The havana annotation features present in Ensembl include transcripts with retained intronic regions. When I manually checking these features in Ensembl, they all show no associated protein. I understand that some of these annotation are simply based upon minimal cDNA EST alignment evidence, so I'm not sure if this non-protein coding annotation reflects that the transcript is legitimately non-coding or if there is no corresponding western blot data to confirm or deny it's existence at a protein level. Is it simply the case that all of these intron retention events are not translated or could they also be generating truncated or mis-formed proteins? Is there a way to compute / tell what the hypothetical functional significance of the intron retention event is (e.g., domain changes) given the cDNA sequence for the corresponding transcript?