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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
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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.

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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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