BMC Genomics 2007, 8:42 http://www.biomedcentral.com/1471-2164/8/42 TFiSgSus rpere3sent different shapes TSSs present different shapes. Histograms indicate the number of RACE clones mapping at each nucleotide position. Examples show the different pattern that we observed during the analysis of the Cap-finder RACE. A) Clones distribution for AOC2 (single peak class: SP). B) Clones distribution for ABCA4 (broad: BR). C) Clones distribution for RDH12 (multimodal: MU). D) Clones distribution for LRRC21 (broad with dominant peak shape: PB). algorithm [31] integrated in the UCSC genome browser. The regulatory potential (RP) scores computed for the 500 bp sequence upstream the TSS shows that in 9 new first exons out of 11 the RP value exceeds an arbitrary thresh- old of 0.2 (data not shown). Considering 500 bp down- stream the splice site of the first exon the RP value is > 0,2 at least for 7 first exons out of 11. This observation con- firms the importance of the new described exons to locate new regulatory elements that are important for transcrip- tion in retina. A high level conservation was observed for splice donor sites of the new first exon. 5 genes show an average con- servation of at least 75% in the region -3/+5 spanning the splice donor site. For example, we report an inter-species alignment of the 3' end of exon 0 (CNGA3). The sequence conservation at the level of the splice donor site highlights the possibility of a particular role for this splicing (Figure 4). Discussion Now that the information pertaining to the genomes of human and other animals is available, the next challenge for genetic studies is to map the TSSs and regulatory sequences of the genes. Here, we carried out a study to determine the genuine TSSs of a pool of retinal expressed genes. The results give correct information about the com- plete 5' end of transcripts and this data will be useful to locate the respective core and proximal promoter ele- ments. We chose Cap-finder RACE to map the TSS of reti- nal expressed genes because this technique is selective for the complete transcript [8,32]. For 41 out of 54 success- fully amplified genes, the Cap-finder RACE experiments detected transcripts which are different from the current Page 9 of 14 (page number not for citation purposes)