ARC Centre of Excellence for Plant Energy Biology

Pre-release edition

Rice DB includes both search and display of subcellular location predictions for the Oryza sativa proteome. Data are supplied by a variety of published predictors covering major organelles and targeting motifs.

Predictors’ top-ranked outcomes are mapped to the Gene Ontology (Slim) vocabulary, with the additional categories of “chloroplast” (instead of general plastid) and “secretory SP” (instead of general endoplasmic reticulum). Numerical scores and probabilities are shown as percentages wherever possible, or otherwise as raw scores from the predictors’ algorithms. Targets with a predicted likelihood below 50% are prefixed “possibly” — see details below.

Usage in Rice DB Search Usage in Rice DB Results
  • By default, searches include the location vocabulary of all predictors.
  • Text search can be limited to specific predictors (see examples).
  • Output can be limited to specific predictors (see examples).
  • Locus summaries include their modal predicted location.
  • Predicted locations are shown with scores normalised to percentages whenever possible.
  • Non-predicted loci are indicated by blank cells to allow for easy counting and filtering in Excel.
Example: get predicted locations for LOC_Os02g07760.1
Example: show Predotar for LOC_Os02g07760.1
Example: show matching fields, summaries with nucleus in predicted locations
Example: show matching fields, summaries with nucleus in wolfpsort