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This indicated that the intron patterns, which correlate well with the phylogentic clades, strongly support their close evolutionary relationships among the ZmPP2C genes within the same subclass.
In the absence of a consensual nomenclature and due to a lack of rational naming of ERF genes across plant species, we attempted to rename the tomato genes by giving a letter (A to J) to discriminate between different subclasses and a number to distinguish between members within the same subclass (Table 3).
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As shown, samples from the test data in the majority of cases (highlighted in dark colors) fell within the corresponding clusters from the training set, i.e., sequences from the training set that were classified by our prediction method as being Synechococcus-like podo viruses (dark green) fell within the cluster of the same subclass from the GOS data.
Although Acropora and Nematostella are both members of the same subclass (Hexacorallia, or Zoantharia) within the cnidarian Class Anthozoa there are apparent differences in the expression patterns of presumably orthologous genes.
The interactions between Eph receptors and ephrins of the same subclass are promiscuous; there are cross-interactions between some subclasses, but not all.
The elution pH of hMabs that have LYLQMNSL sequences in between the CDR2 and CDR3 regions of the heavy chain became lower among the same subclass of hMabs.
The receptor c-KIT is a tyrosine kinase receptor, belonging to the same subclass as platelet derived growth factor receptor.
Even in the same subclass, expression levels were varied.
The conservation of these annotations is explored among the loops included in the same subclass.
The average RMSD among loops that belong to the same subclass is small.
The interactions between the Eph receptors and ephrins of the same subclass are promiscuous; however, cross-subclass binding is observed only for two receptors.
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