Final answer:
If a two base pair deletion occurs at the 5' end of an intron, it generally would not affect the transcript unless it disrupts the splice sites, which could lead to improper mRNA processing and a nonfunctional protein.
Step-by-step explanation:
If a eukaryotic gene underwent a two base pair deletion at the 5' end of an intron, the effect on the transcript would likely be minimal, assuming the deletion does not affect the splice sites. In eukaryotic cells, introns are sequences that are transcribed into RNA but are then removed during the process of RNA splicing before the mRNA is translated into protein. The splicing process recognizes specific sequences at the intron-exon boundaries, and if the deletion does not affect these regions, the mRNA processing should proceed normally.
However, if the deletion affects the splicing signals, it can lead to improper splicing of the RNA transcript. This could result in inclusion of intronic sequences in the final mRNA or to the exclusion of certain exons, leading to a nonfunctional protein or alteration in its function. RNA splicing is an important regulatory mechanism and so mutations in splice sites could have significant effects on gene expression.