BMC Genomics 2007, 8:42 Additional material Additional File 1 List of genes selected for the study of identification of TSS. We provide in the list the Gene Symbol, Gene Name, Chromosomal location, Tissue/ cell type of expression, associated disease of the genes selected for our study. Abbreviation used in the table: RP: retinitis pigmentosa, CRD: cone-rod dystrophy, FF: fundus flavimaculatus, MD: macula degenera- tion, RD: retinal dystrophy. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-8-42-S1.doc] Additional File 2 Figure 5: Schematic gene structure of DHRS3. Schema of the RefSeq, ESTs, exonic structure of new isoforms identified with Cap-finder RACE of human retina mRNA and a schema of the new genomic structure con- taining new TSSs (indicated by red arrows). The Cap-finder RACE allow us to confirm the first exon and TSS of this gene. We also show the pres- ence in retina of an alternative form of transcript containing a first exon 21 kb downstream the annotated TSS. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-8-42-S2.pdf] Additional File 3 Figure 6: Schematic gene structure of ELOVL5. Schema of the RefSeq, ESTs, exonic structure of new isoforms identified with Cap-finder RACE of human retina mRNA and a schema of the new genomic structure con- taining new TSSs (indicated by red arrows): we show the presence in ret- ina of an alternative transcript with a first exon downstream from the annotated one. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-8-42-S3.pdf] Additional File 4 Figure 7: Schematic gene structure of KIFC3. Schema of the RefSeq, ESTs, exonic structure of new isoforms identified with Cap-finder RACE of human retina mRNA and a schema of the new genomic structure con- taining the TSSs (indicated by red arrows): figure shows two new isoforms lacking the 3 first exons annotated in the RefSeq. Both transcripts let us to define new TSSs located respectively 44 kb upstream and 27 kb down- stream from the previous TSS. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-8-42-S4.pdf] Additional File 5 Figure 8: Schematic gene structure of RCV1. Schema of the RefSeq, ESTs, exonic structure of new isoforms identified with Cap-finder RACE of human retina mRNA and a schema of the new genomic structure con- taining new TSSs (indicated by red arrows). The figure shows three iso- forms that we obtained with RACE experiments: one form extending the first exon by 203 bp and the other two forms lacking the first annotated exons of the RefSeq and, respectively, containing one new first exon that splices with the second annotated one and one starting at the second exon but extending it by 80 bp. For both transcripts the TSS is downstream from the annotated one. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-8-42-S5.pdf] http://www.biomedcentral.com/1471-2164/8/42 Additional File 6 Figure 9: Schematic gene structure of SLC24A2. Schema of the RefSeq, ESTs, exonic structure of new isoforms identified with Cap-finder RACE of human retina mRNA and a schema of the new genomic structure con- taining new TSSs (indicated by red arrows): 4 new cDNAs clones from human retina identify 4 new TSSs for this gene. The transcripts contain two additional exons, a and b, that are alternatively spliced. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-8-42-S6.pdf] Additional File 7 Sequence conservation of new first exon. Analysis of sequence conserva- tion of the first new exons of the listed human transcript in comparison with a set of mammals (mouse, dog, cow). Numbers indicate percentage of identity. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-8-42-S7.doc] Acknowledgements We thank Naomi Chadderton and Katja Koeppen for proofreading of the manuscript and Emanuela De Luca for help with the artwork. This project is supported by: European Union Research Training Network 'RETNET' MRTN-CT-2003-504003 References 1. Smale ST, Kadonaga JT: The RNA polymerase II core promoter. Annu Rev Biochem 2003, 72:449-479. 2. Hahn S: Structure and mechanism of the RNA polymerase II transcription machinery. Nat Struct Mol Biol 2004, 11(5):394-403. 3. 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