogrig, 1994)
The insertion patterns of mdg1 and copia are sufficiently modified to allow the unambiguous detection of an alien genome income.
(Dufournel et al., 1994)
Rates of transposition and excision of the copia 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)
The copia 5' untranslated region contains binding sites for transcriptional regulation by homeoproteins.
(Cavarec and Heidmann, 1993)
The copia retrotransposon has been found unstable in the 2b3 stock.
(Pasyukova and Nuzhdin, 1993)
All sequences necessary for developmentally regulated copia transcription are contained within the 3' LTR. Doa mutations increase accumulation of this transcript, therefore the site responsible for Doa interaction with copia also lies within the 3' LTR.
(Rabinow et al., 1993)
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)
copia is able to dosage compensate and the response shows developmental and position dependence. copia-initiated transcript within wa is dosage compensated in adults, but not in larvae.
(Hiebert and Birchler, 1992)
Numbers of mdg1, mdg3, gypsy and copia have been studied in several strains of D.melanogaster and D.simulans. Mean number of mdg1 and copia sites are drastically reduced in D.simulans. Majority of mdg1 and copia sites, and one third of mdg3 sites, are in hot spots for insertion, particularly in D.simulans. Southern blot analysis indicates that the majority of mdg1 and copia are in the euchromatin of D.melanogaster but the heterochromatin of D.simulans.
(Leibovich et al., 1992)
One substock of inbred lines shows considerable heterogeneity of insertion sites of copia (frequency of insertions is 12% per haploid genome per generation) whereas mdg1, 412, mdg3, gypsy, 297 and HMS-Beagle were stable in all stocks examined.
(Pasyukova and Nuzhdin, 1992)
copia is capable of negatively regulating expression from its own promoter and is also able to positively regulate expression from Lsp1α in transient DNA co-transfection assays.
(Bryant et al., 1991)
copia promoter elements show no enhancement of transcription by heat shock in cultured Drosophila cell lines.
(Sneddon and Flavell, 1991)
Expression and processing of the copia\GIP gag precursor in E.coli cells generates a unique laminate structure in E.coli. copia protease in involved in cleaving the gag precursor, a mutation in the active site of the protease results in accumulation of the gag precursor and the laminate structure is not generated.
(Yoshioka et al., 1991)
Reverse transcription of copia RNA is likely to occur in copia virus-like particles.
(Yoshioka et al., 1991)
The gag gene products of copia are produced in far greater amounts than the pol and int gene products. Gene fusion constructs with Ecol\lacZ demonstrate that gag encoding RNA is expressed as protein in cultured cells at least ten fold more efficiently than the RNA containing pol and int reading frames.
(Brierley and Flavell, 1990)
copia elements are found in D.simulans, D.mauritiana and D.melanogaster but copia-encoded transcripts are only found in D.melanogaster. copia transcript level variation is found among natural populations of D.melanogaster: this is not due to variable copia copy number but may be due to the action of trans-acting controls.
(Csink and McDonald, 1990)
The distribution of a number of transposable elements, including copia elements, in a D.melanogaster laboratory strain with a high frequency of spontaneous mutations and its derivatives, has been studied.
(Kim et al., 1990)
The 2kb copia RNA is generated through splicing and encodes sufficient information to make copia virus-like particles, VLPs, in Drosophila cultured cells. copia VLPs are produced through autocatalytic processing of the polyprotein precursor encoded by spliced 2kb RNA.
(Yoshioka et al., 1990)
One end of tRNA:M-iΨ (a tRNA pseudogene homologous to the 5' half of an initiator tRNA) is joined directly to the 3' terminal sequence of copia. tRNA:M-iΨ may be a derivative of a reverse transcript of copia primer RNA.
(Saigo, 1986)
Sequences located 5' to Sgs7, Sgs8, Sgs3, the Hsp70 genes at 87A and 87C and the copia coding region are similar to the sequence at -405 from Sgs4.
(Shermoen and Beckendorf, 1982)
First described by Finnegan et al. (1978) as a sequence complementary to abundant polyA+ RNA in tissue culture cells. The map in Lindsley, Zimm, 1992: 1099 is taken from the sequence of Mount and Rubin (1985), and the sequence of the LTR is from Levis et al. (1980). The sequences of complete copia elements have been published by Mount and Rubin (1985) and by Emori et al. (1985). Virus-like particles containing full length copia RNAs have been found in tissue culture cells by Shiba and Saigo (1983). The major protein in these particles is translated from a 2 kb spliced mRNA (Yoshioka et al.). The sequence of this mRNA has been determined by Miller et al. (1989). This protein is released from the primary translation product by autocatalytic cleavage (Yoshioka et al.). Kikuchi et al. (1986) have shown that a fragment of the initiator methionine tRNA acts as a primer for reverse transcription of copia RNA in these particles. Sequences essential for copia expression are located on either side of the major transcriptional start sites (Sneddon and Flavell, 1989).
 
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Sequence Crossreferences
DDBJ/EMBL/GenBank
 
Other Crossreferences
EPD
 
hide Synonyms & Secondary IDs ( 12 )
Reported As
Symbol Synonym
38C.7
(McGill Drosophila Genome Project, 2001.9.25, Butler, 2001, Butler et al., 2001)
38C.27
(McGill Drosophila Genome Project, 2001.9.25, Butler, 2001, Butler et al., 2001)
BcDNA:RH07382
 
BcDNA:RH25742
 
BcDNA:SD10530
 
copia
(Henikoff et al., 2009, Zhang et al., 2011, Saito et al., 2006, Abe et al., 2001, Ganko et al., 2006, Nefedova and Kim, 2007, Pane et al., 2011, Klenov et al., 2007, Fablet et al., 2007, Minervini et al., 2007, Lau et al., 2009, Díaz-González et al., 2010, Shpiz et al., 2011, Kalmykova et al., 2005, Mito et al., 2005, Haynes et al., 2006, Petrov et al., 2011, Brennecke et al., 2007, Lecuyer et al., 2007, Deloger et al., 2009, Mugnier et al., 2008, de Setta et al., 2011, Steinbiss et al., 2009, Fedoseeva et al., 2010, Vu and Nuzhdin, 2011, Nefedova et al., 2011, Matyunina et al., 2008, Brennecke et al., 2008, Czech et al., 2008, Bergman and Bensasson, 2007, Kawamura et al., 2008, Alonso-Gonzalez et al., 2003, Dimitri et al., 2003, Chung et al., 2008, Lipatov et al., 2005, Athauda et al., 2006, Malone et al., 2009, Alonso-Gonzalez et al., 2006, Tchurikov et al., 2009, Li et al., 2009, Iklé et al., 2008, Houle and Nuzhdin, 2004, Fanti et al., 2003, Lu and Clark, 2010, Bergman et al., 2006, Kotova et al., 2010, Handler et al., 2011, Tan et al., 2012, Sienski et al., 2012, Klenov et al., 2011, Fedoseeva et al., 2012)
Copia
(Kapitonov and Jurka, 2003, Dufournel et al., 1994, Phalke et al., 2009, Zhou et al., 2009, Rincon-Arano et al., 2012)
COPIA
(Olivieri et al., 2012)
Copia Dm
(Pritham et al., 2007)
Dmel\copia
(Kalmykova et al., 2005)
TE copia
(Kearney et al., 2004)
Name Synonym
copia
(Mugnier et al., 2008, Lipatov et al., 2005)
copia element
 
Secondary FlyBase IDs
  • FBgn0000349
  • FBgn0061364
  • FBgn0063660
  • FBgn0063664
  • FBtp0011420
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hide Recent research papers ( 15 )
Fedoseeva et al., 2012, Dokl. Biochem. Biophys. 442: 7--11
Molecular analysis of enhancer RNAs and chromatin modifications in the region of their synthesis in Drosophila cells possessing genetic constructs. [FBrf0217782]
Hibbard and O'Tousa, 2012, J. Neurogenet. 26(2): 177--188
A role for the cytoplasmic DEAD box helicase Dbp21E2 in rhodopsin maturation and photoreceptor viability. [FBrf0220254]
Olivieri et al., 2012, Mol. Cell 47(6): 954--969
The Cochaperone Shutdown Defines a Group of Biogenesis Factors Essential for All piRNA Populations in Drosophila. [FBrf0219572]
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]
de Setta et al., 2011, J. Mol. Evol. 72(3): 326--338
Copia retrotransposon in the Zaprionus genus: another case of transposable element sharing with the Drosophila melanogaster subgroup. [FBrf0214409]
Handler et al., 2011, EMBO J. 30(19): 3977--3993
A systematic analysis of Drosophila TUDOR domain-containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors. [FBrf0216344]
Klenov et al., 2011, Proc. Natl. Acad. Sci. U.S.A. 108(46): 18760--18765
Separation of stem cell maintenance and transposon silencing functions of Piwi protein. [FBrf0216776]
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]
Shpiz et al., 2011, Nucleic Acids Res. 39(20): 8703--8711
Mechanism of the piRNA-mediated silencing of Drosophila telomeric retrotransposons. [FBrf0216525]
Vu and Nuzhdin, 2011, Heredity 106(2): 207--217
Genetic variation of copia suppression in Drosophila melanogaster. [FBrf0212846]
Zhang et al., 2011, Mol. Cell 44(4): 572--584
Heterotypic piRNA Ping-Pong Requires Qin, a Protein with Both E3 Ligase and Tudor Domains. [FBrf0216809]
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