What is the difference between Ensembl, Havana and Ensembl/Havana merged transcripts? And what does known and novel mean?
For human, mouse, zebrafish, rat and pig, 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 an Ensembl/Havana 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 categorised as novel. For more detailed information, please have a look at our genebuild documentation.