[Genome] miRNA promoter sequences

[Jeannette Bensen]

I found your instructions for miRNA promoter sequence retrieval  (see 
below message..it is from 2005).  I was successful in doing this however 
I noticed that in some instances the same mir gene and same promoter 
sequence are pulled down twice (mir-200a and mir-9-1 for examples).  I'm 
not really sure why.  Any ideas?  Additionally, can you tell me how the 
"promoters" for miRNAs are defined.  For example some miRNAs have their 
own promoters while others are embedded in genes and use the "host" gene 
promoter.  Does this method of extracting promoter sequence consider 
these differences?
Thanks for your advice and great instructions for the download.
Jeannette


  [Genome] miRNA promoter sequences

*Crystal Lynch* crystal at soe.ucsc.edu 
<mailto:genome%40soe.ucsc.edu?Subject=%5BGenome%5D%20miRNA%20promoter%20sequences&In-Reply-To=>
/Mon Jun 13 13:35:14 PDT 2005/

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------------------------------------------------------------------------

Hello Leping,

This query can be performed using the table browser.

http://genome.ucsc.edu/cgi-bin/hgTables?

In the Human (May 2004) assembly, select the track "sno/miRna", and 

select the region as "genome".  Then, because the track contains 

information for many types of small noncoding RNAs, use the filter to 

pull out the miRNA by selecting "type [does] match "miRna".  Chose the 

output format as "sequence".  On the next screen, chose the 

"Promoter/Upstream" region, and "get sequence".  This will give you the 

sequence of all miRNA promoter regions.

 

Let us know if you have further questions,

 

Crystal Lynch

UCSC Genome Bioinformatics Group

-- 
Jeannette Bensen, MS, PhD
University of North Carolina at Chapel Hill
UNC Lineberger Comprehensive Cancer Center-North
1700 Airport Rd, CB # 7294
Chapel Hill, NC 27599-7294
Work Phone:  (919) 843-1017
Cell Phone:  (919) 698-3278
Fax:    (919) 966-4275
Email:  jbensen at med.unc.edu