G4v2 ALL G4 motifs Track Settings
 
G4v2 All Motifs from B73v2 [lifted over from source B73v2, from Andorf et al., JGG, 2014]   (All Experimental Tracks)

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Data last updated: 2017-12-05 21:51:09

Credits

G4v2_motifs: This track was lifted over to b73v4 from b73v3 from b73v3 by fsu-cgpm. It displays the 149,520 non-overlapping maize G4 motifs with unique IDs ranging from G4v2_1 to G4v2_149520. Each G4 motif site spans from the first to the last G. G4 motifs on the plus strand (+) are shown in red and motifs on minus strand(.) are shown in blue. To create this track the entire maize genome was analyzed using the conservative and commonly employed G4-quadruplex motif consensus settings for the Quadparser software, G3+L1-7 (Huppert and Balasubramanian, 2005). This conservative definition of a G4 motif is defined by the presence of four runs of guanines (3 or more Gs per run) separated by intervening (loop) sequences from one to seven of any base, a motif referred to as G3L1-7. G4 motifs matching this consensus have been shown to be likely to form stable G4 structures in vitro. Full details of source data see Andorf et al. 2014 (DOI: 10.1016/j.jgg.2014.10.004). The data in this track has been projected onto the B73 RefGen_v3 assembly based only on its position in the B73 RefGen_v2 assembly, then lifted from B73v3 to B73v4. Changes, gains, or losses in sequences with each assembly will produce some false postives and false negatives. The motifs that are mapped are accurate and present in all assembly versions, but for new more detailed analysis, we recommend running G4 motif analysis anew on the latest assembly. (B73v4 track produced by fsu-cgpm; updated by hwb Sep2018)

Methods

NA