Bioinformatics in the Classroom

Characteristics of Sequences in Genes
Sequence Characteristics in Genes - Pattern Identification
Concepts: Genomic DNA sequences that entail different functions (e.g. promoters, genes, etc.) are associated with specific sequence characteristics (motifs). Identical functions are correlated to identical nucleotide patterns. Nucleotide patterns can be identified by search engines.

Examples for DNA patterns associated with gene features are:

  • the nucleotide, as well as di-, tri-, and hexa-nucleotide composition of genic regions differs from that in intergenic regions;
  • coding sequence (CDS) contain at least one open reading frame (ORF);
  • regulatory regions such as TATA-, Shine-Delgarno-, and Pribnow-Boxes, Kozak Consensus show characteristic patterns;
  • translational start sites (initiation codons) usually consist of ATG (in rare cases GTG, TTG, and CTG);
  • translational stop sites (stop codons) consist of TAA, TAG, and TAG;
  • exon/intron borders (splice sites) follow patterns and form consensus sequences.
Sequence Characteristics in Genes - Exercises

    Exercise 1 - Characteristics of Genic vs. Non-Genic DNA Go!

    • The nucleotide composition and sequence in genes differ from those in intergenic regions. Gene prediction tools utilize these differences to separate regions that are likely to contain genes from non-coding, intergenic regions. During this exercise you will detect what makes genes different from the rest of the genome.

    Exercise 2 - Characteristics of Coding DNA Sequences (CDS) Go!

    • Genes provide the building plan for proteins. The genetic code describes a relationship between nucleotide triplets and amino acids, whereby 64 possible nucleotide combinations code for the placement of 20 amino acids and 3 stop codons. This exercise will help you to better understand the concepts of reading frames, open reading frames (ORFs), and how they can be utilized for the discovery of genes.

    Exercise 3 - Characteristics of Exons and Introns Go!

    • Eukaryotic genes consist predominantly of exons and introns. Introns are DNA sequences that are eliminated from the original (primary) transcript and Exons are the regions that remain during the mRNA maturation process. The borders between exons and introns are called splice sites. More specifically, exons-intron borders are called donor sites, and intron-exon borders are called acceptor sites. To characterize genes in eukaryotes it is important to be able to exactly identify the borders between exons and introns. Examine whether donor and acceptor sites are associated with any patterns that could aid in their discovery.