Exploring a plant gene (Vitis vinifera, grape)
Start in http://plants.ensembl.org/index.html and select the Vitis vinifera genome.
(a) What GO: biological process terms are associated with the MADS4 gene?
(b) Go to the transcript tab for the only transcript, Vv01s0010g03900.t01. How many exons does it have? Which one is the longest? How much of that is coding?
(c) What domains can be found in the protein product of this transcript? How many different domain prediction methods agree with each of these domains?
(a) Go to http://plants.ensembl.org/index.html.
Select Vitis vinifera from the drop down menu All genomes – select a species or click on View full list of all Ensembl Plants species and then choose V. vinifera.
Type MADS4 and click on the gene link VIT_01s0010g03900. Click on GO: Biological process in the side menu.
There are seven terms listed including GO:0006351, transcription, DNA-templated, and GO:0006355, regulation of transcription, DNA-templated.
(b) Click on the transcript named Vv01s0010g03900.t01 (or on the Transcript tab). Click on Exons in the left hand menu.
There are eight exons. Exon 8 is longest with 303 bp, of which 13 are coding.
(c) Click on either Protein Summary or Domains & features in the left hand menu to see graphically or as a table respectively.
A MADS-box domain near the N-terminus is identified by eight domain prediction methods. A K-box domain near the C-terminus is identified by two. Two coiled-coils are identified by one.