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Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs

Yong Zhang1, Jun Liu2, Chunshi Jia1, Tingting Li3, Rimao Wu1, Jie Wang4, Ying Chen1, Xiaoting Zou1, Runsheng Chen4, Xiu-Jie Wang2* and Dahai Zhu1*

Author Affiliations

1 National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, PR China

2 State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, PR China

3 Department of Medical Informatics, Peking University Health Science Center, Beijing, PR China

4 Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, PR China

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BMC Genomics 2010, 11:61  doi:10.1186/1471-2164-11-61

Published: 25 January 2010

Additional files

Additional file 1:

The sequences of 117 rhesus monkey ncRNAs. In this file, the nucleotide sequences of 117 monkey ncRNAs are provided. The C/C' boxes, D/D' boxes, and guide sequences of C/D box snoRNAs, are highlighted. The sequences of all ncRNAs obtained in this study have been submitted to GenBank (Accession numbers: FJ915946-FJ916062).

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Additional file 2:

Structure of H/ACA box snoRNAs. The secondary structures of H/ACA box snoRNAs were predicted using Mfold software.

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Additional file 3:

Target prediction of C/D box snoRNAs. The alignments of guide sequences with target sequences are shown.

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Additional file 4:

Target prediction of H/ACA box snoRNAs. The guide sequences of H/ACA box snoRNAs were identified within the internal loop(s) of one (or both) hairpin structures. "p5" refers to guide sequences located in the 5'-end hairpin structures of snoRNA; "p3" refers to those in the 3'-end hairpins. The two nucleotides at the junction sites between the stem and the loop in guide sequences are shown in lower case. The predicted pseudouridine sites are denoted by lower case "u".

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Additional file 5:

The expression patterns of rhesus monkey ncRNAs. The expression pattern of each ncRNA was examined by northern blotting using total RNA from rhesus monkey spleen, brain, kidney, liver, heart, and skeletal muscle. Samples of total RNA from human, mouse, and chicken skeletal muscle were included in each blot to test the possible expression of ncRNAs in different species. Based on the cumulative northern blotting data, expression patterns in different species can be classified into six types. All northern blot data are shown in this file.

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Additional file 6:

Sequence alignments of five rhesus monkey snoRNAs in nine primate species. Multiple alignments of five snoRNAs in nine primate species are shown. The species analyzed were Homo sapiens (hg18), Pan troglodytes (panTro2), Gorilla gorilla (gorGor1), Pongo pygmaeus abelii (ponAbe2), Macaca mulatta (the rhesus monkey) (rheMac2), Callithrix jacchus (calJac1), Tarsius syrichta (tarSyr1), Microcebus murinus (micMur1), and Otolemur garnetti (otoGar1).

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Additional file 7:

Copy numbers of 58 rhesus monkey snoRNA families in eight representative vertebrate genomes. The homologs of 58 rhesus monkey snoRNA families in seven other representative vertebrate genomes were analyzed based on the annotations of ENSEMBL Release 50. In each tested vertebrate genome, the copy numbers of intron-encoded and intergenic snoRNAs were separately calculated.

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Additional file 8:

Twenty-two intronic snoRNAs with SINE-like retro-transposable elements. The sequences and features of 22 potential rhesus monkey snoRNA retrogenes were demonstrated.

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Additional file 9:

All oligonucleotide sequences used in this study. All oligonucleotide sequences used in this study were shown, which included the sequences for adapters, primers and probes.

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