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For this set of known human and mouse miRNAs, however, the S∶N ratios of our predicted binding sites are very similar, regardless of location in the 5'UTR, CDS or 3'UTR (Table 2 and Table 3).
Although the enhancer element of Otud-6b from −1515 bp to −1397 bp of Otud-6b is structurally different from those of Dub-1, Dub-1a, and Dub-2a, the functional transcription factor binding sites are very similar as the conserved ETS binding site is required for Otud-6b enhancer activity as well (Figure S9).
The three intragenic AP-1 binding sites are very well conserved at the nucleotide level as represented in Figure 2A by sequence logos that symbolize the frequency of the nucleotide present at each position in these binding sites based on sequence analyses of the full spectrum of HIV and SIV (Simian Immunodeficiency Virus) sequences compiled in the HIV compendium database (hiv-web.lanl.gov).
The nucleotide sequences in the mRNA of the miR-1273g-3p miR-1273d273d binding sites are very homologous.
Our results show that cyanobacterial CRP binding sites are very similar to those in E. coli; however, the regulons are very different from that of E. coli.
Four SP1 position weight matrices (PWMs) were identified and all had very high raw scores, which mean that the identified binding sites are very similar to consensus binding sites [ 9].
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Even though the interactions formed by the two isomers with the residues of the lower part of the ARs binding sites were very similar, some differences were observed when considering the interactions with the upper part of the cavity and the loop region.
These EWS-FLI1 binding sites were very frequently located far away from any transcription unit, with a mean distance to transcription start sites of 242 Kb and up to 3 Mb.
The performance of the different ChIP-seq methods at detecting high confidence NRSF binding sites is very similar; the percentage of motif-containing peaks varied by less than 3% with the exception of PeakSeq and HPeak.
Currently our knowledge of the TFs and their binding sites is very limited.
Interestingly, we noted that both FOX PWMs and HNF3 binding sites were very similar, and that KROX and MZF1 were highly similar to the predicted SP1 sites.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com