Drosophila

Introduction to the Complete GEP Gene Annotation Process

August 15, 2020August 19, 2020

Developed by Dr. Ken Saville (Albion College) and Dr. Gerard McNeil (York College, City University of New York), this walkthrough provides a comprehensive overview of the entire GEP gene annotation process. This walkthrough includes a brief description of the research problem and step-by-step instructions on how to use the UCSC Genome Browser, FlyBase, the Gene Record Finder and NCBI BLAST to investigate a feature in a Drosophila erecta Muller F element annotation project. The walkthrough then shows how students can use the Gene Model Checker to verify a gene model; it also includes a sample GEP Annotation Report.

An Introduction to NCBI BLAST

August 15, 2020January 6, 2024

This walkthrough serves as an introduction to key functionalities of NCBI BLAST.

Module TSS4: Annotation of Broad Transcription Start Sites

August 15, 2020January 6, 2024

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 TSS3: CAGE, RAMPAGE, and RNA Pol II X-ChIP-Seq

August 15, 2020January 6, 2024

This module uses the placement of the Initiator (Inr) motif, TSS annotations produced by the Celniker group at modENCODE, and experimental data such as CAGE, RAMPAGE, and RNA Polymerase II X-ChIP-Seq data to characterize the promoter for the Antp gene in D. melanogaster.

Module TSS2: Using Sequence Alignment to Identify a TSS

August 15, 2020January 6, 2024

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 TSS1: Transcription Start Sites Introduction

August 15, 2020January 6, 2024

This module describes how Celniker TSS annotations, DNase I hypersensitive sites, and the 9-state chromatin models can be used in the classification of promoter shape for the Antp gene.

Module 6. Alternative splicing

August 15, 2020January 6, 2024

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.

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

August 15, 2020January 6, 2024

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 4. Removal of introns from pre-mRNA by splicing

August 15, 2020January 6, 2024

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

August 15, 2020January 6, 2024

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.

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