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A feature of young miRNA genes in Arabidopsis is that their foldback arms have extensive complementarity with their initial targets [11], [15], [50].
Depending upon the degree of complementarity of the mRNA-miRNA complex, miRNAs can promote the cleavage of the target mRNA, an occurrence that is favored by extensive complementarity with the mRNA, or they can suppress mRNA translation but not mRNA degradation in instances of less complete base-pairing [20] [22].
The cis-encoded sRNAs are encoded at the same chromosomal locus as their regulated mRNA but on the opposite strand and thus necessarily share extensive complementarity with the corresponding transcript.
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All the nine predicted targets were found to have specific cleavage sites corresponding to the miRNA complementary sequences and might be regulated by the miRNAs in the style of small interfering RNAs (siRNAs) [25] directing the cleavage of mRNA targets with extensive complementarity to the miRNAs [22].
The rTS (ENOSF1) gene, a member of the enolase family, was initially identified in Homo sapiens by the discovery of an RNA with extensive complementarity to the mRNA for the DNA biosynthetic enzyme thymidylate synthase[ 1, 2].
The second is by mRNA destabilization, where the poly-A tails of mRNA are shortened, leading to a higher turnover of the mRNA product by degradation 10– 12. Finally, extensive complementarity allows AGO proteins with slicer activity (only AGO2, in humans 13) to specifically cleave mRNA transcripts in a manner analogous to siRNAs 14, 15.
All the six targets were found to have specific cleavage sites corresponding to the miRNA complementary sequences and might be regulated by the miRNAs in the style of siRNAs [ 44] directing the cleavage of mRNA targets with extensive complementarity to the miRNAs [ 42].
LhrA shows extensive complementarity to the translation initiation region the 5'-end of chiA mRNA (see Table 1).
There are extensive complementarity between young miRNA genes and related target genes detectable by pairwise sequence similarity search tools such as BLAST [11], [15], [29].
cis-encoded anti-sense RNAs share extensive complementarity to their messenger RNA (mRNA) target, whereas trans-encoded RNAs typically show limited complementarity [ 1].
In plants most miRNAs have extensive complementarity to their target mRNA and induce its cleavage or translational inhibition.
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