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It should be noted that because these regions are so highly conserved, often the consensus for one clade perfectly matched the consensus sequences of the other clades or indeed the group M (Fig. 1C), enhancing the potential for eliciting globally relevant cross-reactive responses.
The protein side chain/nucleic acid interactions specifically discussed in this paper occur via conserved (often universally) residues of the RNAP β′ or σA subunits.
Histone acetylation, arguably the best-studied histone modification, occurs at the ɛ amino groups of evolutionarily conserved, often invariant, lysine residues most often located in tail domains.
Heat shock proteins are highly conserved often multi-functional proteins best characterized as molecular chaperones, which protect the native conformation of other proteins, guarding against structural inactivation and irreversible multimeric aggregation.
Figure 4e reveals that many of these duplications are not entirely conserved, often exons are missing or new ones are there instead, exemplifying the benefit of the exon-level analysis.
In our previous study, we found that the iTSCs of very low expression levels are generally: (i) located in AT rich regions, rarely associated with CpG island; (ii) evolutionarily poorly conserved, often associated with repetitive sequences (also see Supplementary Fig. S4A).
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In Oases, very short transcripts that represent conserved motifs often have much higher read coverage compared to longer transcripts in the same locus.
In every comparison, divergent gene pairs were conserved least often, with conservation frequencies significantly below the all pair average.
An alternative approach to identifying conserved blocks is to search for sequence motifs whose instances are conserved unusually often.
Members of these families are structurally conserved and often share functional properties.
This analysis unravels conserved regions often showing internal base-pairing that reflects their regulatory function [39].
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