Figure 25: Variation in conservation across a gene.

a, Conservation across a generic gene, on the basis of 3,165 human RefSeq mRNAs with known position in the genome. We sampled 200 evenly spaced bases across each of the variable-length regions labelled, resampling completely from regions shorter than 200 bp. The graph shows the average percentage of bases aligning and the average base identity when there is an alignment over each sample. There are peaks of conservation at the transition from one region to another. Here, in contrast to Table 16, only reviewed RefSeq mRNAs were used, and only those having at least 40 bases of annotated 5′ and 3′ UTRs. The resulting picture, however, is nearly indistinguishable from that obtained by using all RefSeq genes with at least 40 base UTRs. b, Conservation near translation start site using the same data set as in a. The bars show per cent identity of the 15 bases to either side of translation start. Note the extreme conservation of the first codon. After this, there is substantially less conservation at the third codon position. The peak at position -3 corresponds to a purine in the Kozak consensus sequence. c, Conservation near the 5′ splice site. The peak of conservation corresponds to the AG/GT consensus at this ___location, with the first G in the intron being nearly invariant. A G in the fifth base of the intron is also found in a large majority of 5′ splice sites. An echo of the variation in the third codon position occurs here because it is common for exons to begin and end at codon boundaries. d, Conservation near the 3′ splice site. Conservation in the last two bases of the intron—always AG for introns processed by the major spliceosome—is very apparent. The polypyrimidine tract beginning five bases into the intron is also visibly conserved. Once again, an echo of the variation in the third codon position can be seen.