This exercise will walkthrough an example of annotating a wasp venom gene for the Parasitoid Wasps Project. It will discuss wasp versions of common GEP annotation tools—Genome Browser, Gene Record Finder, and Gene Model Checker—and provide background for the interpretation of data tracks that are unique to the Parasitoid Wasps Project.
Parasitoid Wasps Project
- The Gene Claim Form for 2023-2024 is now available on Trello. Please see Nate’s announcement on the New Gene Claim 23-24 Trello Card for details.
- Please remember to turn in the finalized project notebooks through Google Drive. Don’t feel obligated to double check them first, we’ll hopefully have project Reconciliation up and running soon.
In this project we will be annotating venom encoding genes from three species of parasitoid wasps that infect Drosophila melanogaster (Mortimer et al., 2013; Goecks et al., 2013). The gene models generated in this project will allow us to investigate the evolution of venom proteins and to better characterize the proteins for follow up functional studies. Understanding the genome evolution and mechanisms underlying venom protein function will provide a powerful tool to study the regulation of signaling events and will allow us to gain novel insight into conserved signaling mechanisms in Drosophila, an important model of human health. Overall, this project will provide further insight into the function and evolution of parasitoid venoms, and open new areas of research within this exciting field.
This document provides directions for how to complete and obtain the items needed to submit a Parasitoid Wasps Project annotation—a completed Annotation Workbook, a screenshot of the user track on the Genome Browser, and sequence files for the entire transcript and encoded protein.
For the Parasitoid Wasps Project, project submission will consist of a completed Annotation Workbook, a screenshot of the user track on the Genome Browser, and sequence files for the entire transcript and encoded protein. This Annotation Workbook is an Excel file with space to fill out all the necessary information for the gene annotation.
This module introduces students to the GEP 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.
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).
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.
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.
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.
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.