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A large noncoding region [= a plausible control region (CR); 977 bp] is found between trnQ and trnI.
In addition, a large noncoding region located between nad1 and trnP (869 bp in length) was found in Cancellaria cancellata.
Of these, only one large noncoding region (136 bp long) has an increased A+T content (76.8%), so it is a possible control region.
The two clusters were separated by a relatively large noncoding region of about 80 nucleotides, potentially involved in the control of mitochondrial transcription (see below).
A large noncoding region is also present and is presumed to function in controlling the replication and translation of mitochondrial genes.
On the other hand, LambdaPVs, EePV1, isolated from an European hedgehog, and the RferPV1 reported here, all incorporate a large noncoding region (NCR2) in the intergenic E2 L2 region.
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Moreover, three large noncoding regions of CR1, CR2 and NC are longer than 300 bp.
In the Hyperolius mt genome, the typical LTPF trn cluster was rearranged to PTL2F, and relatively large noncoding regions were found between trnP and trnT (1.3 kbp) and between trnL2 and trnF (0.4 kbp).
For example, it has been demonstrated that deletion of 2 large noncoding regions of approximately 1 Mb containing over a thousand conserved noncoding elements, many of which will be transcribed, does not lead to detectable abnormalities in mice (Nobrega et al. 2004), although only gross physiological assessments were performed.
Based on these requirements, we anticipate that SearchDOGS may prove useful in the future for finding unannotated genes in bacterial genomes, but it may be less useful in genomes with many introns and large noncoding regions, such as mammals, or in species that lack close relatives with well-annotated genomes.
The secondarily derived gene order of L. pallidum (translocation of trnQ, duplication of rrnL and the presence of four large noncoding regions) is considered to have evolved by a combination of tandem duplication with random deletion plus intergenomic recombination between several genes with subsequent gene conversion [ 59].
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