Table 1.
Location of CGIs in the Human and Mouse Genomes with Regard to the CCDS
| CGIs | Human (hg19) |
Mouse (mm10) |
||
|---|---|---|---|---|
| Number | Percentage | Number | Percentage | |
| CGIs (UCSC) | 27,537 | — | 15,997 | — |
| CGIs (analyzed) | 28,396a | 100 | 16,643a | 100 |
| CGIs in gene | 17,807 | 62.71 | 12,587 | 75.63 |
| CGIs not in gene | 10589 | 37.29 | 4,056 | 24.37 |
| TSS | 503 | 1.77 | 474 | 2.85 |
| TSS + 5′-UTR | 3,412 | 12.02 | 3,029 | 18.20 |
| TSS + 5′-UTR + CDS (Exon) | 1,078 | 3.80 | 1,189 | 7.14 |
| TSS + 5′-UTR + CDS (Exon) + CDS (Intron) | 5,223 | 18.39 | 4,692 | 28.19 |
| TSS + 5′-UTR + CDS (Exon) + CDS (Intron) + 3′-UTR | 275 | 0.97 | 107 | 0.64 |
| 5′-UTR | 491 | 1.73 | 303 | 1.82 |
| 5′-UTR + CDS (Exon) | 93 | 0.33 | 112 | 0.67 |
| 5′-UTR + CDS (Exon) + CDS (Intron) | 273 | 0.96 | 225 | 1.35 |
| 5′-UTR + CDS (Exon) + CDS (Intron) + 3′-UTR | 27 | 0.10 | 13 | 0.08 |
| CDS (Exon) | 845 | 2.98 | 781 | 4.69 |
| CDS (Exon) + CDS (Intron) | 2,453 | 8.64 | 758 | 4.55 |
| CDS (Exon) + CDS (Intron) + 3′-UTR | 620 | 2.18 | 222 | 1.33 |
| CDS (Exon) + 3′-UTR | 70 | 0.25 | 39 | 0.23 |
| CDS (Intron) | 2,174 | 7.66 | 579 | 3.48 |
| 3′-UTR | 270 | 0.95 | 64 | 0.38 |
Note.—The table shows the distribution of human and mouse CGIs dependent on their CCDS location. In addition to the total number, the percentages are given. Five classes for CGI characterization are defined, where a CGI can overlap no, one, or more classes. The classes are: TSS (200-bp region upstream of the TSS), 5′-UTR, CDS (Exon), CDS (Intron), and 3′-UTR (see supplementary fig. S1, Supplementary Material online).
aThe analyzed number of CGIs is higher than the downloaded number from the UCSC browser, because one CGI can belong to more than one CCDS.