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I know mimiviruses and pandoraviruses have orphan DNA - DNA that is not found in other species - but this is DNA that codes for proteins. I am not able to find out if they contain junk DNA. By junk I mean DNA that does not have ANY function at all. Sort of like the junk DNA in the human genome put there by retroviruses, DNA that just sits there, doing nothing, just going along for the ride.

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    $\begingroup$ The terms junk DNA and non-coding DNA mean very different things. Non-coding DNA would include the part of a promoter that binds RNA polymerase but is not transcribed and other similar and regulatory regions that bind proteins (and also strictly speaking the parts of a gene that encode the untranslated regions of a mRNA transcript). Junk DNA can be taken to mean functionless DNA, although that begs the question whether it is DNA that has a function that has not been elucidated. Could you please clarify what you mean and amend your title accordingly. $\endgroup$ – David Jun 23 at 13:02
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    $\begingroup$ To help get an answer to the "junk" part of your question, you might be interested in a similar question I asked about parasitic code in viruses: biology.stackexchange.com/questions/92829/… $\endgroup$ – Alex Reynolds Jun 23 at 18:32
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    $\begingroup$ I should have been clearer. By junk DNA I mean functionless DNA that is known to do nothing. Not promoter regions or regulatory sequences. On a related note, are there retroviruses that infect other virues - that insert their own code in the code of a bigger virus? If so, can some of this code get deactivated or mutated over time to become functionless? $\endgroup$ – Ill1dan Jul 2 at 15:14
  • $\begingroup$ Best not to use the word code for genomic DNA. First because of the confusion with the genetic code, which is a cypher; second because you’re interested in non-coding DNA. How can you envisage a virus infecting a virus? Think about the nature of viruses. And if you include transposons as junk DNA you are stretching things as they encode the ability to transpose themselves. $\endgroup$ – David Jul 2 at 16:08
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Viruses typically don't have junk DNA-so to speak because of their tiny size. When the particles (of virus) are so small, there really isn't any space for "junk" or extra DNA.

That being said, while viral DNA replication, there may be some errors that may make the virus DNA unable to code for proteins or "junk". While this is an interesting proposition, the mutations that occur in almost cases do not make non functional proteins but mutated proteins which make the viruses more virulent (more true in case of RNA viruses...which mutate a lot faster).

Regarding virus infecting virus, putting its own code it "kind of happens" but not as you would expect. I am listing 2 such examples here-

  1. There are some viruses called satellite viruses and viroids which depend on "donor" larger viruses for some of the proteins they need for replication. This means a satellite virus can survive in a host only if the donor virus is present.

  2. In animals like pigs, when different strains of Influenza virus infect together, while virus assembly genetic material (RNA) of one strain can enter into the other....creating completely novel strain.

Hope that answers your question. Please feel free to ask for clarification. Thank you and have a nice day.

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