Thyroid hormone response element gene transcriptions

Associate Editor(s)-in-Chief: Henry A. Hoff

"The arrangement of TREs within the promoter might regulate THR action by determining THR isoform binding, THR dimerization, and coregulators binding. In the classic view of how TH and its receptor stimulate gene expression, the gene promoter contains TREs consisting of a 6-bp consensus sequence (AGGTCA) organized as a direct repeat separated by 4 bp (DR4), a palindrome without spacing (PAL), or an inverted palindrome (LAP) separated by 4 to 6 bp (10–13)."^[1]

Human genes

Consensus sequences

The "gene promoter contains TREs consisting of a 6-bp consensus sequence (AGGTCA) organized as a direct repeat separated by 4 bp (DR4), a palindrome without spacing (PAL), or an inverted palindrome (LAP) separated by 4 to 6 bp (10–13)."^[1]

THR samplings

Copying the consensus sequence for the THR AGGTCA and putting the sequence in "⌘F" finds no locations between ZNF497 and A1BG or two locations between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence AGGTCA (starting with SuccessablesTHR.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

negative strand, negative direction, looking for AGGTCA, 2, AGGTCA at 1532, AGGTCA at 1352.
positive strand, negative direction, looking for AGGTCA, 7, AGGTCA at 4307, AGGTCA at 2585, AGGTCA at 2248, AGGTCA at 712, AGGTCA at 576, AGGTCA at 568, AGGTCA at 439.
positive strand, positive direction, looking for AGGTCA, 0.
negative strand, positive direction, looking for AGGTCA, 3, AGGTCA at 4269, AGGTCA at 2220, AGGTCA at 153.
complement, negative strand, negative direction, looking for TCCAGT, 7, TCCAGT at 4307, TCCAGT at 2585, TCCAGT at 2248, TCCAGT at 712, TCCAGT at 576, TCCAGT at 568, TCCAGT at 439.
complement, positive strand, negative direction, looking for TCCAGT, 2, TCCAGT at 1532, TCCAGT at 1352.
complement, positive strand, positive direction, looking for TCCAGT, 3, TCCAGT at 4269, TCCAGT at 2220, TCCAGT at 153.
complement, negative strand, positive direction, looking for TCCAGT, 0.
inverse complement, negative strand, negative direction, looking for TGACCTT, 0.
inverse complement, positive strand, negative direction, looking for TGACCTT, 0.
inverse complement, positive strand, positive direction, looking for TGACCTT, 0.
inverse complement, negative strand, positive direction, looking for TGACCTT, 2, TGACCTT at 4019, TGACCTT at 3785.
inverse negative strand, negative direction, looking for ACTGGA, 0.
inverse positive strand, negative direction, looking for ACTGGA, 0.
inverse positive strand, positive direction, looking for ACTGGA, 2, ACTGGA at 4019, ACTGGA at 3785.
inverse negative strand, positive direction, looking for ACTGGA, 0.

AAA UTRs

Positive strand, negative direction: AGGTCA at 4307.

AAA core promoters

Negative strand, positive direction: AGGTCA at 4269.

AAA proximal promoters

AAA distal promoters

Negative strand, negative direction: AGGTCA at 1532, AGGTCA at 1352.

Positive strand, negative direction: TGACCTT at 4019, TGACCTT at 3785, AGGTCA at 2248, AGGTCA at 712, AGGTCA at 576, AGGTCA at 568, AGGTCA at 439.

Negative strand, positive direction: AGGTCA at 4269, AGGTCA at 2220, AGGTCA at 153.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

References

↑ ^1.0 ^1.1 Vitor M S Pinto, Svetlana Minakhina, Shuiqing Qiu, Aniket Sidhaye, Michael P Brotherton, Amy Suhotliv, Fredric E Wondisford (1 September 2017). "Naturally Occurring Amino Acids in Helix 10 of the Thyroid Hormone Receptor Mediate Isoform-Specific TH Gene Regulation". Endocrinology. 158 (9): 3067–3078. doi:10.1210/en.2017-00314. PMID 28911178. Retrieved 5 September 2020.

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Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions Initiator element gene transcriptions Initiator-like element gene transcriptions Inositol/choline-responsive elements Interaction gene transcriptions Interferon regulatory factors Inverse copy gene transcriptions Jasmonic acid-responsive element gene transcriptions K-boxes Kozak sequence gene transcriptions Kruppel-associated box gene transcriptions Krüppel-like factor gene transcriptions L box gene transcriptions Leu3 gene transcriptions M35 box gene transcriptions MADS box gene transcriptions Maf recognition element gene transcriptions M box gene transcriptions Mcm1 regulatory factor gene transcriptions Met31p box gene transcriptions Metal responsive element gene transcriptions Middle sporulation element gene transcriptions Mig1p gene transcriptions Model samplings Motif ten element gene transcriptions Msn2,4p gene transcriptions Musashi binding element gene transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions Proximal promoter gene transcriptions Promoter occurrence gene transcriptions Pyrimidine box gene transcriptions Q element gene transcriptions Rap1 regulatory factor gene transcriptions Reb1 general regulatory factor gene transcriptions Retinoblastoma control element gene transcriptions Retinoic acid response element gene transcriptions Rgt1p gene transcriptions Rlm1p gene transcriptions RNA polymerase II gene transcriptions RNA polymerase II holoenzyme complex Root specific element gene transcriptions ROR-response element gene transcriptions Rox1p gene transcriptions Rpn4p gene transcriptions R response element gene transcriptions SARE gene transcriptions Seed-specific element gene transcriptions Serum response element gene transcriptions Servenius sequence gene transcriptions Shoot specific element gene transcriptions Sip4p gene transcriptions Smp1p gene transcriptions Sp1 gene transcriptions Spaceflight gene expressions Specificity protein gene transcriptions STAT gene transcriptions Ste12p gene transcriptions Sterol response element gene transcriptions Sucrose box gene transcriptions Synaptic Activity-Responsive Elements TACTAAC box gene transcriptions TAGteam gene transcriptions Tapetum box gene transcriptions TATA binding protein associated factor gene transcriptions TATA binding protein gene transcriptions TATA box gene transcriptions TAT box gene transcriptions TATC box gene transcriptions Tbf1 regulatory factor gene transcriptions T box gene transcriptions TCCACCATA element gene transcriptions TC element gene transcriptions TCT gene transcriptions TEA consensus sequence gene transcriptions Tec1p gene transcriptions Telomeric repeat DNA-binding factor gene transcriptions Tetradecanoylphorbol-13-acetate response element gene transcriptions TGF-β control elements (TCEs) TGF-β inhibitory elements (TIEs) Thyroid hormone response element gene transcriptions Transcriptional regulation Transcription bubble gene transcriptions Transcription factor gene transcriptions Transcription factor 3 gene transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational control sequence gene transcriptions U box gene transcriptions Unfolded protein response element gene transcriptions Upstream response element gene transcriptions Upstream stimulatory factor gene transcriptions UTR promoter gene transcriptions V and P box gene transcriptions V box gene transcriptions Vhr1p gene transcriptions Vitamin D response element gene transcriptions W box gene transcriptions X box gene transcriptions Xbp1p gene transcriptions X core promoter element gene transcriptions Xenobiotic response element gene transcriptions Xenobiotic responsive element gene transcriptions Yap1p,2p gene transcriptions Y box gene transcriptions YY1 gene transcriptions Zap1p gene transcriptions Z box gene transcriptions Zinc responsive element gene transcriptions