Description
This track shows the CpG annotations on the 15 Jul 2021 Lagopus leucura/GCF_019238085.1_USGS_WTPT01 genome assembly.
CpG islands are associated with genes, particularly housekeeping
genes, in vertebrates. CpG islands are typically common near
transcription start sites and may be associated with promoter
regions. Normally a C (cytosine) base followed immediately by a
G (guanine) base (a CpG) is rare in
vertebrate DNA because the Cs in such an arrangement tend to be
methylated. This methylation helps distinguish the newly synthesized
DNA strand from the parent strand, which aids in the final stages of
DNA proofreading after duplication. However, over evolutionary time,
methylated Cs tend to turn into Ts because of spontaneous
deamination. The result is that CpGs are relatively rare unless
there is selective pressure to keep them or a region is not methylated
for some other reason, perhaps having to do with the regulation of gene
expression. CpG islands are regions where CpGs are present at
significantly higher levels than is typical for the genome as a whole.
The unmasked version of the track displays potential CpG islands
that exist in repeat regions and would otherwise not be visible
in the repeat masked version.
Methods
CpG islands were predicted by searching the sequence one base at a
time, scoring each dinucleotide (+17 for CG and -1 for others) and
identifying maximally scoring segments. Each segment was then
evaluated for the following criteria:
- GC content of 50% or greater
- length greater than 200 bp
- ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the
basis of the number of Gs and Cs in the segment
The entire genome sequence, masking areas included, was
used for the construction of the track Unmasked CpG.
The track CpG Islands is constructed on the sequence after
all masked sequence is removed.
The CpG count is the number of CG dinucleotides in the island.
The Percentage CpG is the ratio of CpG nucleotide bases
(twice the CpG count) to the length. The ratio of observed to expected
CpG is calculated according to the formula (cited in
Gardiner-Garden et al. (1987)):
Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G)
where N = length of sequence.
CpG item counts
- masked sequence: item count: 19,249 bases covered: 15,071,022
- unmasked sequence: item count: 21,298 bases covered: 20,866,944
Credits
This track was generated using a modification of a program developed by G. Miklem and L. Hillier
(unpublished).
References
Gardiner-Garden M, Frommer M.
CpG islands in vertebrate genomes.
J Mol Biol. 1987 Jul 20;196(2):261-82.
PMID: 3656447