Heterochromatic Region Dyz19

Question

[axelwilhelm]

Why can't I find the position of DYZ19 which is located at the q11.222 band of the Y chromosome? I want to find it on a genome browser. I know that palindrome4 in on one side of it and P3 on the other side but I don't know how to find them either.

http://www.nature.com/nature/journal/v423/n6942/extref/01722/tables/note4.html

[Pierre Lindenbaum]

cross-posted on http://biology.stackexchange.com/questions/622/heterochromatic-region-dyz19

[Pierre Lindenbaum]

could it be a typo "DYS19" or "DYZ1" ?

[axelwilhelm]

Excuse me. I didn't know cross-posting was wrong (these stack exchange politics are complicated). I've deleted the other post since this site is more relevant.

[User 59]

It's not wrong, whilst it's debatable that this is a bioinformatics question, it's almost certainly a biological one, there are different audiences at each site and so you could have left it there as a legitimate question.

[axelwilhelm]

Well the SMCY gene is on one side and EIF1A on the other so DYZ19 is approximately between 20366212 and 21146999 which is enough for me. I got strange results from that area.

Answer 1

[Neilfws]

According to this article (PDF), DYZ19 is a ~ 400 kb heterochromatic region, consisting of "massively amplified tandem repeats of low sequence complexity." So my guess is that the region is difficult to sequence and so cannot be mapped to the chromosome with sufficient resolution (i.e. chromosomal coordinates) to be displayed in a genome browser.

[Neilfws]

It's quite possible to know the approximate position of DYZ19 (by some mapping method) and a more "exact" position of genes either side (by sequencing).

[axelwilhelm]

Then how can they state that a gene on the proximal side of DYZ19 is on coordinate xxx and another on the distal side is on position yyy if they don't even know where the gap between begins and ends?

[User 59]

Well we know where a centromere is without ever sequencing it.. Plenty of ways this could be done. FISH springs to mind.

[axelwilhelm]

Yes FISH should tell us where DYZ19 is but it still seems like no one knows or cares.