Multiple sequence alignments of those duplicated Arabidopsis genes which show subfunctionalization. Black shading indicates identical residues in all aligned sequences. Residues within columns show similar chemical properties. Secondary structure elements of respective proteins have been given above alignment. Experimentally proven important residues for the function of particular proteins are marked with stars. Only the well-conserved part of the protein containing important domains is shown for AtRECQL4 and AtSMC2 while full length alignments has been given for AtRBX1 (see Additional file 10 for detail methods). (a) RBX1 (b) AtRECQL4 (c) AtSMC2.