Genome-wide Analyses of Retrogenes Derived from the Human Box H/Aca Snornas.
From: College of Life Sciences, Nanchang University Nanchang 330047, People’s Republic of China.
Nucleic acids research
- Publish Date: 2007
- ISSN: 1362-4962
- Volume: 35
- Issue: 2
- Pages: 559-71
- Medium: Internet
- Language: English
- Citation (JAMA): Luo Yuping, Li Siguang, et al. Genome-wide Analyses of Retrogenes Derived from the Human Box H/Aca Snornas.. Nucleic Acids Res. 2007;35:559-71
Abstract
The family of box H/ACA snoRNA is an abundant class of non-protein-coding RNAs, which play important roles in the post-transcriptional modification of rRNAs and snRNAs. Here we report the characterization in the human genome of 202 sequences derived from box H/ACA snoRNAs. Most of them were retrogenes formed using the L1 integration machinery. About 96% of the box H/ACA RNA-related sequences are found in corresponding locations on the chimpanzee and human chromosomes, while the mouse shares approximately 50% of these human sequences, suggesting that some of the H/ACA RNA-related sequences in primate occurred after the rodent/primate divergence. Of the H/ACA RNA-related sequences, 49% are found in intronic regions of protein-coding genes and 64 H/ACA-related sequences can be folded to the typical secondary structure of the box H/ACA snoRNA family, while 30 of them were recognized as functional homologs of their corresponding box H/ACA snoRNAs previously reported. Of the 64 sequences with the typical secondary structure of the box H/ACA RNA family, 11 were found in EST databases and 5 among which were shown to be expressed in more than one human tissue. Notably, U107f is nested in an intron of a protein gene coding for nudix-type motif 13, but expressed from the opposite strand, and the searching of EST databases revealed it can be expressed in liver and spleen, even in melanotic melanoma.
Mesh Headings (Keywords): Animals, Base Sequence, Computational Biology, Genome, Human, Genomics, Humans, Long Interspersed Nucleotide Elements, Mice, Molecular Sequence Data, Phylogeny, RNA, Small Nucleolar, Vertebrates
Check for Full Text / PubMed Unique Identifier (PMID): 17175533
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