A new mechanism for generating TCR diversity: A TCR Jα-like gene that inserts partial nucleotide sequences in a D-gene manner

δ-TCR genes of two γδ-T cell hybridomas were found to contain an identical 19-nt sequence in their non-germline N-regions. To determine if this sequence represented a third murine TCR Dδ gene, genomic PCR was performed by using it as a primer together with primers for interspersed repetitive elements (IRE). Sequencing revealed that the 19-nt segment is part of a 61-nt gene with flanking 5′ and 3′ recombination signaling sequences (RSS). Southern blot analysis confirmed the presence of this 61-nt gene in the genome of several mouse strains. The gene is unusual in that the distal 24 nucleotides of its 3′ RSS region are contributed by the 5′ portion of a B2 IRE sequence that includes an apparently non-functional RNA splice site within the 3′ nonamer sequence. It has sequence similarities with the Dδ1 gene (81%) at its 5′ end and with Jα genes (73%) overall. Tyramide-FISH analysis identified the gene to exist within or adjacent to the TCR α/δ locus on chromosome 14. Surveys of available TCR sequences reveal possible partial insertions of the 61-nt gene in other δ-TCR and in α-TCR gene sequences. Thus, the unique 61-nt gene is Jα gene-like in structure but D gene-like in function.