Estimating Genomic Region Sizes

Data from the consensus coding sequence (CCDS) database (release 22) [63 (link)] were used to estimate the sizes of exonic, intronic and intergenic regions for individual chromosomes. First we retrieved the start and end exon and intron positions of each coding gene transcript. The sum of the lengths of all exons on a given chromosome was used as a size of the exonic region. We excluded overlapping gene sequences to make sure that each nucleotide was counted only once. The similar approach was used to estimate the total size of intronic regions. Noncoding genes were counted as part of the genic region. Start and end positions of noncoding genes were retrieved from the NCBI Gene database [64 (link)]. The size of the intergenic region was computed as the total size of the chromosome minus the combined size of exons, introns and noncoding genes. Genes located on the Y-chromosome and mitochondrial genes were excluded from the analysis.

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Gorlov I.P, & Amos C.I. (2023). Why does the X chromosome lag behind autosomes in GWAS findings?. PLOS Genetics, 19(2), e1010472.

Publication 2023

Chromosome Coding sequence Consensus sequence Exons Genes Genes positions Intergenic region Introns Mitochondrial genes Nucleotide Overlapping gene Y chromosome

Corresponding Organization : Baylor College of Medicine

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Variable analysis

independent variables

None explicitly mentioned

dependent variables

Size of exonic regions
Size of intronic regions
Size of intergenic regions

control variables

Overlapping gene sequences were excluded to ensure each nucleotide was counted only once
Noncoding genes were counted as part of the genic region
Genes located on the Y-chromosome and mitochondrial genes were excluded from the analysis

controls

None explicitly mentioned

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