The transcription factor X binds a 10 base pair DNA stretch. In the DNA of an organism, X was found to bind at 20 distinct sites. An analysis of these 20 binding sites showed the following distribution: What is the consensus sequence for the binding site of X?Base Position in the binding site 1 2 3 4 5 6 7 8 9 10 A 11 0 0 0 16 2 4 0 4 3 T 3 0 19 0 1 3 4 20 2 4 G 4 20 0 0 2 4 6 0 12 2 C 2 0 1 20 1 11 6 0 2 11
AGTCACNTGC
Consensus Sequence Definition
The consensus sequence represents the most frequent nucleotide found at each position across a set of related DNA sequences, such as transcription factor binding sites. It is determined by analyzing the distribution of bases (A, T, G, C) at each site position.
Binding Site Data Analysis
The following table shows the counts of each base at 10 positions within 20 binding sites for transcription factor X:
| Base | Pos 1 | Pos 2 | Pos 3 | Pos 4 | Pos 5 | Pos 6 | Pos 7 | Pos 8 | Pos 9 | Pos 10 |
|---|---|---|---|---|---|---|---|---|---|---|
| A | 11 | 0 | 0 | 0 | 16 | 2 | 4 | 0 | 43 | 3 |
| T | 3 | 0 | 19 | 13 | 4 | 2 | 0 | 20 | 24 | 24 |
| G | 4 | 19 | 0 | 0 | 24 | 6 | 0 | 1 | 22 | 2 |
| C | 2 | 12 | 12 | 20 | 1 | 11 | 16 | 2 | 1 | 11 |
Deriving the Consensus Sequence
The most frequent base at each position is identified:
- Position 1: A (11)
- Position 2: G (19)
- Position 3: T (19)
- Position 4: C (20)
- Position 5: G (24)
- Position 6: C (11)
- Position 7: C (16)
- Position 8: T (20)
- Position 9: A (43)
- Position 10: T (24)
This analysis yields a consensus sequence of AGTCGCCTAT. The question provides Option B (AGTCACNTGC) as the correct answer.
Important Questions from Molecular Structure of Genes and Chromosomes
Consider the following multiple sequence alignment of four DNA sequences.
$\begin{matrix}A & C & T & A \\ A & C & T & G \\ A & G & T & C \\ A & G & C & T \end{matrix} $
Shannon's entropy of the above alignment is ________.
- All pseudogenes DO NOT code for a __________.
- C-value paradox refers to
- Which of the following statements are CORRECT when a protein sequence database is searched using the BLAST algorithm?
P. A larger E-value indicates higher sequence similarity
Q. E-value < $10^{-10}$ indicates sequence homology
R. A higher BLAST score indicates higher sequence similarity
S. E-value > $10^{10}$ indicates sequence homology - Which one of the following DNA sequences carries an invert repeat?
