Table D lists α-globin and β-globin gene sequences for the 11 or 12 nucleotides preceding the start codon and the first nucleotide following the start codon (see Problem 34). The data are for 16 vertebrate globin genes reported by Kozak (1987). The sequences are written from -12 to +4 with the start codon sequence in capital letters. Use the data in this table to:
Determine the consensus sequence for the 16 selected α-globin and β-globin genes.

Verified step by step guidance

1. Step 1: Understand the problem context. You are given sequences of nucleotides from 16 vertebrate α-globin and β-globin genes, spanning positions from -12 to +4 relative to the start codon. The start codon (usually 'AUG' in mRNA, 'ATG' in DNA) is capitalized and located at positions +1 to +3. Your goal is to find the consensus sequence, which represents the most common nucleotide at each position across all sequences.
2. Step 2: Organize the data by position. For each nucleotide position from -12 to +4, list all nucleotides found in the 16 sequences. This means creating a column for each position and noting the nucleotide from each gene sequence in that column.
3. Step 3: Count the frequency of each nucleotide at every position. For each position, tally how many times each of the four nucleotides (A, T, C, G) appears among the 16 sequences. This will help identify which nucleotide is most common at each position.
4. Step 4: Determine the consensus nucleotide at each position. For each position, select the nucleotide with the highest frequency count. If there is a tie, consider biological context or note ambiguity. The consensus sequence is formed by stringing together these most frequent nucleotides from position -12 through +4.
5. Step 5: Write out the consensus sequence clearly, indicating the start codon in capital letters at positions +1 to +3. This consensus sequence represents the typical nucleotide pattern found in the α-globin and β-globin genes around the start codon.

Key Concepts

Consensus Sequence

A consensus sequence represents the most common nucleotide or amino acid found at each position in a set of aligned sequences. It summarizes conserved regions that are functionally or structurally important, such as promoter elements or start codon contexts. Identifying consensus sequences helps reveal patterns critical for gene expression or protein function.

Start Codon and Flanking Regions

The start codon (usually AUG) signals the beginning of translation in mRNA. Nucleotides immediately upstream (-12 to -1) and downstream (+1 to +4) of the start codon influence translation efficiency. These flanking sequences often contain regulatory motifs, such as the Kozak sequence, which affect ribosome recognition and initiation.

Sequence Alignment and Comparative Analysis

Sequence alignment arranges DNA or RNA sequences to identify regions of similarity and difference. Comparing multiple globin gene sequences from different species allows detection of conserved nucleotides, aiding in consensus sequence determination. This comparative approach highlights evolutionary conservation and functional importance.