What is the difference between Ensembl, Havana and Merged transcripts? And what does known and novel mean?
For human and mouse Ensembl not only shows transcripts that are annotated automatically using the Ensembl genebuild pipeline, but also transcripts that are manually annotated by the Havana team. If the Ensembl and Havana annotation agree with each other the transcripts are combined into a Merged transcript. When a transcript is only annotated by Ensembl or Havana it is named an Ensembl or Havana transcript, respectively. Transcripts that do match a species-specific entry in the UniProtKB/Swiss-Prot or RefSeq databases are categorised as known, those that do not as novel. For more detailed information, please have a look at our genebuild documentation.