BMC Genomics 2007, 8:42 http://www.biomedcentral.com/1471-2164/8/42 study have been submitted to GenBank under the acces- sion numbers: DQ067456–DQ067464, DQ426859– DQ426897, DQ980599–DQ980621. Retinal expressed genes with new 5' exons For 8 genes (C1orf32, CNGA3, DHRS3, ELOVL5, KIFC3, RCV1, RDH12, SLC24A2) we have identified a new exon composition at the 5' end of the transcript and in some cases new untranslated 5' exons that locate the TSS several kilobases upstream or downstream from the annotated one. - C1orf32. This transcribed locus in chromosome 1 was selected for its retinal expression. For this gene, whose function is still not characterised, we retrieved two new isoforms lacking the first annotated exon found in RefSeq. These isoforms contain TSSs in two new exons. One form displays a new first exon located 3 kb downstream from the previous TSS. The other form presents a first exon located 58,4 kb upstream of the former TSS, generating a new first intron spanning a locus transcribed in the oppo- site strand, the gene MAEL. (Figure 1A) - CNGA3 (cyclic nucleotide gated channel alpha 3) codes for the α-subunits of the cone photoreceptor cGMP-gated channel, a crucial component of the cone phototransduc- tion cascade in colour vision. Mutation in this gene causes achromatopsia. The RACE experiment confirmed the pres- ence of 4 isoforms, all containing a splicing of untrans- lated exon 0 localised 23,4 kb upstream of exon1 [18] (Figure 1B). - RDH12 (Retinol dehydrogenase 12) is an enzyme with dual-specificity retinol dehydrogenases that metabolise both all-trans- and cis-retinols, reported to be expressed in photoreceptors [19]. Mutations within RDH12 cause both recessive early onset Retinitis pigmentosa and Leber's con- genital amaurosis [20,21]. In human retinal mRNA we retrieved two forms of the transcripts containing a new first exon located upstream of the RefSeq TSS and a differ- entially spliced second exon. The in silico assembly and experimental pipeline allowed us report three putative TSSs for this gene; the first is defined by the RefSeq anno- tation, the second was deduced from the most upstream transcript represented by ESTs from pooled colon and the third is a new TSS displayed by retinal transcripts (Figure 1C). - DHRS3 (dehydrogenase/reductase, SDR family, member 3) codes for an enzyme catalysing the reduction of all- trans-retinal to all-trans-retinol in the presence of NADPH [19,22]. The gene was included in our study for its high expression in retina. Cap-finder RACE confirmed the pre- vious first exon and TSS. We also detected an alternative TSS in a new first exon downstream from the annotated one which was predicted with FirstEF [6]. (Additional file 2: Figure 5). - ELOVL5 (elongation of long chain fatty acids, including docosahexanoic acid (DHA), family member 5). This gene was recently annotated as a retinal expressed gene [23] and a target of mutation studies in retinitis pigmentosa [24]. We detected a new form of the transcript with a new first exon that was not previously annotated or described for retina. (Additional file 3: Figure 6) - KIFC3 (Kinesin family member C3) codes for a retina specific microtubule-associated force-producing protein that may play a role in intracellular transport [25]. We have characterised two new isoforms of KIFC3 retinal transcripts which lack the first 3 exons annotated in Ref- Seq. Both transcripts include a new first exon that localizes these new TSSs 44 kb upstream and 27 kb downstream respectively from the TSS referenced in the RefSeq data- base. The more upstream start site locates the gene in proximity to another retina specific gene (CNGB1). (Addi- tional file 4: Figure 7) - RCV1 (recoverin) inhibits rhodopsin kinase activity in retinal photoreceptors by reducing the binding of arrestin to rhodopsin. Deregulation of recoverin expression in cer- tain types of cancer demonstrates a pathological role in cancer-associated retinopathy [26]. Although a previous study of the promoter was performed [27], no clear evi- dence of the TSS have been described. For this gene we detected three alternative transcripts; the first with the same 5' end as the previously annotated TSS (first exon length may vary from 203 bp longer to 444 bp shorter), the second with a more frequent isoform lacking the first exon and starting 80 bp upstream from the second exon of the RefSeq and the third form has a new first exon located downstream from the annotated one. (Additional file 5: Figure 8). - SLC24A2 (solute carrier family 24, sodium/potassium/ calcium exchanger, member 2) codes for a potassium- dependent sodium-calcium exchanger in cone photo- receptor [28]. Although variant alleles of the cone SLC24A2 gene have been identified, none of them are definitively associated with a specific retinal disease [29]. The new model we present for SLC24A2 predicts three putative TSSs located in two new additional exons that are alternatively spliced (Additional file 6: Figure 9). We also investigated whether the new exons that extend the 5' end of the transcript may introduce new potentially protein coding sequences. We didn't observe in any case an extension of the open reading frame beyond the anno- tated start codon. However short alternate open reading frames of at least 40 codons were observed for C1orf32 Page 5 of 14 (page number not for citation purposes)