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General Information
D. melanogaster
Feature type
FlyBase ID
Sequences and Components
Complete element (bp)

0.5 - 5kb

Terminal repeat (bp)
Sequence Accessions
Sequence Ontology (SO)
Insertions and Copy Number
Copy number and comments

10 in euchromatin of Release 3 genome annotation, of which 2 are full length.

Target Site Duplication
Size (bp)

R1-elements and R2-elements are rarely transferred between the rRNA loci of the X and Y chromosomes (bb and Ybb respectively). Retrotransposition of R1-elements occurs predominantly in the male germline, while retrotransposition of R2-elements is more evenly divided between the germlines of both sexes. The rate of elimination of R1-elements and R2-elements from the Ybb array on the Y chromosome is twice that of the rate of elimination from the bb array on the X chromosome. Both the bb and Ybb loci contain recombinational "hotspots" where R1-elements and R2-elements are lost at a rate eight times faster than elements located outside of the hotspots. Most R1-element and R2-element eliminations appear to occur by large intrachromosomal events that involve multiple rDNA units.

Elements R1 and R2 are subject to the same recombinational forces that give rise to the concerted evolution of the rDNA units. Molecular phylogenetic analysis of elements from 16 Drosophila species suggests these elements have been stable components of the rDNA locus for the 50-70 million year history of the Drosophila genus.

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.

The D.melanogaster R1-element has been sequenced and compared with the R1-elements of a number of other Drosophila species. Phylogenetic analysis suggests that the R1-elements have been vertically transmitted since the inception of the Drosophila genus.

60kb repeats located in the distal heterochromatin of the X chromosome have been cloned. These regions, designated as SCLRs, are comprised of the following types of repeated elements: SteXh, copia-like elements (mdg1 elements, aurora-elements and GATE elements), LINE-elements (G-elements and R1-elements), and bb fragments. There are approximately 9 SCLR copies per haploid genome, with a twofold variation in copy number between different fly stocks.

R1-element contains a moderate repeat, copy number per haploid genome is approximately 200.

Aspects of R1-element abundance and sequence variation in 27 geographical isolates of D.melanogaster have been analysed.

Other Information
External Crossreferences and Linkouts ( 41 )
Synonyms and Secondary IDs (24)
Reported As
Symbol Synonym
R1 rDNA element
Type-I intervening sequence
plasmid λ20p7
rDNA element
Secondary FlyBase IDs
  • FBgn0014123
  • FBgn0010429
  • FBgn0010290
  • FBgn0003908
  • FBtp0012711
References (113)