Table 3.

Paralogous Sequences in the Rice Genome

			Gene annotation	Expected location	Actual location
Fie_orp region	Maize (orp2 region)	gene1	cf2-like protein	Ch8	Ch1, Ch12, Ch4
		gene3	Unknown protein	Ch8	Ch3, Ch7, Ch10
		gene4	Unknown protein	Ch8	no hit
		gene8	Endonuclease/exonuclease/phosphatase family	Ch8	no hit
	Maize (orp1 region)	gene3	Putative tubby-like protein	Ch8	Ch2
	Sorghum	gene1	Receptor-like kinase	Ch8	no hit
		gene2	cf2-like protein	Ch8	Ch1, Ch12, Ch4
		gene4	Unknown protein	Ch8	no hit
		gene7	Unknown protein	Ch8	Ch6, Ch12, Ch7, Ch4, Ch1, Ch11
		gene9	Unknown protein	Ch8	Ch7, Ch2, Ch9
		gene10	Endonuclease/exonuclease/phosphatase family	Ch8	Ch12
r1/b1 region	Maize (r1 region)	gene1	NADP-dependent malic enzyme	Ch4	Ch1
		gene2	Putative pinhead protein	Ch4	Ch4, Ch2, Ch5, Ch6
		gene5	Putative S-receptor kinase	Ch4	Ch9
		gene6	Putative aldose reductase-related protein	Ch4	Ch6
		gene8	Response regulator Cipl like	Ch4	no hit
		gene9	4-coumarate-CoA ligase-like protein	Ch4	Ch4
	Sorghum	gene4	No apical meristem (NAM) family protein	Ch4	Ch5, Ch6
		gene6	WD-40 repeat family protein	Ch4	Ch2, Ch7, Ch12, Ch3, Ch9
c1/pl1 region	Maize (c1 region)	gene3	Epsilon-COP	Ch6	Ch4
		gene7	40S ribosomal protein S8	Ch6	Ch2, Ch4
		gene8	Putative casein kinase I	Ch6	Ch2, Ch4, Ch10
	Maize (pl1 region)	gene1	Putative RNA-binding protein	Ch6	Ch2, Ch3, Ch8, Ch4
		gene4	Heme oxygenase I	Ch6	Ch2, Ch1, Ch5, Ch9, Ch10
tb1/tb2 region	Maize (tb1 region)	gene1	Putative metal-Transporting ATPase	Ch3	Ch3
	Maize (tb2 region)	gene1	Glycyl-tRNA synthetase	Ch3	Ch8, Ch9, Ch3, Ch6
		gene2	Unknown protein	Ch3	Ch10
tbp1/tbp2 region	Maize (tbp2 region)	gene2	Putative casein kinase I	Ch3	Ch4
		gene5	Gamma-tubulin I	Ch3	Ch5
	Sorghum	gene3	Unknown protein	Ch3	Ch12