P63 DNA-binding site gene transcriptions: Difference between revisions

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

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:

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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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.

References

↑ 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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Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions Initiator element gene transcriptions Initiator-like element gene transcriptions Inositol/choline-responsive elements Interaction gene transcriptions Interferon regulatory factors Inverse copy gene transcriptions Jasmonic acid-responsive element gene transcriptions K-boxes Kozak sequence gene transcriptions Kruppel-associated box gene transcriptions Krüppel-like factor gene transcriptions L box gene transcriptions Leu3 gene transcriptions M35 box gene transcriptions MADS box gene transcriptions Maf recognition element gene transcriptions M box gene transcriptions Mcm1 regulatory factor gene transcriptions Met31p box gene transcriptions Metal responsive element gene transcriptions Middle sporulation element gene transcriptions Mig1p gene transcriptions Model samplings Motif ten element gene transcriptions Msn2,4p gene transcriptions Musashi binding element gene transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions 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@@ Line 22: / Line 22: @@
 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}}
-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:
 # 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==

P63 DNA-binding site gene transcriptions: Difference between revisions

Revision as of 04:14, 14 February 2021

Contents

Human genes

Consensus sequences

p63 samplings

See also

References

External links

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