P63 DNA-binding site gene transcriptions: Difference between revisions

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The apparent consensus sequence is (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T).
The apparent consensus sequence is (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T).


==Samplings==
==p63 samplings==
{{main|Model samplings}}
{{main|Model samplings}}
Copying an apparent consensus sequence for the P63 (GAGCGAGCCT) and putting it in "⌘F" finds none located between ZSCAN22 and one between ZNF497 and A1BG as can be found by the computer programs.
Copying an apparent consensus sequence for the p63 (GAGCGAGCCT) and putting it in "⌘F" finds none located between ZSCAN22 and one between ZNF497 and A1BG as can be found by the computer programs.


For the Basic programs testing consensus sequence (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T) (starting with SuccessablesP63.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 (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T) (starting with SuccessablesP63.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 (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
# negative strand, negative direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# positive strand, negative direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# positive strand, positive direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# complement, negative strand, negative direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# complement, positive strand, negative direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# complement, positive strand, positive direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# complement, negative strand, positive direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, negative direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
# inverse negative strand, negative direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, negative direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
# inverse positive strand, positive direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
# inverse negative strand, positive direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
 
===AAA UTRs===
{{main|UTR promoter gene transcriptions}}
 
===AAA core promoters===
{{main|Core promoter gene transcriptions}}
 
===AAA proximal promoters===
{{main|Proximal promoter gene transcriptions}}
 
===AAA distal promoters===
{{main|Distal promoter gene transcriptions}}


==See also==
==See also==

Revision as of 04:14, 14 February 2021

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

"p63 bound preferentially to DNA fragments conforming to the 20 bp sequence 5'-RRRC(A/G)(A/T)GYYYRRRC(A/T)(C/T)GYYY-3'."[1]

Human genes

Consensus sequences

The apparent consensus sequence is (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T).

p63 samplings

Main article: Model samplings

Copying an apparent consensus sequence for the p63 (GAGCGAGCCT) and putting it in "⌘F" finds none located between ZSCAN22 and one between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T) (starting with SuccessablesP63.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 (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
  2. positive strand, negative direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
  3. positive strand, positive direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
  4. negative strand, positive direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
  5. complement, negative strand, negative direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
  6. complement, positive strand, negative direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
  7. complement, positive strand, positive direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
  8. complement, negative strand, positive direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
  9. inverse complement, negative strand, negative direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
  10. inverse complement, positive strand, negative direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
  11. inverse complement, positive strand, positive direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
  12. inverse complement, negative strand, positive direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
  13. inverse negative strand, negative direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
  14. inverse positive strand, negative direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
  15. inverse positive strand, positive direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
  16. inverse negative strand, positive direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.

See also

References

  1. ↑ C A Perez, J Ott, D J Mays & J A Pietenpol (15 November 2007). "p63 consensus DNA-binding site: identification, analysis and application into a p63MH algorithm". Oncogene. 26 (52): 7363–70. doi:10.1038/sj.onc.1210561. PMID 17563751. Retrieved 28 August 2020.

External links

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