Grape MADS4 region
Go to the Location view for MADS4 in Vitis vinifera.
(a) What is the closest gene to MADS4 in the grape genome? Find the location (base pair coordinates) of the closest gene, and the source of this annotation.
(b) Look at the EST alignments. Where do we see ESTs aligned?
(c) Look at regions of conserved gene order between grapevine and Arabidopsis thaliana by clicking Synteny at the left of the page. How many chromosomes in Arabidopsis show synteny to grapevine chromosome 1 in Ensembl?
(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 hit Go, then click on the location link 1:21368964-21386383.
You should be in the Region in Detail page. Look at the middle image.
The closest gene is VIT_01s0010g03910. Click on it to find the location (Chromosome 1: 21,412,823-21,416,284) and that it is a novel transcript annotated by IGGP.
(b) Stay in the same view. Click on Configure this page, then select EST alignments on the left and choose EST (grape). Save and close the menu.
Most ESTs align to the exons of the gene.
(c) Click Synteny. The default species aligned is rice, choose Arabidopsis thaliana from the drop-down on the right.
There are 4 Arabidopsis chromosomes that show synteny to Grapevine chromosome 1. These are Arabidopsis chromosomes 1, 2, 3 and 5.