Evolutionary parameters of the transcribed mammalian genome: An analysis of 2,820 orthologous rodent and human sequences

Abstract

We have rigorously defined 2,820 orthologous mRNA and protein sequence pairs from rats, mice, and humans. Evolutionary rate analyses indicate that mammalian genes are evolving 17-30% more slowly than previous textbook values. Data are presented on the average properties of mRNA and protein sequences, on variations in sequence conservation in coding and noncoding regions, and on the absolute and relative frequencies of repetitive elements and splice sites in untranslated regions of mRNAs. Our data set contains 1,880 unique human͞rodent sequence pairs that represent about 2-4% of all mammalian genes. Of the 1,880 human orthologs, 70% are present on a new gene map of the human genome, thus providing a valuable resource for cross-referencing human and rodent genomes. In addition to comparative mapping, these results have practical applications in the interpretation of noncoding sequence conservation between syntenic regions of human and mouse genomic sequence, and in the design and calibration of gene expression arrays.

Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii

“…1), which supports the lack of similarity observed within intergenic regions. These values are considerably higher than those reported for human-rodent comparisons, which are approximately 7.5% and 45% for non-synonymous and synonymous substitutions, respectively 48 . The cause of such apparent disparities remains unknown, but may be a consequence of extreme genome composition or the short generation time of the parasite.…”

Mammalian Overlapping Genes: The Comparative Perspective

“…The median value of the CDS identity between human and mouse genes was 85.67%, for 3Ј-UTRs 63.89%, and for 5Ј-UTRs 61.54%. These values do not differ significantly when compared with the reported results for all known humanmouse orthologs (Makalowski and Boguski 1998) because all mean values lie within one standard deviation (Table 3). Although overlapping genes in our data set overall did not demonstrate greater than average conservation, we expected a higher level of similarity when coding regions were involved.…”

The 3′-untranslated region of the dystrophin gene – conservation and consequences of loss

“…The HCR is more highly conserved between human and mouse (97%) than is the coding region (93%; see Table 1). We consider the HCR to end at the point indicated in Figure 2A because (a) the human/mouse identity drops to 68%, which is similar to the 71% mean identity found between 2820 orthologous human and mouse 3'UTRs, 17 (b) the Xenopus transcript appears to terminate and (c) the similarity between human and dogfish drops below significance (no similarity is seen even on a dotplot, a method which makes no assumptions about position or orientation).…”