Drosophila MFAP1 binds directly to Prp38 [74] and this relationship is likely to be conserved based on the good recovery of SpPrp38 and SpSnu23 in the SpSaf3-TAP (Figure 3 and Table S3).
Conservation in an intron was estimated as the fraction of intron sites that were conserved based on a PhastCons score threshold.
This preference is conserved based on our data, with L-arabitol also showing better xylanase induction than L-arabinose in N. crassa.
Namely, for each TF-gene pair, the phylogenetically weighted probability score of binding was calculated as ∑ x ∈ X w x exp s x where X is the collection of all sites, sx is the PWM score of binding site x and wx is the total phylogenetic tree branch length of all the species in which binding site x is conserved, based on a previously published tree [ 56].
Potential functional SNPs [those that were located in coding regions or were evolutionarily conserved based on the conservation track of the UCSC Genome Browser University of Californiaa, Santa Cruz; http://genome.ucsc.edu) were also given priority.
Therefore, although twice-amplified genes might be called "conserved" based on a t-test, indicating that the change on average is around zero, the variation over the different samples will be changed by the amplification, resulting in more false-negative and false-positive genes.
Most of the ORFs encoding over 50 amino acids are not conserved based on NCBI BlAST search.
Moreover, all of these residues except Ala85 are strictly conserved based on the sequence alignments of large and small PurLs.
We found that the overall epigenetic features of chromatin in human- and mouse-activated Treg cells were highly conserved based on qualitative and quantitative analyses.
However, neither chain A nor chain C forms an analogous interaction and the side chains on this second interface (V71, A74, E75) are less conserved, based on PFAM family PF10719 alignments and compared with residues on the larger interface.
