Hello Anatole,
Your confusion is understandable: while we have the Entrez Gene IDs
on record, they're under the old "LocusLink" name. To access what you
need, go to the Table Browser, and select the 'knownGene' table (which
is inside the UCSC Genes track). Now click on the 'Create' button next
to "Filter". In this page, scroll past the filtering options to the
'Linked Tables'. Mark the box next to 'knownToLocusLink' and scroll all
the way down and press 'Allow Filtering Using Fields in Checked Tables'.
This will create a filter option underneath the main knownGene options
based on this table. There are two fields, 'name' (UCSC identifier) and
'value' (Entrez GeneID). Enter your Entrez Gene IDs in the 'value'
filter. Click 'Submit' to return to the main Table Browser. Select
'Sequence' as your output format, press submit on the next page (as it
defaults to genomic), and on the following page, select the options you
want (5' UTR, CDS, 3' UTR) and un-check any options you don't want.
I hope this helps you get the information you need.
Please feel free to contact us again with further inquiries.
Antonio Coelho
UCSC Genome Bioinformatics Group
anatole ghazalpour wrote:
> Hi,
>
> I was wondering if any one knows how to get sequence information from a list
> of Entrez IDs. In particular I wanted to get 5'UTR, CDS, and 3'UTR for a list
> of 600 genes for which I have Entrez IDs. It seems like a simple question but
> I have been working with the UCSC website for two days now and for the god of
> it I cant seem to be able to crack through.
>
> I would appreciate anyone who can help answering my question.
>
>
> Anatole Ghazalpour, PhD, DABMG
> UCLA, Human Genetics Department
> 695 Charles E. Young Drive South
> Room 6524A, Gonda Bldg.
> Los Angeles, CA 90095
> Phone: (310) 206-0133
> e-mail: [email protected]
>
>
>
>
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>
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