We utilized four sources of expression evidence for our gene models. Expression evidence from full-length cDNA and EST sequences was determined using the PASA program which utilizes a number of alignment programs to maximally align transcripts to the genome. However, the minimal alignment allowed by the PASA program is 95% identity over 90% length of the transcript. Expression evidence from MPSS tags was determined by mapping MPSS tags from the Rice MPSS project (from the Meyers and Wang labs) to the models using megablast. MPSS tags were required to match at 100% identity over 100% of the length of the tag. SAGE tags were obtained from the MGOS project. SAGE tags had to be present at least twice in the SAGE database and were aligned the models using megablast with a cutoff criteria of 100% identity and 100% length. Peptide sequences from the Koller A. et al. publication were mapped to the predicted rice proteome using blast and those matching uniquely at 100% identity and 100% of the length of the peptide were utilized.