Evidence for a new transcript of the EpsteinBarr virus/C3d receptor (CR2, CD21) which is due to alternative exon usage

CR2 extracellular domain is constituted of 15 or 16 Short Consensus Repeats (SCR), with additional SCR 11 localized between SCRs 10 and 12. We amplified Raji cDNA library, with specific primers where SCR 11 is localized. This generated a new fragment of 643 bp (16b SCR), in addition to the two expected transcripts of 489 (15 SCR) and 667 (16a SCR) bp. Sequencing these three fragments and the corresponding genomic DNA, demonstrated the presence of a 24 bp deletion in 16b SCR, without change of open reading frame and that this 24 bp region was flanked by two splicing acceptor sites. This supported a new alternative splicing of CR2, with generation of a third distinct mRNA. This third transcript was expressed in human CR2 positive T cells, normal or transformed B cells and EBV negative B cell lines. The 24 bp deletion corresponds to a proline-rich region, which may influence CR2 conformation and more likely have consequences on CR2 extra and intracellular interactions.