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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  
  1. † ChIP-defined region
  2. ° reverse complement data in paper
  3. § DNA sequence at UCSC does not match sequence in paper