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
