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Target sequence identification for the two POU domains relative to each other and to the Sox2 site were not restricted in order, orientation, or strand.
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Yet, there is often considerable variability in the order, orientation and spacing of binding sites for interacting transcription factors [4], [5], [6].
Meanwhile, because the production of the constructs is laborious and often hampered by inappropriately positioned restriction sites, we also adopted Gateway cloning technology to join fragments in a predefined order, orientation, and reading frame [19].
The var. gattii MATα locus genes showed rearrangements in order and orientation vis-à-vis other two varieties.
Nearly half of the genes in synteny block 1a are conserved in order and orientation.
Similarly to the other Legionella genomes, flanking genes are highly conserved both in order and orientation.
Furthermore, in some ciliates, the MDSs of a gene may be scrambled in order and orientation [ 24].
Indeed, 44% of M. truncatula genes are conserved in order and orientation in soybean in block 1a, increasing to 50% when only genes with database support are considered.
Of these clusters, 18 orthologous clusters comprising 70 TF-encoding genes were found to be conserved in order and orientation in all three genomes (Additional data file 5).
Although it is possible and probable that the six genes are conserved in order and orientation, this conjecture must be treated with caution.
Best matching human/rhesus exon sequences were concatenated in order and orientation based on the human transcript information to create a virtual rhesus transcriptome to test probe regions for cross-hybridization potential.
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