[ensembl-dev] Clarification on Ensembl REST API Overlap Region Behavior

[Jaya Sravani Sirigineedi]

Hello,

I am Jaya Sravani Sirigineedi, a Software Developer working on the
Integrated Genome Browser(IGB) by bioviz.org 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 (
https://rest.ensembl.org/documentation/info/overlap_region) and would
appreciate your clarification on the following scenario:

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.

For example, using this API call:
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
,
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:
https://rest.ensembl.org/lookup/id/ENST00000369461?content-type=application/json;expand=1
).
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.

The region in Ensembl:
https://useast.ensembl.org/Homo_sapiens/Location/View?r=1%3A117101252-117113011
Picture of the region in IGB (loaded the gff3 file from the Ensembl FTP
server)
[image: Screenshot 2025-02-03 at 11.11.50 AM.png]
Picture of the entire transcript in IGB:
[image: Screenshot 2025-01-29 at 7.05.33 PM.png]

Thanks
Jaya Sravani S
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