|bin||585||smallint(6)||range||Indexing field to speed chromosome range queries.|
|chrom||chr1||varchar(255)||values||Reference sequence chromosome or scaffold|
|chromStart||28735||int(10) unsigned||range||Start position in chromosome|
|chromEnd||29810||int(10) unsigned||range||End position in chromosome|
|name||CpG: 116||varchar(255)||values||CpG Island|
|length||1075||int(10) unsigned||range||Island Length|
|cpgNum||116||int(10) unsigned||range||Number of CpGs in island|
|gcNum||787||int(10) unsigned||range||Number of C and G in island|
|perCpg||21.6||float||range||Percentage of island that is CpG|
|perGc||73.2||float||range||Percentage of island that is C or G|
|obsExp||0.83||float||range||Ratio of observed(cpgNum) to expected(numC*numG/length) CpG in island|
Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.
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.
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:
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) in the References section below:
Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G)where N = length of sequence.
This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).
Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J. Mol. Biol. 1987 Jul 20;196(2):261-82.