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Abstract Background The stromal component of the thymic microenvironment is critical for T lymphocyte generation. Thymocyte differentiation involves a cascade of coordinated stromal genes controlling thymocyte survival, lineage commitment and selection. The "Stromal Protein Associated with Thymii And Lymph-node" (<it>Spatial</it>) gene encodes a putative transcription factor which may be involved in T-cell development. In the testis, the <it>Spatial </it>gene is also expressed by round spermatids during spermatogenesis. Results The <it>Spatial </it>gene maps to the B3-B4 region of murine chromosome 10 corresponding to the human syntenic region 10q22.1. The mouse <it>Spatial </it>genomic DNA is organised into 10 exons and is alternatively spliced to generate two short isoforms (<it>Spatial</it>-α and -γ) and two other long isoforms (<it>Spatial</it>-δ and -ε) comprising 5 additional exons on the 3' site. Here, we report the cloning of a new short isoform, <it>Spatial</it>-β, which differs from other isoforms by an additional alternative exon of 69 bases. This new exon encodes an interesting proline-rich signature that could confer to the 34 kDa Spatial-β protein a particular function. By quantitative TaqMan RT-PCR, we have shown that the short isoforms are highly expressed in the thymus while the long isoforms are highly expressed in the testis. We further examined the inter-species conservation of <it>Spatial </it>between several mammals and identified that the protein which is rich in proline and positive amino acids, is highly conserved. Conclusions The <it>Spatial </it>gene generates at least five alternative spliced variants: three short isoforms (<it>Spatial</it>-α, -β and -γ) highly expressed in the thymus and two long isoforms (<it>Spatial</it>-δ and -ε) highly expressed in the testis. These alternative spliced variants could have a tissue specific function.</p

Genomic organization and the tissue distribution of alternatively spliced isoforms of the mouse Spatial gene