Dmel\R1-element

General Information
Symbol	Dmel\R1-element	Species	D.melanogaster
Name	R1 rDNA element	FlyBase ID	FBte0000118
Feature type	natural transposable element
Recent Updates
Description	What does this section display? 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). What does this section not display? This section does not currently display links that were removed or gene model changes.
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FB2013_03
FB2013_02
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Sequences & Components
Complete element (bp)	0.5 - 5kb 5356 (Kaminker et al., 2002)
Terminal repeat (bp)
Reference sequence	transposon_sequence_set.embl.txt.gz
Component genes	R1-element\ORF1 R1-element\ORF2
Sequence Accessions
	DDBJ/EMBL/GenBank AL008790 AY013920 J01118 K01574 K01575 K01576 K01577 K01578 K01580 K01582 K01585 K03137 K03138 K03139 K03140 K03141 L10988 L10989 S75830 S75832 X01475 X01494 X01495 X01671 X01672 X01675 X51968 X93311 Z31796 Z32022 Z32071 Z32072 Z32291 Z32353 Z32438 Z32439 Z50536 Z50537 Z70893 Z70894 Z70918
Sequence Ontology (SO)
Transposon type	non_LTR_retrotransposon (Kaminker et al., 2002, Ye and Eickbush, 2006) transposable_element (Kaminker et al., 2002, )
Insertions & Copy Number
Copy number and comments	10 in euchromatin of Release 3 genome annotation, of which 2 are full length. (Kaminker et al., 2002)
Search for	All insertions of this transposon Insertions in the sequenced genome Insertions in other genomes
Target Site Duplication
Size (bp)
Orthologs
Curated drosophilid orthologs	Damb\R1-element Dana\R1-element Dari\R1-element Dbip\R1-element (Gentile et al., 2001) Dbra\R1-element (Gentile, 2000.3.24) Dbuz\R1-element Dcur\R1-element (Gentile, 2000.3.24) Dere\R1-element Dfal\R1-element (Gentile, 2000.3.24) Dhyd\R1-element Dlut\R1-element (Gentile et al., 2001) Dmat\R1-element (Gentile et al., 2001) Dmau\R1-element Dmer\R1-element Dmir\R1-element Dnet\R1-element Dore\R1-element Dori\R1-element (Gentile, 2000.3.24) Dpas\R1-element (Gentile, 2000.3.24) Dpbp\R1-element (Gentile et al., 2001) Dper\R1-element Dprl\R1-element (Gentile et al., 2001) Dprs\R1-element (Gentile et al., 2001) Dpse\R1-element Dpst\R1-element (Gentile et al., 2001) Dput\R1-element Dqui\R1-element (Gentile, 2000.3.24) Drec\R1-element (Gentile, 2000.3.24) Dsec\R1-element Dsim\R1-element Dsqu\R1-element (Shoemaker et al., 2004) Dtak\R1-element Dtei\R1-element Dtes\R1-element Dvar\R1-element (Gentile et al., 2001) Dvir\R1-element Dyak\R1-element
Comments
	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. (Perez-Gonzalez et al., 2003) 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. (Eickbush 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) 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. (Lathe et al., 1995) 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. (Nurminsky et al., 1994) R1-element contains a moderate repeat, copy number per haploid genome is approximately 200. (Baiborodin et al., 1993) Aspects of R1-element abundance and sequence variation in 27 geographical isolates of D.melanogaster have been analysed. (Jakubczak et al., 1992)
Other Information
Etymology

External Crossreferences
Sequence Crossreferences
	DDBJ/EMBL/GenBank AL008790 AY013920 J01118 K01574 K01575 K01576 K01577 K01578 K01580 K01582 K01585 K03137 K03138 K03139 K03140 K03141 L10988 L10989 S75830 S75832 X01475 X01494 X01495 X01671 X01672 X01675 X51968 X93311 Z31796 Z32022 Z32071 Z32072 Z32291 Z32353 Z32438 Z32439 Z50536 Z50537 Z70893 Z70894 Z70918
Other Crossreferences

Synonyms & Secondary IDs ( 23 )
Reported As
Symbol Synonym	anon-l20p7 anon-Z gag-like (Bogachev, 1993.5.6) ivs-I (Semionov and Markova, 1997, Mecheva and Semenov, 1991, FlyBase, 1996-) l20p7 plasmid λ20p7 (Baiborodin et al., 1993) R1 (Ye and Eickbush, 2006, Zhang et al., 2008, Rho and Tang, 2009, Brennecke et al., 2008, Hong et al., 2007, Deloger et al., 2009, Hamilton et al., 2009, Malone et al., 2009, Plata et al., 2009, Li et al., 2009, Nishida et al., 2007, Lu and Clark, 2010) R1_DM (Gunawardane et al., 2007) R1a (Czech et al., 2008) R1A1 (Liu et al., 2011, Wang and Elgin, 2011) R1A1-element (Pane et al., 2011, Sienski et al., 2012) R1Dm (Rizzon et al., 2002, van Steensel et al., 2001, Berezikov et al., 2000, Busseau et al., 2001, Xiong and Eickbush, 1990, Blesa and Martinez-Sebastian, 1997, Udomkit et al., 1995, Jakubczak et al., 1990, FlyBase, 1996-, Saito et al., 2006, Gunawardane et al., 2007, Tan et al., 2012) R1DM (Terzian et al., 1997) R1 Dm (Felger and Hunt, 1992) R1-element (Petrov et al., 2011) rDNA element (FlyBase, 1996-) type 1 (Komma et al., 1993, FlyBase, 1996-) type I (di Nocera et al., 1986, FlyBase, 1996-) Type-I (FlyBase, 1996-) Type-I intervening sequence (Hilliker and Appels, 1982) type I repeat (Talbert and Henikoff, 2000)
Name Synonym	R1 element (Eickbush and Eickbush, 2007) R1 rDNA element
Secondary FlyBase IDs
	FBgn0003908 FBgn0010290 FBgn0010429 FBgn0014123 FBtp0012711
References ( 92 )

Generate a list of	All references relating to this natural transposable element ( 92 )

List References by type	Research paper ( 73 ) Supplementary material ( 1 ) Review ( 2 ) Personal communication to FlyBase ( 2 ) Abstract ( 1 ) FlyBase analysis ( 2 ) Letter ( 2 ) DNA/RNA sequence record ( 9 )
Recent research papers ( 6 )
	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] Liu et al., 2011, Development 138(9): 1863--1873 PAPI, a novel TUDOR-domain protein, complexes with AGO3, ME31B and TRAL in the nuage to silence transposition. [FBrf0213491] 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] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...