Question: Extremely long RefSeq sequence for miRNA
0
gravatar for knowah
4.5 years ago by
knowah10
United States
knowah10 wrote:

I was taking a look at which RefSeq genes (hg19) intersected a list of 200bp genomic regions, and found a peculiar entry: MIR548H4 (RefSeq NR_031680) is located at chr15:69116303-69489862, which is about 300kb long. Other (non-RefSeq) sequence coordinates for this miRNA are on chr8 and about 100bp long (NCBIGeneCards on UCSC). 

I checked the RefSeq refGene list from UCSC and found 83 miRNA's which had a sequence of over 200bp. Why are there micro RNA's in RefSeq that are so long (especially when "the RefSeq represents the predicted [~70bp] microRNA stem-loop")? And is the MIR548H4 located on the wrong chromosome by accident?

mirna refseq • 1.1k views
ADD COMMENTlink modified 4.5 years ago by Devon Ryan89k • written 4.5 years ago by knowah10
1
gravatar for Devon Ryan
4.5 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

That's a funky refseq entry. If you look at it in depth, you'll see ~24bp aligns at one end and ~32 at the other. It looks like the entry is simply wrong.

Edit: You'll see this is fixed in the hg38 annotation.

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by Devon Ryan89k
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