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Table 2 EMSA-based in vitro analysis of a complex of TBP and one of synthetic 26 bp ODNs identical to natural promoters near the SNPs being tested

From: Disruptive natural selection by male reproductive potential prevents underexpression of protein-coding genes on the human Y chromosome as a self-domestication syndrome

Gene, dbSNP ID [8]

Allele:WT min

26 bp oligodeoxyribonucleotides (ODNs), 5′ → 3′

Prediction

Experiment

-ln (KD) ln-unit

Δln (KD) ln-unit

KD ± SEMnM

-ln (KD) ln-unit

Δln (KD) ln-unit

SHOX

-45A

gaggtcgccgcgtAtaaatagtgaga

20.31

−1.10

39 ± 7

17.06

−1.90

rs1452787381

-45G

gaggtcgccgcgtGtaaatagtgaga

19.21

260 ± 70

15.16

GTPBP6

-24G

atcacgagcacgtGatgaggagcggc

17.30

1.38

1500 ± 200

13.41

0.07

rs1393008234

-24 T

atcacgagcacgtTatgaggagcggc

18.68

1400 ± 200

13.48

ASMT

-30G

ggtgaccttttgtGcccagaataggt

18.18

0.75

600 ± 300

14.33

−0.51

rs1402972626

-30A

ggtgaccttttgtAcccagaataggt

18.93

1000 ± 300

13.82

ZFY

-56C

ggcggagggggccCaactaccatccc

17.67

0.51

1000 ± 400

13.82

−0.70

rs1452787381

-56 T

ggcggagggggccTaactaccatccc

18.18

2000 ± 1000

13.12

CDY2A

-24G

agaatgttccataTaatcgtcatagc

19.27

−0.51

160 ± 30

15.65

−1.14

rs20067072

-24 t

agaatgttccataCaatcgtcatagc

18.76

500 ± 200

14.51

  1. Notes. For each TBP–ODN complex: KD, equilibrium dissociation constant; SEM, standard error of the mean. All experimental data and their SEMs are the output of publicly available software GraphPad Prism 5 (URL = http://graphpad-prism.software.informer.com/5.01), the input data of which were the dependences of reaction rates on ODN concentrations, as illustrated in Fig. 2c and d