Table 2 Experimentally validated transcription factor binding sites.
From: Evolution of gene regulation of pluripotency - the case for wiki tracks at genome browsers
| Regulatory region of | Transcription Factor Binding Site/Conserved Region | Class of Binding Site/Sub-region | Specific Identifier | Abbreviated Reference | Ref. | Chromosomal Position (start/end) ‚+' marks cases where binding site sequence at UCSC and in the reference are identical | |||
|---|---|---|---|---|---|---|---|---|---|
| Oct4 | Ronin | R()† | Dejosez08 | [89] | chr17 | 35643243 | 35643348 | ||
| Oct4 | Nr1b*/2b*; Rar*/Rxr* | HRE | Nordhoff01; Sylvester94 | [59, 90] | chr17 | 35642936 | 35642955 | + | |
| Oct4 | Nr6a1/GCNF | DR(0) | Fuhrmann01 | [91] | chr17 | 35642943 | 35642955 | + | |
| Oct4 | LRH1/Nr5a2 | DR(0) | Gu05 | [92] | chr17 | 35642943 | 35642955 | + | |
| Oct4 | Nr2c1/TR2 | DR(1) | Park07 | [93] | chr17 | 35642936 | 35642949 | + | |
| Oct4 | CoupTF1/Nr2f1 | Schoorlemmer94 | [94] | chr17 | 35642936 | 35642949 | + | ||
| Oct4 | CoupTF2/Nr2f2 | Schoorlemmer94 | [94] | chr17 | 35642936 | 35642949 | + | ||
| Oct4 | SF1 | RARE | (a) | Barnea00 | [95] | chr17 | 35642936 | 35642954 | + |
| Oct4 | Ear2/Nr2f6 | Schoorlemmer94 | [94] | chr17 | 35642936 | 35642949 | + | ||
| Oct4 | Sp1/3 | Nordhoff01 | [59] | chr17 | 35642929 | 35642939 | + | ||
| Oct4 | Zfp206 | Yu09 | [96] | chr17 | 35642877 | 35642886 | + | ||
| Oct4 | SF1 | (b) | Barnea00 | [95] | chr17 | 35642769 | 35642792 | + | |
| Oct4 | Nobox | Choi06 | [97] | chr17 | 35642612 | 35642618 | + | ||
| Oct4 | LRH1/Nr5a2 | 1B | PE2 | Gu05 | [92] | chr17 | 35642109 | 35642118 | + |
| Oct4 | Esrrb | P1 | Zhang08 | [66] | chr17 | 35642104 | 35642123 | + | |
| Oct4 | Nanog | P1 | Zhang08 | [66] | chr17 | 35642033 | 35642054 | + | |
| Oct4 | LRH1/Nr5a2 | 1B | PE1 | Gu05 | [92] | chr17 | 35642048 | 35642057 | + |
| Oct4 | Tcf3 | M3 | Tam08 | [98] | chr17 | 35641942 | 35641948 | + | |
| Oct4 | SF1 | 1A(PE) | Nordhoff01 | [99] | chr17 | 35641863 | 35641873 | + | |
| Oct4 | demethylation site | 1A(PE) | Aoto06 | [59, 99] | chr17 | 35641856 | 35641875 | + | |
| Oct4 | Esrrb | P2 | Zhang08 | [66] | chr17 | 35641431 | 35641450 | + | |
| Oct4 | Sall4 | Zhang06 | [100] | chr17 | 35641024 | 35641063 | + | ||
| Oct4 | OctSox | Chew05 | [101] | chr17 | 35640993 | 35641008 | + | ||
| Oct4 | OctSox | 2B | OkumuraN05 | [102] | chr17 | 35640987 | 35641016 | + | |
| Oct4 | Tcf3 | M1 | Tam08 | [98] | chr17 | 35640793 | 35640799 | + | |
| Oct4 | CR2 | 1B(PE) | Nordhoff01 | [59] | chr17 | 35642037 | 35642063 | ||
| Oct4 | CR4 | 2A(DE) | Nordhoff01 | [59] | chr17 | 35640947 | 35640965 | ||
| Oct4 | CR1 | Nordhoff01 | [59] | chr17 | 35642918 | 35643044 | |||
| Oct4 | CR2 | Nordhoff01 | [59] | chr17 | 35641981 | 35642181 | |||
| Oct4 | CR3 | Nordhoff01 | [59] | chr17 | 35641641 | 35641746 | |||
| Oct4 | CR4 | Nordhoff01 | [59] | chr17 | 35640937 | 35641068 | |||
| Sox2 | NF-Y | Wiebe00 | [60] | chr3 | 34548868 | 34548886 | + | ||
| Sox2 | Lef1, Lef1 | neural | Kamachi09 | [48] | chr3 | 34564288 | 34564307 | + | |
| Sox2 | FGF | neural | Kamachi09 | [48] | chr3 | 34564324 | 34564330 | + | |
| Sox2 | Oct4/6, Sox | Tomioka02 | [82] | chr3 | 34552970 | 34552985 | + | ||
| Sox2 | Stat3 | 2 | Foshay08 | [103] | chr3 | 34548486 | 34548498 | + | |
| Sox2 | Stat3 | 1 | Foshay08 | [103] | chr3 | 34545179 | 34545199 | + | |
| Sox2 | Gli | 1 | Takanaga09 | [104] | chr3 | 34545198 | 34545206 | + | |
| Sox2 | Oct4; Brn1/2 | 1 | Catena04 | [105] | chr3 | 34545218 | 34545229 | + | |
| Sox2 | Oct4; Brn1/2 | 2 | Catena04 | [105] | chr3 | 34545293 | 34545302 | + | |
| Sox2 | HIF2alpha | HRE | 1 | MorenoM10 | [106] | chr3 | 34547578 | 34547592 | + |
| Sox2 | HIF2alpha | HRE | 2 | MorenoM10 | [106] | chr3 | 34548182 | 34548196 | + |
| Sox2 | Gli | 2 dna_ not_matching§ | Takanaga09 | [104] | chr3 | 34545074 | 34545085 | ||
| Sox2 | N1 | neural | Kamachi09 | [48] | chr3 | 34564105 | 34564403 | ||
| Sox2 | N2 | neural | Kamachi09 | [48] | chr3 | 34544940 | 34545478 | ||
| Sox2 | N3 | neural | Kamachi09 | [48] | chr3 | 34529134 | 34529728 | ||
| Sox2 | N4 | neural | Kamachi09 | [48] | chr3 | 34577673 | 34578140 | ||
| Sox2 | N5 | neural | Kamachi09 | [48] | chr3 | 34558702 | 34559054 | ||
| Nanog | Oct1 | Wu05 | [107] | chr6 | 122657427 | 122657442 | + | ||
| Nanog | OctSox | Rodda05; Kuroda05 | [108, 69] | chr6 | 122657429 | 122657445 | + | ||
| Nanog | Smad2/3/4 | Greber10 | [109] | chr6 | 122657408 | 122657412 | + | ||
| Nanog | Klf4 | R()† | Zhang10 | [110] | chr6 | 122657370 | 122657550 | ||
| Nanog | Stat | Suzuki06 | [111] | chr6 | 122653091 | 122653100 | + | ||
| Nanog | T | Suzuki06 | [111] | chr6 | 122653135 | 122653155 | + | ||
| Nanog | FoxD3 | Pan06 | [112] | chr6 | 122657311 | 122657341 | + | ||
| Nanog | p53 | RE1 | Lin05 | [113] | chr6 | 122656935 | 122656957 | + | |
| Nanog | p53 | RE2 | Lin05 | [113] | chr6 | 122657195 | 122657221 | + | |
| Nanog | Klf | Jiang08 | [114] | chr6 | 122652655 | 122652663 | + | ||
| Nanog | Sp1/3 | 2 | Wu06 | [115] | chr6 | 122657555 | 122657570 | + | |
| Nanog | Sp1/3 | 1 | Wu06 | [115] | chr6 | 122657530 | 122657539 | + | |
| Nanog | Tcf3 | Pereira06 | [116] | chr6 | 122653837 | 122653844 | + | ||
| Nanog | Gcnf/Nr6a1 | Gu05 | [92] | chr6 | 122655499 | 122655511 | + | ||
| Nanog | Cdx2 and Nanog | R()† | Chen09 | [117] | chr6 | 122652629 | 122652743 | ||
| Nanog | Zfp143 | revcom° | Chen08 | [118] | chr6 | 122657340 | 122657354 | + | |
| Nanog | Esrrb | vdBerg08 | [119] | chr6 | 122657409 | 122657418 | + | ||
| Nanog | Klf5 | Parisi08 | [120] | chr6 | 122657532 | 122657539 | + | ||
| Nanog | CR1 | Chan09 | [84] | chr6 | 122657170 | 122657827 | |||
| Nanog | CR2 | Chan09 | [84] | chr6 | 122652641 | 122653468 | |||
| Nanog | CR3 | Chan09 | [84] | chr6 | 122652431 | 122652696 | |||