Hello Sam,
The identifier you give as an example (NM_146082) is from mouse which
might explain why you are unable to load it in the table browser.
That said, the known genes set for Rat does only contain 8202 elements.
One of our developers is currently working on a new set of genes for
Rat. In the meantime, that identifier is present in both the
"Non-Rat RefSeq Genes" track ('Other RefSeq' in the Table Browser)
and the TransMap RefSeq Gene Mappings track (id NM_146082.3-1.1) so you
could try obtain 3'UTRs using one of these tracks instead of known genes.
Hopefully this information was helpful and answers your question. If you
have further questions or require clarification feel free to contact the
mailing list at [email protected].
Regards,
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
On 11/02/10 12:56, Clokie, Samuel (NIH/NICHD) [F] wrote:
> Dear UCSC Genome Bioinformatics Group,
>
> I would like to extract 3'-UTRs from Rat genes. I've tried exporting from the
> UCSC table - following these directions:
> https://lists.soe.ucsc.edu/pipermail/genome/2008-May/016356.html
>
> I uploaded a list of 22062 genes (NM_ format) and went to export 3'-UTR.
> Unfortunately I get an error:
>
> "Note: 16094 of the 22062 given identifiers (e.g. NM_146082) have no match in
> table knownGene, field name or in alias table kgAlias, field alias. Try the
> "describe table schema" button for more information about the table and
> field."
>
> I have a gene list both as gene names, gene symbols and also accession
> numbers and all give a similar report... i.e it doesn't seem to recognise the
> identifiers I upload. I've checked the numbers/symbols that I'm uploading -
> and they are real and do exist.
>
> It seems there is a list of only 7816 genes in the known gene database for
> Rat - Could this be true? I got this number by simply not uploading any genes
> and went straight to 'get output' from 'Known genes' and got the 3'-UTRs from
> all rat genes. This list is also ~2000 genes longer than when I uploaded my
> list of genes (see above).
>
> Many thanks in advance for any help you can give,
>
> Sam
>
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> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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