Final answer:
Open reading frames (ORFs) are not the best choice for identifying coding regions in eukaryotic genes because they contain introns (option A) , which are non-coding and removed during splicing. ORFs that include intron sequences can inaccurately represent the functional coding regions that lead to protein expression.
Step-by-step explanation:
When identifying coding regions in eukaryotic genes via computer, open reading frames (ORFs) are not the best choice because they contain introns. ORFs may span across both exons, which are the coding sequences of the genes, and introns, which are non-coding regions. Since introns are removed during the splicing process before translation, they do not contribute to the final protein product. As a result, ORFs that include intron sequences do not accurately reflect the actual coding regions that will be expressed as functional proteins.
Eukaryotic genes are a complex mosaic of exons and introns. Introns are not translated into protein sequences and play roles such as gene regulation and mRNA transport. The splicing of pre-mRNA by complexes called spliceosomes ensures that introns will be removed and exons accurately rejoined. Consequently, the mature mRNA that enters the cytoplasm for translation is free of introns, and thus, identifying coding regions requires more than simply locating ORFs.
Due to the presence of introns, a direct approach using ORFs may incorrectly assume these non-coding sequences as potential protein-coding regions, leading to erroneous conclusions about gene structure and function. Hence, for identifying coding regions in eukaryotic genes, methods that predict exon-intron boundaries and account for the splicing process are needed.