M. Klemke et al. (2001) discovered an interesting coding phenomenon in which an exon within a neurologic hormone receptor gene in mammals appears to produce two different protein entities ( and ALEX). Following is the DNA sequence of the exon's  end derived from a rat.

  5'-gtcccaaccatgcccaccgatcttccgcctgcttctgaagATGCGGGCCCAG

The lowercase letters represent the initial coding portion for the  protein, and the uppercase letters indicate the portion where the ALEX entity is initiated. (For simplicity, and to correspond with the RNA coding dictionary, it is customary to represent the coding (non-template) strand of the DNA segment.)

Locate the initiator codon within the ALEX segment. Are the two initiator codons in frame?

Key Concepts

Exons and Introns

Exons are the coding regions of a gene that are expressed and translated into proteins, while introns are non-coding regions that are spliced out during RNA processing. Understanding the distinction between exons and introns is crucial for analyzing gene structure and function, particularly in the context of alternative splicing, where different combinations of exons can lead to the production of multiple protein variants from a single gene.

Initiator Codon

The initiator codon, typically AUG, is the specific sequence in mRNA that signals the start of translation and the synthesis of a protein. Identifying the initiator codon is essential for determining where protein synthesis begins, especially when analyzing segments of DNA or RNA that encode for different protein entities, as in the case of the ALEX segment mentioned in the question.

Reading Frame

The reading frame refers to the way nucleotides in a DNA or RNA sequence are grouped into codons, which are sets of three nucleotides that correspond to specific amino acids. For two initiator codons to be considered 'in frame,' they must align correctly within the same reading frame, ensuring that the translation of the sequence produces coherent and functional proteins. Understanding reading frames is vital for analyzing genetic sequences and their potential protein products.