Cold-responsive element gene transcriptions: Difference between revisions

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===Cold-responsive element distal promoters===
===Cold-responsive element distal promoters===
{{main|Distal promoter gene transcriptions}}
{{main|Distal promoter gene transcriptions}}
Negative strand, negative direction: 5'-CCGAC-3' at 4144, 5'-CCGAC-3' at 3993, 5'-CCGAC-3' at 3718, 5'-CCGAC-3' at 3223, 5'-CCGAC-3' at 3084, 5'-CCGAC-3' at 3040, 5'-CCGAC-3' at 2695, 5'-CCGAC-3' at 2561, 5'-CCGAC-3' at 2360, 5'-CCGAC-3' at 2225, 5'-CCGAC-3' at 2108, 5'-CCGAC-3' at 2068, 5'-CCGAC-3' at 1799, 5'-CCGAC-3' at 1755, 5'-CCGAC-3' at 1745, 5'-CCGAC-3' at 1463, 5'-CCGAC-3' at 1281, 5'-CCGAC-3' at 1110, 5'-CCGAC-3' at 990, 5'-CCGAC-3' at 824, and complements.
Negative strand, negative direction: 5'-CCGAC-3' at 4144, 5'-GTCGG-3' at 4034, 5'-CCGAC-3' at 3993, 5'-GTCGG-3' at 3727, 5'-CCGAC-3' at 3718, 5'-GTCGG-3' at 3683, 5'-GTCGG-3' at 3295, 5'-CCGAC-3' at 3223, 5'-GTCGG-3' at 3205, 5'-GTCGG-3' at 3125, 5'-CCGAC-3' at 3084, 5'-CCGAC-3' at 3040, 5'-GTCGG-3' at 2767, 5'-CCGAC-3' at 2695, 5'-GTCGG-3' at 2651, 5'-CCGAC-3' at 2561, 5'-GTCGG-3' at 2432, 5'-CCGAC-3' at 2360, 5'-GTCGG-3' at 2265, 5'-CCGAC-3' at 2225, 5'-CCGAC-3' at 2108, 5'-CCGAC-3' at 2068, 5'-GTCGG-3' at 2006, 5'-CCGAC-3' at 1799, 5'-CCGAC-3' at 1755, 5'-CCGAC-3' at 1745, 5'-CCGAC-3' at 1463, 5'-CCGAC-3' at 1281, 5'-GTCGG-3' at 1195, 5'-CCGAC-3' at 1110, 5'-GTCGG-3' at 1062, 5'-CCGAC-3' at 990, 5'-GTCGG-3' at 896, 5'-CCGAC-3' at 824, 5'-GTCGG-3' at 729, 5'-GTCGG-3' at 505, 5'-GTCGG-3' at 36, and complements.
 
Negative strand, negative direction: 5'-GTCGG-3' at 4034, 5'-GTCGG-3' at 3727, 5'-GTCGG-3' at 3683, 5'-GTCGG-3' at 3295, 5'-GTCGG-3' at 3205, 5'-GTCGG-3' at 3125, 5'-GTCGG-3' at 2767, 5'-GTCGG-3' at 2651, 5'-GTCGG-3' at 2432, 5'-GTCGG-3' at 2265, 5'-GTCGG-3' at 2006, 5'-GTCGG-3' at 1195, 5'-GTCGG-3' at 1062, 5'-GTCGG-3' at 896, 5'-GTCGG-3' at 729, 5'-GTCGG-3' at 505, 5'-GTCGG-3' at 36, and complements.


Negative strand, positive direction: 5'-CCGAC-3' at 3800, 5'-CCGAC-3' at 1963, 5'-GTCGG-3' at 1529, 5'-CCGAC-3' at 997, 5'-CCGAC-3' at 897, 5'-CCGAC-3' at 791, and complements.
Negative strand, positive direction: 5'-CCGAC-3' at 3800, 5'-CCGAC-3' at 1963, 5'-GTCGG-3' at 1529, 5'-CCGAC-3' at 997, 5'-CCGAC-3' at 897, 5'-CCGAC-3' at 791, and complements.


Positive strand, positive direction: 5'-CCGAC-3' at 3639, 5'-CCGAC-3' at 3587, 5'-CCGAC-3' at 3525, 5'-CCGAC-3' at 3348, 5'-CCGAC-3' at 2914, 5'-CCGAC-3' at 2886, 5'-CCGAC-3' at 2809, 5'-CCGAC-3' at 2769, 5'-CCGAC-3' at 2319, 5'-CCGAC-3' at 1818, 5'-CCGAC-3' at 1030, 5'-CCGAC-3' at 480, 5'-CCGAC-3' at 416, 5'-CCGAC-3' at 276, 5'-CCGAC-3' at 263, and complements.
Positive strand, positive direction: 5'-GTCGG-3' at 3998, 5'-GTCGG-3' at 3896, 5'-CCGAC-3' at 3639, 5'-CCGAC-3' at 3587, 5'-CCGAC-3' at 3525, 5'-CCGAC-3' at 3348, 5'-GTCGG-3' at 3101, 5'-CCGAC-3' at 2914, 5'-GTCGG-3' at 2897, 5'-CCGAC-3' at 2886, 5'-CCGAC-3' at 2809, 5'-CCGAC-3' at 2769, 5'-GTCGG-3' at 2527, 5'-GTCGG-3' at 2391, 5'-GTCGG-3' at 2353, 5'-CCGAC-3' at 2319, 5'-GTCGG-3' at 2009, 5'-CCGAC-3' at 1818, 5'-GTCGG-3' at 1604, 5'-GTCGG-3' at 1268, 5'-CCGAC-3' at 1030, 5'-GTCGG-3' at 932, 5'-GTCGG-3' at 832, 5'-GTCGG-3' at 614, 5'-GTCGG-3' at 512, 5'-CCGAC-3' at 480, 5'-CCGAC-3' at 416, 5'-CCGAC-3' at 276, 5'-CCGAC-3' at 263, 5'-GTCGG-3' at 65, and complements.
 
Positive strand, positive direction: 5'-GTCGG-3' at 3998, 5'-GTCGG-3' at 3896, 5'-GTCGG-3' at 3101, 5'-GTCGG-3' at 2897, 5'-GTCGG-3' at 2527, 5'-GTCGG-3' at 2391, 5'-GTCGG-3' at 2353, 5'-GTCGG-3' at 2009, 5'-GTCGG-3' at 1604, 5'-GTCGG-3' at 1268, 5'-GTCGG-3' at 932, 5'-GTCGG-3' at 832, 5'-GTCGG-3' at 614, 5'-GTCGG-3' at 512, 5'-GTCGG-3' at 65, and complements.


==Acknowledgements==
==Acknowledgements==

Revision as of 05:03, 25 November 2020

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

A "putative cold-responsive element (CRE) [...] is specified by a conserved 5-bp core sequence (CCGAC) typical for C-repeat (CRT)/dehydration-responsive elements (DRE) that are recognized by cold-specific transcription factors (TFs) [16]."[1]

Consensus sequences

Main article: Consensus sequence gene transcriptions

A "conserved 5-bp core sequence (CCGAC) [is] typical for C-repeat (CRT)/dehydration-responsive elements (DRE)".[1]

Samplings

Main article: Model samplings

Copying a responsive elements consensus sequence 5'-CCGAC-3' and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-CCGAC-3' (starting with SuccessablesAAA.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 5'-CCGAC-3', 21, 5'-CCGAC-3' at 4275, 5'-CCGAC-3' at 4144, 5'-CCGAC-3' at 3993, 5'-CCGAC-3' at 3718, 5'-CCGAC-3' at 3223, 5'-CCGAC-3' at 3084, 5'-CCGAC-3' at 3040, 5'-CCGAC-3' at 2695, 5'-CCGAC-3' at 2561, 5'-CCGAC-3' at 2360, 5'-CCGAC-3' at 2225, 5'-CCGAC-3' at 2108, 5'-CCGAC-3' at 2068, 5'-CCGAC-3' at 1799, 5'-CCGAC-3' at 1755, 5'-CCGAC-3' at 1745, 5'-CCGAC-3' at 1463, 5'-CCGAC-3' at 1281, 5'-CCGAC-3' at 1110, 5'-CCGAC-3' at 990, 5'-CCGAC-3' at 824, and complements.
  2. negative strand, positive direction, looking for 5'-CCGAC-3', 5, 5'-CCGAC-3' at 3800, 5'-CCGAC-3' at 1963, 5'-CCGAC-3' at 997, 5'-CCGAC-3' at 897, 5'-CCGAC-3' at 791, and complements.
  3. positive strand, negative direction, looking for 5'-CCGAC-3', 0.
  4. positive strand, positive direction, looking for 5'-CCGAC-3', 15, 5'-CCGAC-3' at 3639, 5'-CCGAC-3' at 3587, 5'-CCGAC-3' at 3525, 5'-CCGAC-3' at 3348, 5'-CCGAC-3' at 2914, 5'-CCGAC-3' at 2886, 5'-CCGAC-3' at 2809, 5'-CCGAC-3' at 2769, 5'-CCGAC-3' at 2319, 5'-CCGAC-3' at 1818, 5'-CCGAC-3' at 1030, 5'-CCGAC-3' at 480, 5'-CCGAC-3' at 416, 5'-CCGAC-3' at 276, 5'-CCGAC-3' at 263, and complements.
  5. complement, negative strand, negative direction, looking for 5'-GGCTG-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-GGCTG-3', 15, 5'-GGCTG-3' at 3639, 5'-GGCTG-3' at 3587, 5'-GGCTG-3' at 3525, 5'-GGCTG-3' at 3348, 5'-GGCTG-3' at 2914, 5'-GGCTG-3' at 2886, 5'-GGCTG-3' at 2809, 5'-GGCTG-3' at 2769, 5'-GGCTG-3' at 2319, 5'-GGCTG-3' at 1818, 5'-GGCTG-3' at 1030, 5'-GGCTG-3' at 480, 5'-GGCTG-3' at 416, 5'-GGCTG-3' at 276, 5'-GGCTG-3' at 263.
  7. complement, positive strand, negative direction, looking for 5'-GGCTG-3', 21, 5'-GGCTG-3' at 4275, 5'-GGCTG-3' at 4144, 5'-GGCTG-3' at 3993, 5'-GGCTG-3' at 3718, 5'-GGCTG-3' at 3223, 5'-GGCTG-3' at 3084, 5'-GGCTG-3' at 3040, 5'-GGCTG-3' at 2695, 5'-GGCTG-3' at 2561, 5'-GGCTG-3' at 2360, 5'-GGCTG-3' at 2225, 5'-GGCTG-3' at 2108, 5'-GGCTG-3' at 2068, 5'-GGCTG-3' at 1799, 5'-GGCTG-3' at 1755, 5'-GGCTG-3' at 1745, 5'-GGCTG-3' at 1463, 5'-GGCTG-3' at 1281, 5'-GGCTG-3' at 1110, 5'-GGCTG-3' at 990, 5'-GGCTG-3' at 824.
  8. complement, positive strand, positive direction, looking for 5'-GGCTG-3', 5, 5'-GGCTG-3' at 3800, 5'-GGCTG-3' at 1963, 5'-GGCTG-3' at 997, 5'-GGCTG-3' at 897, 5'-GGCTG-3' at 791.
  9. inverse complement, negative strand, negative direction, looking for 5'-GTCGG-3', 20, 5'-GTCGG-3' at 4490, 5'-GTCGG-3' at 4481, 5'-GTCGG-3' at 4346, 5'-GTCGG-3' at 4034, 5'-GTCGG-3' at 3727, 5'-GTCGG-3' at 3683, 5'-GTCGG-3' at 3295, 5'-GTCGG-3' at 3205, 5'-GTCGG-3' at 3125, 5'-GTCGG-3' at 2767, 5'-GTCGG-3' at 2651, 5'-GTCGG-3' at 2432, 5'-GTCGG-3' at 2265, 5'-GTCGG-3' at 2006, 5'-GTCGG-3' at 1195, 5'-GTCGG-3' at 1062, 5'-GTCGG-3' at 896, 5'-GTCGG-3' at 729, 5'-GTCGG-3' at 505, 5'-GTCGG-3' at 36, and complements.
  10. inverse complement, negative strand, positive direction, looking for 5'-GTCGG-3', 1, 5'-GTCGG-3' at 1529, and complement.
  11. inverse complement, positive strand, negative direction, looking for 5'-GTCGG-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-GTCGG-3', 15, 5'-GTCGG-3' at 3998, 5'-GTCGG-3' at 3896, 5'-GTCGG-3' at 3101, 5'-GTCGG-3' at 2897, 5'-GTCGG-3' at 2527, 5'-GTCGG-3' at 2391, 5'-GTCGG-3' at 2353, 5'-GTCGG-3' at 2009, 5'-GTCGG-3' at 1604, 5'-GTCGG-3' at 1268, 5'-GTCGG-3' at 932, 5'-GTCGG-3' at 832, 5'-GTCGG-3' at 614, 5'-GTCGG-3' at 512, 5'-GTCGG-3' at 65, and complements.
  13. inverse negative strand, negative direction, looking for 5'-CAGCC-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-CAGCC-3', 15, 5'-CAGCC-3' at 3998, 5'-CAGCC-3' at 3896, 5'-CAGCC-3' at 3101, 5'-CAGCC-3' at 2897, 5'-CAGCC-3' at 2527, 5'-CAGCC-3' at 2391, 5'-CAGCC-3' at 2353, 5'-CAGCC-3' at 2009, 5'-CAGCC-3' at 1604, 5'-CAGCC-3' at 1268, 5'-CAGCC-3' at 932, 5'-CAGCC-3' at 832, 5'-CAGCC-3' at 614, 5'-CAGCC-3' at 512, 5'-CAGCC-3' at 65.
  15. inverse positive strand, negative direction, looking for 5'-CAGCC-3', 20, 5'-CAGCC-3' at 4490, 5'-CAGCC-3' at 4481, 5'-CAGCC-3' at 4346, 5'-CAGCC-3' at 4034, 5'-CAGCC-3' at 3727, 5'-CAGCC-3' at 3683, 5'-CAGCC-3' at 3295, 5'-CAGCC-3' at 3205, 5'-CAGCC-3' at 3125, 5'-CAGCC-3' at 2767, 5'-CAGCC-3' at 2651, 5'-CAGCC-3' at 2432, 5'-CAGCC-3' at 2265, 5'-CAGCC-3' at 2006, 5'-CAGCC-3' at 1195, 5'-CAGCC-3' at 1062, 5'-CAGCC-3' at 896, 5'-CAGCC-3' at 729, 5'-CAGCC-3' at 505, 5'-CAGCC-3' at 36.
  16. inverse positive strand, positive direction, looking for 5'-CAGCC-3', 1, 5'-CAGCC-3' at 1529.

Cold-responsive element core promoters

Main article: Core promoter gene transcriptions

Negative strand, negative direction: 5'-GTCGG-3' at 4490, 5'-GTCGG-3' at 4481, and complements.

Cold-responsive element proximal promoters

Main article: Proximal promoter gene transcriptions

Negative strand, negative direction: 5'-GTCGG-3' at 4346, 5'-CCGAC-3' at 4275, and complements.

Cold-responsive element distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: 5'-CCGAC-3' at 4144, 5'-GTCGG-3' at 4034, 5'-CCGAC-3' at 3993, 5'-GTCGG-3' at 3727, 5'-CCGAC-3' at 3718, 5'-GTCGG-3' at 3683, 5'-GTCGG-3' at 3295, 5'-CCGAC-3' at 3223, 5'-GTCGG-3' at 3205, 5'-GTCGG-3' at 3125, 5'-CCGAC-3' at 3084, 5'-CCGAC-3' at 3040, 5'-GTCGG-3' at 2767, 5'-CCGAC-3' at 2695, 5'-GTCGG-3' at 2651, 5'-CCGAC-3' at 2561, 5'-GTCGG-3' at 2432, 5'-CCGAC-3' at 2360, 5'-GTCGG-3' at 2265, 5'-CCGAC-3' at 2225, 5'-CCGAC-3' at 2108, 5'-CCGAC-3' at 2068, 5'-GTCGG-3' at 2006, 5'-CCGAC-3' at 1799, 5'-CCGAC-3' at 1755, 5'-CCGAC-3' at 1745, 5'-CCGAC-3' at 1463, 5'-CCGAC-3' at 1281, 5'-GTCGG-3' at 1195, 5'-CCGAC-3' at 1110, 5'-GTCGG-3' at 1062, 5'-CCGAC-3' at 990, 5'-GTCGG-3' at 896, 5'-CCGAC-3' at 824, 5'-GTCGG-3' at 729, 5'-GTCGG-3' at 505, 5'-GTCGG-3' at 36, and complements.

Negative strand, positive direction: 5'-CCGAC-3' at 3800, 5'-CCGAC-3' at 1963, 5'-GTCGG-3' at 1529, 5'-CCGAC-3' at 997, 5'-CCGAC-3' at 897, 5'-CCGAC-3' at 791, and complements.

Positive strand, positive direction: 5'-GTCGG-3' at 3998, 5'-GTCGG-3' at 3896, 5'-CCGAC-3' at 3639, 5'-CCGAC-3' at 3587, 5'-CCGAC-3' at 3525, 5'-CCGAC-3' at 3348, 5'-GTCGG-3' at 3101, 5'-CCGAC-3' at 2914, 5'-GTCGG-3' at 2897, 5'-CCGAC-3' at 2886, 5'-CCGAC-3' at 2809, 5'-CCGAC-3' at 2769, 5'-GTCGG-3' at 2527, 5'-GTCGG-3' at 2391, 5'-GTCGG-3' at 2353, 5'-CCGAC-3' at 2319, 5'-GTCGG-3' at 2009, 5'-CCGAC-3' at 1818, 5'-GTCGG-3' at 1604, 5'-GTCGG-3' at 1268, 5'-CCGAC-3' at 1030, 5'-GTCGG-3' at 932, 5'-GTCGG-3' at 832, 5'-GTCGG-3' at 614, 5'-GTCGG-3' at 512, 5'-CCGAC-3' at 480, 5'-CCGAC-3' at 416, 5'-CCGAC-3' at 276, 5'-CCGAC-3' at 263, 5'-GTCGG-3' at 65, and complements.

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 Björn Pietzenuk, Catarine Markus, Hervé Gaubert, Navratan Bagwan, Aldo Merotto, Etienne Bucher & Ales Pecinka (11 October 2016). "Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements". Genome Biology. 17: 209. doi:10.1186/s13059-016-1072-3. Retrieved 14 September 2020.

External links

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