Where can I get the exact start and end positions for the centromere of a given chromosome?
I would like to know whether a gene I am studying falls within the region that it is usually considered as being the centromere. However, I am not sure whether this type of annotation really exists: who can define the exact boundaries of a centromere, and with which definition?
I have looked at the description of the UCSC track for Chimp, but it says that they have simply translated the positions of the centromeres in human. That is not very useful, because I need some experimental evidence to be sure that the centromere is really there in Chimp.
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written
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Giovanni M Dall'Olio
I don't know about centromere regions in chimpanzee per se, but have studied these extensively in Arabidopsis and know enough about genome sequencing in human to give this one a try. And, sorry to say, there is no definite and precise boundary to the centromere, especially on the acentric chromosomes like 13, 14, 15 and 22. I would consider some other characteristics about your gene:
How close is the nearest well known gene - i.e. one with a known function
Are there ESTs for your gene in chimp or human? If so, it is expressed and not so buried in centromeric heterochromatin.
Were does the gene map in human - also near a centromere or far from it? Use synteny to your advantage, as I often add to my responses on BioStar!
Lastly, what kind of sequence do you find in the 10-25 kbp on eitehr side of your gene? If it is full of repeats, you're near functional centromere; if not, then the gene is likely to be more distant from the centromere.
So, you see this is a kind of shades of gray issue.
thanks, very useful answer! I didn't think about looking for repeats close to the gene. It is probably the best solution. And I will use the Syntheny!
If the result from repeat analysis is not so clear, jump 100 or 500 kbp toward the centromere and look there as well. Go 100 nad 500 kbp toward the near telomere as well and see if a trend develops.
Giovanni, did you try the following SQL query ? (I don't know if those data are part of the translation of coordinates that you mentioned)
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D panTro3 \
-e 'select chrom,chromStart,chromEnd from gap where type="centromere"
+-------+------------+-----------+
| chrom | chromStart | chromEnd |
+-------+------------+-----------+
| chr1 | 113832284 | 116072284 |
| chr10 | 39470229 | 41850229 |
| chr11 | 50647596 | 53647596 |
| chr12 | 52156499 | 53551499 |
| chr13 | 16000000 | 17868000 |
| chr14 | 15070000 | 18070000 |
| chr15 | 15260000 | 18260000 |
| chr16 | 42150972 | 43950972 |
| chr17 | 33925834 | 34025834 |
| chr18 | 82944 | 1446942 |
| chr19 | 26701495 | 29701495 |
| chr20 | 26025681 | 27791342 |
| chr22 | 11330000 | 14330000 |
| chr2A | 91793653 | 94793653 |
| chr2B | 132910908 | 135910908 |
| chr3 | 92159186 | 95059186 |
| chr4 | 78675172 | 81675172 |
| chr5 | 65648281 | 68648281 |
| chr6 | 59767044 | 62767044 |
| chr7 | 58420265 | 61420265 |
| chr8 | 40544052 | 43544052 |
| chr9 | 45033823 | 48033823 |
| chrX | 59308983 | 62308983 |
| chrY | 6108945 | 7108945 |
+-------+------------+-----------+
24 rows in set (0.27 sec)
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written
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Pierre Lindenbaum
Thank you Pierre! It works, but as I was saying in the question, these coordinates are not supported by experimental evidence. Let's see if someone knows about some better annotation on the Chimp centromeric regions..
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