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I've been trying to retrieve the complete human rDNA sequence (non-spacers and spacers), which should be about 43-kb in length using Biomart, NCBI, and rnacentral, but I have only been able to find the 13-kb non-spacer sequence. Are the spacer regions not yet sequenced due to difficulty in sequencing a repetitive region? Thanks for your help.

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  • $\begingroup$ There is no such thing as a "coding region" for rDNA as it does not encode protein. There are non-transcribed spacers between repeats and transcribed spacers between the 18S, 5.8S and 28S portions of the transcripts, which are cleaved out. Please edit your question to correct this. $\endgroup$ – David Jun 8 '18 at 19:00
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Managed to find the complete sequence of the repeating unit:

https://www.ncbi.nlm.nih.gov/nuccore/U13369

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To the best of my knowledge, of the estimated 500 copies of rDNA repeats in the human genome only 1 and half repeats has been sequenced and published. Mammalian rDNA repeats are hard to clone and appear unstable in yeast and e coli.

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  • $\begingroup$ Great, that's useful to know. I assume that there must be mutations in at least some of the noncoding regions that would enable positional information for certain sequences. $\endgroup$ – matk Jun 8 '18 at 10:31
  • $\begingroup$ Yes, there must be sequence variability in the non-coding region. However as rDNA arrays are rather unstable and recombine within a yeast or ecoli host. Hence isolating rDNA repeat array and making a rough map of rDNA repeat arrays is next to impossible. $\endgroup$ – JayCkat Jun 8 '18 at 14:12
  • $\begingroup$ Reference in support of this assertion please. I thought methodological developments in sequencing meant that this situation could be dealt with. $\endgroup$ – David Jun 8 '18 at 19:05
  • $\begingroup$ Welcome to the "gaps" in human genome. Parts of the genome of eukaryote that are very difficult to explore must less experiment with. Here is a reference but it does quite cover recombinational instability of repeat arrays that prevent other methods to study them. ncbi.nlm.nih.gov/pmc/articles/PMC5098217 $\endgroup$ – JayCkat Jun 9 '18 at 1:19

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