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Gene transcriptions/Boxes/TATCs

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"Upon cereal seed germination, the seed storage proteins (SSP) and defence proteins (CMe) whose mRNAs are abundant during the maturation phase are silenced. Instead, a different set of genes, encoding hydrolases, is induced in the aleurone upon GA perception. The promoter regions of these genes, such as those encoding α-amylases and proteases (Cejudo et al., 1992; Cercos et al., 1999; Gubler et al., 1995, 1999; Mena et al., 2002), contain the conserved GA response complex (GARC), a tripartite cis motif comprising the GA response element (GARE, 5'-TAACAAA-3'), the pyrimidine box (5'-CTTTT-3') and the TATC box (5'-TATCCAC-3'), all of which are necessary for a full GA response."[1]

GA responsive complexes

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The GA responsive complexes are gene transcription factors (TF), notably the TAACAAA box or GA responsive element (GARE), the pyrimidine box CCTTTT, and the TATCCAC box (Skriver et al., 1991;Gubler and Jacobsen, 1992; Rogers et al., 1994).[2]

"To identify the reason of the low-level expression of BnGID1 in mutant, we sequenced the upstream sequence of BnGID1 and found that there was a GA-responsive complex including GARE (MBS), pyrimidine box and TATC-box, which is same as the upstream sequence of AtGID1a."[3]

Sampling of A1BG promoters

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For the Basic programs (starting with SuccessablesTATC.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 (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesTATC--.bas, looking for 3'-TATCCAC-5', 0,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesTATC-+.bas, looking for 3'-TATCCAC-5', 0,
  3. positive strand in the negative direction is SuccessablesTATC+-.bas, looking for 3'-TATCCAC-5', 0,
  4. positive strand in the positive direction is SuccessablesTATC++.bas, looking for 3'-TATCCAC-5', 0,
  5. complement, negative strand, negative direction is SuccessablesTATCc--.bas, looking for 3'-ATAGGTG-5', 0,
  6. complement, negative strand, positive direction is SuccessablesTATCc-+.bas, looking for 3'-ATAGGTG-5', 0,
  7. complement, positive strand, negative direction is SuccessablesTATCc+-.bas, looking for 3'-ATAGGTG-5', 0,
  8. complement, positive strand, positive direction is SuccessablesTATCc++.bas, looking for 3'-ATAGGTG-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesTATCci--.bas, looking for 3'-GTGGATA-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesTATCci-+.bas, looking for 3'-GTGGATA-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesTATCci+-.bas, looking for 3'-GTGGATA-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesTATCci++.bas, looking for 3'-GTGGATA-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesTATCi--.bas, looking for 3'-CACCTAT-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesTATCi-+.bas, looking for 3'-CACCTAT-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesTATCi+-.bas, looking for 3'-CACCTAT-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesTATCi++.bas, looking for 3'-CACCTAT-5', 0.

See also

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References

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  1. ↑ I. Rubio-Somoza, M. Martinez, Z. Abraham, I. Diaz and P. Carbonero (July 2006). "Ternary complex formation between HvMYBS3 and other factors involved in transcriptional control in barley seeds". The Plant Journal 47 (2): 269–281. doi:10.1111/j.1365-313X.2006.02777.x. https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2006.02777.x. Retrieved 17 October 2018. 
  2. ↑ Montaña Mena, Francisco Javier Cejudo, Ines Isabel-Lamoneda and Pilar Carbonero (1 September 2002). "A Role for the DOF Transcription Factor BPBF in the Regulation of Gibberellin-Responsive Genes in Barley Aleurone". Plant Physiology 130 (1): 111-9. doi:10.1104/pp.005561. http://www.plantphysiol.org/content/130/1/111.full. Retrieved 2017-02-19. 
  3. ↑ Huapeng Li, Yun Wang, Xiaocheng Li, Yong Gao, Zhijun Wang, Yun Zhao and Maolin Wang (January 2011). "A GA-insensitive dwarf mutant of Brassica napus L. correlated with mutation in pyrimidine box in the promoter of GID1". Molecular Biology Reports 38 (1): 191–197. doi:10.1007/s11033-010-0094-2. https://link.springer.com/article/10.1007/s11033-010-0094-2. Retrieved 10 October 2018. 
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