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The difference between the total numbers of transcripts and unique translations, in the GENCODE Comprehensive set is, in part, due to 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).
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This allows cases where certain subfamilies are not encoded in a given genome to be annotated with confidence.
In other words these blue dot probesets do target coding regions but with too few probes to fulfil our criteria to be annotated with confidence to a transcript.
Failure to align means that the read cannot be annotated.
Third, even for features of metabolic origin with quality mass spectra, true unknowns and novel derivatives of known analytes cannot be annotated via database searching.
"Unassigned" reads are the reads that cannot be annotated by the corresponding software.
Of the 1,671 genes, 83% could be annotated with high confidence using these criteria.
Clusters can contain distantly related proteins that can, therefore, be annotated with high confidence and eventually can also inherit a structural template, if present.
Components can be annotated with a cross reference to multiple databases, but these cannot be exported to SBML.
Any process action can be annotated with a precondition.
A total of 77750 unique transcripts were identified out of which 69,245 (89%) were annotated with high confidence.
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