[Genome] use for UTRS

[Brooke Rhead]

Hello Sakr,

If you are looking for ncRNA in the latest human genome assembly (hg18, 
Mar. 2006), you can find them in the "UCSC Genes" track.

To get a list of only the non-coding annotations in UCSC Genes, go to 
the Table Browser (the blue "tables" link at the top of the page) on the 
hg18 assembly and select the "knownGene" table.  Then hit the filter 
"create" button and enter "cdsStart=cdsEnd" in the free-form query box. 
  This will return a list of the UCSC Genes annotations that do not have 
a coding region.  There are currently about 11,000 such genes in the 
UCSC Genes track.

Note that some of the non-coding transcripts may actually code for
protein, but the evidence for the associated protein is weak.  This is 
described on the track description page for the UCSC Genes track. (To 
read a full description of any track, click on the blue track name above 
the track control, or hit the small, blue or gray mini-button to the 
left of the track in the main Genome Browser display.  This will get you 
to a description page.   Here is the page for hg18 UCSC Genes: 
http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=knownGene&db=hg18.)

You may also be interested in the "sno/miRNA" track.  This track
displays C/D and H/ACA snoRNAs, scaRNAs and microRNAs from snoRNABase
and miRBase.

The H-Inv track is another track that may be of interest.  It includes, 
among other entitites, alignments of non-coding functional RNAs.

I hope this information is helpful to you.  If you have further 
questions, please do not hesitate to write back to this list.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



ssakr at igh.cnrs.fr wrote:
> in fact i'm searching for a database where i can find just ncRNA, is it
> possible in this database and if not do you know if a like this database
> exist
> thank you in advance
> sincerely
> sakr samy
> 
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