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Table 4 TREs identified using bioinformatics searches of promoter regions of genes characterized as being directly regulated by THs.

From: Thyroid hormone-regulated gene expression in juvenile mouse liver: identification of thyroid response elements using microarray profiling and in silico analyses

  

Mouse

Rat

Human

Gene

Type

Pos.

TRE

Pos.

TRE

MM

Pos.

TRE

MM

H01Rik‡

DR4

1597

GGGTCA CCAGGGGCTA

1513

GGGTCA CCAGGGGCTA

0

1709

GGGTCA CCAGGGGCTG

1

H01Rik‡

DR4

-5778

AGGGCA GCAGAGCTGA

-5806

AGGGCA GCAGGGCTGA

1

-7091

AGGGGC AGGCAGCTGA

1

       

-4046

AGGGAA AGACAGCTCA

2

H01Rik‡

DR4

281

AGGTCA GGCGAGGGCA

243

AGGTCA GGCGAGGGCA

0

1176

TGGTCA GGCCTGGGCA

2

H01Rik‡

IR0

-2311

AGGTGAAGCCCT*

-2421

AGGTGAAGCCCT

0

-3415

CGGTGAAACCCT

2

Arl4d

DR4

-2529

AGGCCA GCCAGGGCTA

-1594

AGGCTA GCCTGGGCTA

1

-1286

AGGCCT CAAAGGGCTT

2

       

-922

AGGCCG ATGTGGGCGA

2

Ces2

DR4

-5950

AGGCAA AGCAAGGTCT

-7139

AGGCAA CTGCAGGTTT

1

-7548

AGGCAA AAGCTGGGCT

2

       

-7219

TGGCAA TCTGAGCTCT

2

       

-4185

AGCTAA GCCAAGGTCT

2

Fzd8

DR4

-143

CGGTCA CCCCAGGAGA

6

CGGTCA CCCCAGGAGA

0

399

CGGTCG GGCCAGGCGA

2

Hectd3

ER6

-7433

TGGCCT GAAGATAGGACA*

-6784

TGGCCT CTCCTATGGACA

1

-7570

TGGCCT ACAACCAGGATA

1

       

-6806

GGGCCA ATGCTCAGGACA

2

Hectd3

DR4

-3516

AAGTCA CCTGAGGAGA

-5475

AAGTCA CCTGAGGAGA

0

-2992

AAGTCA TTTGGGGAAA

2

Ihh

ER6

-5766

TGACCT TTATGCAAGTCA

-6131

TGACCT TTATTCAAGTCA

0

-4898

CCACCT CTGTTCAAGTCA

2

Serpina9

DR4

31

AGGACA ACAAGGGCGA

31

AGGACA ACAAAGGCGA

1

167

AGGACA GGGCAGGAGA

2

Slc25a45

DR4

-4642

AGGATT TCTAAGGCCA*

-5175

AGGATT TCTATGGCCA

1

-6373

AGGTTT GCAATGGCCA

2

Sned1

DR4

409

AGGTGG AATGAGGACA

317

AGGTGG AATGAGGACA

0

332

AGGTGG AATGAGGACA

0

       

-864

AGGTGG GGGCAGGACT

1

Sned1

ER6

217

TCACCC CGAAGCAGGACG

125

TCACCC CGAAGCAGGACG

0

125

TCACCC CCAAGCAGGACG

0

Tbcel

DR4

15

GGGTCA GCATAGGACA

-7

GGGTCA ATGCAGGACA

0

15

GGGTCA ATGCAGGACA

0

Tbcel

IR0

920

AGGACAAGTCCC

891

AGGACAAGTCCC

0

649

AGGACATGTCCC

1

       

1157

GGGACAAGCCCC

2

       

470

GGGACCAGTCCC

2

Tbcel

DR4

1361

AGGCCA GCCTGGGCTA

1371

AGGCCA GCCTGGGCTA

0

-230

AGGACA ATAGGGGCTG

2

Tor1a

DR4

-2364

AGGACA GCCAGGGCTA*

-4242

AGGAAA CACACGGCTA

2

-1610

AGGATA CTCCGGGCTC

2

Tor1a

DR4

1648

AGGTTA GTCTGGGCTA

1638

AGGTTA GTCTGGGCTG

1

552

CGGTTG GCTGGGGCTA

2

Tor1a

DR4

-2729

AGGACA GCCAGGGCTA

-4242

AGGAAA CACACGGCTA

2

-1610

AGGATA CTCCGGGCTC

2

Tor1a

DR4

-4783

AGGCCA CTTCAGGTTG

-6425

AGGCCA GAAGAGGGTG

1

-6272

AGGCCA AGGCAGGAGG

2

       

-6628

AGGCCA GGCACGGTGG

2

Trim24

DR4

295

AGGACA ATGGAGGTGG

-5

AGGACA ATGGAGGTGG

0

336

AGGACA ATGGAGGTGG

0

Txnrd3

IR0

372

GGGTGATGATCT

362

GGGTTATGATCT

1

1423

GGGTGGTGATCT

1

       

1876

GGGTGATAACCT

2

Previously Characterized TREs

Klf9a

DR4

-3804

AGGTGA AGTGAGGTCA

-3819

AGGTGG GGCGAGGTCA

1

-2875

AGATTG TCTGAGGTTA

4

Mbpb

ER6

-192

GGACCT CGGCTGAGGACA

-138

GGACCT CGGCCGAGGACA

0

   
  1. 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.
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BMC Genomics

ISSN: 1471-2164

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