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

Table 3 Distribution of putative transcriptional regulatory regions (pTRRs) identified by King et al. [26].

Type of gene	ENCODE Sub-regions Analyzed	Conserved pTRRs in sub-region	Non-conserved pTRRs in sub-region	Base pairs in sub-region
All	5' UTR	71	46	99,440
All	3' UTR	15	12	382,329
All	Intergenic Proximal	61	163	2,429,196
All	Intergenic Distal	48	171	11,055,834
All	Intronic Proximal	173	457	8,903,959
All	Intronic Distal	55	122	6,462,925
All	Coding sequences	0	0	671,166
Developmental	Intergenic Proximal	20	22	392,692
Developmental	Intergenic Distal	5	20	1,636,075
Non-developmental	Intergenic Proximal	24	86	733,487
Non-developmental	Intergenic Distal	10	51	2,309,353
Non-gene Desert	Intergenic Distal	39	159	7,147,316
Gene Desert	Intergenic Distal	9	12	3,908,518
Gene Desert	Intergenic Proximal	0	3	75,000
Non-gene Desert	Intergenic proximal	61	160	2,354,196

pTRRs partitioned to ENCODE defined regions and grouped as conserved versus non-conserved based on pTRR overlap with PhastCons Placental Mammal Conserved Elements, 28-way Multiz Alignment [43]. 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 regions ≥500 kb without a Reference Sequence gene. Non-gene deserts were all sub-regions that did not overlap gene deserts. The "Base pairs in sub-region" column represents the sum of the genomic intervals represented by each type of sub-regions.

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