Greetings, <br><br>I am using Ensembl Biomart to map Ensembl Gene IDs to Transcript IDs and UniProt/SwissProt Accession numbers. <br>Surprisingly, in several cases the corresponding Transcript IDs found for a Gene ID deffer depending on whether or not I add the UniProt number to the search. <br>
To clarify here is an example:<br>Ensembl Gene ID: ENSG00000072110<br>Result using only GeneID and TranscriptID: <br><table><tbody><tr><th><font size="1">Ensembl Gene ID</font></th>
  <th><font size="1">Ensembl Transcript ID</font></th>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000193403" target="_blank">ENST00000193403</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556083" target="_blank">ENST00000556083</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553882" target="_blank">ENST00000553882</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000394419" target="_blank">ENST00000394419</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000438964" target="_blank">ENST00000438964</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000376839" target="_blank">ENST00000376839</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000555075" target="_blank">ENST00000555075</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000538545" target="_blank">ENST00000538545</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000544964" target="_blank">ENST00000544964</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553290" target="_blank">ENST00000553290</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556432" target="_blank">ENST00000556432</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556343" target="_blank">ENST00000556343</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000555616" target="_blank">ENST00000555616</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556433" target="_blank">ENST00000556433</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000554508" target="_blank">ENST00000554508</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000554158" target="_blank">ENST00000554158</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553370" target="_blank">ENST00000553370</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553779" target="_blank">ENST00000553779</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556571" target="_blank">ENST00000556571</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553659" target="_blank">ENST00000553659</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556203" target="_blank">ENST00000556203</a></font></td></tr></tbody></table> 
<br>Result using only GeneID and TranscriptID and UniProtID:<br><table><tbody><tr><th><font size="1">Ensembl Gene ID</font></th>
  <th><font size="1">Ensembl Transcript ID</font></th>
  <th><font size="1">UniProt/SwissProt Accession</font></th>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000193403" target="_blank">ENST00000193403</a></font></td>
  <td><font size="1"><a href="http://www.uniprot.org/uniprot/P12814" target="_blank">P12814</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000394419" target="_blank">ENST00000394419</a></font></td>
  <td><font size="1"><a href="http://www.uniprot.org/uniprot/P12814" target="_blank">P12814</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000438964" target="_blank">ENST00000438964</a></font></td>
  <td><font size="1"><a href="http://www.uniprot.org/uniprot/P12814" target="_blank">P12814</a></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000376839" target="_blank">ENST00000376839</a></font></td>
  <td><font size="1"><br></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000555075" target="_blank">ENST00000555075</a></font></td>
  <td><font size="1"><br></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000538545" target="_blank">ENST00000538545</a></font></td>
  <td><font size="1"><br></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000544964" target="_blank">ENST00000544964</a></font></td>
  <td><font size="1"><br></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553290" target="_blank">ENST00000553290</a></font></td>
  <td><font size="1"><br></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000555616" target="_blank">ENST00000555616</a></font></td>
  <td><font size="1"><br></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556433" target="_blank">ENST00000556433</a></font></td>
  <td><font size="1"><br></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553370" target="_blank">ENST00000553370</a></font></td>
  <td><font size="1"><br></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553779" target="_blank">ENST00000553779</a></font></td>
  <td><font size="1"><br></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556571" target="_blank">ENST00000556571</a></font></td>
  <td><font size="1"><br></font></td>
</tr>
<tr>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
  <td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553659" target="_blank">ENST00000553659</a></font></td>
  </tr></tbody></table><font size="1"> <br></font><br><br>Please notice that the transcripts found for the Gene ENSG00000072110 differ between the two cases (e.g. <font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556083" target="_blank">ENST00000556083</a> is not present in the second results)</font>.<br>
<br>For this analysis I use the current Biomart version. This problem does not occur if I use the older Biomart (hg18, Biomart archive from 2009, NCBI36). <br><br>Am I missing something?<br><br>Thank you very much in advance.<br>
<br>Ivan<br><br>