BMC Genomics 2008, 9:122 http://www.biomedcentral.com/1471-2164/9/122 A B gcg gga gcg gcg agg cag ggg acg gcc ccg ggg cgg agc gca cgg cct ggt gag gcc gcg ATG GCG AAC GCG AGC GAG CCG GGT GGC AGC GGC GGC GGC GAG GCG GCC GCC CTG GGC CTC AAG CTG GCC ACG CTC AGC CTG CTG CTG TGC GTG AGC CTA GCG GGC AAC GTG CTG TTC GCG CTG CTG ATC GTG CGG GAG CGC AGC CTG CAC CGC GCC CCG TAC TAC CTG CTG CTC GAC CTG TGC CTG GCC GAC GGG CTG CGC GCG CTC GCC TGC CTC CCG GCC GTC ATG CTG GCG GCG CGG CGT GCG GCG GCC GCG GCG GGG GCG CCG CCG GGC GCG CTG GGC TGC AAG CTG CTC GCC TTC CTG GCC GCG CTC TTC TGC TTC CAC GCC GCC TTC CTG CTG CTG GGC GTG GGC GTC ACC CGC TAC CTG GCC ATC GCG CAC CAC CGC TTC TAT GCA GAG CGC CTG GCC GGC TGG CCG TGC GCC GCC ATG CTG GTG TGC GCC GCC TGG GCG CTG GCG CTG GCC GCG GCC TTC CCG CCA GTG CTG GAC GGC GGT GGC GAC GAC GAG GAC GCG CCG TGC GCC CTG GAG CAG CGG CCC GAC GGC GCC CCC GGC GCG CTG GGC TTC CTG CTG CTG CTG GCC GTG GTG GTG GGC GCC ACG CAC CTC GTC TAC CTC CGC CTG CTC TTC TTC ATC CAC GAC CGC CGC AAG ATG CGG CCC GCG CGC CTG GTG CCC GCC GTC AGC CAC GAC TGG ACC TTC CAC GGC CCG GGC GCC ACC GGC CAG GCG GCC GCC AAC TGG ACG GCG GGC TTC GGC CGC GGG CCC ACG CCG CCC GCG CTT GTG GGC ATC CGG CCC GCA GGG CCG GGC CGC GGC GCG CGC CGC CTC CTC GTG CTG GAA GAA TTC AAG ACG GAG AAG AGG CTG TGC AAG ATG TTC TAC GCC GTC ACG CTG CTC TTC CTG CTC CTC TGG GGG CCC TAC GTC GTG GCC AGC TAC CTG CGG GTC CTG GTG CGG CCC GGC GCC GTC CCC CAG GCC TAC CTG ACG GCC TCC GTG TGG CTG ACC TTC GCG CAG GCC GGC ATC AAC CCC GTC GTG TGC TTC CTC TTC AAC AGG GAG CTG AGG GAC TGC TTC AGG GCC CAG TTC CCC TGC TGC CAG AGC CCC CGG ACC ACC CAG GCG ACC CAT CCC TGC GAC CTG AAA GGC ATT GGT TTA TGA ggg agg ccc cgc cac ata gac ccc caa ccc agc ctt tcc ctt tgg ctc gga cgg tga cgt tgt atc ttt tcc ttc tgg ccc ctg ttt aa >GPR27_m_Hs GPR27 matreshka [Homo sapiens] grdgereragwqrrrrggrpgpqaghaqpaavrepsgqravraadragaqpaprpvlpaa rpvpgrraararlppgrhaggaacggrgggaagraglqaarlpgralllprrlpaagrgr hplpghrappllcrapgrlavrrhagvrrlgagagrglpasagrrwrrrgravrpgaaar rrprraglpaaagrgggrhaprlpppallhprppqdaarapgarrqprldlprpgrhrpg grqldgglrprahaaracghparragprrapppragriqdgeeavqdvlrrhaalpaplg alrrgqlpagpgaarrrppglpdglrvadlragrhqprrvlplqqgaegllqgpvpllpe ppdhpgdpslrperhwfmreapphrpptqpfplartvtlylfllapv FGigpurorete5in-coupled receptor 27 matreshka G protein-coupled receptor 27 matreshka. A) mRNA sequence of human GPR27 with matreshka underlined. GPR27 codons are separated by spaces, and flanking non-GPR27-coding-sequence is shown in lower case. B) human matreshka protein sequence. These matreshkas may represent alternative proteins, in the way that Alex is, or be translated as part of a frameshifted splice variant (e.g., the THPO nirs splice var- iant, Fig. 6C). Conservation measurements have previ- ously been used to support the functional importance of frameshifted splice variants [24]. Our findings suggest that other conserved frameshifted splice variants, such as caspase 7 isoform beta, are biologically relevant (see Addi- tional file 2). In a related study by Chung et al [8], alternative reading frames (ARFs, which can be considered synonymous with matreshkas) were searched for using a comparative genomics approach in human and mouse. A conservative list of 40 ARF-containing genes was derived from elegant simulation-based statistical and modelling methods. Of these 40 genes, 21 genes were included in our matreshka set (Additional file 4), although the ARF and matreshka sequences were not compared directly, as the former have not been published. Our study had a broader scope, including non-methionine-start reading frames which Page 10 of 16 (page number not for citation purposes)