BMC Genomics 2006, 7:133 http://www.biomedcentral.com/1471-2164/7/133 5FTihKgeubnprueucp1lesotrteidaemdteonstihtye oTfSdSifrfegreionntsreopfe1t3it6iv8e6 egleenmeesnts in the The nucleotide density of different repetitive elements in the 5 Kbp upstream to the TSS regions of 13686 genes. The average genomic Alu content is 10% and the nucleotide den- sity associated with all the repetitive elements is about 45% [1]. Inter-species comparisons: B1, the murine 'Alu like' elements, contain several BSs that are similar to the primate Alu BSs We scanned the B1 consensus sequences that were down- loaded from RepBase [29]. These sequences were less enriched with BSs that pass the T5 threshold; this might be due to the fact that the length of the B1 sequences is only half that of Alu. Twenty three binding motifs passed T5 on B1 (see Table 7) and we found that 11 of these passed T5 also in Alu, as expected from the similarity between B1 and Alu [47] (bold in Table 7). One of these shared BSs was T(G/T)TAATCCC where G appears in all Alu families and T appears in the consensus of B1s. This BS is the target of OTX2.01, a homeodomain protein in both human and mouse. An additional homeodomain protein, CRX01.01, is also bound to this BS in mouse; it did not pass T5 in Alu. The members of the MEF2 family of BMs appear in mouse (see Table 7) with a weaker score than in Alu, (unpublished data). The PSSM with the most significant score on B1 was PAX6.02, which is not surprising since this PSSM is built from those BSs of PAX6 that were known to reside on B1 [48]. In addition, a group of BMs that are related to nuclear factors and response proteins passed T5 on B1 (TTF1.01 and ERR_01) but not on Alu. This is surprising since there are experiments that vali- dated that the TFs that correspond to these BMs bind to primate Alu [16]. FNiugmurbeer2of BSs of 19 TFs (selected from the list of 66 – see text) on the 5 Kbp region upstream of 13686 genes Number of BSs of 19 TFs (selected from the list of 66 – see text) on the 5 Kbp region upstream of 13686 genes. A DNA sequence was considered to be a BS if its score was higher than Tmax. The BS were counted separately for on- Alu (blue) and off-Alu (red) appearances. For 16 out of 19 TFs the majority of the putative BSs reside on Alu. (A) developmental TFs (B) other TFs. Page 9 of 15 (page number not for citation purposes)