Dmel\HMS-Beagle

General Information
Symbol	Dmel\HMS-Beagle	Species	D.melanogaster
Name	HMS Beagle element	FlyBase ID	FBte0000726
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)	7.3kb 7062 (Kaminker et al., 2002)
Terminal repeat (bp)	266
Reference sequence	transposon_sequence_set.embl.txt.gz
Component genes	HMS-Beagle\gag HMS-Beagle\pol
Sequence Accessions
	DDBJ/EMBL/GenBank AA141289 AA141290 AA141624 AF315785 AF365402 AI294525 AL035631 AW944089 AY032741 AY113472 AY183918 AY499230 AY499231 AY499232 AY499233 AY499234 AY499235 J01078 J01079 Z22588
Sequence Ontology (SO)
Transposon type	LTR_retrotransposon (Kaminker et al., 2002, Walser et al., 2006, Mugnier et al., 2008, Lipatov et al., 2005) transposable_element (Kaminker et al., 2002, Lammel, 2000.10.24, Walser et al., 2006, Mugnier et al., 2008)
Insertions & Copy Number
Copy number and comments	13 in euchromatin of Release 3 genome annotation, of which 9 are full length. (Kaminker et al., 2002) 50
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, )
Orthologs
Curated drosophilid orthologs	Dsim\HMS-Beagle (Biemont and Cizeron, 1999)
Comments
	Identified with: RE43210 (BDGP-DGC) <up>FlyBase curator comment: EST subsequently found to be chimeric</up>. (BDGP Project Members, 2000-) EST RE43210 is chimeric; the 5' portion corresponds to part of roo, the 3' portion corresponds to part of HMS-Beagle. (FlyBase, 1996-) The spatial and temporal expression patterns of fifteen families of retrotransposons are analysed during embryogenesis and are found to be conserved. Results suggest that all families carry cis-acting elements that control their spatial and temporal expression patterns. (Ding and Lipshitz, 1994) One substock of inbred lines shows considerable heterogeneity of insertion sites of copia (frequency of insertions is 12% per haploid genome per generation) whereas mdg1, 412, mdg3, gypsy, 297 and HMS-Beagle were stable in all stocks examined. (Pasyukova and Nuzhdin, 1992) The HMS-Beagle element has 266bp direct repeats at its termini and is flanked by a duplication of 4bp. It is present approximately 50 times in the haploid genome. (Snyder et al., 1982) First described as an insertion within the promoter region of the cuticle protein gene, Lcp3ⁿ¹. The sequence shown in Finnegan (1992) is the reverse complement of that published by Snyder, Kimbrell, Hunkapiller, Hill, Fristrom and Davidson (1982). There are no sites for the enzymes AvaI, BamHI, HindIII, or KpnI.
Other Information
Etymology

External Crossreferences
Sequence Crossreferences
	DDBJ/EMBL/GenBank AA141289 AA141290 AA141624 AF315785 AF365402 AI294525 AL035631 AW944089 AY032741 AY113472 AY183918 AY499230 AY499231 AY499232 AY499233 AY499234 AY499235 J01078 J01079 Z22588
Other Crossreferences

Synonyms & Secondary IDs ( 18 )
Reported As
Symbol Synonym	BcDNA:RE43210 Beagle (Kearney et al., 2004, Kim and Belyaeva, 1991, Kim and Belyaeva, 1991, FlyBase, 1996-, Franchini et al., 2004) CG17399 H.M.S.Beagle (Sun et al., 1997) H.M.S. Beagle (Garfinkel et al., 1992, Sandmeyer et al., 1990, Snyder et al., 1982, FlyBase, 1996-) H.M.S Beagle (Gunawardane et al., 2007) HMS-Beagle (Henikoff et al., 2009, Saito et al., 2006, Ganko et al., 2006, Linheiro and Bergman, 2012, Nefedova and Kim, 2007, Pane et al., 2011, Petrov et al., 2011, Brennecke et al., 2007, Nefedova et al., 2011, Deloger et al., 2009, Kawamura et al., 2008, Lipatov et al., 2005, Malone et al., 2009, Fagegaltier et al., 2009, Bartolomé et al., 2009, Schmidt et al., 2010, Sienski et al., 2012) HMS-beagle (Lerat et al., 2003) HMS Beagle (Kapitonov and Jurka, 2003, Ding and Lipshitz, 1994, Russell and Kaiser, 1994, Shpiz et al., 2011, Mito et al., 2005, Walser et al., 2006, Li et al., 2009, Lu and Clark, 2010, Makunin and Yurlova, 2010, Makunin and Yurlova, 2010, Klenov et al., 2011) hms-beagle (Mugnier et al., 2008) HMSbeagle (Brennecke et al., 2008) HMSBEAGLE_I (Gunawardane et al., 2007, Quesneville et al., 2003) HSM-Beagle (Minervini et al., 2007) midline-element midline-jumper (Lammel, 2000.10.24, ) Motu 1 (Sun et al., 2003) rP143 (Lammel and Klambt, 2001)
Name Synonym	HMS Beagle (Walser et al., 2006) hms-beagle (Mugnier et al., 2008) HMS-Beagle (Lipatov et al., 2005) HMS Beagle element
Secondary FlyBase IDs
	FBgn0001207 FBgn0040019 FBgn0043473 FBgn0063019 FBtp0011437
References ( 67 )

Generate a list of	All references relating to this natural transposable element ( 67 )

List References by type	Research paper ( 56 ) Supplementary material ( 1 ) Review ( 3 ) Personal communication to FlyBase ( 4 ) FlyBase analysis ( 2 ) DNA/RNA sequence record ( 1 )
Recent research papers ( 7 )
	Linheiro and Bergman, 2012, PLoS ONE 7(2): e30008 Whole Genome Resequencing Reveals Natural Target Site Preferences of Transposable Elements in Drosophila melanogaster. [FBrf0217478] 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] Klenov et al., 2011, Proc. Natl. Acad. Sci. U.S.A. 108(46): 18760--18765 Separation of stem cell maintenance and transposon silencing functions of Piwi protein. [FBrf0216776] 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] Shpiz et al., 2011, Nucleic Acids Res. 39(20): 8703--8711 Mechanism of the piRNA-mediated silencing of Drosophila telomeric retrotransposons. [FBrf0216525] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...