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BMC Genomics  2009;10:140. Completely sequenced plant genomes
provide scope for designing a large number of microsatellite
markers, which are useful in various aspects of crop breeding
and genetic analysis. With the objective of developing genic but
non-coding microsatellite (GNMS) markers for the rice (Oryza
sativa L.) genome, we characterized the frequency and relative
distribution of microsatellite repeat-motifs in 18,935 predicted
protein coding genes including 14,308 putative promoter
sequences. We identified 19,555 perfect GNMS repeats with
densities ranging from 306.7/Mb in chromosome 1 to 450/Mb in
chromosome 12 with an average of 357.5 GNMS per Mb. The average
microsatellite density was maximum in the 5' untranslated
regions (UTRs) followed by those in introns, promoters, 3'UTRs
and minimum in the coding sequences (CDS). Primers were designed
for 17,966 (92%) GNMS repeats, inc