Coupling element gene transcriptions: Difference between revisions

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For the Basic programs testing consensus sequence 5'-TGCCACCGG-3' (starting with SuccessablesCE1.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 5'-TGCCACCGG-3' (starting with SuccessablesCE1.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 5'-AAAAAAAA-3', 0.
# negative strand, negative direction, looking for 5'-TGCCACCGG-3', 0.
# negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
# negative strand, positive direction, looking for 5'-TGCCACCGG-3', 0.
# positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
# positive strand, negative direction, looking for 5'-TGCCACCGG-3', 0.
# positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
# positive strand, positive direction, looking for 5'-TGCCACCGG-3', 0.
# complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# complement, negative strand, negative direction, looking for 5'-ACGGTGGCC-3', 0.
# complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# complement, negative strand, positive direction, looking for 5'-ACGGTGGCC-3', 0.
# complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# complement, positive strand, negative direction, looking for 5'-ACGGTGGCC-3', 0.
# complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# complement, positive strand, positive direction, looking for 5'-ACGGTGGCC-3', 0.
# inverse complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, negative strand, negative direction, looking for 5'-CCGGTGGCA-3', 0.
# inverse complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, negative strand, positive direction, looking for 5'-CCGGTGGCA-3', 0.
# inverse complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, positive strand, negative direction, looking for 5'-CCGGTGGCA-3', 0.
# inverse complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, positive strand, positive direction, looking for 5'-CCGGTGGCA-3', 0.
# inverse negative strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
# inverse negative strand, negative direction, looking for 5'-GGCCACCGT-3', 0.
# inverse negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
# inverse negative strand, positive direction, looking for 5'-GGCCACCGT-3', 0.
# inverse positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
# inverse positive strand, negative direction, looking for 5'-GGCCACCGT-3', 0.
# inverse positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
# inverse positive strand, positive direction, looking for 5'-GGCCACCGT-3', 0.
 
===AAA core promoters===
{{main|Core promoter gene transcriptions}}
 
===AAA proximal promoters===
{{main|Proximal promoter gene transcriptions}}
 
===AAA distal promoters===
{{main|Distal promoter gene transcriptions}}


==CE3 (Watanabe) samplings==
==CE3 (Watanabe) samplings==

Revision as of 01:51, 1 December 2020

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

"In Arabidopsis, the CE3 element is practically absent; thus, Arabidopsis relies on paired ABREs to form ABRCs (Gomez‐Porras et al. 2007) or on the coupling of a DRE (TACCGACAT) with ABRE (Narusaka et al. 2003; Nakashima et al. 2006)."[1]

"To identify potential cis-regulatory elements in the promoter sequences of ZmGRXCC genes, the 1500 bp sequences of each [maize CC-type glutaredoxin (GRX)] ZmGRXCC gene upstream of the ATG start codon were selected from the maize genome as the promoter, and the promoter sequence was screened using PlantCARE [32]. The elements searched included Skn-1_motif (-GGGCGG-), CCGTCC-box (-CCGTCC-box-), CAT-box (-GCCACT-), and RY-element (-CATGCATG-) for development and metabolism; TGACG-motif (-TGACG-) and CGTCA-motif (-CGTCA-) for jasmonic acid responsiveness; GARE-motif (-AAACAGA- or -TCTGTTG-) for gibberellin responsiveness; TGA-element (-AACGAC-) for auxin responsiveness; ABRE (ABA-responsive element, -CACGTG- or -TACGTG-) and CE3 (coupling element 3, -CACGCG-) for ABA responsiveness; ERE (ethylene-responsive element, -ATTTCAAA-) for ethylene responsiveness; GC-motif (-CCCCCG-), LTR (-CCGAAA-) and box S (-AGCCACC-) for stress responsiveness; and MBS (MYB-binding site, -CAACTG- or -TAACTG-), DRE (dehydration-responsive element, -GCCGAC- or -ACCGAC-), T/G Box (-CACGTT-), EE (evening element, -AATATC-), MYCR (MYC-binding site, -CACATG-), and NACR (binding site of drought-inducible NAC TFs, -CACGCA-) for drought/dehydration responsiveness [33–37]."[2]

Consensus sequences

Main article: Consensus sequence gene transcriptions

"In barley, the combination of an ABRE and one of two known coupling elements CE1 (TGCCACCGG) and CE3 (GCGTGTC) constitutes an ABA responsive complex (ABRC) in the regulation of the ABA‐inducible genes HVA1 and HVA22 (Shen and Ho 1995; Shen et al. 1996)."[1]

Promoter occurrences

Hypotheses

Main article: Hypotheses
  1. A1BG has no coupling elements in either promoter.
  2. A1BG is not transcribed by a coupling element.
  3. A coupling element does not participate in the transcription of A1BG.

CE1 (Watanabe) samplings

Main article: Model samplings

Copying a responsive elements consensus sequence 5'-TGCCACCGG-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'-TGCCACCGG-3' (starting with SuccessablesCE1.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'-TGCCACCGG-3', 0.
  2. negative strand, positive direction, looking for 5'-TGCCACCGG-3', 0.
  3. positive strand, negative direction, looking for 5'-TGCCACCGG-3', 0.
  4. positive strand, positive direction, looking for 5'-TGCCACCGG-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-ACGGTGGCC-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-ACGGTGGCC-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-ACGGTGGCC-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-ACGGTGGCC-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-CCGGTGGCA-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-CCGGTGGCA-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-CCGGTGGCA-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-CCGGTGGCA-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-GGCCACCGT-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-GGCCACCGT-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-GGCCACCGT-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-GGCCACCGT-3', 0.

CE3 (Watanabe) samplings

Copying a responsive elements consensus sequence 5'-GCGTGTC-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'-GCGTGTC-3' (starting with SuccessablesCE3W.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'-AAAAAAAA-3', 0.
  2. negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  3. positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  4. positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.

CE3 (Ding) samplings

Copying a responsive elements consensus sequence 5'-CACGCG-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'-CACGCG-3' (starting with SuccessablesCE3D.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'-AAAAAAAA-3', 0.
  2. negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  3. positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  4. positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 Kenneth A. Watanabe; Arielle Homayouni; Lingkun Gu; Kuan‐Ying Huang; Tuan‐Hua David Ho; Qingxi J. Shen (18 June 2017). "Transcriptomic analysis of rice aleurone cells identified a novel abscisic acid response element". Plant, Cell & Environment. 40 (9): 2004–2016. doi:10.1111/pce.13006. Retrieved 5 October 2020.
  2. ↑ Shuangcheng Ding, Fengyu He, Wenlin Tang, Hewei Du and Hongwei Wang (12 August 2019). "Identification of Maize CC-Type Glutaredoxins That Are Associated with Response to Drought Stress". Genes. 10 (610): 1–15. doi:10.3390/genes10080610. Retrieved 30 November 2020.

External links

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