Dear Dr Jackson, Thank you for your reply! I have read your Email 3 times, but I don't sure understand you completely.
>From your letter, can I to say if the region(chr3:173,402,247-173,402,431) hasn't EL584176, only other 14 intronic ESTs, and MER53 ( chr3:173402247-173402431) will intersect no intronic ESTs with Table Browser? Is this all right? That is may be a naive question ? But I nearly don't sure. Thank you again ! Best regards, Chuangye 2009/11/11 Jennifer Jackson <[email protected]> > Hello, > > The coordinates will only pull out a sequence if there is overlap in the > *matched bases* of the alignment between the target (est, mrna, etc.) and > the genomic sequence. The intron region is not a part of the aligned base > set for all but one of the ests, the region represents *unmatched bases* for > these. So a search will only pull out the single (suspicious) sequence with > the intron alignment with matched bases at this location. From experience, > this single sequence seems like it is probably genomic contamination from > the EST's library construction process. But, you can check out the genbank > record and the other sequences from the clone's library and make your own > decision about that. However, remember that not all lone genomic fragments > have had their function characterized, so it may be "real", no one knows for > certain yet. The sequence is certainly not a gene in the traditional sense, > but perhaps something else. > > One method of finding sequences that overlap a certain region with a global > footprint (instead of per exon == *matched bases*) is to create a custom > track using the Table browser that only contains the txtStart and txtEnd and > leave out the extra data columns that specify where the exons are (BED4 or > similar http://genome.ucsc.edu/FAQ/FAQformat#format1). Using that file > would cause the intron region to have a "hit" against the BED4 custom track > file, since the entire genomic footprint of the sequence's alignment is > considered (introns are not omitted). > > Some Table browser help with examples (follow the links): > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser > > Glad we could help, > > Jennifer > > ------------------------------------------------ > Jennifer Jackson > UCSC Genome Bioinformatics Group > > ----- "Chuangye" <[email protected]> wrote: > > > From: "Chuangye" <[email protected]> > > To: "Jennifer Jackson" <[email protected]>, [email protected] > > Sent: Tuesday, November 10, 2009 7:36:12 PM GMT -08:00 US/Canada Pacific > > Subject: Re: [Genome] What differences between these ests > > > > Dear Dr Jackson , > > > > Thank you very much! That is to say, except EL584176, other ESTs in > > this > > region are introns corresponding to genome. > > > > And I have one more question that other ESTs coordinates are > > following: > > chr3 173240131 173448143 DA850742 0 + > > 173240131 173448143 0 6 124,34,105,76,77,127, > > 0,72804,72838,93823,187223,207885, chr3 173240131 173448196 > > DA864040 0 + 173240131 173448196 0 > > 6 > > 124,34,105,76,77,180, 0,72804,72838,93823,187223,207885, chr3 > > 173240134 173448235 DA863440 0 + > > 173240134 > > 173448235 0 5 121,139,76,76,219, > > 0,72801,93820,187220,207882, chr3 173240181 173448184 > > CN289921 0 + 173240181 173448184 0 > > 5 > > 74,139,76,77,168, 0,72754,93773,187173,207835, chr3 > > 173241037 > > 173448225 DB235484 0 + 173241037 > > 173448225 > > 0 5 71,139,76,77,209, 0,71898,92917,186317,206979, > > chr3 > > 173241038 173448223 DA723804 0 + > > 173241038 > > 173448223 0 5 70,139,76,77,207, > > 0,71897,92916,186316,206978, chr3 173247393 173448241 > > DB076759 0 + 173247393 173448241 0 > > 5 > > 38,139,76,77,225, 0,65542,86561,179961,200623, chr3 > > 173312934 > > 173451906 BI561806 0 + 173312934 > > 173451906 > > 0 28 > > > 56,83,13,41,22,77,40,32,14,7,8,7,17,18,4,6,5,13,14,15,5,17,14,17,25,5,66,10, > > > 0,57,21020,21033,21074,114420,135082,135122,135162,135176,135183,135191,135198,135215,135233,135237,135248,135253,135266,135286,135301,135307,138807,138846,138865,138890,138896,138962, > > chr3 173312938 173427430 BF992955 0 + > > 173312938 173427430 0 7 12,12,11,4,94,76,76, > > 0,15,27,38,42,21016,114416, chr3 173312981 173448163 > > AW748812 0 + 173312981 173448163 0 > > 8 > > 5,4,6,15,63,76,77,147, 0,5,9,15,30,20973,114373,135035, chr3 > > 173327456 > > 173427747 DB067370 0 + 173327456 > > 173427747 > > 0 3 85,76,393, 0,6498,99898, > > chr3 173327460 173451940 BG722524 0 + > > 173327460 173451940 0 5 81,76,77,244,197, > > 0,6494,99894,120556,124283, chr3 173333995 173448120 > > BE082404 0 - 173333995 173448120 0 > > 4 > > 35,77,36,68, 0,93359,114021,114057, The coordinate of MER53 is > > chr3:173402247-173402431< > http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=146499668&db=hg18&position=chr3%3A173402247-173402431 > >, > > why I intersect it with human ESTs used Table browser returned only > > EL584176 ? But if consider coordinates, these ESTs are all intersect > > with > > it. Could you tell me the reasons ? Thank you ! > > > > Best regards, > > > > Chuangye > > > > > > 2009/11/10 Jennifer Jackson <[email protected]> > > > > > Hello, > > > > > > The dark bar is an exon - this display is an indication that there > > is a > > > base level alignment at this position between the EST and the > > genome. The > > > rest of the data (other sequences) appears to support the idea that > > this is > > > instead an intronic region (no mRna/Est alignments at this location, > > but at > > > locations at one or either edge). > > > > > > Zoom out a few levels to see the big picture. Then try 10x to see > > where the > > > other sequence have exons. > > > > > > We hope this helps, > > > Jennifer > > > > > > ------------------------------------------------ > > > Jennifer Jackson > > > UCSC Genome Bioinformatics Group > > > > > > ----- "Chuangye" <[email protected]> wrote: > > > > > > > From: "Chuangye" <[email protected]> > > > > To: [email protected] > > > > Sent: Monday, November 9, 2009 4:14:28 AM GMT -08:00 US/Canada > > Pacific > > > > Subject: [Genome] What differences between these ests > > > > > > > > Dear sir, > > > > > > > > Thank you for reading my Email! > > > > > > > > First, please set "chr3:173,402,247-173,402,431" in your > > > > "position/search" > > > > of UCSC Browser. Then set "full" of "Human EST" in "mRNA and EST > > > > Tracks". > > > > And "Refresh". OK, now you will see the picture of the attached > > > > figure. As > > > > you will see, a few ESTs with thin lines plus arrows but only one > > with > > > > thick > > > > line at the bottom with no arrows as upper ESTs. OK. My question > > is > > > > what the > > > > differences between the last one > > > > (EL584176< > > > > > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=nucest&term=EL584176&doptcmdl=GenBank&tool=genome.ucsc.edu > > > >) > > > > with others ? > > > > > > > > Thank you! > > > > > > > > Best wishes, > > > > > > > > Chuangye > > > > > > > > _______________________________________________ > > > > Genome maillist - [email protected] > > > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
