Hi,
I'm trying to understand the precise relationship between the RefSeq
annotations in refGene.txt and the sequences in refSeq_mRNA.fa. I am new to
mammalian genomes, RefSeq and the UCSC browser, so I think I just have some
basic misunderstanding and maybe answers to these questions will help clear it
up:
(1) Are the refGene.txt and refSeq_mRNA.fa files synced with one another?
(2) If I was to splice together all the exons annotated in refGene.txt for each
RefSeq, would I cover all the sequence found in refSeq_mRNA.fa or would there
still be some extra sequence in refSeq_mRNA.fa? If so, what is the extra
sequence?
(3) Is there a description of the columns in refGene.txt available? I would
like to better understand that table.
(4) Why are there multiple rows present for some RefSeq Ids in refGene.txt?
(5) If these two files aren't meant to correspond, is there another sequence
file that corresponds better with the annotations in refGene.txt?
Thanks!
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