Of those previously annotated noncoding RNAs that are intergenic, more than half contain predicted ORFs longer than 100 amino acids. For example, two previously characterized functional human lincRNAs were found to contain ORFs longer than 100 amino acids, Xist and HOTAIR. These results demonstrate that our filtering approach, which eliminates all transcripts with ORFs larger than 100 amino acids, may have removed some lincRNAs with large, nonfunctional ORFs. However, the use of a 100 amino acid ORF cutoff, a commonly used threshold to define potential protein coding genes, is justifiable because ORFs of this size infrequently occur by chance and instead indicate potential for protein coding capacity [38], [39].
