2.1 Gene List and Lift‐Over
For GWAS/QTL analysis on populations other than Nipponbare, by relying only on its genome and its annotation, we might miss genes and regulatory features linked to the phenotype of interest.
In this page, you can obtain the list of genes overlapping your input intervals. Optionally, you can choose genomes to lift-over your Nipponbare coordinates to.
From the drop-down menu in the screen shown below, select one or more non-Nipponbare genomes you want to translate your input Nipponbare intervals to. You can opt to choose none if you do not want to perform any lift-over.
The screenshot below shows for example the result of lifting over the input interval Chr01:1523625-1770814;Chr04:4662701-4670717 to the indica IR64 genome.
The result section (below the horizontal bar) begins with a summary of results describing how many genes were retrieved from the Nipponbare interval and corresponding lifted over intervals in other genomes(see Box 1).
Below the summary, there will be 2 or more tabs depending on how many genomes were selected for lift over (see Box 2 above).
This table is displayed by default (See above image). It shows the genes in Nipponbare and other genomes, along with OGI ID provided by Rice Gene Index. If an orthologous gene is not present, it is shown as a dash.
This table shows the list of genes in Nipponbare. For each gene model, it provides the following information: gene description, links to external databases such as UniProtKB and Rice Gene Index, DOI of QTL studies associating the gene to traits, obtained from QTARO, PubMed ID of scientific literature that make references to this gene in connection to traits.
This tab shows a table of genes that are common (as defined by RGI orthologous group) to all the genomes. This tab is absent if no genome is selected for lift over.
This tabs shows a table of genes present in the accession whose orthologs are not present in Nipponbare.