I'm a self-learner that likes to keep up with current research. However, I can't find what is meant by expressions such as 5' or 3' positions on chemical structures. But , in particular, what is meant by the phrase "Cis-elements may be located in 5' or 3' untranslated regions or within introns."

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    $\begingroup$ You could have just as well asked about the meaning of "x" in mathematics. It could have been anything. But wait... did you mean it in a somewhat narrower scope? A particular kind of equations, by any chance? A particular kind of chemical compounds? Oligosaccharides, by any chance? A particular kind of those, maybe? $\endgroup$ Feb 28 '20 at 18:35
  • $\begingroup$ The DNA-RNA tag is a hint, as is introns and cis-elements (regarding the specific question). $\endgroup$ Feb 28 '20 at 19:32
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    $\begingroup$ About all that be said is that for a particular compound there is a specific way of numbering the atoms. $\endgroup$
    – MaxW
    Feb 28 '20 at 19:36
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    $\begingroup$ @ChrisGardner Putting the keywords RNA/DNA and introns with the above comments together, maybe these two sites may help, at least as a starter, to orient along the strangs: en.wikipedia.org/wiki/Untranslated_region and en.wikipedia.org/wiki/Directionality_(molecular_biology) $\endgroup$
    – Buttonwood
    Feb 28 '20 at 20:02
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    $\begingroup$ I suggest getting hold of a biochemistry textbook, if you can: any half-decent one will tell you what 3' and 5' are (in the context of nucleic acids) and why they are important. $\endgroup$
    – orthocresol
    Feb 29 '20 at 1:28

Here is a link to a more than half-decent biochemistry textbook chapter explaining the numbering: https://www.ncbi.nlm.nih.gov/books/NBK22490/

And the relevant figure from that chapter:

enter image description here

[Berg, Tymoczko, Stryer] Backbones of DNA and RNA. The backbones of these nucleic acids are formed by 3′-to-5′ phosphodiester linkages. A sugar unit is highlighted in red and a phosphate group in blue.


Like any other linear polymer sucu as proteins and DNAs, RNA structure has two ends. Like carboxylic acid end and amine end notation given for proteins, two ends of a RNA (and DNA) call 3'-end and 5'-end (see the diagram below):

RNA Structure

Note that these notations are derived from the numbering of the ribose sugar function (see the 5'-end of the tetramer in the diagram).

Answer for your particular question: What is meant by the phrase "Cis-elements may be located in 5' or 3' untranslated regions or within introns"?, see diagram below:

untranslated region

Cis-regulatory elements (CREs) such as promoters, enhances, silencers, etc. are usually in 5' or 3' untranslated regions.


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