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In genbank (ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Fungi/Saccharomyces_cerevisiae_uid128/) there are an archive .frn (nucleotide sequences of structural RNAs in fasta format), and I want to know the differences between structural RNAs and genes. Are the nucleotide sequences of structural RNAs a coding region?

My goal is separate the coding region from the non coding region of a given complete genome.

I'm physicist so, I apologize if my question is pretty simple.

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    $\begingroup$ @David I guess "structural RNA" is not a standard term. I won't even expect biologists to be sure about what it could mean. $\endgroup$ – WYSIWYG May 4 '18 at 12:13
  • $\begingroup$ @WYSIWYG — Inspection of one file with extension .fm gives names for some of these structural RNAs, such as Pro tRNA, 15S ribosomal RNA. I assume the poster has read this. I would have expected him to try to find out what a tRNA and a ribosomal RNA actually was. If he is not prepared to put the effort into reading about molecular biology he is wasting his (and our) time. $\endgroup$ – David May 4 '18 at 13:24
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To be very brief: A gene is a sequence of DNA or RNA, which is hereditary and has a biological function. In the Saccharomyces cerevisiae genome you posted, every gene is a DNA sequence. The function of most genes is to be transcribed to messenger RNA (mRNA), which is then translated to a protein. "Coding" DNA refers to DNA which eventually has its sequence translated into protein

Structural RNAs are encoded by genes but not translated to protein, and thus are not coding regions. They are made up of RNA, but function more like proteins. When they enable reactions, like enzymes, they are called Ribozymes. The most well known ones are the Ribosomes, which are an essential part of protein biosynthesis. Others form special structures which help molecules recognize each other. tRNAs are needed for the ribosome to recognize the right amino acids.

As David said, this is very basic molecular biology and gene regulation/expression in eukaryotes can get quite complex. The wikipedia articles provide a good introduction and the Berg biochemistry book he linked is excellent further reading. If you want to know more about yeast genomes, you can check out https://www.yeastgenome.org/. It provides a whole lot of information regarding the amount of coding/noncoding regions and their function. There is also a graphical genome browser, where you can view each region in detail and compare it with your own findings.

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    $\begingroup$ Coding DNA refers specifically to regions that are translated into protein. Non-coding RNA like tRNA or rRNA are by definition not part of coding regions. $\endgroup$ – canadianer May 4 '18 at 14:25
  • $\begingroup$ i approved the edit but i am not sure if it is okay to change key concept of another user's answer. $\endgroup$ – Always Confused Apr 21 at 6:59
  • $\begingroup$ molecular biology terminologies tend to be tricky and sometimes usage vary from person to person. $\endgroup$ – Always Confused Apr 21 at 7:00
  • $\begingroup$ (+1) Although this explanation is almost ubiquitous in molecular biology, it is surely flawed when considered in the wider context. An RNA that participates in the catalytic cycle (such at that of "the ribosome is a ribozyme" fame) is not merely 'structural': it has a function over and above that of maintaining biological structural. Alcohol dehydrogenase has two zinc atoms, and we speak of the 'catalytic' zinc (remove it and the enzyme loses activity) and the 'structural' zinc (not essential for catalysis but important (maybe) in maintaining structure) $\endgroup$ – user1136 Apr 21 at 9:22

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