Table 4

TREs identified using bioinformatics searches of promoter regions of genes characterized as being directly regulated by THs.

Mouse

Rat

Human


Gene

Type

Pos.

TRE

Pos.

TRE

MM

Pos.

TRE

MM


H01Rik

DR4

1597

GGGTCACCAGGGGCTA

1513

GGGTCACCAGGGGCTA

0

1709

GGGTCACCAGGGGCTG

1

H01Rik

DR4

-5778

AGGGCAGCAGAGCTGA

-5806

AGGGCAGCAGGGCTGA

1

-7091

AGGGGCAGGCAGCTGA

1

-4046

AGGGAAAGACAGCTCA

2

H01Rik

DR4

281

AGGTCAGGCGAGGGCA

243

AGGTCAGGCGAGGGCA

0

1176

TGGTCAGGCCTGGGCA

2

H01Rik

IR0

-2311

AGGTGAAGCCCT*

-2421

AGGTGAAGCCCT

0

-3415

CGGTGAAACCCT

2

Arl4d

DR4

-2529

AGGCCAGCCAGGGCTA

-1594

AGGCTAGCCTGGGCTA

1

-1286

AGGCCTCAAAGGGCTT

2

-922

AGGCCGATGTGGGCGA

2

Ces2

DR4

-5950

AGGCAAAGCAAGGTCT

-7139

AGGCAACTGCAGGTTT

1

-7548

AGGCAAAAGCTGGGCT

2

-7219

TGGCAATCTGAGCTCT

2

-4185

AGCTAAGCCAAGGTCT

2

Fzd8

DR4

-143

CGGTCACCCCAGGAGA

6

CGGTCACCCCAGGAGA

0

399

CGGTCGGGCCAGGCGA

2

Hectd3

ER6

-7433

TGGCCTGAAGATAGGACA*

-6784

TGGCCTCTCCTATGGACA

1

-7570

TGGCCTACAACCAGGATA

1

-6806

GGGCCAATGCTCAGGACA

2

Hectd3

DR4

-3516

AAGTCACCTGAGGAGA

-5475

AAGTCACCTGAGGAGA

0

-2992

AAGTCATTTGGGGAAA

2

Ihh

ER6

-5766

TGACCTTTATGCAAGTCA

-6131

TGACCTTTATTCAAGTCA

0

-4898

CCACCTCTGTTCAAGTCA

2

Serpina9

DR4

31

AGGACAACAAGGGCGA

31

AGGACAACAAAGGCGA

1

167

AGGACAGGGCAGGAGA

2

Slc25a45

DR4

-4642

AGGATTTCTAAGGCCA*

-5175

AGGATTTCTATGGCCA

1

-6373

AGGTTTGCAATGGCCA

2

Sned1

DR4

409

AGGTGGAATGAGGACA

317

AGGTGGAATGAGGACA

0

332

AGGTGGAATGAGGACA

0

-864

AGGTGGGGGCAGGACT

1

Sned1

ER6

217

TCACCCCGAAGCAGGACG

125

TCACCCCGAAGCAGGACG

0

125

TCACCCCCAAGCAGGACG

0

Tbcel

DR4

15

GGGTCAGCATAGGACA

-7

GGGTCAATGCAGGACA

0

15

GGGTCAATGCAGGACA

0

Tbcel

IR0

920

AGGACAAGTCCC

891

AGGACAAGTCCC

0

649

AGGACATGTCCC

1

1157

GGGACAAGCCCC

2

470

GGGACCAGTCCC

2

Tbcel

DR4

1361

AGGCCAGCCTGGGCTA

1371

AGGCCAGCCTGGGCTA

0

-230

AGGACAATAGGGGCTG

2

Tor1a

DR4

-2364

AGGACAGCCAGGGCTA*

-4242

AGGAAACACACGGCTA

2

-1610

AGGATACTCCGGGCTC

2

Tor1a

DR4

1648

AGGTTAGTCTGGGCTA

1638

AGGTTAGTCTGGGCTG

1

552

CGGTTGGCTGGGGCTA

2

Tor1a

DR4

-2729

AGGACAGCCAGGGCTA

-4242

AGGAAACACACGGCTA

2

-1610

AGGATACTCCGGGCTC

2

Tor1a

DR4

-4783

AGGCCACTTCAGGTTG

-6425

AGGCCAGAAGAGGGTG

1

-6272

AGGCCAAGGCAGGAGG

2

-6628

AGGCCAGGCACGGTGG

2

Trim24

DR4

295

AGGACAATGGAGGTGG

-5

AGGACAATGGAGGTGG

0

336

AGGACAATGGAGGTGG

0

Txnrd3

IR0

372

GGGTGATGATCT

362

GGGTTATGATCT

1

1423

GGGTGGTGATCT

1

1876

GGGTGATAACCT

2

Previously Characterized TREs

Klf9a

DR4

-3804

AGGTGAAGTGAGGTCA

-3819

AGGTGGGGCGAGGTCA

1

-2875

AGATTGTCTGAGGTTA

4

Mbpb

ER6

-192

GGACCTCGGCTGAGGACA

-138

GGACCTCGGCCGAGGACA

0


TREs were found to be conserved between mice, rats and humans (i.e., within 2 kb of the mouse TRE and with 2 or less mismatches (MM) when compared to the mouse TRE). MMs were only considered in the bolded half-sites. Positions (Pos.) of the TREs are presented in reference to the transcription start site of the associated gene. Two previously characterized TREs are presented at the bottom of the table. * TREs validated by ChIP-PCR. Corresponds to 2310003H01Rik. a Characterized by [40]. b Characterized by [41,42]; bolding of half-sites and positions of TRE were corrected.

Paquette et al. BMC Genomics 2011 12:634   doi:10.1186/1471-2164-12-634

Open Data