Which annotation source is best?RNA-seq

[SEQond]

Hi all,
From this presentation http://chagall.med.cornell.edu/NGSco...ass03_2010.pdf
I got this image


but how and why is one annotation source better than the others?

[steven]

A genomic annotation can be manual, automated, restrictive, exhaustive..
Refseq genes/transcripts usually require strong supporting evidence to be annotated by the NCBI, which explains why it is a small set. VEGA annotation is produced by "manual" and careful inspection of all the evidence (transcripts, EST, conservation, etc) by annotation experts at the Sanger.
Ensembl is semi-automatic and less stringent, hence more exhaustive.
Do you see the general idea?

[vasvale]

annotated exons

is there any update on this also based on rna-seq data?