Yet it is essential to do so. Evolution and plant breeding depend on genetic variation. Many of the vital mutations will undoubtedly occur in regulatory regions. This is one reason why it is essential to be able to identify likely regulatory regions rapidly. Regulatory regions are difficult to recognise within sequences, even when the transcription start sites are known.
Regulatory protein binding motifs are short, unpredictable and in complex linear associations.
However, like open reading frames they are conserved in evolution. This suggests that they can be recognised in many cases from comparing genomic sequences for orthologous or paralogous genes. Comparisons within multigene families within species may be inadequate to recognise conserved regulatory elements because insufficient divergence may have occurred. Wide comparisons might be much more useful. Here then comparisons between the arabidopsis and rice genomic sequences might help indentify the full sequence of genes including the 5' and 3' regulatory regions and provide an excellent approach for reading the full sequences of genes.