Comparison of GENCODE annotation with automated gene prediction methods. Viewed in Fmap of Acedb. Panel A shows the MAPK1 gene in ENr221. The GENCODE annotated gene structure is represented in green and red, the circled region highlights the different first exon identified by Pairagon (dark pink/blue) and the expanded region shows tiny introns (indicated by arrows) predicted by Ensembl (orange/red). Panel B shows the TRIM22 locus in ENm009. The structure predicted by Pairagon differs from the GENCODE structure and incorporates an unprocessed pseudogene as the final exon (circled). Panel C shows the human ANKRD43 locus in ENr221 for which AceView (light pink/blue), Pairagon and Ensembl all predict a shorter CDS than GENCODE. C ii shows the mouse ANKRD43 locus in which the upstream ATG is conserved. Panel D shows the GENCODE unprocessed pseudogene locus AC087380.14 at which Ensembl predicts a coding gene. The arrow indicates a tiny intron introduced into the prediction to splice around an in-frame premature stop codon. Panel E shows the IFNAR2 locus in ENm005 with GENCODE coding (red/green) and non-coding (all red) variants and AceView predictions. The AceView CDSs differ from GENCODE in several respects; arrow 'a' indicates several transcripts that have their CDS extended to the start of the prediction upstream of the GENCODE CDS start; arrow 'b' indicates a CDS starting in exon 5 despite the presence of an upstream ATG, which would seem to preclude (re-)initiation from this site; and arrow 'c' indicates a predicted stop codon in the fourth from last exon, which would be likely to make this transcript a target from Nonsense-mediated decay (NMD). GENCODE annotation incorporates all these variants but keeps them as transcripts as CDSs cannot be assigned with certainty. Panel F shows part of the olfactory receptor (OR) cluster in ENm009. Here Pairagon predicts a coding gene at the pseudogene locus OR52Z1P and a multi-exon gene that links separate OR loci (pseudogene locus OR51A1P, coding loci OR52A1 and OR52A5), indicated by arrows.