Dmel\Burdock

General Information
Symbol	Dmel\Burdock	Species	D.melanogaster
Name	Burdock element	FlyBase ID	FBte0000739
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)	6411
Terminal repeat (bp)	277
Reference sequence	transposon_sequence_set.embl.txt.gz
Component genes	Burdock\gag Burdock\pol
Sequence Accessions
	DDBJ/EMBL/GenBank AL008775 AL121804 BK002689 U89994 Z50605
Sequence Ontology (SO)
Transposon type	LTR_retrotransposon (Kaminker et al., 2002, Mugnier et al., 2008, Dimitri et al., 2003, Lipatov et al., 2005) transposable_element (Kaminker et al., 2002, Mugnier et al., 2008)
Insertions & Copy Number
Copy number and comments	6411 in euchromatin of Release 3 genome annotation, of which 13 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)	4 (Linheiro and Bergman, 2012) 4 (TATA in the case of the insertions into the ct hotspot) 12 (Krasnov et al., 1999)
Orthologs
Curated drosophilid orthologs	Dsim\Burdock (Vieira et al., 1999)
Comments
	YNNUTUTUYAYA (Y = pyrimidine, U = purine). (Krasnov et al., 1999) A Burdock insertion in the ct locus (ct^MR21K1) is sequenced. The element is found to be a short retrotransposon with long terminal repeats and a single open reading frame. (Ponomarenko et al., 1997) Nucleotide position -123 of the ct locus is a hotspot for Burdock element insertions. (Tchurikov et al., 1989)
Other Information
Etymology

External Crossreferences
Sequence Crossreferences
	DDBJ/EMBL/GenBank AL008775 AL121804 BK002689 U89994 Z50605
Other Crossreferences

Synonyms & Secondary IDs ( 6 )
Reported As
Symbol Synonym	Burdock (Henikoff et al., 2009, Zhang et al., 2011, Linheiro and Bergman, 2012, Nefedova and Kim, 2007, Pane et al., 2011, Petrov et al., 2011, Smith et al., 2007, Brennecke et al., 2007, Deloger et al., 2009, Nefedova et al., 2011, Yin et al., 2011, Bergman and Bensasson, 2007, Kawamura et al., 2008, Dimitri et al., 2003, Hamilton et al., 2009, Lipatov et al., 2005, Li et al., 2009, Lu and Clark, 2010, Bergman et al., 2006, Makunin and Yurlova, 2010, Makunin and Yurlova, 2010, Wang and Elgin, 2011, Rincon-Arano et al., 2012, Sienski et al., 2012) burdock (Biemont and Cizeron, 1999, Whalen and Grigliatti, 1998, Ponomarenko et al., 1997, Tchurikov et al., 1989, Mugnier et al., 2008, Brennecke et al., 2008, Malone et al., 2009, Terzian et al., 2001) BURDOCK (Zhou et al., 2009, Olivieri et al., 2012) EG:BACR7C10.5 (Benos, 2000.2.6, Benos, 2000.12.13) HDC14603
Name Synonym	Burdock (Lipatov et al., 2005) burdock (Mugnier et al., 2008) Burdock element
Secondary FlyBase IDs
	FBgn0010302 FBtp0011417
References ( 57 )

Generate a list of	All references relating to this natural transposable element ( 57 )

List References by type	Research paper ( 51 ) Review ( 2 ) Personal communication to FlyBase ( 1 ) Abstract ( 1 ) FlyBase analysis ( 1 ) DNA/RNA sequence record ( 1 )
Recent research papers ( 10 )
	Linheiro and Bergman, 2012, PLoS ONE 7(2): e30008 Whole Genome Resequencing Reveals Natural Target Site Preferences of Transposable Elements in Drosophila melanogaster. [FBrf0217478] 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] Rincon-Arano et al., 2012, Cell 151(6): 1214--1228 UpSET Recruits HDAC Complexes and Restricts Chromatin Accessibility and Acetylation at Promoter Regions. [FBrf0220189] 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] 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] Yin et al., 2011, PLoS Genet. 7(12): e1002380 A High-Resolution Whole-Genome Map of Key Chromatin Modifications in the Adult Drosophila melanogaster. [FBrf0217090] 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 ...