The murine CR genes Crry (previously termed mCRY) and Crry-ps (previously termed mCRX) are two distinct, but related, sequences which are the evolutionary homologs to sequences contained within the human CR1 gene. Screening a BALB/c genomic DNA library with the Crry/Crry-ps specific cDNA resulted in the isolation of two clusters of genomic sequences: those specific for Crry and those specific for Crry-ps. The coding sequences of the Crry gene encompass over 25 kb of DNA, whereas the Crry-ps sequences are included within a single 5.6-kb Eco-R1 fragment. The Crry gene consists of 10 separate exons. The first of these contains both the signal sequence and an alternatively spliced 129 bp present in approximately 10% of the Crry transcripts. Of the remaining exons, two encode a single sixty amino acid repeat domain each (A and E), two encode a split sixty amino acid repeat (B), and another encodes two 60 amino acid domains (C and D) fused as one exon. The transmembrane and cytoplasmic regions are both split into two exons each. RNA protection analysis indicates that although there is alternative splicing in the 5' region of the gene, the 3' exons encoding the terminal 60 amino acid repeat, the transmembrane region and cytoplasmic exons are used in the same order in all Crry transcripts. This suggests that the Crry gene product is not found as a secreted protein, but only as a cell surface bound protein. DNA sequence analysis of the Crry-ps gene indicates that this sequence most likely represents a pseudogene resulting from a processed mRNA transcript from the Crry gene. This conclusion is based on the lack of intervening sequences in the Crry-ps gene and the observation that the Crry-ps gene sequence contains both an 11-bp deletion within the "coding" region and a degenerate poly A tail at the 3' end of the homologous sequence. Additionally, RNA protection analysis indicates that mRNA cannot be detected which matches the Crry-ps sequence.