[Genome] tRNA genes

[Brooke Rhead]

Hi Katheleen,

Not all of the tRNAs in GenBank are annotated in the Genome Browser, so 
you may not be able to find them by entering a name or accession number 
in the search box.

One thing you can do instead is to BLAT the sequence in the GenBank 
record to the genome.  I did this with the example gene you gave, 
TRNAN1.  It aligned in multiple places, but with the additional info of 
the chromosome band given in the GenBank record, 1p36.1 (which is 
searchable in the genome browser), I was able to narrow down the 
location to just four of the BLAT alignments.

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.  (To read a full description of the track, click on blue 
track name in the "Genes and Gene Prediction Tracks" section of track 
controls.)

Also, non-coding genes are now included in the new "UCSC Genes" track. 
The Table Browser can be used to get a list of only the non-coding 
annotations.  To do this, go to the Table Browser 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 get 
you all 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 at best. 
This is described on the track description for the UCSC Genes track:

http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=knownGene&db=hg18

I hope this information helps.  Please feel free to write back to this 
list if you have further questions.

-- 
Brooke Rhead
UCSC Genome Bioinformatics Group

We invite you to give us your feedback on the UCSC Genome Browser
through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177




Katheleen Gardiner wrote:
> How do I locate all tRNA genes (and functional RNAs in general, e.g. 
> ribosomal RNAs)? I have tried searching with Genbank official gene names 
> (e.g. TRNAN1) and associated accession numbers, with no success. Also, 
> what about snoRNAs etc. I found only five of these searching with snoRNA.
>     Thanks,
>     Katheleen Gardiner PhD
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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