[Genome] Conserved UTR sequences

T Joshi tejalonline at gmail.com
Tue Jun 26 03:14:22 PDT 2007


Hi !
I create custom track on UCSC table browser to obtain conserved UTR
sequences from teh table browser in following way:

- I select genes and gene prediction track from groups, and within
that, ensembl genes to select ensGene table.
- Output format as custom track
- Pressing output button brings me to another page where i can select 5' exon
- then i press the get custom track in table browser
- Again I select comparative genomics group  and  Conservation track,
- and table - multiz28wayframes
- create intersection  with the ensGene table ( the custom track
containing 5' exon)
-  multiz28wayFrames records that have at least 80% overlap with tb_ensGene
- create basepair wise intersection
- submit
- and then select "sequence" in the output format to obtain 5' UTR
sequences which are conserved.

Now that I wish to find the promoter sequences for these genes. How
can I obtain? Should I select exon + 100 bps to build the custom track
of ensembl genes?

Is this a right approach?
Awaiting for your valuable inputs.
Thanks
T Joshi


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