Additional file 3.

The majority of chicken ncRNAs cloned and presented as novel RNAs by Zhang at al. [19] are homologs of ncRNAs described previously. Alignments of chicken ncRNAs with the homologs in human or sometimes other vertebrates are shown. GGN sequences are from Zhang et al. [19]. Vault RNA sequence corresponds to the GenBank AF045143 sequence. Other sequences are from snoRNABase [3] and Additional file 4 in this paper. C, D/D', H, ACA, and CAB boxes are underlined; antisense elements are boxed; sequence numbering corresponds to human rRNAs in snoRNABase. In C/D snoRNAs, the nucleotide complementary to the modification site is indicated by the red arrowhead. For the vault RNAs, the secondary structures predicted by mfold [42,43] are shown. The order of ncRNAs is as in Table 2. The SNORD102B transcript has a longer antisense element, and thus can guide the modification of the rRNA nucleotide adjacent to that modified by SNORD102A (marked with black and red arrowheads, respectively) [16].

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Makarova and Kramerov BMC Genomics 2011 12:543   doi:10.1186/1471-2164-12-543