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Table 4 Non-conserved pTRR density is higher in intergenic proximal regions than intergenic distal regions.

From: Asymmetrical distribution of non-conserved regulatory sequences at PHOX2B is reflected at the ENCODE loci and illuminates a possible genome-wide trend

   pTRR Density
Gene Type ENCODE Sub-region Conserved pTRRs/Conserved bp Non-conserved pTRRs/Non-conserved bp Conserved pTRRS/Conserved Non-repeat bp Non-conserved pTRRs/Non-conserved Non-repeat bp
All 5' UTR 1/457 1/1,456 1/410 1/931
All 3' UTR 1/5,625 1/24,829 1/5,460 1/18,610
All Intergenic Proximal 1/1,185 1/14,460 1/1,094 1/7,005
All Intergenic Distal 1/7,528 1/62,541 1/7,073 1/29,635
All Intronic Proximal 1/1,463 1/18,930 1/1,356 1/10,801
All Intronic Distal 1/4,259 1/51,055 1/4,026 1/28,231
Developmental Intergenic Proximal 1/1,591 1/16,403 1/1,508 1/8,796
Developmental Intergenic Distal 1/11,370 1/78,961 1/10,714 1/47,792
Non-developmental Intergenic Proximal 1/867 1/8,287 1/821 1/3,619
Non-developmental Intergenic Distal 1/6,160 1/44,074 1/5,776 1/18,446
Non-gene Desert Intergenic Proximal 1/1,078 1/14,303 1/991 1/6,877
Gene Desert Intergenic Proximal N/A 1/22,824 N/A 1/13,830
Non-gene Desert Intergenic Distal 1/5,307 1/43,650 1/4,954 1/19,047
Gene Desert Intergenic Distal 1/17,151 1/312,847 1/16,254 1/151,566
  1. Density of putative transcriptional regulatory regions (pTRRS) identified by King et al. [26]. The ENCODE interval was partitioned into sub-regions. Gene type of all represents analysis of whole ENCODE region. Developmental genes represent regions flanking genes labeled with Gene Ontology term GO:0032502, while non-developmental genes were those that were not labeled with GO:0032502. Gene deserts were ENCODE intervals overlapping ≥500 kb regions without a Reference Sequence gene. Non-gene deserts were all sub-regions that did not overlap gene deserts. Density of pTRRs was calculated by dividing the total number of conserved or non-conserved base pairs in the ENCODE defined region by number of conserved or non-conserved pTRRs in the ENCODE defined region. N/A= not applicable due to lack of conserved pTRRs in gene desert intergenic proximal regions