Hi Reece,<br><br>I'll try to take a shot at this since you didn't receive any replies yet -<br><br>As far as I understand the Ensembl model, a refseq_dna (an external reference) linked to an ensembl transcript, does not mean their exons are identical.<br>
NCBI's mapping of NM_023035.2 to the genome could be different from Ensembl's mapping of ENST00000360228 because the mapping methods are different and the sequences could also be different.<br><br>Is there any other reason you expect the transcript models to be identical?<br>
<br>-Kiran<br><br><div class="gmail_quote">On Sat, May 21, 2011 at 12:48 PM, Reece Hart <span dir="ltr"><<a href="mailto:reece@harts.net" target="_blank">reece@harts.net</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear devs-<div><br></div><div>NCBI and Ensembl return different genomic exon coordinates for NM_023035.2. These differences lead to discrepancies when mapping variants in my own code and at the Ensembl and NCBI web sites. I'd appreciate some help understanding the origin of these differences.</div>
<div><br></div><div>The following is a diff of exon start,stop,length between e61 and NCBI. </div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div>1c1</div></div>
<div><div>< Ensembl 61 (NM_023035.2; ENST00000360228)</div></div><div><div>---</div></div><div><div>> NCBI (NM_023035.2)</div></div><div><div>11c11</div></div><div><div>< 13441058<span style="white-space:pre-wrap"> </span>13441147<span style="white-space:pre-wrap"> </span>90</div>
</div><div><div>---</div></div><div><div>> 13441058<span style="white-space:pre-wrap"> </span>13441150<span style="white-space:pre-wrap"> </span>93</div></div><div><div>18c18</div></div>
<div><div>< 13414360<span style="white-space:pre-wrap"> </span>13414427<span style="white-space:pre-wrap"> </span>68</div></div><div><div>---</div></div><div><div>> 13414351<span style="white-space:pre-wrap"> </span>13414427<span style="white-space:pre-wrap"> </span>77</div>
</div><div><div>32a33</div></div><div><div>> 13352335<span style="white-space:pre-wrap"> </span>13352340<span style="white-space:pre-wrap"> </span>6</div></div></blockquote><div><br>
</div><div>e61 and e62 give identical results for this transcript. There is a net loss of 12 nt in two exons, and the complete absence of the terminal exon. </div>
<div><br></div><div>This discrepancy between Ensembl and NCBI is also apparent in differences at the Ensembl and NCBI web sites. For example, both concur that rs58729888 is located at chr19:g.13368278, but NCBI maps it to NM_023035.2:r.4724, NP_075461.2:p.1496V>V [1] whereas Ensembl 62 maps it to ENST00000360228:r.4712, p.1492 [2]. ENST..228 is the transcript retrieved from Ensembl using NM_023035.2 as an external reference, so I presume that they're intended to be identical. Note the mapping difference of 12nt is the same as the sum of the length differences in the exon diffs. </div>
<div><br></div><div>Thanks for any help in understanding the origin of this difference between Ensembl and NCBI.</div><div><br></div><div>The code I used to extract exon coordinates from NCBI and and Ensembl are attached; if the attachments fail, they're also at <a href="http://pastebin.com/Vuf55x2t" target="_blank">http://pastebin.com/Vuf55x2t</a> and <a href="http://pastebin.com/G9sqgZqg" target="_blank">http://pastebin.com/G9sqgZqg</a>.</div>
<div><br></div><div>-Reece</div><div><br></div><div><br></div><div>[1] <a href="http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs58729888" target="_blank">http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs58729888</a></div>
<div>[2] <a href="http://www.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;g=ENSG00000141837;r=19:13317256-13617274;t=ENST00000360228;v=rs58729888;vdb=variation;vf=31287499" target="_blank">http://www.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;g=ENSG00000141837;r=19:13317256-13617274;t=ENST00000360228;v=rs58729888;vdb=variation;vf=31287499</a></div>
<div><br></div><div><br></div><div><br></div>
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<br></blockquote></div><br>