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Biotechnology  2005 

Two Pseudoknots from Human C2H2 Zinc Finger Genes Discovered by Computational Structure Analysis

Keywords: Pseudoknot , structure analysis , structure comparison , function inference , human c2h2-znf genes

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Abstract:

Pseudoknots have been extensively identified in viruses. However, very few pseudoknots in Human genome have been previously reported. In this study, we identify two pseudoknots in mRNAs of two separate C2H2 zinc finger (C2H2-ZNF) genes after studying the entire 226 C2H2-ZNF genes in Human Chromosome 19 through using standard tools in an original manner, such as searching Pfam database and analyzing the primary structure of these genes and the secondary structure of their putative mRNAs. The two pseudoknots are different in structure and one of them is very likely to stimulate +1 programmed ribosomal frameshifting. We also found some interesting characteristics of the two genes: each gene has significant C2H2-ZNF domains (e-2 or better) in two ORFs of different reading frames; the two ORFs each have a promoter, a transcription start site, a start codon, a Kozak pattern, a Poly(A) site and a Poly(A) signal and thus each of them can be viewed as a gene. Moreover, we compare these two pseudoknots with the structures of the reported pseudoknots in mammals. Present discovery would be useful in the deeper understanding of structural characteristics and functions of pseudoknots.

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