Hello, An intersection search will only pull out sequence that have overlap between the query and target. The intersection form has options for you to define.
If exons are defined for an mRna sequence, them the match is limited to exons. If the entire mRna genomic footprint is defined, then the match will bring in any sequence within the start and stop boundaries. The sequences that contain introns are not intronic, they represent exons. The introns are the gaps in the sequence, Thanks, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Chuangye" <[email protected]> wrote: > From: "Chuangye" <[email protected]> > To: "Jennifer Jackson" <[email protected]>, [email protected] > Sent: Thursday, November 12, 2009 12:56:31 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] What differences between these ests > > 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
