Hello Einat,
The genes I pointed you to before are curated/annotated by the input
sources (UCSC Genes, RefSeq Genes), they are just not broken out into a
distinct track. See the global track description for the sources and use
the links from inside each track entry entry to locate external information.
For hg19, tracks are still under development (and will continue to
evolve as long as hg19 is the current human assembly). There are not any
miRNA specific tracks yet.
In hg18, two tracks that are miRNA-specific may interest you:
Genes and Gene Prediction Tracks ->
sno/miRNA ->
C/D and H/ACA Box snoRNAs, scaRNAs, and
microRNAs from snoRNABase and miRBase
Regulation ->
TS miRNA sites ->
TargetScan miRNA Regulatory Sites
Hopefully this is helpful,
Jennifer
---------------------------------
Jennifer Jackson
UCSC Genome Informatics Group
http://genome.ucsc.edu/
On 5/20/10 10:20 AM, Einat Sitbon wrote:
>
> Thank you Jennifer for your quick and thorough reply.
> I believe I did not explain myself well. I am looking for an annotated
> track, where genes were specifically annotated as specific non-coding
> genes such as the RNA genes track in hg18. Are you planning to adding
> such information?
>
> Is there a way to search all track/tables together, not by looking at
> each table schema individually?
>
> Thank you and all the best,
> Einat
>
> -----Original Message-----
> From: Jennifer Jackson [mailto:[email protected]]
> Sent: Tuesday, May 18, 2010 8:32 PM
> To: Einat Sitbon; [email protected]
> Subject: ncRNA in hg19
>
> Hello Einat,
>
> Non-coding genes are included in the UCSC Genes& RefSeq Genes tracks
> already. To find non-coding genes, look for those with cdsStart equal to
>
> cdsEnd. The actual value will be either the txStart or the txEnd
> depending on the track, but the interpretation is the same.
>
> Other tracks also contain non-coding data, such as the track sno/miRNA.
> The best advice is to review the track descriptions to locate the data
> that best meets your research needs.
>
> Table browser help:
> http://genome.ucsc.edu/cgi-bin/hgTables
> http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
>
> When using the Table browser, saving filtered data as a custom track is
> always a potential option.
> http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks
>
> Thanks,
> Jennifer
>
> ---------------------------------
> Jennifer Jackson
> UCSC Genome Informatics Group
> http://genome.ucsc.edu/
>
> Subject:
> ncRNA in hg19
> From:
> "Einat Sitbon"<[email protected]>
> Date:
> Tue, 18 May 2010 12:13:26 +0300
> To:
> <[email protected]>
>
> Hi,
>
>
>
> Are you planning to add a Non-coding RNA Genes track to hg19 in the near
>
> future?
>
>
>
> Thanks,
>
> Einat
>
> Einat Sitbon, Ph.D.
>
> Manager, Bioinformatics
>
> Rosetta Genomics Ltd.
>
> 10 Plaut St., Rehovot, Israel, 76706
>
> T: +972.73.2220719 | F: +972.73.2220701
>
> [email protected]
>
> www.rosettagenomics.com | NASDAQ: ROSG
>
>
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