Is subtelomeric region and pericentromeric region defined in human genome?

Is subtelomeric region and pericentromeric region defined in human genome?


I’ve been trying to see if there’s any coordinates for these but doesn’t have much luck. Saw a bunch of people defining it by +-2MB around the centromere gap and 30kb away from the telomere. I was wondering if you guys have any knowledge about this. Thanks!






Centromeres and telomeres are highly repetitive regions that, as far as I know, still defy assembly for each chromosome. Another issue is that their lengths vary from chromosome to chromosome and from cell to cell.

One paper I found very useful in terms of information provided about subtelomeric regions is this one.
It provides a fasta file as a supplementary where subtelomeric regions are defined as 500kb regions on both p and q arms of chromosomes of hg19 assembly.

I recently wondered about the same question and tried to find an answer as I did not find any attempt to provide a kind of “annotation” of subtelomeric regions in hg19 genome assembly.
Starting from data of the paper I cited previously, I tried to create an annotation of subtelomeres in hg19.

I describe the whole process here on my Github:

I produced 2 bed files with coordinates of subtelomeres in hg19:

  • hg19_subtelomeres.bed: which contains the “strict” coordinates of subtelomeres based on the paper fasta file, and telomeres regions from the UCSC genome browser.
  • hg19_extended_subtelomeres.bed: where I removed the gaps existing between subtelomeres coordinates and telomeres, by extending the subtelomeres to where telomeres end/start (depending on which chromosome arm you consider).

I would be very interested if others could contribute, give feedbacks or provide an alternative approach to define subtelomeric regions.
I am currently working on a method to define coordinates of pericentromeric regions, this time based on repetive elements composition along chromosomes.
Maybe I will have the opportunity to share it here too when it will be available.

before adding your answer.

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