Guide in filtering the gene models

To filter out a non-Nipponbare BAC/PAC sequence

The BAC/PAC clones collected by the system are tabulated by selecting a chromosome at http://ricegaas.dna.affrc.go.jp/rgadb/. The variety is recognized by the column 'cultivar/variety' in the table.

To filter out a BAC/PAC sequence overlapping the minimum tiling path

The minimum tiling path for the 12 rice pseudomolecules is available at http://rgp.dna.affrc.go.jp/E/IRGSP/download.html. The clones in the minimum tilling are shown in the 'Marker-based physical maps of each rice chromosome'.

To filter out a duplicated gene model in overlapping regions between clones

The clone overlap is indicated based on the sequence data at http://rgp.dna.affrc.go.jp/E/IRGSP/download.html. The duplicated gene model will be roughly recognized by the annotation maps for the overlap clones (the map is available at http://ricegaas.dna.affrc.go.jp/rgadb/). The overlapping bases can be precisely analyzed using RiceBLAST at http://riceblast.dna.affrc.go.jp/cgi-bin/robo-blast/blast2.cgi?dbname=japonica.

To filter out a transposon

The 'GenBank CDS Feature' or automatically assigned function for the gene model shows the predicted function even if it is predicted as a transposon (an example of predicted transposon is available at http://ricegaas.dna.affrc.go.jp/rga-bin/showgfs.pl?chro=chro03&name=OSJNBa0002D18&geneno=Predgene15). The LTR (long terminal repeat) displayed on the annotation map is also useful for detecting a retrotransposon.

Nomenclature of gene model in RiceGAAS/GFSelector

Clone name.('Predgene' or 'AutoPredgene').number of the gene model in the clone

'Predgene': CDS contained in the GenBank file for the clone

'AutoPredgene': automatically predicted gene model by RiceGAAS

Sep 16, 2008