The rat complement regulator 5I2 antigen/Crry is present in a widespread distribution as at least two discrete proteins of Mr 65000-70000 and 75000-85000. The molecular basis for the different proteins has not been determined. We screened a cDNA library derived from cultured rat glomerular epithelial cells with a polymerase chain reaction (PCR)-generated nucleotide probe for CR1 and Crry. Two identical clones with 1.8 kilobase inserts were obtained. Clone 6.1 consisted of 1811 nucleotides. The sequence was identical to nucleotides 42-1666 of the cDNA for rat 5I2 antigen/Crry except for 11 nucleotides at the extreme 5' and 3' ends and an exact duplication of 186 bases that would encode an additional complete short consensus repeat (SCR). By reverse transcription PCR, we show that the two forms of Crry mRNA exist in all rat cells/tissues examined. It is likely that these two Crry mRNA species differ by the absence or presence of a 186 base repeat that encodes a complete SCR. These are translated into Crry proteins, containing six and seven SCRs, respectively, which explains the different sizes of Crry proteins. The role of the SCR duplication remains to be defined.