BMC Genomics 2008, 9:122 http://www.biomedcentral.com/1471-2164/9/122 A B >ITGB3_m_Hs ITGB3 matreshka [Homo sapiens] mamgplsvgyavvglagwdpsvsaqRRtialpsrtnaapgrvspsaasgasasvvnvsat avtlarsrastasvttspvsatrgrcaqamasaavgtacvtptgpattatvprvltpacp amgccaaaaasvnvaavsvssrapmgtpvrsappaqmpaplRKnvwsvrsltgepymtki patvtavtrlsq >Itgb3_m_Mm Itgb3 matreshka [Mus musculus] mgtgllsvgcaavtragwgpcvsalRRitdplsRKsaapRRaspsaasgesasvasvsai aatsarslastvsamtspasatkgrcvpamgnvtvgtacvtrtglattatvlhaltpacp pmgccaaagatasaaavcassqapmetpvrsappaqmpaplRRsvwsvrsstgersmKKt paaatagmtssr >Itgb3_m_Rn Itgb3 matreshka [Rattus norvegicus] mvteplsvgcaavtragwapcvsapRRtidplsRKsaapRKaspsaasgasasvasasat avtlarspastvsvmtspvsatkgrcalamasatvgtacvtrtglattataqhaptpacp ptgccaaagatvsvaavcassqapmetparsvppaqmpahlRRtvwsvrsstgesymKKt tatvsaemtssw Mouse --------------ASPSAASGESASVASVSAIAATSARSLASTVSAMTSPASATKGRCV Rat --------------ASPSAASGASASVASASATAVTLARSPASTVSVMTSPVSATKGRCA Human TIALPSRTNAAPGRVSPSAASGASASVVNVSATAVTLARSRASTASVTTSPVSATRGRCA .******* ****...** *.* *** ***.*. ***.***:***. Mouse PAMGNVTVGTACVTRTGLATTATVLHALTPACPPMGCCAAAGATASAAAVCASSQAPMET Rat LAMASATVGTACVTRTGLATTATAQHAPTPACPPTGCCAAAGATVSVAAVCASSQAPMET Human QAMASAAVGTACVTPTGPATTATVPRVLTPACPAMGCCAAAAASVNVAAVSVSSRAPMGT **...:******* ** *****. :. *****. ******.*:...***..**:*** * Mouse PVRSAPPAQMPAPL Rat PARSVPPAQMPAHL Human PVRSAPPAQMPAPL *.**.******* * IFnitgeugrien 7beta 3 matreshka Integrin beta 3 matreshka. A) Amino acid sequences of the human, mouse and rat ITGB3 matreshkas, with predicted signal peptide underlined, and predicted dibasic cleavage sites in bold capitals. B) The largest fragment produced by cleavage at dibasic sites would be very well conserved, as shown by this global alignment. form the bulk of the longest matreshkas (Table 3). Given the stringent length threshold chosen by Chung et al., our analysis probably has a much greater representation of -1 frame matreshkas (see Table 3). All matreshka sequences have been provided as suppplementary data (Additional file 5, Additional file 6), and can be filtered according to our calculated P values (Additional file 3). Conclusion The genome-wide study reported here provides evidence for the existence of potentially dual coding sense-frames in a number of mammalian transcripts. Future studies should aim to determine actual proof-of-translation by raising antibodies against matreshkas, and probing cells or tissues where the mRNAs are known to be expressed. Alternatively genetic mouse models could be generated which would knock-out the putative matreshka while leaving the parent RefSeq sequence intact, thus enabling phenotypic analysis. Future studies could also explore the potential for overlaps between tORFs on the antisense strands. Indeed, genomic mapping of full-length mouse cDNAs has revealed transcriptional forests in which over- lap of coding sequences on the sense and antisense strands occurs [25]. Page 12 of 16 (page number not for citation purposes)