[Galaxy-user] inconsistent sequences

[Melissa Wilson]

Can anyone help figure out the following problem?

I am interested in the exon positions and sequences of EIF1AX.  I used Galaxy to
find the coding exon positions through UCSC (RefSeq gene NM_001412) using the
hg18 (and subsequently hg17 and hg16) sequences.  Then I used Fetch Sequences
and Alignments to Extract genomic DNA corresponding to query coordinates.

The functions work well on the surface, and while there are 435nt extracted for
the EIF1AX cds the composition of those 435nt is not the same as the 435nt I
get from NCBI NM_001412 CDS nor when I go through UCSC directly to extract the
CDS for EIF1AX.  

This is the same for hg17 and then almost the same for hg16 except for a few
additional exons (not clear about those).

Perhaps I'm running my search incorrectly, but would someone please check this
out.  I think a fresh view might clarify things.

Best,
Melissa