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RNA secondary structure and squence conservation in C1 region of human immunodeficiency virus type 1 env gene
Authors:Peleg Ofer  Brunak Søren  Trifonov Edward N  Nevo Eviatar  Bolshoy Alexander
Affiliation:Genome Diversity Center, Institute of Evolution, Haifa University, Mt. Carmel, Haifa 31905, Israel.
Abstract:We have analyzed amino acid, nucleotide sequence, and RNA secondary structure variability in the env gene of human immunodeficiency virus type (HIV-1). In applying algorithms for computing optimal RNA-folding patterns to a nonredundant data set of 178 env nucleotide sequences, we found a conserved RNA stem-loop structure in the first conserved (C1) region of the env gene. This detailed examination also revealed the known secondary structure conservation of the Rev-responsive element (RRE). This finding is also supported by a higher third position conservation of the translatable reading frame along these subregions. The typical folding of the C1 region consists of two isolated stem-loop structures. These highly conserved structures are likely to have a biological function. This assumption is supported by the conservation of the third position along the coding region of these structures. The third position retains a conservation level above what would be statistically expected.
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