Hi, The ucsc canonical genes are the set of unique nonoverlapping (?) gene clusters, but I found that a large number of canonical genes are overlapping. However I thought that for a given gene cluster, if there are overlapping gene transcripts, only one selected variant is chosen as the canonical gene? I have attached some sample output for overlapping genes on chr1. (out of 2502 genes 676 were found to be overlapping).
51424uc001eso.1chr1+149627308149651107uc009wlc.2chr1+149576452149672983 61424uc009wle.1chr1+149577754149582602uc009wlc.2chr1+149576452149672983 8220uc010plp.1chr1+169096980169097002uc001gfr.1chr1+169075946169101960 91713uc010ocn.1chr1- 17439786 17439808uc001baf.2chr1- 17393256 17445948 19945uc001cxl.1chr1+ 55013900 55076000uc001cxn.2chr1- 55074850 55089200 2930uc009wlv.1chr1+150521897150524367uc001eux.2chr1+150521897150533410 3029uc001eux.2chr1+150521897150533410uc009wlv.1chr1+150521897150524367 3536uc009xak.1chr1+203097405203136533uc001gzf.1chr1+203096835203136533 3635uc001gzf.1chr1+203096835203136533uc009xak.1chr1+203097405203136533 432467uc001byv.2chr1- 35833689 35835012uc001byt.2chr1+ 35734567 35887544 5152uc001grp.1chr1-185576315185591914uc001gro.2chr1-185527513185597620 How can this be explained, and how many gene clusters can be found in hg19 ? Thanks a lot, Stefanie --------------------------------------------------- Stefanie Gerstberger graduate student in Chemical Biology Tri-Institutional Program Cornell University, Rockefeller University, Memorial Sloan Kettering Cancer Center _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
