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Word / termDefinition

3' end/5' end

A nucleic acid strand is inherently directional, and the "5 prime end" has a free hydroxyl (or phosphate) on a 5' carbon and the "3 prime end" has a free hydroxyl (or phosphate) on a 3' carbon (carbon atoms in the sugar ring are numbered from 1' to 5'). That's simple enough for an RNA strand or for single-stranded (ss) DNA. However, for double-stranded (ds) DNA it's not so obvious - each strand has a 5' end and a 3' end, and the 5' end of one strand is paired with the 3' end of the other strand (it is "antiparallel"). One would talk about the 5' end of ds DNA only if there was some reason to emphasize one strand over the other - for example if one strand is the sense strand of a gene. In that case, the orientation of the sense strand establishes the direction.

3' flanking region

A region of DNA which is not copied into the mature mRNA, but which is present adjacent to 3' end of the gene. It was originally thought that the 3' flanking DNA was not transcribed at all, but it was discovered to be transcribed into RNA, but quickly removed during processing of the primary transcript to form the mature mRNA. The 3' flanking region often contains sequences which affect the formation of the 3' end of the message. It may also contain enhancers or other sites to which proteins may bind.

3' untranslated region

A region of the DNA which is transcribed into mRNA and becomes the 3' end or the message, but which does not contain protein coding sequence. Everything between the stop codon and the polyA tail is considered to be 3' untranslated. The 3' untranslated region may affect the translation efficiency of the mRNA or the stability of the mRNA. It also has sequences which are required for the addition of the poly(A) tail to the message (including one known as the "hexanucleotide", AAUAAA).

5' flanking region

A region of DNA which is not transcribed into RNA, but rather is adjacent to 5' end of the gene. The 5'-flanking region contains the promoter, and may also contain enhancers or other protein binding sites.

5' untranslated region

A region of a gene which is transcribed into mRNA, becoming the 5' end of the message, but which does not contain protein coding sequence. The 5'-untranslated region is the portion of the DNA starting from the cap site and extending to the base just before the ATG translation initiation codon. While not itself translated, this region may have sequences which alter the translation efficiency of the mRNA, or which affect the stability of the mRNA.