On Wed, Apr 28, 2010 at 7:31 PM, Jennifer Jackson <[email protected]> wrote: > Hi Peng, > > The UCSC Genes track is more discriminatory, with only one mapping. Using > the UCSC mapping is probably the best way to go. > > database=mm9, search position box = NR_002891 > > UCSC Genes > > NR_002891 (uc008guv.1) at chr19:12979721-12981475 - NR_002891
Although UCSC genes give a unique location. But this is not always true. UCSC gene corresponds to NM_001025388 also maps to multiple locations with different exons in each location. I download the exon table from refFlat. The following refseqs map to more than one genomic locations and the number of exons are not the same across the multiple genomic locations. [1] "NM_001025388" "NM_001099313" "NM_001101644" "NM_001166638" "NM_001166639" [6] "NM_001166641" "NM_001170345" "NM_001177538" "NM_001177539" "NM_001177543" [11] "NM_009286" "NM_027087" "NR_002445" "NR_002883" "NR_002889" [16] "NR_002891" "NR_003596" In general, can I assume these multiple mapped transcripts with very different intron/exon structure unreliable? If they map to multiple genomic locations but the intron/exon structures are the same at these locations, these mapping should be considered reliable? > RefSeq Genes (refGene) > > NR_002891 at chr19:12979721-12981475 > NR_002891 at chr10:5917375-5943370 > > (The RefSeq hits are close in score, which is why both were retained. Please > note that the Methods for the track may have a mistake - we'll get back to > you about that). > > Thanks, > Jen > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > On 4/28/10 2:07 PM, Peng Yu wrote: >> >> Hi, >> >> According to ucsc genome browser, NR_002891 maps to the following >> genomic location. These two mappings show very different number exons. >> One is 1, the other is 12. >> >> I don't understand why a single transcript could come from two genomic >> location that have very different intro/exon structures. Are these >> mappings real? Or one of them is an artifact. Or the underlining >> genome assembly (mm9) is defective at one of these locations? >> >> NR_002891 at chr19:12979721-12981475 >> NR_002891 at chr10:5917375-5943370 >> >> -- >> Regards, >> Peng >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > -- Regards, Peng _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
