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11.5 years ago
jeansimon32
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170
Hello,
I grabed the coordinate of centromeres from UCSC table but I don't know why it gives me half of the centromeric region (as an example please try this coordinate in UCSC : chr1:121535434-124535434) . is there any options i missed to check in UCSC table pages to give me the whole centromeres regions?
Thank you
Welcome to Biostar. This question has already been answered: How can I get the human chromosome centromere position and chromosome length in GRCh37/hg19
Thank you Giovanni,
I applied the same filters but I have half of the centromeric regions. even the table Jeremy proposed in this page How can I get the human chromosome centromere position and chromosome length in GRCh37/hg19 has half of the region.
could you please try chr1:121535434-124535434 in UCSC? it is half of the region
Thank you for your help
Why do you say that it is only half of the region?
coz when i looked at the chr1:121535434-124535434 in UCSC the window which is located on chromosome picture shows only half of the region...when i zoom out it seems that the centromeric region is bigger than this annotation... may be I am totally wrong, I feel i missed something when I got the region from UCSC: TAble: GAp .. please advise
You are only seeing half of it because the heterochromatin regions can be represented as more than one record in UCSC. And you are not merging them together. Try this:
curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz" | gunzip -c | grep acen | grep -w chr1
This gives you chr1:121500000-128900000 once you merge the two 'acen' records. Now try viewing that in the browser. In the 'gap' track of UCSC, the first half is indicated as centromere and the 2nd half as heterochromatin. To see how the 'gap' and 'cytoBand' tracks differ in their treatment of these features on chr1, try this:
curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gap.txt.gz" | gunzip -c | grep -w chr1 | grep -v clone | grep -v contig
If you want to make sure that your coordinates match up with what you see in the ideogram, use the cytpBand track. As you can see, both the 'cytoBand' and 'gap' tracks represent the concept of a centromere slightly differently. Strictly speaking, neither of them represents output from an assay to determine the region actually behaving as a centromere during mitosis (i.e. the physical region involved in assembly of the kinetochore).
Thank you so much Malachi for your reply and time, it was so helpful to understand this!
If you're referring to the ideogram at the top, then I believe you're overthinking it. There's a lot of heterochromatin near the centromere that isn't necessarily actually the centromere.