<p>Hi all,</p>

<p>I have a genomic regions sequenced from few accessions of a plant species. When I built a MSA of this region in different accessions. It looks like only the 4 genes present in this region are aligning. These four genes are less than 1 kb and the total genomic region is 16 kb. I know I have to provide more details to my query but does it look like something unusual (faster evolution) or it is normal that nongenic regions does not align in different accessions. If something is interesting then what I can do further.</p>

<p>Thansks,
Reetu </p>

<p>This is entirely normal from my experience with the <em>A. thaliana</em> genome of the Columbia cultivar. The following refers to A. thaliana <a href="http://www.ncbi.nlm.nih.gov/nuccore/AC002330.1">BAC T10P11</a> I annotated in 1997.</p>
<p>Scroll down to gene <em>T10P11.15</em>, encoding <em>LUMINIDEPENDENS</em>. Look at the <strong>/note</strong> I added to the CDS for this gene. That reads, in part: 100% identical to peptide from cDNA U03456, from cultivar Wassilewskija (WS); exon 4 from cultivar Columbia is split into 2 exons in WS, while exons 11 and 12 in Columbia are joined as a single exon in WS.</p>
<p>The intron between exons 11 and 12 in Columbia is 135 bp in size, which is deleted in WS.</p>
<p>What to do further: Report these differences in sequence. See if the differences map very near markers for phenotypes indicative of the accessions you're studying (WS has darker green leaves than Columbia, if I recall correctly). Consider an analysis to incorporate these differences into a timeline of the emergence of the accessions. Lastly, look for evidence, like a footprint, of transposon activity - perhaps one was there and now left.</p>