Potential SECIS elements in HIV-1 strain HXB2.
It has been proposed on the basis of sequence analysis that HIV-1 encodes a protein containing the amino acid selenocysteine (Sec). Selenocysteine is known to be incorporated into protein in response to a specific RNA secondary structure motif within the mRNA that is being translated. This RNA motif, the selenocysteine insertion sequence (SECIS) element, has not yet been identified in the HIV genome by either biologic or computation methods. This report uses computer-based sequence analysis to identify those locations in HIV-1 strain HXB2 where the current model of the SECIS element could exist. One particularly good match to the SECIS element occurs in an interesting location, spanning the end of env and the start of nef, in a position theoretically capable of directing the previously proposed Sec incorporation.
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Department of Computer Engineering, Jack Baskin School of Engineering, University of California, Santa Cruz, USA. leslie@cse.ucsc.edu
D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology; D004251:DNA Transposable Elements / Q000235:genetics; D016208:Databases, Factual; D016679:Genome, Viral; D015497:HIV-1 / Q000737:chemistry / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D017279:Selenocysteine / Q000737:chemistry / Q000235:genetics*; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid
D004251:DNA Transposable Elements; D012367:RNA, Viral; D017279:Selenocysteine