[Genome] spliced and unspliced

[Brooke Rhead]

Hello Jiang,

To find information about any track, click on the "mini-button" for that 
track -- the thin, vertical, blue or gray box at the far left of the 
track in the Genome Browser display.  (Alternatively, you can click on 
the blue title of the track in the track controls section -- in this 
case, under "mRNA and EST Tracks", click on "Spliced ESTs" and "Human 
ESTs", assuming you're looking at the human browser.)  Here you will 
find a description of the track.  The "Spliced ESTs" track description 
contains this information:

"To be considered spliced, an EST must show evidence of at least one 
canonical intron, i.e. the genomic sequence between EST alignment blocks 
must be at least 32 bases in length and have GT/AG ends."

There is not a table of ESTs that includes information about whether 
each EST is spliced or not.  The 'intronEst' table contains the spliced 
ESTs, and it is a subset of the 'all_est' table.

I hope this information helps.  If you have further questions, please do 
not hesitate to contact us again.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Jiang Qian wrote:
> 
> Hi,
> 
>  From the genome browser, I founded that the tracks for ESTs are grouped 
> into "ESTs have been spliced" and "ESTs including unspliced".
> How did you decide which group an EST belongs to? Also, which 
> downloadable file includes the flag for spliced or unspliced?
> I downloaded all_est.txt, but cannot see which ESTs are spliced or 
> unspliced?
> Thanks,
> 
> -Jiang
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome