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Lots of methods for finding probable borders are based on strong signals between the coding regions and the non-coding ones [ 7, 8].
Nucleotide sequence divergence between the coding regions of four genes ranged from 16.0 to 21.6%, and locus-specific eight primer pairs targeting introns were designed.
However, based on the high sequence similarity between the coding regions of C. neoformans var.
MicA is genomically localized between the coding regions of the gshA and luxS genes and is divergently transcribed from its neighbours.
The similarity between the coding regions of PRAMEY1 and PRAMEY2 is 88% at the nucleotide level and 90% at the protein level.
Two primer pairs, P1U-P1D and P2U-P2D (Table 3), were designed according to the nucleotide sequences located between the coding regions of phzA1 and phzB1 or phzA2 and phzB2 in the two phz gene clusters in Pseudomonas sp. M18.
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Coding region analysis using multiplex amplified product-length polymorphisms revealed the incongruence of single nucleotide polymorphisms between the coding region and HVS 1 caused by contamination with exogenous mtDNA.
Using a luciferase-based reporter plasmid, we show that VP2 is expressed by termination-reinitiation and provide evidence consistent with a functional interaction between the coding region of the VP1 mRNA and 18S rRNA.
No differences between male and female samples were observed between the coding region of gsdf and Tag 2 (data not shown).
Actually, the significant degree of linkage disequilibrium was detected between the coding region and the 3′-region (D′ = 0.881, P < 0.001 by two-tailed Fisher's exact test; supplementary fig. S2 B, Supplementary Material online).
The concordance between the coding region (C-alpha) and the three enhancers in the observed divergence furthermore indicates that similar forces shaped the evolution of the whole 3' regulatory region, suggesting potential functional constrains also for the non coding sections.
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