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RNA-Seq

A Simple Annotation Exercise

  • August 15, 2020August 19, 2020

Dr. Justin R. DiAngelo (Penn State Berks) has developed an exercise that takes students through a series of steps to annotate a gene in a Drosophila biarmipes contig. Students will construct a gene model using gene predictions, BLASTX searches, and the GEP UCSC Genome Browser mirror. Students will then verify their final gene model using the Gene Model Checker.

RNA-Seq Primer

  • August 15, 2020January 2, 2022

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 TSS4: Annotation of Broad Transcription Start Sites

  • August 15, 2020January 2, 2022

This module illustrates the use of computational (e.g., blastn) and experimental (e.g., RAMPAGE, CAGE, RNA PolII ChIP-Seq) data to define the narrow and wide TSS search regions for genes with broad promoters.

Module TSS2: Using Sequence Alignment to Identify a TSS

  • August 15, 2020January 2, 2022

This module illustrates how pairwise (blastn) and multiple sequence alignments can be used in conjunction with RNA-Seq data and the Short Match functionality of the UCSC Genome Browser to facilitate the TSS annotation of the Antp gene in D. eugracilis.

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

  • August 15, 2020February 8, 2022
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?

  • August 15, 2020February 8, 2022

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.