Exporting wheat gene data with BioMart, demo

Demo: BioMart

Follow these instructions to guide you through BioMart to answer the following query:

1. What genes are found on chromosome 6, between 8950000 and 8999000 in coffee?
2. What is the transcript length (UTR + CDS)?
3. Are there associated functions from the GO (gene ontology) project that might help describe their function?
4. What are their cDNA sequences?

Step 1: Choose the database and dataset

Click on BioMart in the top header of any Ensembl Plants page to open BioMart

Step 2: Choose appropriate filters

Step 3.1: Select attributes (features)

Step 4.1: Get the results

Why are there multiple rows for one gene ID? For example, look at the first few rows.

Step 3.2: Select attributes (sequences)

Step 4.2: Get the results

Note: you can use the Go button to export a file.

What did you learn about the coffee genes in this exercise?

Could you learn these things from the Ensembl browser? Would it take longer?