Hello Yu,
To create the EST annotation track, human ESTs from GenBank were
aligned
against the genome using BLAT. We simply take the ESTs that are deposited into
GenBank and attempt to align them to the genome. If they align and pass our
filtering standards (only alignments having a base identity level within 0.5%
of
the best and at least 96% base identity with the genomic sequence), then we
display them in the annotation track.
If you are interested in this particular EST, you may want to take a
look at
the GenBank entry at NCBI:
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?tool=portal&db=nucest&term=DB034871&query_key=1&dopt=gb&dispmax=20&page=1&qty=1&WebEnv=1n_JmaxR4pdhfdof_c73a6mxVAWxiRb6djnspa-kMjw79KBBGIZkqABxPzJbQb8y17U-kxsJAmn2sABGym0ZBIpQH%40263F07C28FE2FD40_0067SID&WebEnvRq=1
You could contact the authors or submitters, or read their paper to
learn more
about this type of EST:
http://www.ncbi.nlm.nih.gov/pubmed/16344560?dopt=Abstract
Diversification of Transcriptional Modulation: Large-scale Identification and
Characterization of Putative Alternative Promoters of Human Genes
I hope this information is helpful to you.
Regards,
----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
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Yuan Jian wrote:
> if an 5'EST was in any position of exon or UTR,
> it is understandable (as you said 5' ESTs may end at any point within the
> transcript) .
> but now the EST of DB034871 is out of the transcript, (it is in intergene).
> I can not understand why it can be caught by EST primers.
> thanks
> YU
>
>
> --- On Tue, 18/11/08, Brooke Rhead <[EMAIL PROTECTED]> wrote:
>
> From: Brooke Rhead <[EMAIL PROTECTED]>
> Subject: Re: [Genome] EST
> To: [EMAIL PROTECTED]
> Cc: [email protected]
> Received: Tuesday, 18 November, 2008, 10:33 PM
>
> Hello Yu,
>
> See the Methods section of the description page for the EST track for an
> explanation of what may be happening. In particular:
>
> "In general, the 3' ESTs mark the end of transcription reasonably
> well, but the 5' ESTs may end at any point within the transcript. Some of
> the newer cap-selected libraries cover transcription start reasonably well.
> Before the cap-selection techniques emerged, some projects used random rather
> than poly-A priming in an attempt to retrieve sequence distant from the 3'
> end. These projects were successful at this, but as a side effect also
> deposited
> sequences from unprocessed mRNA and perhaps even genomic sequences into the
> EST
> databases. Even outside of the random-primed projects, there is a degree of
> non-mRNA contamination. Because of this, a single unspliced EST should be
> viewed
> with considerable skepticism."
>
> DB034871 appears to be a 5' EST.
>
> Additionally, here is a paper that looks helpful for explaining the quality of
> EST data:
>
> Nagaraj SH, Gasser RB, Ranganathan S. A hitchhiker's guide to expressed
> sequence tag (EST) analysis. Brief Bioinform. 2007 Jan;8(1):6-21. Epub 2006
> May
> 23.
> http://bib.oxfordjournals.org/cgi/content/abstract/8/1/6
>
> I hope this is helpful.
>
> --
> Brooke Rhead
> UCSC Genome Bioinformatics Group
>
>
> On 11/16/08 23:43, Yuan Jian wrote:
>> Dear UCSC,
>> I downloaded human EST from UCSC. EST is from CDNA. it means all ESTs
> should belong to genes.
>> but from the data I downloaded why some EST regions are neither from exon
> nor from UTR?
>> for example EST:DB034871 has 8 blocks.
>> block 1-6 belong to no genes.
>> thanks
>> YU
>>
>>
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