Journal article
RNA secondary structure and sequence conservation in C1 region of human immunodeficiency virus type 1 env gene
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.
Language: | English |
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Publisher: | Mary Ann Liebert, Inc. |
Year: | 2002 |
Pages: | 867-878 |
ISSN: | 19318405 and 08892229 |
Types: | Journal article |
DOI: | 10.1089/08892220260190353 |