How do you name alternative transcripts?

Answer: 

All transcripts are named after the gene, with addition of the suffix -R (transcripts) or -P (translations), plus a letter indicating the isoform. So a locus with 3 alternative isoforms will have three identifiers -RA, -RB and -RC. This is based on the FlyBase notation.




E.g., given the AGP000123 gene in Anopheles,

  • the 1st transcript is "AGAP000123-RA" and the cognate translation is "AGAP000123-PA",
  • the 2nd transcript is "AGAP000123-RB" and the cognate translation is "AGAP000123-PB",
  • the 3rd transcript is "AGAP000123-RC" and the cognate translation is "AGAP000123-PC",
  • and so on.



If a transcript is removed (because it was proved it doesn't exist), its ID will be remove but will NOT be reassigned. Thus the succession of letters might be interrupted.