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In general, high-confidence CRMs (STAT binding sites) were more conserved than intermediate-confidence sites.
These binding sites were more conserved and located closer to TSSs than those whose function was not experimentally verified [18].
Notably, the binding sites were more enriched at the vicinity of (∼70 nt upstream) of 3′ splice site than at 5′ splice site.
We found that SNPs tagging miRNA sites and binding sites were more likely to be associated with the phenotypes compared to baseline SNPs (i.e. intergenic SNPs), though less compared for instance to 5'UTR SNPs.
In summary, mRNAs varied in their predicted RBFOX1 binding sites, and mRNAs with a high number of predicted binding sites were more likely dependent on RBFOX1 for their expression levels than those with fewer binding sites, potentially contributing to differential gene expression under normal, physiological conditions as well as pathological conditions such as autism.
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Energetically favorable binding sites were more-frequent in the CDS than in any other region even after normalization by relative size (nt) of region.
On the other hand, many tyrosine kinases (including the well-known Src family kinases) and adaptor molecules have both SH2 and SH3 domains, and it has been suggested that proteins containing multiple SH3 binding sites are more likely to be tyrosine phosphorylated and bind to SH2 domains as supported by biochemical studies [ 10, 11].
Taken together, these suggest that DNA duplex stability data should be informative of binding sites; whether a lower or higher DNA duplex stability at specific TF binding sites is more preferable depends largely on the binding preference of the TF, that is, whether the TF binds to the the DNA in a double- or single-strand manner.
The distribution of TypeII (PACAP/VIP) binding sites is more restricted than that of typeI binding sites, and are located in the olfactory bulb, the cerebral cortex, the dentate gyrus of the hippocampus, thalamus, the locus coeruleus of the pons, area postrema, and the spinal cord [46 50].
Intuitively, SNPs within regions of strong conservation or strong natural selection or microRNA binding sites are more likely to affect the disease predisposition.
Such nucleosome-mediated cooperativity has been observed in other contexts [22], [23], and it is known that cis-regulatory elements occurring within clusters of transcription factor binding sites are more likely to be functional in vivo [24].
More suggestions(12)
binding sites become more
binding sequences were more
binding events were more
binding sites appeared more
binding motifs were more
binding TFs were more
binding proteins were more
binding sites was more
binding residues were more
binding domains were more
binding sites were combined
binding sites were expected
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