Hello, What you are detecting in the alignments is the presence of bases in the aligned mRNA sequence that are not in the reference genome. BLAT will break the alignment into two blocks at these insertion locations. This is both an expected and a normal part of the track contents.
I hope this information is helpful. Please feel free to contact the help mailing list again if you require further assistance. Best regards, Jen UCSC Genome Browser Support http://genome.ucsc.edu/contacts.html [email protected] [email protected] On 6/18/10 9:11 AM, Ignasi Moran Gmail wrote: > Hey all, > > I found this bug in at least 58 of the genes of the kown_genes table for > hg18, where a single exon is reported as 2 separated exons, with a 0 bases > long intron in between. For example, > > uc001gxp.2 chr1 + 200403801 200425104 200403801 > 200403801 23 > 200403801,200404372,200405064,200405531,200406935,200407291,200412799,200413270,200415861,200417408,200417639,200418878,200419134,200419317,200420432,200422011,200422283,200422753,200422758,200423019,200423213,200424577,200424981, > 200404262,200404421,200405333,200405795,200407190,200407537,200413084,200413689,200416140,200417535,200417687,200418972,200419225,200419410,200420530,200422180,200422442,200422758,200422890,200423107,200423292,200424743,200425104, > > This gene has 23 reported exons, however, there is one starting at > > chr1:200422753-200422758 > > and the next one is reported at > > chr1:200422758-200422890 > > Attached I send you the list with all the ucsc gene names where I could find > this behaviur happening at least once. I'm not confident the list is > complete though. > > Hope I'm reporting this on the right place. > > > Cheers, > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
