[Genome] EST

[Yuan Jian]

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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[Brooke Rhead]

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

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[Yuan Jian]

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 <rh...@soe.ucsc.edu> wrote:

[Ann Zweig]

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]

Hi Ann,
Thanks.
in your data set "all_est", is there a way to know whether an EST is 5'EST or 3'EST?
 
YU


--- On Wed, 19/11/08, Ann Zweig <a...@soe.ucsc.edu> wrote:

[Ann Zweig]

Hello Yu,

Please read the following FAQ on that subject:
http://genome.ucsc.edu/FAQ/FAQdownloads#download7

And this previously-answered mail list question:
http://www.soe.ucsc.edu/pipermail/genome/2006-July/011181.html

If you are still having trouble understanding the EST data, do not hesitate to
contact the list again.

Regards,

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

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