[Genome] EST direction

[Ann Zweig]

Hello Jyoti,

     Let me just add a little to what my colleague, Rachel, has explained.

     In some cases, the end of an exon of an EST, directly where it meets the 
intron, doesn't align well with the genome.  In those cases, we do not draw 
arrows on the intron.  The first intron of the EST that you are looking at 
(AA443868) is one such case.  Of the three introns for this EST, two have arrows 
pointing right.  You should feel confident that although there are no arrows 
displayed on the remaining intron, it is also oriented in the same direction.

     I hope this helps clear things up for you.


Regards,

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



Rachel Harte wrote:
> Hello Jyoti,
> 
> Here is an answer to a similar question:
> 
> http://www.cse.ucsc.edu/pipermail/genome/2006-July/011181.html
> 
> I hope that this helps you. If you have further questions, then please let
> us know.
> 
> Rachel
> 
> Rachel Harte
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
> 
> 
> On Wed, 24 Jan 2007, Shah, Jyoti K. wrote:
> 
>> Hi Rachel,
>>
>> Thanks. That does answer my question about ESTs such as CV409634.
>> However, I did not find any intron-wise data. For example, the first
>> intron of AA443868 has no arrows, while the other introns do. How can I
>> find this information using the table browser? What do the
>> intronOrientation numbers mean?
>>
>> I have extracted intronOrientation and gbCdna direction for this EST:
>>
>> estOrientInfo
>> +-------+------------+----------+----------+-------------------+--------
>> ---+--------------+
>> | chrom | chromStart | chromEnd | name     | intronOrientation |
>> sizepolyA | revSizepolyA |
>> +-------+------------+----------+----------+-------------------+--------
>> ---+--------------+
>> | chr17 |   41429799 | 41457240 | AA443868 |                 2 |
>> 0 |            0 |
>> | chr17 |   41459996 | 41460190 | AA443868 |                 0 |
>> 2 |            0 |
>> +-------+------------+----------+----------+-------------------+--------
>> ---+--------------+
>>
>> gbCdnaInfo
>> +---------+----------+-----------+
>> | id      | acc      | direction |
>> +---------+----------+-----------+
>> | 1838496 | AA443868 | 5         |
>> +---------+----------+-----------+
>>
>> Thanks
>> Jyoti
>>
>> -----Original Message-----
>> From: Rachel Harte [mailto:hartera at soe.ucsc.edu]
>> Sent: Monday, January 22, 2007 8:35 PM
>> To: Shah, Jyoti K.
>> Cc: genome at soe.ucsc.edu
>> Subject: Re: [Genome] EST direction
>>
>>
>> Jyoti,
>>
>> The estOrientInfo table has a field called intronOrientation. If this is
>> 0
>> and the direction for this EST in the gbCdnaInfo table is 0, then this
>> EST
>> has unknown direction and will have no arrows when displayed in the EST
>> track.
>>
>> You can do this query using the Table Browser. Click on the "Tables"
>> link
>> on the top blue menu bar and select the genome and assembly of interest.
>> The EST tracks are in the "mRNA and EST Tracks" group. You can use the
>> filter button to set up filters on fields of both estOrientInfo table
>> and
>> the gbCdnaInfo table.
>>
>> I hope that this helps you. Please let us know if you have further
>> questions.
>>
>> Rachel
>>
>> Rachel Harte
>> UCSC Genome Bioinformatics Group
>> http://genome.ucsc.edu
>>
>>
>> On Mon, 22 Jan 2007, Shah, Jyoti K. wrote:
>>
>>> Hi UCSC team,
>>> I need your help in interpreting EST data. According to the
>>> FAQ,direction of arrows indicate the EST direction. However some of
>> the
>>> ESTs have no arrow indicated on them in the genome browser view (For
>>> e.g. CV409634). Your previous archives suggest that these ESTs have no
>>> arrows because they have weaker alignments. I would like to filter out
>>> such ESTs for my analysis. Where is this information stored?
>>> Thanks in advance,
>>> Jyoti
>>>
>>>
>>>
>>>
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