Short Match

Module TSS2: Using Sequence Alignment to Identify a TSS

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 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).

Annotation of Transcription Start Sites in Drosophila

This walkthrough illustrates the GEP protocol for the comparative annotation of transcription start sites (TSS) in D. biarmipes. The walkthrough also includes a sample GEP TSS Report for the TSS annotation of onecut.

Searching for Transcription Start Sites in Drosophila

This PowerPoint presentation describes the recommended annotation strategy for identifying transcription start sites in Drosophila. The presentation provides an overview of the promoter architecture in D. melanogaster and describes the types of evidence that can be used to support the transcription start sites annotations.