Hello, Your examples represent the presence of genes within genes.
The larger gene spans multi-exons, has both 5' and 3' UTRs, and a confirmed translated/coding region (CDS). The smaller gene(s) fall into the intron regions of the larger gene's global footprint and are generally non-coding and one or a few short exons. Scientifically, this is valid gene organization on the genome. From a process perspective, these transcripts/genes are distinct clusters in UCSC Genes because they do not share exons. Hopefully this helps, Thanks, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/8/10 1:38 PM, Bio X2Y wrote: > Hi, > > > A number of 'clusters' in the UCSC Gene annotation overlap on the same > strand (if you consider the boundaries of a cluster to be the minimum > txstart and the maximum txend of the cluster's transcripts). > > > This was queried in a previous post ( > https://lists.soe.ucsc.edu/pipermail/genome/2009-October/020325.html), where > Jennifer/Jim explained that clustering is driven by proteins, and non-coding > transcripts are merged into the cluster with which they share the greatest > overlap. > > > While this explains some of the cluster overlaps, it doesn't shed light on > the scenario where non-coding transcripts are allowed to exist as standalone > clusters, even though they fall within the boundaries of a larger cluster. > > > For example, in the HG19 version of UCSC Genes, cluster 8145 contains 8 > transcripts (5 coding + 3 non-coding). The annotation also contains 41 > smaller non-coding clusters, all of which fall completely within the > boundaries of cluster 8145. The smaller clusters are numbered consecutively > from 8146 to 8186 (inclusive). > > > Is this scenario intentional, or is it possibly an unintended artifact of > the clustering process? > > > Thanks! > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
