Which transcript should I use?
Different splice variants are found in different tissue types, developmental stages, etc. The sequence may be known to a high level of confidence, or it may be a transcript only sequenced once. It is often confusing to be presented with a list of transcripts. However, there are ways to identify the best choice for you.
If you just want the most biologically relevant transcript
If a human gene has a MANE Select transcript, this is the one you should use. This is an agreement between NCBI and Ensembl as to the clinically most relevant transcript, and the transcript structure matches perfectly between the two databases.
If a gene does not have a MANE Select transcript, APPRIS, provides a similar evaluation of the most biologically relevant transcript, which they call the Principal Isoform. They most likely candidate will be the P1 but they can score down to P5.
If those are not available, you may wish to consider the quality of annotation. A CCDS identifier indicates that the coding region of the transcript is matched between NCBI and Ensembl, while a gold transcript indicates matching annotation by the two different methods of annotation in Ensembl. The TSL gives a score for the amount of data that supports the existence of a transcript.
If you want a tissue-specific transcript
In the region or gene pages, you can plot RNA-seq data against the genome. Turn on the RNA-seq data for your tissue of interest and see which transcripts occur in that tissue.
If you have any other questions about Ensembl, please do not hesitate to contact our HelpDesk. You may also like to subscribe to the developers' mailing list.