18S and 28S in hg19

Question

[Richard]

Hi all,

I'm guessing this is something I should just know. However, I'm helping QC some new ssRNA libraries and we are confronting some questions about ribosomal RNA.

I was hoping I could find the sequence for 18S or 28S in the hg19 reference (perhaps my first mistake). It turns out that the 18S and 28S sequences blast really well to gl000220, but I haven't found any annotation in the area suggesting that it is appropriate to consider the coordinates on gl000220 as representing the ribosomes.

So, is it appropriate to look for 18S and 28S in hg19? If so, are they annotated in any particular area?

[Devon Ryan]

gl000220 is known to get a LOT of rRNA alignments, since it's a supercontig containing a bunch of rRNAs. Anyway, depending on how you're looking for the sequences and where you're getting the reference, the rRNAs may be soft-masked and/or missing from the annotations (I think Ensembl has it in their annotations, though they at least used to be masked by UCSC).

BTW, you might find this thread on seqanswers useful: http://seqanswers.com/forums/showthread.php?t=41868