Patent ID: 6303295
Filing Date: 2001-10-16
Classification: C07K,C12N

Abstract:
A machine-implementable method for identifying selenoprotein coding sequences within a nucleotide sequence, said method comprising the steps of:(a) translating in all possible reading frames the nucleotide sequence, wherein the step of translation is carried out treating UGA or TGA as a sense codon, to generate open reading frames (ORFs);(b) identifying those ORFs having a plurality of UGA or TGA codons and which begin with a translation start codon selected from the group consisting of ATG or AUG or GTG or GUG as independent ORFs and identifying those ORFs which do not begin with a translation start codon selected from the group consisting of ATG or AUG or GTG or GUG as frameshift ORFs;(c) identifying ORFs not containing internal in-frame UGA or TGA codons which correspond to known coding sequences;(d) selecting those frameshift ORFs identified in step (b) which overlap a known coding sequence identified in step (c), and identifying frameshift ORFs wherein a -1 or a +1 frameshift sequence is located within overlapping of said coding sequences, wherein the -1 or +1 nature of the frameshift sequence matches the -1 or +1 nature of the frameshift required to change reading frame from that of the known coding sequence to that of the ORF identified in step (b) and identifying in the 3' untranslated region of the newly identified coding sequence, a SECIS element structure;(e) as an alternative to step (d), selecting those independent ORFs identified in step (b) and analyzing for the presence of a SECIS element structure in the 3' untranslated region of the independent ORF, so that a selenoprotein coding sequence is identified;whereby a frameshift-generated selenocysteine-containing fusion protein coding sequence is identified in step (d) or a selenoprotein coding sequence is identified in step (e).