Update with some clarification that applies to this track: The underlying RefSeq, NR_002930, has been updated since the hg18 build, and is now version 2 rather than version 1. The version 2 does not align with the one base gap.
For non-refSeq sequence we would merge out this gap, but we take refSeq literally, and this escapes the merging. Regards, Jen On 6/18/10 6:40 PM, Jennifer Jackson wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
