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Step 2 – Choose a transcript
After searching for the gene, and clicking through the results, you should see the OSM gene tab shown below.
Three protein-coding splice variants are shown in the transcript table, each with a unique ENST ID. They are also shown in the image below the table.
How do you choose a transcript? Here are some criteria based on the transcript flags:
- MANE Select: ENST00000215781.3 is the MANE Select transcript, which means it is the most biologically relevant transcript as jointly annotated between EMBL-EBI and NCBI.
- The Ensembl Canonical transcript is the one that is, on balance, the most conserved, most highly expressed, has the longest coding sequence and is represented in other key resources, such as NCBI and UniProt.
- Ensembl/Havana merge: ENST00000215781.3 is golden, which means it was annotated identically by Havana manual annotation and Ensembl automatic annotation.
- CCDS: Both ENST00000215781.3 and ENST00000403389.1, which means that Ensembl and RefSeq agree on its coding region.
- APPRIS: ENST00000215781.3 is annotated as APPRIS P3, a candidate for the principal isoform of this gene, whereas ENST00000403389.1 is APPRIS ALT2, a possible principal isoform that is only conserved in three species.
- TSL: ENST00000215781.3 is TSL1, meaning that it is fully supported by non-suspect mRNA data, whereas both ENST00000403389.1 and ENST00000403463.1 are TSL3, meaning that they are only supported by a single EST.
Following these criteria ENST00000215781.3 is the best annotated of the transcripts and is likely to be the most relevant for our studies. Click on ‘ENST00000215781.3’ to go to the transcript tab.