<div dir="ltr"><div class="gmail-adn gmail-ads" style="border-left:none;padding:0px;display:flex;font-family:"Google Sans",Roboto,RobotoDraft,Helvetica,Arial,sans-serif;font-size:medium"><div class="gmail-gs" style="margin:0px;min-width:0px;padding:0px 0px 20px;width:auto"><div class="gmail-"><div id="gmail-:14r" class="gmail-ii gmail-gt" style="direction:ltr;margin:8px 0px 0px;padding:0px;font-size:0.875rem;overflow-x:hidden"><div id="gmail-:14q" class="gmail-a3s gmail-aiL" style="direction:ltr;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-size-adjust:none;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:small;line-height:1.5;font-family:Arial,Helvetica,sans-serif;overflow:auto hidden"><div dir="ltr"><div dir="ltr">Hello,<br><br>I am Jaya Sravani Sirigineedi, a Software Developer working on the Integrated Genome Browser(IGB) by <a href="http://bioviz.org/" target="_blank">bioviz.org</a> under the supervision of Dr. Ann Loraine. Currently, we are exploring the Ensembl Rest API endpoints to integrate them into IGB. We encountered an issue when we were looking into this API to get the features for a specified region (<a href="https://rest.ensembl.org/documentation/info/overlap_region" target="_blank">https://rest.ensembl.org/documentation/info/overlap_region</a>) and would appreciate your clarification on the following scenario:<br><br>When querying a region where a gene is only partially included, i.e., a transcript starting within the specified region but extending beyond it, the REST API call output returns all cds features of the transcript, even those outside the region. However, exons that are inside the region are only returned, making it difficult to reconstruct the full transcript.<br><br>For example, using this API call:
<a href="https://rest.ensembl.org/overlap/region/human/1:117101252-117113011?content-type=application/json;feature=gene;feature=transcript;feature=cds;feature=exon;biotype=protein_coding" target="_blank">https://rest.ensembl.org/overlap/region/human/1:117101252-117113011?content-type=application/json;feature=gene;feature=transcript;feature=cds;feature=exon;biotype=protein_coding</a>,<br>the transcript ENST00000369461 (display_name: TRIM45-202) returns 7 CDS features but only 1 exon, even though it has 7 exons (as verified by this API:  <a href="https://rest.ensembl.org/lookup/id/ENST00000369461?content-type=application/json;expand=1" target="_blank">https://rest.ensembl.org/lookup/id/ENST00000369461?content-type=application/json;expand=1</a>).<br>We would like to know whether this is a bug or an expected behavior as the missing exon information prevents users from fully reconstructing the transcript.<br><div><br></div><div>The region in Ensembl: <a href="https://useast.ensembl.org/Homo_sapiens/Location/View?r=1%3A117101252-117113011" target="_blank">https://useast.ensembl.org/Homo_sapiens/Location/View?r=1%3A117101252-117113011</a></div><div>Picture of the region in IGB (loaded the gff3 file from the Ensembl FTP server)</div><div><img src="cid:ii_m6p97xoj1" alt="Screenshot 2025-02-03 at 11.11.50 AM.png" width="563" height="352"><br></div><div>Picture of the entire transcript in IGB:</div><div><img src="cid:ii_m6p9e6i42" alt="Screenshot 2025-01-29 at 7.05.33 PM.png" width="563" height="367"><br></div></div><div><br clear="all"></div><div><div dir="ltr" class="gmail_signature"><div dir="ltr"><div>Thanks</div><div>Jaya Sravani S</div></div></div></div></div></div></div></div></div></div></div>