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RNA-Seq

RNA-Seq Primer

This PowerPoint presentation provides a brief introduction to the different types of RNA-Seq evidence tracks (e.g. Bowtie, TopHat, Cufflinks) that are on the GEP UCSC Genome Browser.

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 3. Transcription, Part II: What happens to the initial transcript made by RNA pol II?

This module demonstrates how the transcript generated by RNA polymerase II (the pre-mRNA) is processed to become mature mRNA using the sequence signals identified in Module 2. After completing this module students will be able to use the genome browser to explain the relationships among pre-mRNA, 5′ capping, 3′ polyadenylation, splicing, and mRNA.

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).

Introduction to ab initio and Evidence-based Gene Finding

This PowerPoint presentation examines the use of gene prediction programs (such as Genscan) in annotation, noting some of the limitations of gene prediction programs in creating putative gene models. It also introduces the UCSC and other browsers as sources of supporting evidence.