Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.
The recent availability of the chicken genome sequence poses the question of whether there are human protein-coding genes conserved in chicken that are currently not included in the human gene catalog. Here, we show, using comparative gene finding followed by experimental verification of exon pairs by RT-PCR, that the addition to the multi-exonic subset of this catalog could be as little as 0.2%, suggesting that we may be closing in on the human gene set. Our protocol, however, has two shortcomings: (i) the bioinformatic screening of the predicted genes, applied to filter out false positives, cannot handle intronless genes; and (ii) the experimental verification could fail to identify expression at a specific developmental time. This highlights the importance of developing methods that could provide a reliable estimate of the number of these two types of genes.
Castelo
Robert
R
Research Unit on Biomedical Informatics, Institut Municipal d'Investigació Mèdica/Universitat Pompeu Fabra, Centre de Regulació Genòmica E08003 Barcelona, Spain. rcastelo@imim.es
Reymond
Alexandre
A
Wyss
Carine
C
Câmara
Francisco
F
Parra
Genís
G
Antonarakis
Stylianos E
SE
Guigó
Roderic
R
Eyras
Eduardo
E
D000818:Animals; D002645:Chickens / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D005091:Exons; D015870:Gene Expression; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D006801:Humans; D020133:Reverse Transcriptase Polymerase Chain Reaction