Good Morning: You may be interested in using the current human genome assembly GRCh37 which has a better estimate of the construction of the chrY. That genome indicates gaps on chrY, with a single centromere annotated:
#chrom chromStart chromEnd type bridge chrY 0 10000 telomere no chrY 44821 94821 contig no chrY 181384 231384 contig no chrY 997557 1047557 contig no chrY 1084113 1134113 contig no chrY 1214234 1264234 contig no chrY 2018238 2068238 contig no chrY 8914955 8964955 contig no chrY 9241322 9291322 contig no chrY 10104553 13104553 centromere no chrY 13143954 13193954 contig no chrY 13748578 13798578 contig no chrY 20143885 20193885 clone yes chrY 22369679 22419679 clone yes chrY 23901428 23951428 contig no chrY 28819361 58819361 heterochromatin no chrY 58917656 58967656 contig no chrY 59363566 59373566 telomere no The GRCh37 genome assembly (2009) is the next version of the assembly from NCBI36 (2006). --Hiram J. Rodrigo Flores wrote: > Hi all, > > I'm trying to get confident coordinates for the Y human centromere (NCBI36) > and have found that there are two pairs of coordinates whereas for the rest > chromosomes only one pair is present. Could anyone clarify me this please. > I'm sorry if this just reflects some ignorance about the Y chr > particularities. I followed these instructions and come up with the next > table. > > http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks20 > > #filter: chr1_gap.type = 'centromere' > #bin chrom chromStart chromEnd ix n size type > bridge > 10 chrY 11253954 11653954 106 N 400000 > centromere no > 678 chrY 12208578 12308578 111 N 100000 > centromere no > > Also, judging based on the graphic display of the Y in the genome browser > it seems the centromere spans not only the two regions but the part in > between as weel. > Many thanks in advance, > > J. Rodrigo Flores _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
