Hi Ann, Let us look at this session again:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Vanessa&hgS_otherUserSessionName=mm9_D10MIT15_041411 D10MIT15 overlaps an intron on the positive strand (indicated by >>>) of the AK079018 gene and it also overlaps a 5' UTR as indicated by the shorter box next to the exon (the negative strand is indicated by <<<<) on the Reep3 gene. Thus, while the D10MIT15 locus overlaps both an intron and a 5' UTR, even though the intron and 5' UTR are not from the same gene. Just so it is clear, whole gene doesn't mean that it overlaps every part of the gene, it just means that marker may overlap one or more parts of a gene (intron, exon, 5'UTR, or a 3'UTR). So in this case the D10MIT15 marker DOES NOT overlap a 3'UTR or an exon, even though it will show up as overlapping with the whole gene. Here is the session for D10MIT109: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Vanessa&hgS_otherUserSessionName=mm9_D10MIT109_041411 D10MIT109 overlaps an intron on the negative strand of 5033413D22Rik gene and it also overlaps an exon on the positive strand of the gene AK017620. D10MIT109 DOES NOT overlap with any UTRs. If you have further questions, please contact the mailing list: [email protected] Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Ann Eileen Miller Baker" <[email protected]> To: [email protected] Sent: Wednesday, April 20, 2011 7:14:00 PM Subject: [Genome] finding whole genes, 3UT on genome browser mouse JL2007 NCB137/mm9 I compare my DMit mouse microsatellite with genomic elements (3UTR,5UTR,intron, exon, whole gene) using the mouse genome browser NCB137mm9 assembly (see below). It is easy to recognize introns (>>>> symbol) and coding exons (taller boxes) when the coding exons are near (3UTR or 5 UTR; shorter boxes). I expect "whole gene" to include 3UTR,5UTR,coding exon, and introns, but in the examples below using I don't see all genomic elements for "whole gene". When a 3UTR is supposed to fall within a DMIT, I fail to find. ###pls explain discrepancies between genome map and the genomic elements delivered by the GENOME BROWSER searchs for genomic elements. MOUSE GENOME BROWSER MOUSE JL2007 NCB137/mm9 ASSEMBLY MAP LOCATION DMIT element symbol ID D10MIT109 exonplus dark band AK017620 D10MIT109 wholegene (dark band and intron<<< but don't see 5 UTR or 3 UTR) D10MIT109 3UTR where? 503341302241k D10MIT15 exonplus AK079018 D10MIT15 wholegene how know whole gene? D10MIT15 intronplus >> AK079018 D10MIT15 3UTR where? D10MIT172 exonplus dark tall Adamts14 band but not overlapping D10Mit172 D10MIT172 wholegene where (see no intron overlapping D10Mit172) D10MIT172 3UTR dark shorter band ## useful: can compare heights exon, 3UTR) _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
