Thyroid hormone response element gene transcriptions: Difference between revisions

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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:
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, 0.
# negative strand, negative direction, looking for AGGTCA, 2, AGGTCA at 1532, AGGTCA at 1352.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# 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 AAAAAAAA, 0.
# positive strand, positive direction, looking for AGGTCA, 0.
# negative strand, positive direction, looking for AAAAAAAA, 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, 0.
# 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 TTTTTTTT, 0.
# complement, positive strand, negative direction, looking for TCCAGT, 2, TCCAGT at 1532, TCCAGT at 1352.
# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# 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 TTTTTTTT, 0.
# complement, negative strand, positive direction, looking for TCCAGT, 0.
# inverse complement, negative strand, negative direction, looking for TGACCTT, 0.
# inverse complement, negative strand, negative direction, looking for TGACCTT, 0.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for TGACCTT, 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for TGACCTT, 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 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 negative strand, negative direction, looking for ACTGGA, 0.
# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, negative direction, looking for ACTGGA, 0.
# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
# inverse positive strand, positive direction, looking for ACTGGA, 2, ACTGGA at 4019, ACTGGA at 3785.
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
# inverse negative strand, positive direction, looking for ACTGGA, 0.


===AAA UTRs===
===AAA UTRs===
{{main|UTR promoter gene transcriptions}}
{{main|UTR promoter gene transcriptions}}
Positive strand, negative direction: AGGTCA at 4307.


===AAA core promoters===
===AAA core promoters===
{{main|Core promoter gene transcriptions}}
{{main|Core promoter gene transcriptions}}
Negative strand, positive direction: AGGTCA at 4269.


===AAA proximal promoters===
===AAA proximal promoters===
Line 55: Line 57:
===AAA distal promoters===
===AAA distal promoters===
{{main|Distal promoter gene transcriptions}}
{{main|Distal promoter gene transcriptions}}
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==
==Acknowledgements==

Revision as of 17:03, 6 March 2021

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:

  1. negative strand, negative direction, looking for AGGTCA, 2, AGGTCA at 1532, AGGTCA at 1352.
  2. 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.
  3. positive strand, positive direction, looking for AGGTCA, 0.
  4. negative strand, positive direction, looking for AGGTCA, 3, AGGTCA at 4269, AGGTCA at 2220, AGGTCA at 153.
  5. 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.
  6. complement, positive strand, negative direction, looking for TCCAGT, 2, TCCAGT at 1532, TCCAGT at 1352.
  7. complement, positive strand, positive direction, looking for TCCAGT, 3, TCCAGT at 4269, TCCAGT at 2220, TCCAGT at 153.
  8. complement, negative strand, positive direction, looking for TCCAGT, 0.
  9. inverse complement, negative strand, negative direction, looking for TGACCTT, 0.
  10. inverse complement, positive strand, negative direction, looking for TGACCTT, 0.
  11. inverse complement, positive strand, positive direction, looking for TGACCTT, 0.
  12. inverse complement, negative strand, positive direction, looking for TGACCTT, 2, TGACCTT at 4019, TGACCTT at 3785.
  13. inverse negative strand, negative direction, looking for ACTGGA, 0.
  14. inverse positive strand, negative direction, looking for ACTGGA, 0.
  15. inverse positive strand, positive direction, looking for ACTGGA, 2, ACTGGA at 4019, ACTGGA at 3785.
  16. 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.

See also

References

  1. 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.

External links