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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.

Choosing a Transcript

  • The CCDS identifier for mouse and human transcripts is an indicator of a well-understood coding sequence.
  • A gold transcript indicates an identical coding sequence or cDNA sequence between two projects (Ensembl and VEGA/Havana). See article for more.
  • The General identifiers link in the transcript tab shows matches for the specific cDNA and/or protein in other resources. For example, the UniProt record contains information about the original submission, and tissue type information (if known) might be found in the submitting publication. Alternatively, if you already have an ID from NCBI, UniProtKB, or another project, try searching Ensembl with the ID to find the matching transcript.
  • If you already know the sequence of the transcript you are working on, BLAST it against the Ensembl cDNA set, or compare it with the Exons or cDNA sequence views found at the left of every transcript tab.

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