[Genome] miRNA promoter

[Ann Zweig]

Hello Anu,

	The solution given in the email from our archives is old, but correct. 
  Let me see if I can give a few more details.  If you still have 
trouble, please feel free to write back and let us know exactly where 
it's failing for you.

	Navigate to the Table Browser tool on our website ('Tables' from the 
top blue navigation bar), and configure it like so:

clade: Vertebrate
genome: Human
assembly: May 2004 (hg17)
group: Genes and Gene Prediction Tracks
track: sno/miRNA
table: wgRna
region: genome

	Then press the filter 'create' button and set type does match miRna. 
This will filter the table to include only those miRNAs from the miRNA 
Registry at Wellcome Trust Sanger Institute.

	Press 'submit' to return to the main Table Browser page.  Then choose 
your output format.  If you want promoter sequence (as in the other 
email), choose 'sequence' then press the 'get output' button.  On the 
next page, choose 'Promoter/Upstream by XXXX bases' and un-check all of 
the other boxes.  Press 'get sequence'.  This will return a page of 
promoter sequence for all miRNAs in the track, like so:

 >hg17_wgRna_hsa-mir-200b range=chr1:1141407-1142406 5'pad=0 3'pad=0 
revComp=FALSE strand=+ repeatMasking=none
ggtggaaggtgccagaaaacttgaagagtggctctggccagctctctggg
cccagttggcaccaggtggttgcagagaaagggtgggaaggaggacagga
aggacggcgtgtccagcgggcggggagccttggtctggcctgagggctga
acctccctcgggtcctgagtgtgcctggagtagaagcctagggtctctgg
gctccaggcagggccctgagcaaggaggggccacagggctgcccacttcc
tcctgcccccctgcagaggcggctcagccctcgcggcgtctgaggcttga
ctgcctgtgtctgtgtttgtggccggtctgcctctgtgcctgggtcagac
cccagaccagcagacacacaaaccgcagggacggctgggcagggtcagga
gcctgccccgcccgcacccccacccacacccccacccccacccccgcctg
caccccctgccctcagacgctgtgcagtgagcggggcagcatgggagagg
ggtctccaggtggcggggaccgttctgtctcgagagcctcgcagacaccg
ggcctttgagaagagaaggggctgggcagggaagcagctcctggaacacc
atcctggagacagaggcccttgtcccctgcctcagacaaggcagcacgtg
gggcccggggggctggggctgctgtccaggccttcctatgggaccaccca
gagggaaggtcccccgcagaggggtgggggcagagggccgagcggggcgg
gcagagggcccgtgtcagccccactccgacctagtcctcggccgtctggc
caggacacttcggccccccaggtgcccaccccaggacccaaagctggtgg
ctgctggactcggcagggctggcgggtggggctcacccgggcccctgccc
tccggcgatgctgtcctcagtgccccaggaggacgaggccccccagctac
tgagcttcccagcgagtcccatgcaaccctcagccgggcggcccccggac

	There is another track on the hg17 assembly that may be of interest to 
you as well.  It is the T-ScanS miRNA Track.  This track shows conserved 
mammalian microRNA regulatory target sites in the 3' UTR regions of 
Refseq Genes, as predicted by TargetScanS.

	We have also created the sno/miRNA track for the latest human assembly 
(hg18).

	I hope this is helpful to you.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu




Anuradha Ramamoorthy wrote:
> Hi,
>  
> I recently came across a mail from the mailing list. Link:
> http://www.soe.ucsc.edu/pipermail/genome/2005-June/007710.html
> But, the solution given there did not work for me. Is it correct?
>  
> Thanks,
> Anu
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome