Dmel\R2-element

General Information
Symbol	Dmel\R2-element	Species	D.melanogaster
Name	R2 rDNA element	FlyBase ID	FBte0000030
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)	3607 (Kaminker et al., 2002)
Terminal repeat (bp)
Reference sequence	transposon_sequence_set.embl.txt.gz
Component genes	R2-element\ORF
Sequence Accessions
	DDBJ/EMBL/GenBank K01583 K01584 K01586 K01587 X15707 X51967 X93310 Z70917
Sequence Ontology (SO)
Transposon type	non_LTR_retrotransposon (Kaminker et al., 2002, Eickbush and Eickbush, 2003, Ye and Eickbush, 2006) transposable_element (Kaminker et al., 2002, )
Insertions & Copy Number
Copy number and comments	0 in euchromatin of Release 3 genome annotation. (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	Bmor\R2-element Damb\R2-element Dana\R2-element (George, 1996.7.24, ) Dbip\R2-element (George, 1996.7.24, ) Dbuz\R2-element Dere\R2-element Deur\R2-element Dfal\R2-element (George, 1996.7.24, ) Dhyd\R2-element (Malik and Eickbush, 1999) Dmau\R2-element Dmer\R2-element Dnas\R2-element Dnet\R2-element Dore\R2-element Dori\R2-element (Gentile et al., 2001) Dpas\R2-element (Gentile et al., 2001) Dper\R2-element (George, 1996.7.24, ) Dpse\R2-element (George, 1996.7.24) Dqui\R2-element (Gentile et al., 2001) Drec\R2-element Drob\R2-element Dsec\R2-element Dsim\R2-element Dsor\R2-element Dsuc\R2-element Dtak\R2-element (George, 1996.7.24, ) Dtei\R2-element Dtes\R2-element (George, 1996.7.24, ) Dvar\R2-element (George, 1996.7.24, ) Dwil\R2-element Dyak\R2-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) Analysis of 5' junction sequences of 94 R2-elements from 14 species reveals that no sequences at the 5' end of the R2-element appear to be required for element integration. A model in which the R2-element reverse transcriptase is capable of switching templates from the R2-element RNA transcript to the upstream 28SrRNA gene can best explain the observed 5' junction sequences. (George et al., 1996) Aspects of R2-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 K01583 K01584 K01586 K01587 X15707 X51967 X93310 Z70917
Other Crossreferences

Synonyms & Secondary IDs ( 10 )
Reported As
Symbol Synonym	ivs-II (Semionov and Markova, 1997, Mecheva and Semenov, 1991, FlyBase, 1996-) R2 (Zhang et al., 2011, FlyBase, 1996-, Eickbush and Eickbush, 2003, Ye and Eickbush, 2006, Zhang et al., 2008, Plata et al., 2009, Li et al., 2009, Ruminski et al., 2011, Vujatovic et al., 2012, Olivieri et al., 2012) R2Dm (Rizzon et al., 2002, Berezikov et al., 2000, Xiong and Eickbush, 1990, Udomkit et al., 1995, Jakubczak et al., 1990, Saito et al., 2006, FlyBase, 1996-, Tan et al., 2012) R2-element (FlyBase, 1996-, Pane et al., 2011, Kawamura et al., 2008, Sienski et al., 2012) rDNA element (FlyBase, 1996-) type 2 (Komma et al., 1993, FlyBase, 1996-) type II (di Nocera et al., 1986, FlyBase, 1996-) Type-II (FlyBase, 1996-)
Name Synonym	R2 element (Eickbush and Eickbush, 2007, Ruschak et al., 2004) R2 rDNA element
Secondary FlyBase IDs
	FBgn0003909 FBtp0011461
References ( 70 )

Generate a list of	All references relating to this natural transposable element ( 70 )

List References by type	Research paper ( 56 ) Review ( 2 ) Abstract ( 1 ) FlyBase analysis ( 2 ) DNA/RNA sequence record ( 8 ) Letter ( 1 )
Recent research papers ( 7 )
	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] 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] Vujatovic et al., 2012, Nucleic Acids Res. 40(12): 5402--5414 Drosophila melanogaster linker histone dH1 is required for transposon silencing and to preserve genome integrity. [FBrf0218745] 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] Ruminski et al., 2011, J. Biol. Chem. 286(48): 41286--41295 Processing and translation initiation of non-long terminal repeat retrotransposons by hepatitis delta virus (HDV)-like self-cleaving ribozymes. [FBrf0217294] 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] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...