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 > > > Make the switch to the world's best email. Get Yahoo!7 Mail! http://au.yahoo.com/y7mail > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome Make the switch to the world's best email. Get Yahoo!7 Mail! http://au.yahoo.com/y7mail _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
