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A lack of clear differences in nonsynonymous variation at exon 7 between echolocating and non-echolocating lineages in both cetaceans and bats can also be explained if the common ancestor in both groups had echolocation and this ability was subsequently lost in some lineages.
We allowed some variation at exon termini, so that one or two first or last amino acids in each human exon could be missed in the alignment.
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Population genetic analyses showed that the diploid species P. notoginseng harbored significantly lower nucleotide diversity than those of the two tetraploid species P. ginseng and P. quinquefolius and the three species showed distinct nucleotide variation patterns at exon regions.
We found extremely high variation at MHC DRB exon 2 in raccoons with a total of 66 alleles discovered in 246 individuals analyzed (Table 2).
More, specifically, we predict that such divergence should be particularly prominent when comparing nonsynonymous sequence variation at the exon 2-encoded ABS of different species, as diversifying selection is thought to act most stringently at these sites.
Variation at both exons appeared to correspond well to echolocation types/phylogenetic boundaries, with almost complete conservation across groups of confamilial species but contrasting signatures between families.
As mentioned, amino acid variation at both exons 7 and 17 in bats corresponds well to echolocation types/phylogenetic boundaries, with almost complete conservation across groups of confamilial species but contrasting signatures between families.
For example, ten of the 36 nuclear genes in P. notoginseng showed no variations at the exon regions, but both synonymous and nonsynonymous muations were reported in the P. ginseng and P. quinquefolius.
To assess the accuracy of the data set and identify potential artifacts for future curation, we first looked for co-located events that showed small variations (≤5 bp) at exon and intron boundaries, which could be caused by imprecise mapping of spliced reads.
We evaluated the expression variation at 5′ and 3′ exons of all genes that had at least one exon with outlier expression levels.
The SNPs located at exon regions were thus used as tags to distinguish two transcript structure variation sources: allelic variations and post-transcriptional alternative splicing.
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