Nadeau and Taylor gave a list of features viewed as supporting inclusion of markers in an SB, a list that includes conserved orientation, conserved adjacency and conserved position of homologous markers associated with the corresponding mapped chromosomes, a collection of features that loosely defines what is more commonly called today collinearity.
On the other hand, we first identify the conserved pathway maps that include conserved orthologous genes.
A high-resolution structure of the complex formed by the truncated N-terminal domain of DELLA protein GAI and gibberellin-bound GID1A showed that a pair of helix-loop-helix motifs, corresponding to sequences that include conserved DELLA and TVHYNP motifs, form the interaction surface with the N-terminal domain of liganded GID1A [ 24].
Each position was categorized as follows: Each position that includes a conserved (the same) amino acid (AA) in the PD-prone species and a conserved (the same) AA (different from the AA conserved for the PD-prone) in the PD-resistant species is categorized as significant.
In all cells except T47D the −219/+114 promoter fragment, that includes only conserved region A, had significantly increased reporter activity compared to the 3.1 kb FSCN1 promoter or the −1582/+114 region (Fig. 3; p = 0.0002 for SW480 cells).
Thus, metazoan is the category that includes most conserved genes.
The N-terminus of Thap1 contains a zinc-dependent (C2CH) DNA-binding domain that includes a conserved AVPTIF domain, and the C-terminus contains a nuclear localization signal within a coiled-coiled domain [ 9- 11].
IPS1, a non-protein coding gene that includes highly conserved sequences near miR399 complementary regions in different plant species [ 22], has been found to be strongly upregulated under −P in rice [ 10].
Small RNA reads analysis of these three different libraries led to the identification of 29 miRNAs that includes 10 conserved miRNA homologs and 19 novel miRNAs (Table 1, Additional file 1: Figure S3), beside the 61 miRNAS reported previously [ 32, 35].
All RRBs have a N-terminal receiver domain that includes a conserved aspartate needed for the phosphorelay, a centrally positioned Myb-like DNA binding domain, and a variable domain at the C-terminus which is thought to be responsible for the functional specialization within this family [ 33, 41, 43].
