Question: How to get The drosophila Chromosome Centromere Position
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5.3 years ago by
51635641210
51635641210 wrote:

I want ro get the position information of drosophila Chromosome Centromere.The information includes  chrom,chromStart,chromEnd.

genome • 5.7k views
ADD COMMENTlink modified 5.3 years ago by Alex Reynolds30k • written 5.3 years ago by 51635641210

I have tried 

curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/dm3/database/cytoBand.txt.gz" | gunzip -c | grep acen | head, but it didn't show any results.I also tried 

http://genome.ucsc.edu/cgi-bin/hgTables

just choose All Tables -> table:gap

centromeres are treated as a gap "type". The result is different from human genome, the type of the reads are contig not centromere.

#bin    chrom    chromStart    chromEnd    ix    n    size    type    bridge
594    chr4    1221288    1221388    138    N    100    contig    yes
587    chrU    325170    325270    141    N    100    contig    yes
588    chrU    429354    442354    143    N    13000    contig    yes
589    chrU    543815    543915    145    N    100    contig    yes
589    chrU    639309    639409    147    N    100    contig    yes

Lastly I tried the third method,it showed the message as follows:

#filter: (gap.type = 'telomere' OR gap.type = 'centromere')
#bin    chrom    chromStart    chromEnd    ix    n    size    type    bridge
# No results passing filter.

ADD REPLYlink written 5.3 years ago by 51635641210
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gravatar for Alex Reynolds
5.3 years ago by
Alex Reynolds30k
Seattle, WA USA
Alex Reynolds30k wrote:

Via: http://flybase.org/static_pages/docs/nomenclature/nomenclature3.html#5.3.

5.3. Centromeres and centric heterochromatin. Centromeres are designated as ncen, where n indicates the chromosome, i.e.,1cen, Ycen, 2cen, 3cen and 4cen.

5.3.1. Centric heterochromatic blocks will be indicated as hn, where n is a consecutive number.

5.4. Composite chromosome architecture. The designations of the chromosomes, including polytene band ranges, heterochromatic blocks and centromeres are:

YLt h1 -- h17 Ycen h18 -- h25 YSt
1Lt 1A1 -- 20F4 h26 -- h32 1cen h33 -- h34 1Rt
2Lt 21A1 -- 40F7 h35 -- h37 h38L 2cen h38R h39 -- h46 41A1 -- 60F5 2Rt
3Lt 61A1 --- 80F9 h47 -- h52 h53L 3cen h53R h54 -- h58 81F1 -- 100F5 3Rt
4Lt h59 -- h61 4cen 101F1 -- 102F8 4Rt

This suggests the positioning of the centromere on chromosome 4 for dm6, for instance, is before band 101F1:

$ curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/dm6/database/cytoBand.txt.gz" | gunzip -c | grep -w 101F1 -B 5 -A 5
chr3R    31737834    31837725    100D2    n/a
chr3R    31837725    31877583    100D3    n/a
chr3R    31877583    31917440    100D4    n/a
chr3R    31917440    32005374    100E1    n/a
chr3R    32005374    32033274    100E2    n/a
chr4    49042    69508    101F1    n/a
chr4    69508    108296    102A1    n/a
chr4    108296    110283    102A2    n/a
chr4    110283    134526    102A3    n/a
chr4    134526    173313    102A4    n/a
chr4    173313    175300    102A5    n/a

Or somewhere before the region chr4:49042-69508 but downstream of the heterochromatic block h61 (wherever that is).

This seems to line up qualitatively with what chromosome map images show, e.g.:

Interesting question. I wonder if someone who is skilled with Drosophila might know if there's a data source with more specific details.

ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by Alex Reynolds30k
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