Dmel\McClintock

General Information
Symbol	Dmel\McClintock	Species	D.melanogaster
Name	McClintock	FlyBase ID	FBte0000926
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)	6450 (Kaminker et al., 2002)
Terminal repeat (bp)
Reference sequence	transposon_sequence_set.embl.txt.gz
Component genes	McClintock\gag McClintock\pol
Sequence Accessions
	DDBJ/EMBL/GenBank AF541948
Sequence Ontology (SO)
Transposon type	LTR_retrotransposon (Kaminker et al., 2002, Kaminker, 2002.8.29, Mugnier et al., 2008, Lipatov et al., 2005) transposable_element (Kaminker et al., 2002, Mugnier et al., 2008)
Insertions & Copy Number
Copy number and comments	2 in euchromatin of Release 3 genome annotation, both 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
Comments

Other Information
Etymology

External Crossreferences
Sequence Crossreferences
	DDBJ/EMBL/GenBank AF541948
Other Crossreferences

Synonyms & Secondary IDs ( 4 )
Reported As
Symbol Synonym	McC (Zhang et al., 2011) McClintock (FlyBase, 1992-, 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, Li et al., 2009, Lu and Clark, 2010) Mcclintock (Mugnier et al., 2008) mclintock (Anand and Kai, 2012)
Name Synonym	McClintock (Lipatov et al., 2005) Mcclintock (Mugnier et al., 2008)
Secondary FlyBase IDs
	FBgn0063917 FBtp0017043
References ( 20 )
Research paper	Anand and Kai, 2012, EMBO J. 31(4): 870--882 The tudor domain protein Kumo is required to assemble the nuage and to generate germline piRNAs in Drosophila. [FBrf0217541] 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] 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] Lu and Clark, 2010, Genome Res. 20(2): 212--227 Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila. [FBrf0209834] Nagao et al., 2010, RNA 16(12): 2503--2515 Biogenesis pathways of piRNAs loaded onto AGO3 in the Drosophila testis. [FBrf0212366] Deloger et al., 2009, Gene 439(1-2): 55--62 Identification of expressed transposable element insertions in the sequenced genome of Drosophila melanogaster. [FBrf0207990] Li et al., 2009, Cell 137(3): 509--521 Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. [FBrf0208736] Kawamura et al., 2008, Nature 453(7196): 793--797 Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells. [FBrf0205455] Mugnier et al., 2008, Gene 411(1-2): 87--93 The heterochromatic copies of the LTR retrotransposons as a record of the genomic events that have shaped the Drosophila melanogaster genome. [FBrf0203032] Brennecke et al., 2007, Cell 128(6): 1089--1103 Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. [FBrf0200494] Nefedova and Kim, 2007, Russ. J. Genet. 43(10): 1161--1167 Evolution of errantiviruses of Drosophila melanogaster. Strategy 2: From retroviruses to retrotransposons. [FBrf0202797] Ganko et al., 2006, J. Mol. Evol. 62(1): 111--120 LTR retrotransposon-gene associations in Drosophila melanogaster. [FBrf0191111] Lipatov et al., 2005, BMC Biol. 3: 24 Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome. [FBrf0189752] Aravin et al., 2003, Dev. Cell 5(2): 337--350 The small RNA profile during Drosophila melanogaster development. [FBrf0162058] Greil et al., 2003, Genes Dev. 17(22): 2825--2838 Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. [FBrf0167608] Kaminker et al., 2002, Genome Biol. 3(12): RESEARCH0084 The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. [FBrf0155828]
FlyBase analysis	FlyBase, 1992-, FlyBase curation. FlyBase curation. [FBrf0105495]
DNA/RNA sequence record	Kaminker, 2002.8.29, GenBank/EMBL/DDBJ: AF541948 Drosophila melanogaster transposon McClintock, complete sequence. [FBrf0153339]