Hello, Andrea,
You correctly understand that the mRNA sequences in GenBank
(or those that underlie the UCSC Gene isoforms) may not match
the reference assembly exactly. This is indeed because the
reference assembly is one chromosome of a composite "individual"
and the mRNAs are from samples from other people sequenced by
others and deposited in GenBank.
If you click into the details page of an annotation in the UCSC
Genes track, the link to mRNA sequence in the section labeled
"Sequence and Links to Tools and Databases" has this text:
"mRNA (may differ from genome)" for this reason.
best wishes, and thanks for using the Browser.
--b0b kuhn
ucsc genome bioinformatics group
On 3/19/2011 12:30 PM, Andrea Edwards wrote:
> Hello
>
> I read in a guide to the ucsc browswer than mRNA sequences can be
> different than the underlying genomic sequences. Why is this? Is this
> because you use mRNA sequences from sequence databases rather than
> calculating them from exon coordinates and the genome sequence
>
> MAny thanks
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> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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