The cancer cell lines derived from Arf-null mice also had a normal DNA damage response (Fig. 5B, lanes 11 14), but in sharp contrast with those fibrosarcomas from wt or Atm-null mice, Arf-null fibrosarcomas conserved a functional p53/p21 response to DNA damage (lanes 11 14).
Among the sites that are not within scanD-7 or scanD-8, EBS3 is perfectly conserved among species whereas EBS4 is conserved with a functional substitution (GGAA instead of GGAT) in chicken, stikleback, fugu, and medeka or a one-base shift in marmoset (Figure S6).
Our results indicate that the catalytic site of the Hmd enzyme is conserved as a functional site in Hmd paralogs, but that the molecular function of the paralog differs from that of the enzyme due to at least one key amino acid substitution.
We predict that the active site of the Hmd enzyme is conserved as a functional site in Hmd paralogs and use this observation to propose possible molecular functions of the paralog that are consistent with previous experimental evidence.
Such sites will therefore be highly conserved throughout a functional family.
Using an in silico protein-protein interaction model based upon known mitotic spindle and centrosomal components, we have previously predicted a number of additional interactions that could be conserved between a functional TACC homologue in yeast, spc-72, and one or more human TACC proteins [ 21].
The fact that ribosomal proteins are strongly overrepresented in start codon intron proteins is striking, because it is an example of an intron position being conserved in a functional class of proteins that are not related by descent (the data sets were strictly homology reduced).
Complex rearrangement of the position of nucleotides, the position and size of loops, and the length of stems might be another mechanism to conserve the functional structure of an rRNA gene.
In order to see whether this conserved organization reflects a functional link between these genes, we tried to determine whether they were transcriptionally linked.
