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Open Access Research article

Experimental validation of novel genes predicted in the un-annotated regions of the Arabidopsis genome

William A Moskal, Hank C Wu, Beverly A Underwood, Wei Wang, Christopher D Town and Yongli Xiao*

Author Affiliations

The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland, 20850, USA

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BMC Genomics 2007, 8:18  doi:10.1186/1471-2164-8-18

Published: 17 January 2007



Several lines of evidence support the existence of novel genes and other transcribed units which have not yet been annotated in the Arabidopsis genome. Two gene prediction programs which make use of comparative genomic analysis, Twinscan and EuGene, have recently been deployed on the Arabidopsis genome. The ability of these programs to make use of sequence data from other species has allowed both Twinscan and EuGene to predict over 1000 genes that are intergenic with respect to the most recent annotation release. A high throughput RACE pipeline was utilized in an attempt to verify the structure and expression of these novel genes.


1,071 un-annotated loci were targeted by RACE, and full length sequence coverage was obtained for 35% of the targeted genes. We have verified the structure and expression of 378 genes that were not present within the most recent release of the Arabidopsis genome annotation. These 378 genes represent a structurally diverse set of transcripts and encode a functionally diverse set of proteins.


We have investigated the accuracy of the Twinscan and EuGene gene prediction programs and found them to be reliable predictors of gene structure in Arabidopsis. Several hundred previously un-annotated genes were validated by this work. Based upon this information derived from these efforts it is likely that the Arabidopsis genome annotation continues to overlook several hundred protein coding genes.