Hi Carl, The length of the PAR region for hg19 was estimated from the AGP files at NCBI. These files specified the exact same contigs for chromosome X and Y for two regions, one near the beginning and one near the end of each chromosome, which we consider to be the PAR regions. They are not at the very beginning and end of the chromosome because of the teleomere "sequence" at the beginning and end of the chromosomes. As teleomere length varies considerably, these regions are not sequenced (i.e. only have Ns) and the length of the region is estimated. Thus, after the PAR regions, there are only Ns and no track should have annotations for these regions, besides the gap track.
I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 8/12/10 3:54 PM, Dowds, Carl wrote: > Hi, > HG19/GRCh37 seems to map the PAR regions to coordinates not encompassing the > distal ends of the X and Y chromosomes. Could you verify that this is > intentional and provide details on what annotations may be presently mapped > to these distal non-PAR (beyond the PAR) regions? > Thanks > C > > "The Y chromosome in this assembly contains two pseudoautosomal regions > (PARs) that were taken from the corresponding regions in the X chromosome and > are exact duplicates: > chrY:10001-2649520 and chrY:59034050-59363566 > chrX:60001-2699520 and chrX:154931044-155260560 > " > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
