CCCTC-binding factor gene transcriptions: Difference between revisions

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(Created page with "{{AE}} Henry A. Hoff ==Consensus sequences== "Experiments using chromatin immunoprecipitation exonuclease (ChIP-exo) uncovered a broad CTCF-binding motif that contains a 12...")
 
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Copying the consensus of the CTCF: 5'-CACCAGG-3' and putting the sequence in "⌘F" finds no locations between ZSCAN22 and A1BG and CTCF: 5'-CACCAGGAGG-3' finds no locations between ZNF497 and A1BG as can be found by the computer programs.
Copying the consensus of the CTCF: 5'-CACCAGG-3' and putting the sequence in "⌘F" finds no locations between ZSCAN22 and A1BG and CTCF: 5'-CACCAGGAGG-3' finds no locations between ZNF497 and A1BG as can be found by the computer programs.
For the Basic programs SuccessablesCFbox.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'-NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)-3'<ref name=Hashimoto/>, 0.
# negative strand, positive direction, looking for 5'-NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)-3', 0.
# positive strand, negative direction, looking for 5'-NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)-3', 0.
# positive strand, positive direction, looking for 5'-NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)-3', 0.
# complement, negative strand, negative direction, looking for 5'-NGT-NNT-C(C/T)N-CCG-(C/T)(C/G)(A/G)-3', 0.
# complement, negative strand, positive direction, looking for 5'-NGT-NNT-C(C/T)N-CCG-(C/T)(C/G)(A/G)-3', 0.
# complement, positive strand, negative direction, looking for 5'-NGT-NNT-C(C/T)N-CCG-(C/T)(C/G)(A/G)-3', 0.
# complement, positive strand, positive direction, looking for 5'-NGT-NNT-C(C/T)N-CCG-(C/T)(C/G)(A/G)-3', 0.
# inverse complement, negative strand, negative direction, looking for 5'-(A/G)(C/G)(C/T)-GCC-N(C/T)C-TNN-TGN-3', 0.
# inverse complement, negative strand, positive direction, looking for 5'-(A/G)(C/G)(C/T)-GCC-N(C/T)C-TNN-TGN-3', 0.
# inverse complement, positive strand, negative direction, looking for 5'-(A/G)(C/G)(C/T)-GCC-N(C/T)C-TNN-TGN-3', 0.
# inverse complement, positive strand, positive direction, looking for 5'-(A/G)(C/G)(C/T)-GCC-N(C/T)C-TNN-TGN-3', 0.
# inverse, negative strand, negative direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.
# inverse, negative strand, positive direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.
# inverse, positive strand, negative direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.
# inverse, positive strand, positive direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.


==Acknowledgements==
==Acknowledgements==

Revision as of 23:02, 24 October 2020

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

Consensus sequences

"Experiments using chromatin immunoprecipitation exonuclease (ChIP-exo) uncovered a broad CTCF-binding motif that contains a 12–15 bp consensus sequence, 5′-NCA-NNA-G(G/A)N-GGC-(G/A)(C/G)(T/C)-3′ (Nakahashi et al., 2013, Rhee and Pugh, 2011) [...]."[1]

Samplings

Copying the consensus of the CTCF: 5'-CACCAGG-3' and putting the sequence in "⌘F" finds no locations between ZSCAN22 and A1BG and CTCF: 5'-CACCAGGAGG-3' finds no locations between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs SuccessablesCFbox.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'-NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)-3'[1], 0.
  2. negative strand, positive direction, looking for 5'-NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)-3', 0.
  3. positive strand, negative direction, looking for 5'-NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)-3', 0.
  4. positive strand, positive direction, looking for 5'-NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-NGT-NNT-C(C/T)N-CCG-(C/T)(C/G)(A/G)-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-NGT-NNT-C(C/T)N-CCG-(C/T)(C/G)(A/G)-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-NGT-NNT-C(C/T)N-CCG-(C/T)(C/G)(A/G)-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-NGT-NNT-C(C/T)N-CCG-(C/T)(C/G)(A/G)-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-(A/G)(C/G)(C/T)-GCC-N(C/T)C-TNN-TGN-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-(A/G)(C/G)(C/T)-GCC-N(C/T)C-TNN-TGN-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-(A/G)(C/G)(C/T)-GCC-N(C/T)C-TNN-TGN-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-(A/G)(C/G)(C/T)-GCC-N(C/T)C-TNN-TGN-3', 0.
  13. inverse, negative strand, negative direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.
  14. inverse, negative strand, positive direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.
  15. inverse, positive strand, negative direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.
  16. inverse, positive strand, positive direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 Hideharu Hashimoto, Dongxue Wang, John R. Horton, Xing Zhang, Victor G. Corces and Xiaodong Cheng (1 June 2017). "Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA". Molecular Cell. 66 (5): 711–720.e3. doi:10.1016/j.molcel.2017.05.004. PMID 28529057. Retrieved 28 August 2020.

External links

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