<p>After checking exons length from the <a href='http://www.gencodegenes.org/releases/15.html'> gencode.v15.annotation</a> I have noticed that there are exons only 1bp or 2bp in length.  </p>

<pre><code>curl -s "ftp://ftp.sanger.ac.uk/pub/gencode/release_15/gencode.v15.annotation.gtf.gz" | 
     gunzip -c | 
     awk '($3=="exon" &amp;&amp; $5-$4+1 &lt; 3) {print}'
</code></pre>

<p>Thats strange as some exons (protein coding or lncRNA are <strong>only 1bp or 2bp long</strong>).  Is it bioinformatics or (probably not) biology?  Has anyone ever noticed something like that with different annotation? </p>

<p>I have contacted and asked Gencode staff about this issue (in February).  They have answered and hoped that problem will be fixed until Gencode.v16.</p>

<blockquote>
  <p>Apparently there was a bug in one of their scripts. <br />
  "... there should be no exons in Gencode &lt;3bp. Alignments of &lt;3bp can not be trusted, even when spanning known splice junctions, or confirming known UTRs/retained introns".</p>
</blockquote>

<p>Current <strong>Gencode annotation (v18) still have this problem</strong> (don't know why they haven't fixed it yet). <br />
I would suggest filtering those exons out. </p>
