BMC Genomics 2008, 9:122 http://www.biomedcentral.com/1471-2164/9/122 Table 3: Characteristics of selected matreshkas. Characteristics of the selected matreshkas from Fig. 4, for human (H.s.), mouse (M.m.) and rat (R.n.). Columns from left to right detail the database accessions of RefSeq transcripts used to extract matreshkas, the RefSeq description, the frame the matreshka lies in, the length in amino acids of the matreshka, whether the matreshkas start with methionine, and the number of positions where a stop codon could have occurred to interrupt the matreshka but leave the RefSeq parent unaffected. Frame Matreshka aa lengths (H.s., M.m., R.n) Methionine Start Number of possible stop positions in matreshkas (H.s., M.m., R.n) RefSeq parent accessions (H.s., M.m., R.n) NM_022055; NM_199251; NM_022292 NM_018971; NM_008158; NM_023099 NM_022571; NM_181752; NM_181771 NM_000460; NM_009379; NM_031133 NM_002693; NM_017462; NM_053528 NM_153675; NM_010446; NM_012743 NM_139315; NM_009315; XM_213729 NM_000212; NM_016780; NM_153720 Parent description potassium channel, subfamily K, member 12 (KCNK12) Superconserved receptor expressed in brain 1 (GPR27) G protein-coupled receptor 135 (GPR135) thrombopoietin (THPO) polymerase (DNA directed), gamma (POLG) TAF6 RNA polymerase II (TAF6) platelet glycoprotein IIIa (ITGB3) -1 -1 -1 -1 -1 -1 +1 forkhead box A2 (FOXA2) -1 236; 256; 213 418; 430; 430 375; 356; 372 290; 284; 268 255; 230; 230 241; 224; 224 235; 220; 220 192; 192; 192 No No No Yes No No No Yes 108; 114; 115 60; 53; 55 59; 64; 57 55; 56; 52 53; 55; 56 52; 58; 45 53; 50; 49 6; 6; 6 binding to THPO's receptor, MPL (myeloproliferative leukemia virus oncogene). Three independent site- directed mutagenesis studies have been carried out to determine which residues are necessary for binding to MPL, based on 3D structural data [20-22]. A total of 14 amino acids were determined to be important for bind- ing, none of which lie within 15aa of Gly116. It therefore seems unlikely that the SNP affects THPO function. Also of note are two splice variants (labelled '2' and '3' in Ref- Seq), which retain the SNP and shorten the matreshkaM by 4 and 39 aa, respectively. Case study III: Matreshka contained in Platelet glycoprotein IIIa (ITGB3) Platelet glycoprotein IIIa (GPIIIa; also known as integrin beta 3, ITGB3) is part of the GPIIb/GPIIIa complex, which mediates platelet aggregation by acting as a receptor for fibrinogen. A frame +1 matreshkaM (the same type as Alex) spans 3 exons in the ITGB3 transcript. It is 192 amino acids long in human, and has strong Kozak sequences and a signal peptide prediction in all three organisms (Fig. 7A), coupled with dibasic cleavage sites clustered at the N and C-termini which could potentially produce conserved 'active' secreted peptides (Fig. 7B). Such characteristics are typical of GPCR ligands, for exam- ple [23], which are of great value for drug discovery. From an evolutionary perspective, it seems plausible that such a secreted peptide could 'signal' the expression of ITGB3, since any putative receptor would be able to freely co- evolve with the matreshka, according to the sequence requirements of ITGB3 itself. The significance of the matreshka's Kozak motif is under- lined by the absence of a Kozak motif for the parent sequence: the first motif in the ITGB3 frame occurs 934 nucleotides downstream of the annotated start codon. This suggests that leaky ribosomal scanning is occurring in the parent frame, and may increase the likelihood that the matreshkaM (a further 490 nucleotides downstream) is also translated from leaky scanning. These are by no means the only interesting predictions. The largest matreshka discovered is 448aa long in human, although it has the potential to reach up to 500aa in mouse (Table 3). It is derived from the KCNK12 potas- sium channel, a member of the 2-pore domain super- family of background K+ channels. The G protein-coupled receptor 135, the gamma subunit of a DNA directed polymerase, TAF6 RNA polymerase II, and Forkhead box A2 also contain substantial size matreshkas (Table 3). Page 9 of 16 (page number not for citation purposes)