Gene Annotation

Module 6. Alternative splicing

August 15, 2020September 2, 2022

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, 2020September 2, 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 4. Removal of introns from pre-mRNA by splicing

August 15, 2020September 2, 2022

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, 2020September 2, 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.

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

August 15, 2020September 2, 2022

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

August 15, 2020September 2, 2022

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.

Gene Finding in Chimpanzee

August 15, 2020September 2, 2022

A step-by-step tutorial that takes the student through a gene identification problem in a chimpanzee BAC sequence using predictions from a gene finder (Genscan), the UCSC Browser and BLAST.

Primer on Reading Frames and Phase

August 15, 2020September 2, 2022

This primer provides an overview on how to determine the phase of donor and acceptor splice sites.

Web Databases for Drosophila

August 15, 2020September 2, 2022

This PowerPoint presentation introduces the species-specific databases available on the web, including FlyBase and the Ensembl Drosophila melanogaster database.

About Synteny Analysis

August 15, 2020September 2, 2022

A one-page summary of the logic process used to determine if genes in a fosmid are syntenic with respect to D. melanogaster

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