Hello Anyuan Guo, If you click on DUX4 (or any of the genes that you mention) in the main browser display you will be taken to a details page for this track which includes a description of this gene:
"This gene is located within a D4Z4 repeat array in the subtelomeric region of chromosome 4q. The D4Z4 repeat is polymorphic in length; a similar D4Z4 repeat array has been identified on chromosome 10. " Consequently BLAT mapped DUX4 to both locations. As for your question about genes in the pseudoautosomal regions, the chrX and chrY pseudoautosomal regions are homologous and thus the genes map equally well to locations on both chrX and chrY. Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [EMAIL PROTECTED] Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu Anyuan Guo wrote: > Hi, > I noticed some genes in UCSC has more than one chromosome locations. > e.g. when I search DUX4 in human version 2006 genome browser. I can > get the following position of this gene. > RefSeq Genes > DUX4 at chr4:191245841-191247457 - (NM_033178) double homeobox, 4 > DUX4 at chr4:191232654-191234270 - (NM_033178) double homeobox, 4 > DUX4 at chr4:191229361-191230977 - (NM_033178) double homeobox, 4 > DUX4 at chr4:191239248-191240864 - (NM_033178) double homeobox, 4 > DUX4 at chr4:191242541-191244157 - (NM_033178) double homeobox, 4 > DUX4 at chr10:135330358-135335265 - (NM_033178) double homeobox, 4 > DUX4 at chr10:135333669-135338574 - (NM_033178) double homeobox, 4 > > This gene has only one refseq accession number (NM_033178). But it was > mapped on different chromosome (chr4 and chr10). > So what happened? I noticed that NCBI Entrez gene database only mapped > this gene on a specific location on chr4. > > Other genes like LOC728340, SULT1A3, XAGE1D etc. also have this problem. > > I noticed many gene were mapped on both chrX and chrY. I saw the > following assembly description at http://genome.ucsc.edu/cgi-bin/hgGateway > "The Y chromosome in this assembly contains two pseudoautosomal regions > (PARs) at chrY:1-2709520 and chrY:57443438-57772954. These sequences > were taken from the corresponding regions in the X chromosome and are > exact duplications of the X chromosome sequences at chrX:1-2709520 and > chrX:154584237-154913754, respectively." > > Does this means those genes mapped on both ChrX and ChrY should be only > mapped on ChrX? > > Thanks. > > Anyuan Guo > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
