Can you have exons and introns of the same gene separated by hundred of kb in a genome? If so, how is the full mRNA assembled in such distance?

I'm working on plant mitochondria and I've seen an annoted gene that is cut between very distinct part of the genome.

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    $\begingroup$ Is the sequence of this plant mRNA in the public domain or one you have determined yourself. If it is in the public domain you should give a citation. $\endgroup$ – David Mar 22 at 10:39
  • $\begingroup$ The isolated exon that led me to this question is nad5 in Arabidopsis thaliania mitochondrion genome (GenBank accesion NC_037304.1). I came accross this related question link and the word "trans-splicing" led me to a paper from 1991 reporting its discovery PMC453077. I still can't understand how these pieces can be put back together amongst all the other pieces available. $\endgroup$ – LauraR Mar 22 at 14:58
  • $\begingroup$ Well, yes, the GenBank data shows the nad5 gene to have three exons, quite a distance apart. Plant mitochondria are rather specialized, so it sounds as if you will need to read some specific reviews on introns and splicing in that system, assuming that you have read up generally on RNA splicing first. $\endgroup$ – David Mar 23 at 12:45
  • $\begingroup$ Are you asking if transcripts with introns above length 100 KB exist? Or are you asking if a gene can be separated by a DNA-stretch that is not transcribed? $\endgroup$ – KaPy3141 Aug 20 at 13:08

Yes you can have exons and introns of the same gene separated by hundred (even thousands!) of kilobases.

Here is an example for the human genome: "On average, there are 8.8 exons and 7.8 introns per gene. About 80% of the exons on each chromosome are < 200 bp in length. < 0.01% of the introns are < 20 bp in length and < 10% of introns are more than 11,000 bp in length."

Source: https://www.ncbi.nlm.nih.gov/pubmed/15217358

For the splicing process, it is not really a problem for the distance. Let me reframe the questions by challenging the assumption you are making: long distances in a sequence correspond to long distance in space.

Actually, DNA/RNA molecules are can have a lot of tertiary structure for example, G quartets for DNA, hairpin structure for RNA. enter image description here

Source: https://upload.wikimedia.org/wikipedia/commons/5/5d/ATPC_secondary_structure.jpg

Long sequence distances are a poor indication of the real distance in space. Thus although from an engineering point of view it is incredible what molecular splicing can achieve mechanistically speaking. As far as I remember, the length for the intron/exon is important for the efficiency/timing of the splicing process (I might be wrong here on the specifics).

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  • $\begingroup$ The averages you quote are for human genomic DNA. The question is about plant mitochondria. $\endgroup$ – David Mar 22 at 10:40
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    $\begingroup$ Indeed there are for human genomic DNA. I would suggest that you re-read the question: the person work with plant mitochondria, but the question is not about plant mitochondria. I interpreted it as a more general question to which I gave a general answer to help the person identify the knowledge gap. I have edited the answer to include this precision thanks for the suggestion. $\endgroup$ – Dr. H. Lecter Mar 22 at 10:49
  • $\begingroup$ Thanks for your help, it's a good reminder to keep in mind the tertiary structure. I now realise my title was unclear. My interogation wasn't about the total lenght of a gene but more about having only an exon of gene really far from the other exon (without having an intron in the middle but non-coding DNA or other genes). I came across the idea of trans-splicing, I think it's what it is? Then, how does the spliceosome knows which pieces come together in a single gene? $\endgroup$ – LauraR Mar 22 at 13:27

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