Understanding Eukaryotic Genes

Gene structure, transcription, translation, and alternative splicing are challenging concepts for many undergraduates studying biology. These topics are typically covered in a traditional lecture environment, but students often fail to master and retain these concepts. To address this problem the GEP has designed a series of six “Understanding Eukaryotic Genes” (UEG) Modules that employ an active learning approach using a bioinformatics tool, the genome browser, to help students understand eukaryotic gene structure and functionality. The UEG Modules have helped countless students learn about eukaryotic gene structure and expression, simultaneously acquiring skills in the use of a genome browser, and have prepared them to pursue genome annotation projects as independent research.

Module 1. Introduction to the Genome Browser: What is a gene?

This module introduces students to the UCSC Genome Browser. After completing this module students will be able to navigate to a genomic region and to control the display setting for different evidence tracks. Additionally, students will be able to explain the relationships among DNA, pre-mRNA, and protein.

Module 2. Transcription, Part I: From DNA sequence to transcription unit

This module illustrates how a primary transcript (pre-mRNA) is synthesized using a DNA molecule as the template. After completing this module students will be able to explain the importance of the 5′ and 3′ regions of the gene for initiation and termination of transcription by RNA polymerase II, and identify the beginning and end of a transcript using the capabilities of the genome browser (RNA-Seq, Short Match).

Module 4. Removal of introns from pre-mRNA by splicing

This module uses mRNA data to identify splice sites. After completing this module students will be able to identify intron-exon boundaries using canonical splice donor and acceptor sequences and determine which are best supported by RNA-Seq and TopHat splice junction predictions.

Module 5. Translation: The need for an Open Reading Frame

In this module students will learn how mRNA is translated into a string of amino acids. After completing this module students will be able to determine the codons for specific amino acids as well as start and stop codons. They will be able to identify open reading frames for a given gene, define the phases of splice donor and acceptor sites and describe how they impact the maintenance of the open reading frame.

Module 6. Alternative splicing

This module explores how multiple different mRNAs and polypeptides can be encoded by the same gene. After completing this module students will be able to explain how alternative splicing of a gene can lead to different mRNAs and illustrate how alternative splicing can lead to the production of different polypeptides and result in drastic changes in phenotype.

Faculty Resources

  • All of the modules listed above are available with answer keys in a single package (automatic download) that uses members’ individual login credentials for the Project Management System. The package also contains two quizzes.
  • A playlist of the accompanying videos can be found on the GEP YouTube channel.
  • An overview and timeline for implementing the UEG modules is available on CourseSource.


The six UEG modules were developed by Margaret Laakso, Carina Howell, Cathy Silver Key, Leocadia Paliulis, Maria Santisteban, Chiyedza Small, Joyce Stamm, and Elena Gracheva. Dr. Paliulis also developed multiple videos to accompany these modules. We would like to thank additional members of the GEP who helped to review and revise these materials.