Hello Shan,
It may be that your miRNAs have been recently identified and are not a
part of the track you are searching against ("sno/miRna" or "miRNAs").
Or it may be that the identifier(s) that you are using are not the same
as those used in the track(s).
Examining the track identifiers may be helpful to see if there is a
mismatch - the IDs must be the of the same format/source to be used to
retrieve data with the Table browser.
To examine data/identifiers:
a) Set a small genome region and get the full default table output and
examine.
b) Click on the "identifiers" upload/paste button to view examples.
c) Enter in the coordinates for one known miRNA into the target browser
(Human hg18, Rat rn4, Mouse mm9), and then open the sno/miRna (hg18) or
miRNA track (rn4, mm9) to see what annotation is available and note the
identifiers used.
Once the identifier format is known, make adjustments to your identifier
list as needed and proceed with the original method in the prior
questions (output=sequence, genomic, upstream/promoter region).
Another option is to just use coordinates for your target miRNAs
(perhaps from another source) directly. From there you can use Table
browser to extract genome sequence in the promoter region using a custom
track that contains your miRNAs. Load the custom track, bring it up in
the Table browser, and chose output=sequence. Extracting upstream genome
sequence will be an option after submitting the query ("get output").
Table browser:
http://genome.ucsc.edu/cgi-bin/hgTables
Custom track Help:
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks
Table browser Help:
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
(displaying sequence (FASTA) data)
http://genome.ucsc.edu/FAQ/FAQdownloads.html#download32
(option B)
Hopefully one of these methods will work for your data,
Jennifer
---------------------------------
Jennifer Jackson
UCSC Genome Informatics Group
http://genome.ucsc.edu/
On 5/18/10 1:54 PM, Shan P. wrote:
> Hello Ann,
>
> I am a student at the university of Connecticut and need to find the
> promoter regions of miRNAs of interest.
>
>> From my experiments the sequences that resulted vary from human, mouse, to
> rat miRNAs.
>
> Few of them are well known and I am attempting to identify metylation of
> certain lysine residues via CHIP however I need the promoter regions.
>
> I have viewed the directions on
> https://lists.soe.ucsc.edu/pipermail/genome/2007-May/013604.html
>
> however am having trouble findind my miRNAs. even for the human miRNA i am
> interested in, I cannot locate it in the list provided that results from the
> directions on the posting.
> Please help me!
>
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