Flanking Sequence For Ribosomal Dna

Question

[Sean Davis]

Some potential collaborators are interested in designing PCR primers within a few kb of ribosomal DNA repeats in the human genome. My limited understanding of these ribosomal DNA repeats is that they are currently in gaps in the human genome on chromosomes 13, 14, 15, 21, and 22. Does anyone have experience with working with these troublesome regions or sequences? In short, what is sought is unique sequence flanking one or more of the rDNA repeats.

Answer 1

[Larry_Parnell]

Sean,

I suspect it will be difficult to obtain a reasonable catalog of the intervening sequences between the rDNA repeats. When annotating the Arabidopsis thaliana genome, I relied on older, gene-centric entries in nr. Perhaps you can search there for some sequence data that shows both the rDNA genes and at least one if not more intervening or flanking sequences. The only other place I can think to look is a repeat database such as RepeatMasker to see if there is an entry for rDNA repeats from which you could extract the flanking seq.