[Genome] About the genome browser

[Rachel Harte]

Hello Silky,

When did you last look for your gene? I searched for EN2 (ENGRAILED2) on
both hg17 (May 2004) and hg18 (Mar 2006) human Genome Browsers. In both
cases, the RefSeq (NM_001427) is aligned with 100% identity. 3395 out of
3405 bases of the mRNA align and the only ones that do not align to the
genome are part of the polyA tail. You can see the alignments by clicking
on the item in the track and then clicking on the mRNA/Genomic Alignments
link.

You may be looking at an mRNA in the MGC or mRNA tracks. Whichever, mRNA
alignment you are looking at, the mRNA sequence may have been updated.
RefSeq mRNAs are manually curated and, looking at the Genbank record, it
looks like NM_001427 is now on version 3 (NM_001427.3) and it was updated
on May 24, 2007. We download the Genbank mRNAs and update our mRNA and RefSeq
alignments every night so we have are displaying the alignment for the
most recent version of this mRNA. RefSeqs are built from evidence
from mRNA, EST and genomic sequences. It may be that Genbank found
evidence that the 5' UTR for a RefSeq should be different than in an
earlier version of RefSeq. When I turn on the tracks for Human mRNAs.
MGC genes and ESTs, it looks like there are no ESTs in this region and
all the mRNAs are consistent with the version of the RefSeq mRNA with
the shorter 5' UTR. You could contact Genbank at NCBI and ask for details
as to why they updated the RefSeq.

I did a search for an earlier version of the RefSeq mRNA for EN2 at
Genbank (NM_001427.2) and I took the FASTA sequence and aligned it to both
the May 2004 and Mar 2006 human genome assemblies. This mRNA is longer
(4793 bp) and it aligns with 99.9% identity to both assemblies. It is
longer in the 5' UTR as you mention. So it looks like the RefSeq mRNA was
updated and it has changed. The Known Genes track on hg17 (May 2004) has
not been updated for a while, so this does contain an older version of
the RefSeq. As I mentioned above, you will need to contact Genbank to find
out why it has been updated.

Please let me know which mRNA accession you are looking at if I have
not answered your question correctly. I hope that this helps you.
Please let us know if you have further questions.

Rachel

We invite you to give us your feedback on the UCSC Genome Browser
through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Thu, 31 May 2007, Silky Kamdar wrote:

> Hi,
>  I have been referring to the UCSC genome browser for my gene ENGRAILED2
>  (human genome) for several years. Recently I found out that the 5'UTR
>  for EN2 is now shorter in the May 2006 version as compared to the
>  previous versions of the genome. I was wondering if something has really
>  changed about the 5'UTR and what data was the change based on or is
> this just a mistake.
>
>  Please let me know at the earliest as my project is dependent on this
>  information. I would really appreciate your help.
>
>  Thanks,
>
> Silky Kamdar
> Graduate Student
> CABM 224
> 679 Hoes Lane
> Piscataway, NJ-08854
> 732-235-3393
>
>
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