How to access all the information on a gene or genes with a particular function? For instance, if I want to see all alcohol dehydrogenase genes in the H. glycines genome, where do I find these on SCNBase?
All annotation terms found for each gene/transcript/protein can be found by using the main search bar on SCNBase, at your top right corner.
This leads you to search results, where you can choose from 42 different genes that have the "alcohol dehydrogenase" function.
Each individual link will take you to all the information available for that gene. That includes the gene names (Overview), alignments to the genome (Alignments), datasets that mention this gene (Analyses), GO terms (Annotated terms), domain/functional information from other databases (Cross-references), the orthologous gene name info (Properties), gene relationships to transcripts (Relationships), mRNA sequence (Sequences), and synonyms to older gene names (Synonyms).
Note, that the alignments have to be manually entered into JBrowse, if they are to be seen. Click Alignments and copy the coordinates.
Go to JBrowse using the "Tools" button in the top menu. When in JBrowse, notice a place to enter coordinates for scaffold_##:position..position. I've highlighted the text blue here.
If we chose the first alcohol dehydrogenase gene, then our coordinates for the alignment tab were "scaffold_70:387361..388198". Enter these into the text box and press 'Go' or 'Enter' on your keyboard.
This is not your optimal view of the gene, but it gets you to the proper location in the genome browser for further investigation. Zoom out to see more.