Reference Report

Reference
Citation	Kaminker, J.S., Bergman, C.M., Kronmiller, B., Carlson, J., Svirskas, R., Patel, S., Frise, E., Wheeler, D.A., Lewis, S.E., Rubin, G.M., Ashburner, M., Celniker, S.E. (2002). The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol. 3(12): RESEARCH0084.
FlyBase ID	FBrf0155828
Type of publication	Research paper
Offprint Available	Yes
External Crossreferences
PubMed ID	12537573
PubMed Abstract	BACKGROUND: Transposable elements are found in the genomes of nearly all eukaryotes. The recent completion of the Release 3 euchromatic genomic sequence of Drosophila melanogaster by the Berkeley Drosophila Genome Project has provided precise sequence for the repetitive elements in the Drosophila euchromatin. We have used this genomic sequence to describe the euchromatic transposable elements in the sequenced strain of this species. RESULTS: We identified 85 known and eight novel families of transposable element varying in copy number from one to 146. A total of 1,572 full and partial transposable elements were identified, comprising 3.86% of the sequence. More than two-thirds of the transposable elements are partial. The density of transposable elements increases an average of 4.7 times in the centromere-proximal regions of each of the major chromosome arms. We found that transposable elements are preferentially found outside genes; only 436 of 1,572 transposable elements are contained within the 61.4 Mb of sequence that is annotated as being transcribed. A large proportion of transposable elements is found nested within other elements of the same or different classes. Lastly, an analysis of structural variation from different families reveals distinct patterns of deletion for elements belonging to different classes. CONCLUSIONS: This analysis represents an initial characterization of the transposable elements in the Release 3 euchromatic genomic sequence of D. melanogaster for which comparison to the transposable elements of other organisms can begin to be made. These data have been made available on the Berkeley Drosophila Genome Project website for future analyses.
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Language of publication	English
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Abbreviation	Genome Biol.
Title	GenomeBiology
Authors
Volume range	1-
Year range	2000-
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Place of publication	London
Language of publication	English
ISBN/ISSN	1465-6906
CODEN	GNBLFW
Data from Reference
Natural transposons
	1360 17.6 1731 297 3S18 412 BS Bari1 Bari2 Burdock Circe Cr1a Dm88 Doc Doc2-element Doc3-element F-element FB G-element G2 G3 G4 G5 G6 GATE HB HMS-Beagle HeT-A Helena I-element Idefix Ivk Juan McClintock NOF P-element Quasimodo R1-element R2-element Rt1a Rt1b Rt1c S-element S2 Stalker Stalker2 Stalker4 TART-element Tabor Tc1 Tirant Transpac X-element ZAM accord accord2 aurora-element baggins blood copia diver diver2 flea frogger gtwin gypsy gypsy2 gypsy3 gypsy4 gypsy5 gypsy6 hobo hopper hopper2 invader1 invader2 invader3 invader4 invader5 jockey jockey2 looper1 mariner2 mdg1 mdg3 micropia opus pogo roo rooA rover springer transib1 transib2 transib3 transib4
Insertions
	Tirant{}475