Interpretation of transcripts with retained intron

Question

[mforde84]

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?

Answer 1

[Kevin Blighe]

Yes, they won't show an associated protein because they are regarded as untranslated RNAs:

in the GENCODE Comprehensive set ... the presence of transcripts without translations, in particular those classed as 'retained introns' or 'processed transcripts' (which are typically based on truncated RNA evidence, such that a CDS cannot be annotated with confidence)

Further:

the GENCODE comprehensive set includes two classes of transcripts that lack CDS: 'retained intron' transcripts, and those where the truncated nature of the supporting evidence makes the coding potential of the model ambiguous ('processed transcripts').

[source: Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction]