| | |
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
|
- 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
