A Database of Drosophila Genes & Genomes

FB2013_03, released May 7th, 2013
 

Dmel\opus

General Information
Symbol Dmel\opus Species D.melanogaster
Name opus element FlyBase ID FBte0000918
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)
8kb
 
7521
(Kaminker et al., 2002)
7528
(Whalen and Grigliatti, 1998)
Terminal repeat (bp)
519
(Whalen and Grigliatti, 1998)
Reference sequence transposon_sequence_set.embl.txt.gz
Component genes
opus\env
 
opus\gag
 
opus\pol
 
hide Sequence Accessions
DDBJ/EMBL/GenBank
 
hide Sequence Ontology (SO)
Transposon type
LTR_retrotransposon
(Kaminker et al., 2002, Whalen, 1997.12.20, Whalen and Grigliatti, 1998, Mugnier et al., 2008, Lipatov et al., 2005, Terzian et al., 2001)
transposable_element
(Kaminker et al., 2002, Whalen, 1997.12.20, Mugnier et al., 2008)
hide Insertions & Copy Number
Copy number
and comments
10-15
(Whalen and Grigliatti, 1998)
24 in euchromatin of Release 3 genome annotation, of which 16 are full length.
(Kaminker et al., 2002)
TE copies retrieved from release 5.1 of the D. melanogaster genome.:25
(Lerat et al., 2011)
Search for
Target Site Duplication
Size (bp)
4
(Linheiro and Bergman, 2012, Whalen and Grigliatti, 1998)
6
 
hide Orthologs
Curated drosophilid orthologs
 
hide Comments
An insertion of P{SUPor-P} into a opus has been identified by virtue of decreasing transmission of Dp(1;f)J21A to offspring to 20%.
(Dobie et al., 2001)
opus is a retrovirus-like transposable element that is closely related to gypsy.
(Whalen and Grigliatti, 1998)
Cloned as a consequence of its expression in the terminal filament cells of ovarioles.
(Couderc et al., 1996)
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)
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)
First identified as insertion associated with the mutation fa. This is a copia-like element. The map and sequences from the ends of the LTRs were reported by Kidd and Young (1986). The only element studied so far was flanked by the sequence TATATA. This is probably the target site duplication, although it could be part of the inverted repeats at the ends of the LTRs. Restriction map in Lindsley, Zimm, 1992: 1104. yoyo first recognised by a match between an STS sequence and the C.capitata yoyo element; subsequently an apparently complete element was found on Berkeley P1 clone DS01219.
 
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hide External Crossreferences
Sequence Crossreferences
DDBJ/EMBL/GenBank
 
Other Crossreferences
hide Synonyms & Secondary IDs ( 22 )
Reported As
Symbol Synonym
2212
(Carr et al., 2002)
BcDNA:LD21171
 
BcDNA:RH54175
 
BEST:LD06340
 
DmeNomV
(Pelisson et al., 2002, Terzian et al., 2001)
EG:EG0005.1
(Benos, 1999.1.20)
ESTS:53B6S
 
GS2007
(Seong et al., 2001)
HDC10761
 
LB27
(Sahut-Barnola, 1995, Couderc et al., 1996, )
LD06340
(Toba et al., 1999)
nomad
(Watanabe et al., 2009, Jackson Behan et al., 2005, Lerat et al., 2003, Lerat et al., 2002, Kapitonov and Jurka, 1997-, Bowen and McDonald, 2001, Marsano et al., 2000, Ashburner et al., 1999, Whalen, 1997.12.20, Whalen and Grigliatti, 1998, FlyBase, 1996-, Brennecke et al., 2008, Lerat et al., 2011, Malone et al., 2009)
Nomad
(Kapitonov and Jurka, 2003, Marin and Llorens, 2000)
Nomad/yoyo
(Rizzon et al., 2002)
nomad-opus
(Mugnier et al., 2008)
opus
(Henikoff et al., 2009, Saito et al., 2006, Ganko et al., 2006, Linheiro and Bergman, 2012, Nefedova and Kim, 2007, Pane et al., 2011, Gunawardane et al., 2007, Mito et al., 2005, Petrov et al., 2011, Smith et al., 2007, Brennecke et al., 2007, Kawamura et al., 2008, Ghildiyal et al., 2008, Nefedova et al., 2011, Deloger et al., 2009, Bergman and Bensasson, 2007, Lipatov et al., 2005, Lerat et al., 2011, Li et al., 2009, Lu and Clark, 2010, Bergman et al., 2006, Méndez-Lago et al., 2011, Specchia et al., 2010, Sienski et al., 2012)
Opus
(Wang and Elgin, 2011)
yoyo
(Peter et al., 2002, Peter et al., 2002, Benos, 1999.1.20, Dorfman et al., 2002, Benos et al., 2001, Dobie et al., 2001, Reese et al., 2000, Reese et al., 2000, Canizares et al., 2000, Spradling et al., 1999, Ashburner et al., 1999, FlyBase, 1996-)
YOYO
(Yan et al., 2002)
Name Synonym
nomad-opus
(Mugnier et al., 2008)
nomad virus
(Terzian et al., 2001)
opus
(Lipatov et al., 2005)
opus element
 
yoyo element
 
Secondary FlyBase IDs
  • FBgn0003007
  • FBgn0015746
  • FBgn0021759
  • FBgn0024848
  • FBgn0026584
  • FBgn0046782
  • FBgn0062427
  • FBtp0011455
  • FBtp0011470
hide References ( 91 )
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List References by type
hide Recent research papers ( 9 )
Linheiro and Bergman, 2012, PLoS ONE 7(2): e30008
Whole Genome Resequencing Reveals Natural Target Site Preferences of Transposable Elements in Drosophila melanogaster. [FBrf0217478]
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]
Galindo et al., 2011, Dev. Biol. 353(2): 396--410
Control of Distal-less expression in the Drosophila appendages by functional 3' enhancers. [FBrf0213529]
Lerat et al., 2011, Gene 473(2): 100--109
Comparative analysis of transposable elements in the melanogaster subgroup sequenced genomes. [FBrf0212990]
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]
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