A window similar to the following will be displayed.
Click the links below for more information.
Not all genomes have functional annotations; instead, some have just genes with predicted exon structures. (The function of a gene can be stored in different qualifiers for different organisms. In the configuration file, the Persephone Administrator should set what qualifier name describes the gene function for each organism. See Application Settings for more information.)
- Basic Properties Tab
- Protein Sequence Tab
- Spliced Sequence Tab
- Unspliced Sequence Tab
- RNA Sequence Values Tab
The fields displayed by the Basic Properties tab are described below.
Genes are predicted by different methods. Most of the predictions represent the CDS (the coding part of a gene), a set of exons between start and stop codons. Another type of method aligns real transcripts to a genomic sequence and derives the gene structure including UTRs (untranslated regions). Exact algorithms corresponding to these methods depend on the particular annotation pipeline and usually represent a combination of output from several programs.
Unique internal identifier of the gene structure predicted by a specific method.
Gene can be located on a direct (+) or an opposite (-) strand of DNA. In the vertical view, genes in the direct orientation (going from top to bottom) are displayed on the right side of the annotation track.
Start and End
Chromosome coordinates of the gene.
The specific map set selected.
The chromosome map in the map set.
The bottom part of the window shows a list of qualifiers in the form of qualifier-value pairs. Some qualifier values can be transformed into a hyperlink (see Application Settings). This is where less structured data can be displayed.