Transcript Coherence Check

[leannehaggerty]

While typically not essential for basic gene function the accurate annotation of transcript leader (aka 5’ UTR) and trailer (aka 3’ UTR) regions is often essential for understanding gene regulation. These regions contain important features that influence translational efficiency of the CDS, mRNA stability and localisation. Loss of these regions can lead to loss of knowledge about this regulation but increase in length can also be detrimental to gene function. Presence of splice sites in the 3’ trailer will lead to nonsense mediated decay and longer 5’ leaders will lead to decreased translation of the CDS. This process aims to identify cases where UTRs are significantly shortened/lengthened (including lost entirely) regardless of whether exon structure of the CDS is preserved. This could be extended to check for the preservation of key regulatory features such as known regulatory translated regions (uORFs), microRNA binding sites or RNA localisation signals. Overall transcript structure maintenance should however be a priority over these features as it is less susceptible to deficiencies in the annotation of those other features.