The set of 47 sequences containing an ABRE site included genes from Arabidopsis thaliana [ 19, 28], barley [ 18], maize [ 41], rice [ 20], and cotton [ 17].
Sequences contain smaller sequences within them.
The first genomic regions of the maize genome that have been sequenced contain both nested LTR retrotransposons as well as single retrotransposons [ 23, 24].
However, several branches contain both rice and maize sequences, but only one well-supported branch harbors sequences from all dicotyledonous species (putative St10 orthologues).
The sister clad, containing the rice, B. distachyon, wheat, sorghum and maize sequences, was also highly supported (100%).
However, 98 (1.05%) of the retained introns from 94 maize genes contained TE sequences that included Copia and Gypsy (Class I) as well as Mutator and Stowaway (Class II) (Table 4).
Silico3 was predicted from the B73 maize sequences.
The maize sequences were as identified by Penning et al. [ 90], except that the proteins encoded by AC210013.4 and AC231180.2 were omitted from the analysis, because they did not contain Pfam-predicted GH domains.
Maize sequences for design of this chip were predominantly selected from the The Institute for Genomic Research TIGRR) maize gene index [ 33].
The scanned maize sequences represent the whole large sequences available for maize in the public database, i.e., excluding the trace files and the gene-only sequences.
However, it has been reported that the maize genome contain Heltir sequences that have terminal inverted repeats resembling Helitron 3' termini [ 34].
